Companion Page for modENCODE Integrative Worm Paper
modENCODE data file formats
A guide to the data file formats, which describes WIG file format, GFF3 format, and provides an introduction on how to upload and view them on WormBase, modENCODE and UCSC browsers.Figures
Figure 1: Transcriptome Features and Alternative Splicing
Analysis completed using WormBase version WS209 and WS170
Parts A and B
Interpreted data:
- Aggregate Integrated Transcripts
-
External data source
- Genome Res. 2009 Apr;19(4):657-66
Source experimental data
- RNA-seq - early embryo sequences & alignments 3974
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Part C
Interpreted data:
Source experimental data
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
Part D
Source experimental data
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
Figure 2: Expression & Binding Dynamics
Analysis completed using WormBase version WS180
Parts A and B
Source experimental data
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- early embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2855
- late embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2857
- L1 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2860
- L2 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2861
- L3 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2862
- L4 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2863
- Young Adult N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs 2851
Part C
Source experimental data
- embryo A-class motor neurons tiling array 654
- embryo panneural tiling array 455
- embryo GABA motor neurons tiling array 468
- embryo body wall muscle tiling array (v2) 470
- embryo coelomocytes tiling array 458
- embryo intestine tiling array 457
- L2 A-class neuron tiling array 469
- L2 panneural tiling array 462
- L2 GABA neurons tiling array 466
- L2 body wall muscle tiling array 465
- L2 coelomocytes tiling array 657
- L2 intestine tiling array 463
Figure 3: Highly Occupied Target (HOT) Regions
Analysis completed using WormBase version WS190
Part A and B
Interpreted data
Source experimental data:
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_POLII_emb 586
- ChIP-seq - PHA4_POLII_FedL1 587
- ChIP-seq - PHA4_StarvedL1_POLII 588
- ChIP-seq - AMA1_GFP_L4YA 589
- ChIP-seq - AMA1_POLII_L4YA 590
- ChIP-seq - DAF16_GFP_L4YA 591
- ChIP-seq - DAF16_POLII_L4YA 592
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MAB5_POLII_L3 594
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - UNC-130_GFP_L1 2430
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EOR-1_POLII_L3 3160
- ChIP-seq - HLH-8_POLII_L3 2597
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EGL5_POLII_L3 3162
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - PQM-1_GFP_L3 2623
Part C
Source experimental data:
- embryo A-class motor neurons tiling array 654
- embryo all cells reference tiling array 456
- embryo AVA neurons tiling array 459
- embryo body wall muscle tiling array (v2) 470
- embryo coelomocytes tiling array 458
- embryo dopaminergic neurons tiling array 467
- embryo GABA motor neurons tiling array 468
- embryo germline precursor cells tiling array 661
- embryo hypodermal cells tiling array 662
- embryo intestine tiling array 457
- embryo panneural tiling array 455
- gonad from young adult 20dC 42hrs post-L1 N2 tiling array 481
- L2 A-class neuron tiling array 469
- L2 body wall muscle tiling array 465
- L2 coelomocytes tiling array 657
- L2 excretory cell tiling array 464
- L2 GABA neurons tiling array 466
- L2 glutamate receptor expressing neurons tiling array 658
- L2 intestine tiling array 463
- L2 panneural tiling array 462
- L3-L4 dopaminergic neuron tiling array 655
- L3-L4 PVD & OLL neurons tiling array 460
- soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array 485
- young adult 25dC 42hrs post-L1 N2 tiling array 475
- Young Adult Cephalic sheath (CEPsh) tiling array 660
Additional Data Sources
Figure 4: Integrated Regulatory Network
Analysis completed using WormBase version WS170
Interpreted data
Source experimental data:
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_POLII_emb 586
- ChIP-seq - PHA4_POLII_FedL1 587
- ChIP-seq - PHA4_StarvedL1_POLII 588
- ChIP-seq - AMA1_GFP_L4YA 589
- ChIP-seq - AMA1_POLII_L4YA 590
- ChIP-seq - DAF16_GFP_L4YA 591
- ChIP-seq - DAF16_POLII_L4YA 592
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MAB5_POLII_L3 594
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - UNC-130_GFP_L1 2430
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EOR-1_POLII_L3 3160
- ChIP-seq - HLH-8_POLII_L3 2597
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EGL5_POLII_L3 3162
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - PQM-1_GFP_L3 2623
Figure 5: Chromosome-scale Domains of Chromatin Organization
Analysis completed using WormBase version WS170
Source experimental data:
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3880
- RNA-seq - early embryo sequences & alignments 3884
- ChIP-chip - Histone_H3K4me1_N2_EEMB_(AB8895_H3K4ME1733246_N2_EEMB) 2726
- ChIP-chip - Histone_H3K4me1_N2_L3_(AB8895_H3K4ME1733246_N2_L3) 2775
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me3_from_N2_L3_larvae_(AR0169_H3K4me3_N2_L3) 176
- ChIP-chip - Histone_H3K9me1_N2_EEMB_(AB9045_H3K9ME1291918_N2_EEMB) 2646
- ChIP-chip - Histone_H3K9me1_N2_L3_(AB9045_H3K9ME1291918_N2_L3) 2770
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K27ac_N2_EEMB_(WA30634849_H3K27AC_N2_EEMB) 3200
- ChIP-chip - Histone_H3K27ac_N2_L3_(AB4729_H3K27AC361571_N2_L3) 2771
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - Histone_H3K36me1_N2_EEMB_(AB9048_H3K36ME1206009_N2_EEMB) 2604
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 2338
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H4K8ac_N2_L3_(AB15823_H4K8AC487128_N2_L3) 2774
- ChIP-chip - Histone_H4_Tetra_ac_N2_EEMB_(LPAR109_H4TETRAAC109_N2_EEMB) 2766
- ChIP-chip - Histone_H3K20me1_N2_EEMB_(AB9051_H4K20ME1104513_N2_EEMB) 2765
- ChIP-chip - HK00013_H3K27ME31E7_N2_EEMB 3171
- ChIP-chip - UP07448_H3K27ME124439_N2_EEMB 3179
- ChIP-chip - AB15823_H4K8AC487128_N2_EEMB 3181
- ChIP-chip - MP07329_H4K16ACDAM1612187_N2_EEMB 3182
- 3203
- 3205
Figure 6: Chromatin Patterns around Genes
Analysis completed using WormBase version WS170
Source experimental data:
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3880
- RNA-seq - early embryo sequences & alignments 3884
- ChIP-chip - Histone_H3K4me1_N2_EEMB_(AB8895_H3K4ME1733246_N2_EEMB) 2726
- ChIP-chip - Histone_H3K4me1_N2_L3_(AB8895_H3K4ME1733246_N2_L3) 2775
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me3_from_N2_L3_larvae_(AR0169_H3K4me3_N2_L3) 176
- ChIP-chip - Histone_H3K9me1_N2_EEMB_(AB9045_H3K9ME1291918_N2_EEMB) 2646
- ChIP-chip - Histone_H3K9me1_N2_L3_(AB9045_H3K9ME1291918_N2_L3) 2770
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K27ac_N2_EEMB_(WA30634849_H3K27AC_N2_EEMB) 3200
- ChIP-chip - Histone_H3K27ac_N2_L3_(AB4729_H3K27AC361571_N2_L3) 2771
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - Histone_H3K36me1_N2_EEMB_(AB9048_H3K36ME1206009_N2_EEMB) 2604
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 2338
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H4K8ac_N2_L3_(AB15823_H4K8AC487128_N2_L3) 2774
- ChIP-chip - Histone_H4_Tetra_ac_N2_EEMB_(LPAR109_H4TETRAAC109_N2_EEMB) 2766
- ChIP-chip - Histone_H3K20me1_N2_EEMB_(AB9051_H4K20ME1104513_N2_EEMB) 2765
- ChIP-chip - HK00013_H3K27ME31E7_N2_EEMB 3171
- ChIP-chip - UP07448_H3K27ME124439_N2_EEMB 3179
- ChIP-chip - AB15823_H4K8AC487128_N2_EEMB 3181
- ChIP-chip - MP07329_H4K16ACDAM1612187_N2_EEMB 3182
- 3203
- 3205
Figure 7: Statistical Models Predicting TF-binding and Gene Expression from Chromatin Features
Analysis completed using WormBase version WS190
Aggregated Data
Source experimental data
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new) 2409
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB) 2313
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB) 2339
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB) 2338
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB) 174
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB) 2312
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3) 2407
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM) 2408
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 909
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4) 630
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB) 696
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB) 701
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB) 334
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB) 336
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB) 644
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB) 194
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB) 897
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB) 911
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB) 645
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - DAF16_GFP_L4YA 2010
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - PQM-1_GFP_L3 2623
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - UNC-130_GFP_L1 2430
Figure 8: Relative proportion of annotations among constrained sequences
Analysis completed using WormBase version WS190
Supplementary Figures
Figure S1: ChIP-chip and ChIP-seq comparison
Analysis completed using WormBase version WS190
Source experimental data:
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_L4 2440
- ChIP-chip - Pol_II_CTD_N2_EEMB_(ABAB817_8WG16_N2_EEMB) 663
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
-
Figure S2: Correlation of RNA expression levels for young adult between RNA-seq and tiling array platforms
Analysis completed using WormBase version WS190
Source experimental data:
- young adult 25dC 42hrs post-L1 N2 tiling array 475
- RNAseq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3878
Figure S3: Numbers of RNA-seq reads
Analysis completed using WormBase version WS170
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Figure S4: RNA sequencing depth analysis
Part A: Density plots of 20,051 genes in WormBase190
Analysis completed using WormBase version WS190
Source experimental data:
Part B: Pair-wise comparison of the density plots
Analysis completed using WormBase version WS190
Source experimental data:
Part C: Rate of gene discovery
Analysis completed using WormBase version WS190
Source experimental data:
Figure S5: Transcript building
Interpreted data:
Source experimental data
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Figure S6: A complex isoform example
Interpreted data:
Source experimental data
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Figure S7: Features defined by RNAseq as compared to WormBase as of January, 2007 (WS170)
Analysis completed using WormBase version WS170
Figure S8: Number of confirmed splice junctions over time
Analysis completed using WormBase version WS170
Figure S9: Proportion of splice junctions confirmed by various methods
Figure S10: Saturation of discovery of additional ncRNAs and coding exons with additional RNA-seq data sets
Analysis completed using WormBase version WS190
Figure S11: Number of stages and samples where a given gene or splice junction is observed
Analysis completed using WormBase version WS170
Figure S12: Developmental stage-specific expression
Analysis completed using WormBase version WS190
Interpreted data
Source experimental data
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Part B: Expression profiles of the meta-genes for developmental stage-specific transcripts
Analysis completed using WormBase version WS190
Interpreted data
Source experimental data
- RNA-seq - early embryo sequences & alignments 3884
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments 3883
- RNA-seq - embryo him-8 20dC post-L1 sequences & alignments 3905
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments 3882
- RNA-seq - lin-35(n745) mid-L1 25dC 4.0hrs post-L1 sequences & alignments 3910
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments 3880
- RNA-seq - dauer entry daf-2 25dC 48hrs post-L1 sequences & alignments 3902
- RNA-seq - dauer daf-2 25dC 91hrs post-L1 sequences & alignments 3904
- RNA-seq - dauer exit daf-2 25dC 91hrs 15dC 12hrs post-L1 sequences & alignments 3881
- RNA-seq - mid-L3 25dC 25hrs post-L1 sequences & alignments 3879
- RNA-seq - mid-L4 25dC 36hrs post-L1 sequences & alignments 3878
- RNA-seq - soma-only mid-L4 25dC 36hrs post-L1 JK1107 sequences & alignments 3908
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments 3909
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment 3903
- RNA-seq - Adult spe-9 23dC 8days post-L4 molt sequences & alignment 3901
- RNA-seq - pathogen Harposporium 25dC 24hr exposure post-adulthood N2 sequences & alignments 3906
- RNA-seq - pathogen Harposporium control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3907
- RNA-seq - pathogen Smacescens 25dC 24hr exposure post-adulthood N2 sequences & alignment 3911
- RNA-seq - pathogen Smacescens control OP50 25dC 24hr exposure post-adulthood N2 sequences & alignments 3912
Part C: Enrichment of promoter motifs
Analysis completed using WormBase version WS190
Interpreted data
- upstream 1000bp regions (promoters) for selected genes, used for motif identification by MEME
- The enrichement of motifs in promoters of stage specific genes
Figure S13: Lab batch effects
Analysis completed using WormBase version WS180
Parts A and B
Source experimental data
- ChIP-seq - N2_POLII_eemb
- ChIP-seq - N2_POLII_lemb
- ChIP-seq - N2_POLII_L1
- ChIP-seq - N2_POLII_L2
- ChIP-seq - N2_POLII_L3
- ChIP-seq - N2_POLII_L4
- ChIP-seq - N2_POLII_YA
- early embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- late embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- L1 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- L2 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- L3 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- L4 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
- Young Adult N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs
Part C
Source experimental data
- embryo A-class motor neurons tiling array 654
- embryo panneural tiling array 455
- embryo GABA motor neurons tiling array 468
- embryo body wall muscle tiling array (v2) 470
- embryo coelomocytes tiling array 458
- embryo intestine tiling array 457
- L2 A-class neuron tiling array 469
- L2 panneural tiling array 462
- L2 GABA neurons tiling array 466
- L2 body wall muscle tiling array 465
- L2 coelomocytes tiling array 657
- L2 intestine tiling array 463
Figure S14: Cumulative plot of isoform composition distribution
Source experimental data
- RNA-seq - mid-L1 20dC 4hrs post-L1 sequences & alignments
- RNA-seq - early embryo sequences & alignments
- RNA-seq - late embryo 20dC 4.5hrs post-early embryo sequences & alignments
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments
- RNA-seq - male mid-L4 dpy28(y1);him-8(e1489) 25dC 30hrs post-L1 sequences & alignments
- RNA-seq - Young Adult 25dC 46hrs post-L1 sequences & alignment
Figure S15: SOM clusters of transcripts with different developmental expression profiles
Analysis completed using WormBase version WS190
Figure S16: Number of genes and transcripts shared between pairs of SOM clusters
Analysis completed using WormBase version WS190
Figure S17: Classes of distinguishing features between isoforms with different developmental expression profiles based on SOM clustering
Analysis completed using WormBase version WS190
Figure S18: Examples of read count distributions supporting differential expression of alternative transcript isoforms among developmental stages
Analysis completed using WormBase version WS190
Figure S19: A breakdown on how the updated list of C. elegans pseudogenes was created
Analysis completed using WormBase version WS200
Interpreted data
Figure S20: Binning of long TARs built from tiling arrays
Graphics only, no data usedFigure S21: Predicting ncRNAs
Analysis completed using WormBase version WS200 and WS170
Interpreted data:
Source experimental data
- RNA-seq - mid-L2 25dC 14 hrs post-L1 sequences & alignments
Figure S22: TF binding around non-coding RNAs
Analysis completed using WormBase version WS190
Source experimental data
- poly-A RNA sequencing data
- small RNA N2 embryos RNA-seq 634
- small RNA N2 mid-L1 RNA-seq 635
- small RNA N2 mid-L2 RNA-seq 636
- small RNA N2 mid-L3 RNA-seq 637
- small RNA N2 mid-L4 RNA-seq 638
- small RNA N2 young adult RNA-seq 639
- small RNA him-8 males RNA-seq 640
- ChIP-chip - Histone_H3K27ac_N2_EEMB_(AB4729_H3K27AC361571_N2_EEMB) 2740
- ChIP-chip - Histone_H3K4me1_N2_EEMB_(AB8895_H3K4ME1733246_N2_EEMB) 2726
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_POLII_emb 586
- ChIP-seq - PHA4_POLII_FedL1 587
- ChIP-seq - PHA4_StarvedL1_POLII 588
- ChIP-seq - AMA1_GFP_L4YA 589
- ChIP-seq - AMA1_POLII_L4YA 590
- ChIP-seq - DAF16_GFP_L4YA 591
- ChIP-seq - DAF16_POLII_L4YA 592
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MAB5_POLII_L3 594
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - UNC-130_GFP_L1 2430
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EOR-1_POLII_L3 3160
- ChIP-seq - HLH-8_POLII_L3 2597
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EGL5_POLII_L3 3162
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - PQM-1_GFP_L3 2623
Figure S23: Co-occurrence of transcription factors
Analysis completed using WormBase version WS190
Interpreted data
Source experimental data:
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_POLII_emb 586
- ChIP-seq - PHA4_POLII_FedL1 587
- ChIP-seq - PHA4_StarvedL1_POLII 588
- ChIP-seq - AMA1_GFP_L4YA 589
- ChIP-seq - AMA1_POLII_L4YA 590
- ChIP-seq - DAF16_GFP_L4YA 591
- ChIP-seq - DAF16_POLII_L4YA 592
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MAB5_POLII_L3 594
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - UNC-130_GFP_L1 2430
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EOR-1_POLII_L3 3160
- ChIP-seq - HLH-8_POLII_L3 2597
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EGL5_POLII_L3 3162
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - PQM-1_GFP_L3 2623
Figure S24: Comparison of PeakSeq and PeakRanger peak calls
Figure S25: Distribution of TF binding numbers
Analysis completed using WormBase version WS190
Interpreted data
Figure S26: Control experiments for HOT regions
Analysis completed using WormBase version WS190
Part B: DPY-27 only binds to HOT regions on the X chromosome
Analysis completed using WormBase version WS190
Source experimental data:
Interpreted data
Figure 27: HOT regions enrichments
Part A
Source experimental data:
Part B
Source experimental data:
- ChIP-seq - PHA4_GFP_emb 582
- ChIP-seq - PHA4_StarvedL1_GFP 584
- ChIP-seq - PHA4_GFP_FedL1 585
- ChIP-seq - PHA4_POLII_emb 586
- ChIP-seq - PHA4_POLII_FedL1 587
- ChIP-seq - PHA4_StarvedL1_POLII 588
- ChIP-seq - AMA1_GFP_L4YA 589
- ChIP-seq - AMA1_POLII_L4YA 590
- ChIP-seq - DAF16_GFP_L4YA 591
- ChIP-seq - DAF16_POLII_L4YA 592
- ChIP-seq - MAB5_GFP_L3 593
- ChIP-seq - MAB5_POLII_L3 594
- ChIP-seq - CEH-14_GFP_L2 734
- ChIP-seq - DPY27_GFP_emb 2416
- ChIP-seq - EOR-1_GFP_L3 3155
- ChIP-seq - LIN-11_GFP_L2 2429
- ChIP-seq - UNC-130_GFP_L1 2430
- ChIP-seq - HLH-1_GFP_emb 2431
- ChIP-seq - LIN-39_GFP_L3 2432
- ChIP-seq - ALR-1_GFP_L2 3156
- ChIP-seq - N2_POLII_eemb 2435
- ChIP-seq - N2_POLII_lemb 2436
- ChIP-seq - N2_POLII_L1 2437
- ChIP-seq - N2_POLII_L2 2438
- ChIP-seq - N2_POLII_L3 2439
- ChIP-seq - N2_POLII_L4 2440
- ChIP-seq - N2_POLII_YA 2441
- ChIP-seq - PES1_GFP_L4 3157
- ChIP-seq - GEI11_GFP_L4 2451
- ChIP-seq - PHA4_GFP_L2 3158
- ChIP-seq - EGL5_GFP_L3 3159
- ChIP-seq - EOR-1_POLII_L3 3160
- ChIP-seq - HLH-8_POLII_L3 2597
- ChIP-seq - PHA4_GFP_lemb 2598
- ChIP-seq - PHA4_GFP_YA 3161
- ChIP-seq - MEP-1_GFP_emb 2600
- ChIP-seq - MDL-1_GFP_L1 2601
- ChIP-seq - LIN-15B_GFP_L3 2610
- ChIP-seq - BLMP-1_GFP_L1 2612
- ChIP-seq - LIN-13_GFP_emb 2613
- ChIP-seq - ELT-3_GFP_L1 2614
- ChIP-seq - EGL5_POLII_L3 3162
- ChIP-seq - CEH-30_GFP_lemb 2620
- ChIP-seq - EGL-27_GFP_L1 2621
- ChIP-seq - SKN-1_GFP_L1 2622
- ChIP-seq - PQM-1_GFP_L3 2623
Part A
Source experimental data:
Figure S28: Higher gene expression level in HOT regions in RNA-seq
Analysis completed using WormBase version WS190
Source experimental data:
Interpreted data
Part B: Higher gene expression level in HOT regions in tiling arrays
Analysis completed using WormBase version WS190
Source experimental data:
- embryo A-class motor neurons tiling array 654
- embryo all cells reference tiling array 456
- embryo AVA neurons tiling array 459
- embryo body wall muscle tiling array (v2) 470
- embryo coelomocytes tiling array 458
- embryo dopaminergic neurons tiling array 467
- embryo GABA motor neurons tiling array 468
- embryo germline precursor cells tiling array 661
- embryo hypodermal cells tiling array 662
- embryo intestine tiling array 457
- embryo panneural tiling array 455
- gonad from young adult 20dC 42hrs post-L1 N2 tiling array 481
- L2 A-class neuron tiling array 469
- L2 body wall muscle tiling array 465
- L2 coelomocytes tiling array 657
- L2 excretory cell tiling array 464
- L2 GABA neurons tiling array 466
- L2 glutamate receptor expressing neurons tiling array 658
- L2 intestine tiling array 463
- L2 panneural tiling array 462
- L3-L4 dopaminergic neuron tiling array 655
- L3-L4 PVD & OLL neurons tiling array 460
- soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array 485
- young adult 25dC 42hrs post-L1 N2 tiling array 475
- Young Adult Cephalic sheath (CEPsh) tiling array 660
Figure S29: HOT regions are broadly expressed
Analysis completed using WormBase version WS190
Interpreted data
Source experimental data:
- embryo A-class motor neurons tiling array 654
- embryo all cells reference tiling array 456
- embryo AVA neurons tiling array 459
- embryo body wall muscle tiling array (v2) 470
- embryo coelomocytes tiling array 458
- embryo dopaminergic neurons tiling array 467
- embryo GABA motor neurons tiling array 468
- embryo germline precursor cells tiling array 661
- embryo hypodermal cells tiling array 662
- embryo intestine tiling array 457
- embryo panneural tiling array 455
- gonad from young adult 20dC 42hrs post-L1 N2 tiling array 481
- L2 A-class neuron tiling array 469
- L2 body wall muscle tiling array 465
- L2 coelomocytes tiling array 657
- L2 excretory cell tiling array 464
- L2 GABA neurons tiling array 466
- L2 glutamate receptor expressing neurons tiling array 658
- L2 intestine tiling array 463
- L2 panneural tiling array 462
- L3-L4 dopaminergic neuron tiling array 655
- L3-L4 PVD & OLL neurons tiling array 460
- soma-only mid-L4 25dC 36hrs post-L1 JK1107 tiling array 485
- young adult 25dC 42hrs post-L1 N2 tiling array 475
- Young Adult Cephalic sheath (CEPsh) tiling array 660
Additional Data Sources
Figure S30: Pair-wise correlations of PHA-4 binding signal across different stages
Analysis completed using WormBase version WS190
Source experimental data:
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new) 2409
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB) 2313
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB) 2339
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB) 2338
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB) 174
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB) 2312
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3) 2407
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM) 2408
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 909
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4) 630
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB) 696
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB) 701
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB) 334
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB) 336
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB) 644
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB) 194
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB) 897
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB) 911
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB) 645
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
Figure S31: Examples of Pol II binding and expression
Analysis completed using WormBase version WS190
Source experimental data:
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new) 2409
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB) 2313
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB) 2339
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB) 2338
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB) 174
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB) 2312
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3) 2407
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM) 2408
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 909
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4) 630
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB) 696
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB) 701
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB) 334
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB) 336
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB) 644
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB) 194
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB) 897
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB) 911
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB) 645
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
Figure S32: Histone marks distribution over repetitive elements
Analysis completed using WormBase version WS190
Source experimental data:
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new) 2409
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB) 2313
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB) 2339
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB) 2338
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB) 174
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB) 2312
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3) 2407
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM) 2408
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 909
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4) 630
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB) 696
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB) 701
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB) 334
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB) 336
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB) 644
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB) 194
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB) 897
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB) 911
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB) 645
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
Figure S33: Promoters of chromosome X genes have higher GC content compared to autosomes
Analysis completed using WormBase version WS190
Source experimental data:
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new) 2409
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB) 2313
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB) 2443
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB) 2410
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB) 2442
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB) 2339
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB) 2338
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB) 174
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB) 2312
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3) 2407
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM) 2408
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4) 599
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB) 973
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3) 2401
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB) 2444
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3) 2406
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB) 2339
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3) 2398
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB) 909
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3) 2399
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3) 2400
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4) 630
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB) 696
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB) 701
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB) 334
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB) 336
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB) 644
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB) 194
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB) 897
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB) 911
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB) 645
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB) 3197
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB) 3198
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3) 2402
Figure S34: Histone marks aggregation around TSSs and TTSs
Source experimental data:
- ChIP-chip - Histone_H3K4me1_N2_EEMB_(AB8895_H3K4ME1733246_N2_EEMB)
- ChIP-chip - Histone_H3K4me1_N2_L3_(AB8895_H3K4ME1733246_N2_L3)
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB)
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3)
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB)
- ChIP-chip - Histone_H3K4me3_from_N2_L3_larvae_(AR0169_H3K4me3_N2_L3)
- ChIP-chip - Histone_H3K9me1_N2_EEMB_(AB9045_H3K9ME1291918_N2_EEMB)
- ChIP-chip - Histone_H3K9me1_N2_L3_(AB9045_H3K9ME1291918_N2_L3)
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB)
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3)
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB)
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3)
- ChIP-chip - Histone_H3K27ac_N2_EEMB_(WA30634849_H3K27AC_N2_EEMB)
- ChIP-chip - Histone_H3K27ac_N2_L3_(AB4729_H3K27AC361571_N2_L3)
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3)
- ChIP-chip - Histone_H3K36me1_N2_EEMB_(AB9048_H3K36ME1206009_N2_EEMB)
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB)
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3)
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB)
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3)
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB)
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB)
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB)
- ChIP-chip - Histone_H4K8ac_N2_L3_(AB15823_H4K8AC487128_N2_L3)
- ChIP-chip - Histone_H4_Tetra_ac_N2_EEMB_(LPAR109_H4TETRAAC109_N2_EEMB)
- ChIP-chip - Histone_H3K20me1_N2_EEMB_(AB9051_H4K20ME1104513_N2_EEMB)
- ChIP-chip - HK00013_H3K27ME31E7_N2_EEMB
- ChIP-chip - UP07448_H3K27ME124439_N2_EEMB
- ChIP-chip - AB15823_H4K8AC487128_N2_EEMB
- ChIP-chip - MP07329_H4K16ACDAM1612187_N2_EEMB
Figure S35: TF sequence motif discovery
Analysis completed using WormBase version WS190
Figure S36: TFs in the larval network
Figure S37: Network motifs
Analysis completed using WormBase version WS170
Interpreted data
Source experimental data:
- ChIP-seq - PHA4_GFP_emb
- ChIP-seq - PHA4_StarvedL1_GFP
- ChIP-seq - PHA4_GFP_FedL1
- ChIP-seq - PHA4_POLII_emb
- ChIP-seq - PHA4_POLII_FedL1
- ChIP-seq - PHA4_StarvedL1_POLII
- ChIP-seq - AMA1_GFP_L4YA
- ChIP-seq - AMA1_POLII_L4YA
- ChIP-seq - DAF16_GFP_L4YA
- ChIP-seq - DAF16_POLII_L4YA
- ChIP-seq - MAB5_GFP_L3
- ChIP-seq - MAB5_POLII_L3
- ChIP-seq - CEH-14_GFP_L2
- ChIP-seq - DPY27_GFP_emb
- ChIP-seq - EOR-1_GFP_L3
- ChIP-seq - HLH-8_GFP_L3
- ChIP-seq - LIN-11_GFP_L2
- ChIP-seq - UNC-130_GFP_L1
- ChIP-seq - HLH-1_GFP_emb
- ChIP-seq - LIN-39_GFP_L3
- ChIP-seq - NHR-6_GFP_L2
- ChIP-seq - ALR-1_GFP_L2
- ChIP-seq - N2_POLII_eemb
- ChIP-seq - N2_POLII_lemb
- ChIP-seq - N2_POLII_L1
- ChIP-seq - N2_POLII_L2
- ChIP-seq - N2_POLII_L3
- ChIP-seq - N2_POLII_L4
- ChIP-seq - N2_POLII_YA
- ChIP-seq - PES1_GFP_L4
- ChIP-seq - GEI11_GFP_L4
- ChIP-seq - PHA4_GFP_L2
- ChIP-seq - EGL5_GFP_L3
- ChIP-seq - EOR-1_POLII_L3
- ChIP-seq - HLH-8_POLII_L3
- ChIP-seq - PHA4_GFP_lemb
- ChIP-seq - PHA4_GFP_YA
- ChIP-seq - MEP-1_GFP_emb
- ChIP-seq - MDL-1_GFP_L1
- ChIP-seq - LIN-15B_GFP_L3
- ChIP-seq - BLMP-1_GFP_L1
- ChIP-seq - LIN-13_GFP_emb
- ChIP-seq - ELT-3_GFP_L1
- ChIP-seq - EGL5_POLII_L3
- ChIP-seq - NHR-105_GFP_L3
- ChIP-seq - CEH-30_GFP_lemb
- ChIP-seq - EGL-27_GFP_L1
- ChIP-seq - SKN-1_GFP_L1
- ChIP-seq - PQM-1_GFP_L3
Figure S38: TF binding and chromatin features
Analysis completed using WormBase version WS182
Part A: Correlations between whole-genome transcription factor binding signals and chromatin features
Analysis completed using WormBase version WS182
Source experimental data:
- ChIP-chip - Histone_H3_N2_L3_(AB1791_H3_N2_L3_new)
- ChIP-chip - Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB)
- ChIP-chip - Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB)
- ChIP-chip - Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB)
- ChIP-chip - Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB)
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB)
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB)
- ChIP-chip - POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB)
- ChIP-chip - Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB)
- ChIP-chip - Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3)
- ChIP-chip - Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM)
- ChIP-chip - POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4)
- ChIP-chip - Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB)
- ChIP-chip - Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3)
- ChIP-chip - Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB)
- ChIP-chip - Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3)
- ChIP-chip - Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB)
- ChIP-chip - Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3)
- ChIP-chip - Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB)
- ChIP-chip - Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3)
- ChIP-chip - Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3)
- ChIP-chip - DPY-27_N2_L4(JL00001_DPY27_N2_L4)
- ChIP-chip - DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB)
- ChIP-chip - SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB)
- ChIP-chip - DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB)
- ChIP-chip - MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB)
- ChIP-chip - DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB)
- ChIP-chip - HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB)
- ChIP-chip - MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB)
- ChIP-chip - MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB)
- ChIP-chip - SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB)
- ChIP-chip - Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB)
- ChIP-chip - Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB)
- ChIP-chip - Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3)
Part B: Modeling accuracy of models involving either all features or individual features
Analysis completed using WormBase version WS182
Figure S39: Machine learning procedure for modeling TF binding peaks
Graphics only, no data usedFigure S40: TF binding model accuracy
Analysis completed using WormBase version WS182
Source experimental data:
- Histone_H3_N2_L3_(AB1791_H3_N2_L3_new)
- Histone_H3_N2_EEMB_2_(AB1791_H3609253_N2_EEMB)
- Histone_H3K79me3_N2_EEMB_(AB2621_H3K79ME3361576_N2_EEMB)
- Histone_H3K79me1_N2_EEMB_(AB2886_H3K79ME1361912_N2_EEMB)
- Histone_H3K79me2_N2_EEMB_(AB3594_H3K79ME3905021_N2_EEMB)
- Histone_H3K9me3_N2_EEMB_2_(AB8898_H3K9ME3339901_N2_EEMB)
- Histone_H3K36me2_N2_EEMB_(AB9049_H3K36ME2608457_N2_EEMB)
- POL-2_CTD_Mixed_Embryos (ABAB5408_4H8_N2_MXEMB)
- Histone_H3_N2_EEMB_1_(AR0144_H3144_N2_EEMB)
- Histone_H3_N2_L3_2_(AR0144_H3144_N2_L3)
- Histone_H3_N2_L3_1_(AR0144_H3144_N2_L3_LM)
- POL-2_N2_L4_(CVMMS126R_8WG16_N2_L4)
- Histone_H3K36me3_N2_EEMB_(HK00001_H3K36ME313C9_N2_EEMB)
- Histone_H3K36me3_N2_L3_(HK00001_H3K36ME313C9_N2_L3)
- Histone_H3K9me2_N2_EEMB_(HK00008_H3K9ME26D11_N2_EEMB)
- Histone_H3K9me2_N2_L3_(HK00008_H3K9ME26D11_N2_L3)
- Histone_H3K9me3_N2_EEMB_2_(HK00009_H3K9ME32F3_N2_EEMB)
- Histone_H3K9me3_N2_L3_(HK00009_H3K9ME32F3_N2_L3)
- Histone_H3K36me2_N2_EEMB_(HK00012_H3K36ME22C3_N2_EEMB)
- Histone_H3K36me2_N2_L3_(HK00012_H3K36ME22C3_N2_L3)
- Histone_H3K27me3_N2_L3_(HK00013_H3K27ME31E7_N2_L3)
- DPY-27_N2_L4(JL00001_DPY27_N2_L4)
- DPY27_YPT47(V;X)_MXEMB(JL00001_DPY27_YPT47_MXEMB)
- SDC3_YPT47(V;X)_MXEMB(JL00002_SDC3_YPT47_MXEMB)
- DPY-26_N2_Mixed_Embryos_(JL00003_DPY26_N2_MXEMB)
- MIX-1_N2_Mixed_Embryos_(JL00004_MIX1_N2_MXEMB)
- DPY-28_N2_MXEMB_(JL00012_DPY28_N2_MXEMB)
- HCP-3_CENP-A_Mixed_Embryos_(OD00001_HCP3_N2_MXEMB)
- MRG-1_N2_EEMB_(SDQ0790_MRG1_N2_EEMB)
- MES-4_N2_EEMB_(SDQ0791_MES4_N2_EEMB)
- SDC-2_N2_MXEMB_(SDQ3146_SDC2_N2_MXEMB)
- Histone_H3K4me3_N2_EEMB_(WA30534819_H3K4ME3_N2_EEMB)
- Histone_H3K4me2_N2_EEMB_(WA30834809_H3K4ME2_N2_EEMB)
- Histone_H3K4me2_N2_L3_(WA30834809_H3K4ME2_N2_L3)
Figure S41: Average signals of some chromatin marks at the binding- peaks and non-binding-peaks of TFs
Figure S42: Developmental stage-specific models
Analysis completed using WormBase version WS182
Figure S43: Combination of chromatin and sequence features
Analysis completed using WormBase version WS190
Interpreted data:
- positional weighted matrix for HLH-1
- positional weighted matrix for HLH-1 from database
- PPV at different cut-off values
- PPV at different cut-off values
Figure S44: Coverage of evolutionarily constrained regions by genomic features
Analysis completed using WormBase version WS182
Figure S45: Conservation enrichment analysis
Figure S46: PhastCons score correlation with peak centers in modENCODE peak calls
Figure S47: Saturation of TF binding
Analysis completed using WormBase version WS182
Figure S48: Comparison of coverage between ENCODE pilot and modENCODE C. elegans project
Figure S49: RNAPII ChIP-seq signal aggregation in human and C. elegans
Figure S50: Comparison of histone marks in C. elegans early embryos and human CD4T cells
Supplementary Tables
Supplement Table 1: Data overview for RNA sequencing and expression tiling arrays
Interpreted data:Source experimental data:
Supplement Table 1b: ChIP-chip, ChIP-seq, and other chromatin-characterization experiments
Interpreted data:Source experimental data:
Supplement Table 1c: Inferred genomic elements
Interpreted data:Source experimental data:
Supplement Table 2a: Sources of polyA sites in final integrated transcript set
Interpreted data:Source experimental data:
Supplement Table 2b: C. elegans genes not identified as “transcribed†in 19 polyA RNA-seq samples
Interpreted data:Source experimental data:
Supplement Table 3: Developmental stages and tissue samples of small RNA-seq and tiling array experiments
Interpreted data:Source experimental data:
Supplement Table 4: Summary of cell and stage specific tiling array results
Interpreted data:Source experimental data:
Supplement Table 5: Different types of known ncRNAs
Interpreted data:Source experimental data:
Supplement Table 6: Annotated regions used for the training of machine learning methods (21K- set) – tiling array TARs
Interpreted data:Source experimental data:
Supplement Table 7: Performance of our integrated method (21K-set) on tiling array TARsa with three different ways to define element classes in the gold-standard set
Interpreted data:Source experimental data:
Supplement Table 8: Annotated and novel tiling array TARs going into 21K-set of ncRNAs
Interpreted data:Source experimental data:
Supplement Table 9: Co-expression clusters of coding transcripts and novel ncRNA candidates (7K-set)
Interpreted data:Source experimental data:
Supplement Table 10: Total mapped reads, numbers of peaks bound by each of 23 factors (22 TFs and one dosage compensation factor, 28 experiments in total) from ChIP-seq
Interpreted data:Corrected Table S10 Source experimental data:
- ChIP-seq ALR1_L2_peaks
- ChIP-seq BLMP1_L1_peaks
- ChIP-seq CEH14_L2_peaks
- ChIP-seq CEH30_LATEEMBRYO_peaks
- ChIP-seq DPY27_EMB_peaks
- ChIP-seq EGL27_L1_peaks
- ChIP-seq EGL5_L3_peaks
- ChIP-seq ELT3_L1_peaks
- ChIP-seq EOR1_L3_peaks
- ChIP-seq GEI11_L4_peaks
- ChIP-seq HLH1_EMB_peaks
- ChIP-seq LIN11_L2_peaks
- ChIP-seq LIN13_EMB_peaks
- ChIP-seq LIN15B_L3_peaks
- ChIP-seq LIN39_L3_peaks
- ChIP-seq MAB5_L3_peaks
- ChIP-seq MDL1_L1_peaks
- ChIP-seq MEP1_EMB_peaks
- ChIP-seq PES1_L4_peaks
- ChIP-seq PHA4_EMB_peaks
- ChIP-seq PHA4_L1_peaks
- ChIP-seq PHA4_L2_peaks
- ChIP-seq PHA4_LATE_peaks
- ChIP-seq PHA4_STARVED_peaks
- ChIP-seq PHA4_YA_peaks
- ChIP-seq PQM_L3_peaks
- ChIP-seq SKN1_L1_peaks
- ChIP-seq UNC130_L1_peaks
Supplement Table 11: GO analysis of genes associated with HOT regions
Interpreted data:Source experimental data:
Supplement Table 12: Expression correlation of transcription factors with target genes and non- target genes
Interpreted data:Source experimental data:
Supplement Table 13: Overview of PicTar-predicted miRNA target sites within 3'UTRs of the aggregated integrated transcript set
Interpreted data:Source experimental data:
Supplement Table 14: Overlap of 4.1 Mb of residual constrained blocks with various genomic elements
Interpreted data:Source experimental data:
Supplement Table 15: Sample comparison of C. elegans and human TF binding regions
Interpreted data:Source experimental data:
Supplement Table 16: Sample comparison of C. elegans and human transcription
Interpreted data:Source experimental data:
Supplement Table 17: Table of Wormbase versions used
Interpreted data:Source experimental data:
Supplementary Files
Supplement File 1
Genome positions and predicted scores of predicted long ncRNA TARs (set-21K)Supplement File 2
(Dataset S#) Coordinates for PicTar-predicted miRNA target sites within 3'UTRs of the ag1003 transcript setSupplement File 3
Coordinates for HOT regionsSupplement File 4
Predicted ncRNAs, 7K setAnalysis Tools
- Phylogenetic analysis with space/time models (PHAST) software
- The Yale Network Analyzer (tYNA)
- Cytoscape
- Aggregation and Correlation Toolbox
- IQseq
- RSEQtools
- UCSC Genome Browser
- SHRiMP aligner v1.3
- Integrative Genomics Viewer
- AceView
- documented source code for Deepseq9 algorithm at SourceForge, http://deepseq9.sourceforge.net
Companion Papers
- M. Kato, X. Chen, S. Inukai, H. Zao, F. Slack, Age-associated changes in expression of small, non-coding RNAs, including microRNAs, in C. elegans. Genome Res., (submitted).
- X. Feng, L. Stein, High resolution peak calling for Chromatin IP Sequencing. (submitted).
- S. Contrino et al., Accessing modENCODE data. Genome Res., (submitted).
- H. Lei et al., A widespread distribution of genomic CeMyoD binding sites revealed and cross-validated by ChIP-chip and ChIP-Seq techniques. PLoS One, (submitted).
- M. Friedlander, S. Mackowiak, N. Rajewsky, miRDeep 2.0. (manuscript in preparation).
- W. Chung et al., Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res., (submitted).
- B. Ewing, A. Leahey, L. Hillier, C. Davis, P. Green, Targeted closure of the C. elegans transcriptome. (manuscript in preparation).
- N. L. Washington et al., The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details. Genome Res., (submitted).
- W. C. Spencer et al., A spatial and temporal map of C. elegans gene expression. (manuscript in preparation).
- W. Niu et al., Systematic dissection of regulatory networks dictated by C. elegans sequence-specific transcription factors. (manuscript in preparation).
- W. Niu, ..., V. Reinke, Diverse transcription factor binding features revealed by genome-wide ChIP-Seq in C. elegans. Genome Res., (submitted).
- Z. J. Lu et al., Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data. Genome Res., (submitted).
- T. Liu et al., Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res, (submitted).
- C. H. Jan, R. C. Friedman, J. G. Ruby, C. B. Burge, D. P. Bartel, Formation and regulation of 3´ untranslated regions in Caenorhabditis elegans. (manuscript in preparation).
- S. Ercan, Y. Lubling, E. Segal, J. D. Lieb, High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans Genome Res, (submitted).
- M. A. Allen, L. W. Hillier, R. H. Waterston, T. Blumenthal, A global analysis of trans-splicing in C. elegans. Genome Res., (submitted).
All listed URLs
- Short Read Archive
- Gene Expression Omnibus
- WormBase
- Full analysis of C. elegans mirtrons
- modMine
- Methods used to build six-way nematode genome alignments
- Genome sequence of Caenorhabditis briggsae
- Genome sequence of Caenorhabditis remanei
- Genome sequence of Caenorhabditis brenneri
- Genome sequence of Pristionchus pacificus
- Genome sequence of Caenorhabditis japonica
- Phylogenetic analysis with space/time models (PHAST) software
- The Yale Network Analyzer (tYNA)
- Cytoscape
- Aggregation and Correlation Toolbox
- IQseq
- RSEQtools
- UCSC Genome Browser
- SHRiMP aligner v1.3
- Integrative Genomics Viewer
- AceView
- documented source code for Deepseq9 algorithm at SourceForge, http://deepseq9.sourceforge.net