Companion Page for modENCODE Integrative Fly Paper
Figure 1: Overview of the Drosophila modENCODE project
Graphics onlyFigure 2: Coding and non-coding genes and structures
- Lai_GSM280088_S2cells_Ago1IP 2380
- Lai_CantonS_male 2751
- Lai_one day adult female-ENCODE/BS152 2009
- Lai_one day adult male-ENCODE/BS149 2008
- Dev Timecourse Adult Female Eclosion+5d RNA-Seq multimapped reads 2795
- Dev Timecourse Adult Male Eclosion+5d RNA-Seq multimapped reads 2791
- Dev Timecourse Adult Female Eclosion+30d RNA-Seq multimapped reads 2793
- Dev Timecourse Adult Male Eclosion+30d RNA-Seq multimapped reads 2792
Figure 3: Chromatin-based annotation of functional elements
- GAF.S2 - 285
- RNA Pol II (ALG).S2- 329
- H4AcTetra.S2 201
- H3K4Me3(LP).S2 305
- H3K4me2.ab.S2 965
- H3K9ac.S2 309
- H4K16ac(L).S2 319
- H3K79Me2.S2 307
- H2B-ubiq (NRO3).S2 290
- H3K36me3.S2 303
- H3K79Me.S2 963
- H3K27Ac.S2 296
- H4K8ac.S2 322
- H3K18ac.S2 292
- H3K4me1.S2 304
- H4K5ac.S2 321
- H3K23ac.S2 294
- MB8 gene models 2675
- Orc2 BG3 ChIP-Seq 2754
- Bg3 Replication Timing 670
- Bg3 Replication Origins 711
- H3K36me1.S2 3170
- 150-600_mM_Salt_Extracted_Chromatin_H2Av 2525
- 150-600_mM_Salt_Extracted_Chromatin_H3.3 2526
- 150-600_mM_Salt_Extracted_Chromatin_S2 2527
- 150_mM_Salt_Extracted_Chromatin 2503
- 600_mM_Salt_Extracted_Chromatin_Pellet 2502
- 80-150_mM_Salt_Extracted_Chromatin_H2Av 2521
- 80-150_mM_Salt_Extracted_Chromatin_S2 2522
- 80-600_mM_Salt_Extracted_Chromatin_H2Av 2524
- 80-600_mM_Salt_Extracted_Chromatin_H3.3 2523
- 80_mM_Salt_Extracted_Chromatin_H2A 2518
- 80_mM_Salt_Extracted_Chromatin_H2Av 2519
- 80_mM_Salt_Extracted_Chromatin_H3.3 2520
- 80_mM_Salt_Extracted_Chromatin_S2 2517
- Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin 2507
- Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin 2508
- Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin_Pellet 2509
- Fly_embryos_4-6_hr_150_mM_Salt_Extracted_Chromatin 2510
- Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin 2511
- Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet 2512
- Fly_wing_disc_150_mM_Salt_Extracted_Chromatin 2514
- Fly_wing_disc_600_mM_Salt_Extracted_Chromatin 2515
- Fly_wing_disc_600_mM_Salt_Extracted_Chromatin_Pellet 2516
- Fly_wing_disc_80_mM_Salt_Extracted_Chromatin 2513
- H2A_EDTA 2505
- H2Av_EDTA 2504
- Mononucleosomes_H2Av 2529
- Mononucleosomes_H3.3 2528
- Nucleosome_Density_S2 2506
- Orc2 BG3 ChIP-Seq 2754
- Bg3 Replication Timing 670
- Bg3 Replication Origins 711
Figure 4: Discovery and characterization of chromatin states and their functional enrichments
- E0-12h-bab1 628
- E-0-12h-bks 609
- E-0-4h_bks 2569
- pupae-brm ChIP-chip 602
- A-Female_7T_ChIP-seq 2625
- E0-4h_7T_ChIP-seq 2626
- E4-8h_7T_ChIP-seq 2637
- E0-4_GFP_7T ChIP-chip 902
- E0-4_CBP_chip-seq 854
- E0-4_CBP 900
- Embryo 0-12h chinmo ChIP-chip 608
- E0-12h-CNC 627
- E0-12h-D 626
- E0-8_D 2571
- E-0-12h-dCtBP7667 607
- E0-8h_disco 2572
- E-0-12h-dll 606
- ISO1_8-16_Ez 2585
- W3L_EcRGFP_ChIP_seq 2640
- WPP_EcR_GFP_ChIP-seq 2641
- WPP30-33_EcR_GFP_ChIP-seq 2642
- Embryo 7-24h end300 ChIP-chip 611
- E0-12h-ENserum 625
- R13_1-6_eve-GFP 2603
- E0-12h-FTZ-F1 624
- E0-8h_GATAe 2573
- E0-12h-Gro3 623
- E0-12 GROAviva ChIP-chip 597
- Embryo 7-24h gsbnpurif ChIP-chip 610
- E0-8h_h 2574
- E0-8h_hkb 2575
- E-0-12h-INV7657 605
- Embryo 0-12h INV-GFP ChIP-chip 619
- E0-8h_jumu 2576
- E0-12h-KN 618
- E0-8_Kr-D2 ChIP-chip 898
- E0-12h-RUN7659 617
- E4-8_GFP-sens 979
- E4-8h_sens 2577
- E4-8_sens 978
- Pupae-snr1 ChIP-chip 601
- E0-12h-Stat92E 616
- Embryo 0-12h GAF ChIP-chip 23
- Kc167_Trl 2568
- E0-12h-TTK 615
- Embryo 3-8h UBX1 ChIP-chip 613
- Embryo 3-8h UBX2 ChIP-chip 612
- E0-12h-UBX7701 614
- Embryo 3-8h UBX7701 ChIP-chip 603
- Embryo 0-12h ZFH1 ChIP-chip 604
- 7T-E4-8h_GFP 2578
- E0-4h_cad 2570
- Orc2 BG3 ChIP-Seq 2754
- Bg3 Replication Timing 670
- Bg3 Replication Origins 711
- H3K18ac.BG3 291
- H3K18ac.S2 292
- H3K23ac.BG3 293
- H3K23ac.S2 294
- H3K27Ac.BG3 295
- H3K27Ac.S2 296
- H3K27Me3 (Abcam2).BG3 297
- H3K27me3 (Abcam2).S2 298
- H3K36me1.BG3 299
- H3K36me3.BG3 301
- H3K36me3.Kc 302
- H3K36me3.S2 303
- H3K4me1.S2 304
- H3K4Me3(LP).S2 305
- H3K79me1.S2 2572
- H3K79Me2.BG3 306
- H3K79Me2.S2 307
- H3K9ac.S2 309
- H3K9me2-Ab2 (new lot).BG3 310
- H3K9me2 antibody2.S2 311
- H3K9me3 (new lot).BG3 312
- H3K9me3.S2 313
- H4K16ac(L).Clone_8 317
- H4K16ac(L).Kc 318
- H4K16ac(L).S2 319
- H4K16ac(M).S2 320
- mod2.2-VC.BG3 324
- SU(HW)-HB.S2 330
- Su(Hw)-VC.S2 331
- BEAF-HB.S2 274
- CTCF-VC.BG3 282
- CTCF-VC.S2 283
- CP190-VC.S2 280
Figure 5: High-occupancy TF binding regions and their relation to motifs, ORC, and chromatin
- E0-12h-bab1 628
- E-0-12h-bks 609
- E-0-4h_bks 2569
- pupae-brm ChIP-chip 602
- A-Female_7T_ChIP-seq 2625
- E0-4h_7T_ChIP-seq 2626
- E4-8h_7T_ChIP-seq 2637
- E0-4_GFP_7T ChIP-chip 902
- E0-4_CBP_chip-seq 854
- E0-4_CBP 900
- Embryo 0-12h chinmo ChIP-chip 608
- E0-12h-CNC 627
- E0-12h-D 626
- E0-8_D 2571
- E-0-12h-dCtBP7667 607
- E0-8h_disco 2572
- E-0-12h-dll 606
- ISO1_8-16_Ez 2585
- W3L_EcRGFP_ChIP_seq 2640
- WPP_EcR_GFP_ChIP-seq 2641
- WPP30-33_EcR_GFP_ChIP-seq 2642
- Embryo 7-24h end300 ChIP-chip 611
- E0-12h-ENserum 625
- R13_1-6_eve-GFP 2603
- E0-12h-FTZ-F1 624
- E0-8h_GATAe 2573
- E0-12h-Gro3 623
- E0-12 GROAviva ChIP-chip 597
- Embryo 7-24h gsbnpurif ChIP-chip 610
- E0-8h_h 2574
- E0-8h_hkb 2575
- E-0-12h-INV7657 605
- Embryo 0-12h INV-GFP ChIP-chip 619
- E0-8h_jumu 2576
- E0-12h-KN 618
- E0-8_Kr-D2 ChIP-chip 898
- E0-12h-RUN7659 617
- E4-8_GFP-sens 979
- E4-8h_sens 2577
- E4-8_sens 978
- Pupae-snr1 ChIP-chip 601
- E0-12h-Stat92E 616
- Embryo 0-12h GAF ChIP-chip 23
- Kc167_Trl 2568
- E0-12h-TTK 615
- Embryo 3-8h UBX1 ChIP-chip 613
- Embryo 3-8h UBX2 ChIP-chip 612
- E0-12h-UBX7701 614
- Embryo 3-8h UBX7701 ChIP-chip 603
- Embryo 0-12h ZFH1 ChIP-chip 604
- 7T-E4-8h_GFP 2578
- E0-4h_cad 2570
Figure 6: Genome coverage by modENCODE datasets
- E0-12h-bab1 628
- E-0-12h-bks 609
- E-0-4h_bks 2569
- pupae-brm ChIP-chip 602
- A-Female_7T_ChIP-seq 2625
- E0-4h_7T_ChIP-seq 2626
- E4-8h_7T_ChIP-seq 2637
- E0-4_GFP_7T ChIP-chip 902
- E0-4_CBP_chip-seq 854
- E0-4_CBP 900
- Embryo 0-12h chinmo ChIP-chip 608
- E0-12h-CNC 627
- E0-12h-D 626
- E0-8_D 2571
- E-0-12h-dCtBP7667 607
- E0-8h_disco 2572
- E-0-12h-dll 606
- ISO1_8-16_Ez 2585
- W3L_EcRGFP_ChIP_seq 2640
- WPP_EcR_GFP_ChIP-seq 2641
- WPP30-33_EcR_GFP_ChIP-seq 2642
- Embryo 7-24h end300 ChIP-chip 611
- E0-12h-ENserum 625
- R13_1-6_eve-GFP 2603
- E0-12h-FTZ-F1 624
- E0-8h_GATAe 2573
- E0-12h-Gro3 623
- E0-12 GROAviva ChIP-chip 597
- Embryo 7-24h gsbnpurif ChIP-chip 610
- E0-8h_h 2574
- E0-8h_hkb 2575
- E-0-12h-INV7657 605
- Embryo 0-12h INV-GFP ChIP-chip 619
- E0-8h_jumu 2576
- E0-12h-KN 618
- E0-8_Kr-D2 ChIP-chip 898
- E0-12h-RUN7659 617
- E4-8_GFP-sens 979
- E4-8h_sens 2577
- E4-8_sens 978
- Pupae-snr1 ChIP-chip 601
- E0-12h-Stat92E 616
- Embryo 0-12h GAF ChIP-chip 23
- Kc167_Trl 2568
- E0-12h-TTK 615
- Embryo 3-8h UBX1 ChIP-chip 613
- Embryo 3-8h UBX2 ChIP-chip 612
- E0-12h-UBX7701 614
- Embryo 3-8h UBX7701 ChIP-chip 603
- Embryo 0-12h ZFH1 ChIP-chip 604
- 7T-E4-8h_GFP 2578
- E0-4h_cad 2570
- Splice Junction Annotation Adult Female, eclosion + 1d 2712
- Splice Junction Annotation Adult Female, eclosion + 30d 2716
- Splice Junction Annotation Adult Female, eclosion + 5d 2714
- Splice Junction Annotation Adult Male, eclosion + 1d 2713
- Splice Junction Annotation Adult Male, eclosion + 30d 2717
- Splice Junction Annotation Adult Male, eclosion + 5d 2715
- Splice Junction Annotation Embryo 0-2h 2688
- Splice Junction Annotation Embryo 10-12h 2693
- Splice Junction Annotation Embryo 12-14h 2694
- Splice Junction Annotation Embryo 14-16h 2695
- Splice Junction Annotation Embryo 16-18h 2696
- Splice Junction Annotation Embryo 18-20h 2697
- Splice Junction Annotation Embryo 2-4h 2689
- Splice Junction Annotation Embryo 20-22h 2698
- Splice Junction Annotation Embryo 22-24h 2699
- Splice Junction Annotation Embryo 4-6h 2690
- Splice Junction Annotation Embryo 6-8h 2691
- Splice Junction Annotation Embryo 8-10h 2692
- Splice Junction Annotation Larvae L1 2700
- Splice Junction Annotation Larvae L2 2701
- Splice Junction Annotation Larvae L3 12hr post-molt 2702
- Splice Junction Annotation Larvae L3, clear gut PS7-9 2705
- Splice Junction Annotation Larvae L3, dark blue gut PS1-2 2703
- Splice Junction Annotation Larvae L3, light blue gut PS3-6 2704
- Splice Junction Annotation Pupae, WPP + 2d 2709
- Splice Junction Annotation Pupae, WPP + 3d 2710
- Splice Junction Annotation Pupae, WPP + 4d 2711
- Splice Junction Annotation White Prepupae 2706
- Splice Junction Annotation White Prepupae, WPP + 12hr 2707
- Splice Junction Annotation White Prepupae, WPP + 24hr 2708
- Dev Timecourse Adult Female Eclosure+1d RNA-Seq multimapped reads 2794
- Dev Timecourse Adult Female Eclosion+30d RNA-Seq multimapped reads 2793
- Dev Timecourse Adult Female Eclosion+5d RNA-Seq multimapped reads 2795
- Dev Timecourse Adult Male Eclosion+1d RNA-Seq multimapped reads 2790
- Dev Timecourse Adult Male Eclosion+30d RNA-Seq multimapped reads 2792
- Dev Timecourse Adult Male Eclosion+5d RNA-Seq multimapped reads 2791
- Dev Timecourse Embryo 0-2h RNA-Seq multimapped reads 2796
- Dev Timecourse Embryo 10-12h RNA-Seq multimapped reads 2797
- Dev Timecourse Embryo 12-14h RNA-Seq multimapped reads 2798
- Dev Timecourse Embryo 14-16h RNA-Seq multimapped reads 2799
- Dev Timecourse Embryo 16-18h RNA-Seq multimapped reads 2780
- Dev Timecourse Embryo 18-20h RNA-Seq multimapped reads 2801
- Dev Timecourse Embryo 2-4h RNA-Seq multimapped reads 2804
- Dev Timecourse Embryo 20-22h RNA-Seq multimapped reads 2802
- Dev Timecourse Embryo 22-24h RNA-Seq multimapped reads 2803
- Dev Timecourse Embryo 4-6h RNA-Seq multimapped reads 2805
- Dev Timecourse Embryo 6-8h RNA-Seq multimapped reads 2806
- Dev Timecourse Embryo 8-10h RNA-Seq multimapped reads 2807
- Dev Timecourse Larvae L1 RNA-Seq multimapped reads 2808
- Dev Timecourse Larvae L2 RNA-Seq multimapped reads 2809
- Dev Timecourse Larvae L3 12hr RNA-Seq multimapped reads 2810
- Dev Timecourse Larvae L3 PS7-9 RNA-Seq multimapped reads 2813
- Dev Timecourse Larvae L3 PS1-2 RNA-Seq multimapped reads 2811
- Dev Timecourse Larvae L3 PS3-6 RNA-Seq multimapped reads 2812
- Dev Timecourse White Pre-pupae 2 days RNA-Seq multimapped reads 2817
- Dev Timecourse White Pre-pupae 3 days RNA-Seq multimapped reads 2818
- Dev Timecourse White Pre-pupae 4 days RNA-Seq multimapped reads 2819
- Dev Timecourse White Pre-pupae RNA-Seq multimapped reads 2814
- Dev Timecourse White Pre-pupae 12hr RNA-Seq multimapped reads 2815
- Dev Timecourse White Pre-pupae 24hr RNA-Seq multimapped reads 2816
- MB8 gene models 2675
- Directed cDNA Full Insert Sequencing 2550
- Orc2 BG3 ChIP-Seq 2754
- Bg3 Replication Timing 670
- Bg3 Replication Origins 711
- Lai_GSM280088_S2cells_Ago1IP 2380
- 150-600_mM_Salt_Extracted_Chromatin_H2Av 2525
- 150-600_mM_Salt_Extracted_Chromatin_H3.3 2526
- 150-600_mM_Salt_Extracted_Chromatin_S2 2527
- 150_mM_Salt_Extracted_Chromatin 2503
- 600_mM_Salt_Extracted_Chromatin_Pellet 2502
- 80-150_mM_Salt_Extracted_Chromatin_H2Av 2521
- 80-150_mM_Salt_Extracted_Chromatin_S2 2522
- 80-600_mM_Salt_Extracted_Chromatin_H2Av 2524
- 80-600_mM_Salt_Extracted_Chromatin_H3.3 2523
- 80_mM_Salt_Extracted_Chromatin_H2A 2518
- 80_mM_Salt_Extracted_Chromatin_H2Av 2519
- 80_mM_Salt_Extracted_Chromatin_H3.3 2520
- 80_mM_Salt_Extracted_Chromatin_S2 2517
- Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin 2507
- Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin 2508
- Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin_Pellet 2509
- Fly_embryos_4-6_hr_150_mM_Salt_Extracted_Chromatin 2510
- Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin 2511
- Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet 2512
- Fly_wing_disc_150_mM_Salt_Extracted_Chromatin 2514
- Fly_wing_disc_600_mM_Salt_Extracted_Chromatin 2515
- Fly_wing_disc_600_mM_Salt_Extracted_Chromatin_Pellet 2516
- Fly_wing_disc_80_mM_Salt_Extracted_Chromatin 2513
- H2A_EDTA 2505
- H2Av_EDTA 2504
- Mononucleosomes_H2Av 2529
- Mononucleosomes_H3.3 2528
- Nucleosome_Density_S2 2506
- BEAF-HB.S2 274
- CTCF-VC.BG3 282
- CTCF-VC.S2 283
- Chro(Chriz)BR.BG3 275
- Chro(Chriz)BR.Clone_8 276
- Chro(Chriz)BR.Kc 277
- Chro(Chriz)BR.S2 278
- Chro(Chriz)WR.S2 279
- CP190-VC.S2 280
- Ez.S2 284
- H2B-ubiq (NRO3).BG3 288
- H2B-ubiq (NRO3).Kc 289
- H2B-ubiq (NRO3).S2 290
- H3K18ac.BG3 291
- H3K18ac.S2 292
- H3K23ac.BG3 293
- H3K23ac.S2 294
- H3K27Ac.BG3 295
- H3K27Ac.S2 296
- H3K27Me3 (Abcam2).BG3 297
- H3K27me3 (Abcam2).S2 298
- H3K36me1.BG3 299
- H3K36me3.BG3 301
- H3K36me3.Kc 302
- H3K36me3.S2 303
- H3K4me1.S2 304
- H3K4Me3(LP).S2 305
- H3K79Me2.BG3 306
- H3K79Me2.S2 307
- H3K9ac.S2 309
- H3K9me2-Ab2 (new lot).BG3 310
- H3K9me2 antibody2.S2 311
- H3K9me3 (new lot).BG3 312
- H3K9me3.S2 313
- H4K16ac(L).BG3 316
- H4K16ac(L).Clone_8 317
- H4K16ac(L).Kc 318
- H4K16ac(L).S2 319
- H4K16ac(M).S2 320
- H4K5ac.S2 321
- H4K8ac.S2 322
- H4AcTetra.S2 201
- Pc.BG3 325
- Pc.S2 326
- RNA pol II (ALG).Clone_8 327
- RNA pol II (ALG).Kc 328
- RNA pol II (ALG).S2 329
- mod2.2-VC.BG3 324
- SU(HW)-HB.S2 330
- Su(Hw)-VC.S2 331
- Trx-C.S2 332
- GAF.BG3 2651
- GAF.S2 285
- H3K36me1.S2 3170
Figure 7: Properties of the physical regulatory network
- BEAF-HB.S2 274
- CTCF-VC.BG3 282
- CTCF-VC.S2 283
- Chro(Chriz)BR.BG3 275
- Chro(Chriz)BR.Clone_8 276
- Chro(Chriz)BR.Kc 277
- Chro(Chriz)BR.S2 278
- Chro(Chriz)WR.S2 279
- CP190-VC.S2 280
- Ez.S2 284
- H2B-ubiq (NRO3).BG3 288
- H2B-ubiq (NRO3).Kc 289
- H2B-ubiq (NRO3).S2 290
- H3K18ac.BG3 291
- H3K18ac.S2 292
- H3K23ac.BG3 293
- H3K23ac.S2 294
- H3K27Ac.BG3 295
- H3K27Ac.S2 296
- H3K27Me3 (Abcam2).BG3 297
- H3K27me3 (Abcam2).S2 298
- H3K36me1.BG3 299
- H3K36me3.BG3 301
- H3K36me3.Kc 302
- H3K36me3.S2 303
- H3K4me1.S2 304
- H3K4Me3(LP).S2 305
- H3K79Me2.BG3 306
- H3K79Me2.S2 307
- H3K9ac.S2 309
- H3K9me2-Ab2 (new lot).BG3 310
- H3K9me2 antibody2.S2 311
- H3K9me3 (new lot).BG3 312
- H3K9me3.S2 313
- H4K16ac(L).BG3 316
- H4K16ac(L).Clone_8 317
- H4K16ac(L).Kc 318
- H4K16ac(L).S2 319
- H4K16ac(M).S2 320
- H4K5ac.S2 321
- H4K8ac.S2 322
- H4AcTetra.S2 201
- Pc.BG3 325
- Pc.S2 326
- RNA pol II (ALG).Clone_8 327
- RNA pol II (ALG).Kc 328
- RNA pol II (ALG).S2 329
- GAF.S2 285
- mod2.2-VC.BG3 324
- SU(HW)-HB.S2 330
- Su(Hw)-VC.S2 331
- Trx-C.S2 332
- GAF.BG3 2651
- H3K36me1.S2 3170
- E0-12h-CNC 627
- E0-12h-bab1 628
- pupae-brm ChIP-chip 602
- Embryo 0-12h chinmo ChIP-chip 608
- E-0-12h-dCtBP7667 607
- E0-12h-D 626
- E-0-12h-dll 606
- E0-12h-ENserum 625
- Embryo 7-24h end300 ChIP-chip 611
- E0-12h-FTZ-F1 624
- E0-12 GROAviva ChIP-chip 597
- E0-12h-Gro3 623
- Embryo 7-24h gsbnpurif ChIP-chip 610
- E0-12h-H3K36me3 620
- E0-12h-H3K4me3 622
- E0-12h-H3K9me3 621
- E-0-12h-INV7657 605
- Embryo 0-12h INV-GFP ChIP-chip 619
- E0-12h-KN 618
- E0-12h-RUN7659 617
- E-0-12h-bks 609
- Pupae-snr1 ChIP-chip 601
- E0-12h-Stat92E 616
- E0-12h-TTK 615
- E0-12h-UBX7701 614
- Embryo 3-8h UBX7701 ChIP-chip 603
- Embryo 3-8h UBX1 ChIP-chip 613
- Embryo 3-8h UBX2 ChIP-chip 612
- Embryo 0-12h ZFH1 ChIP-chip 604
- E0-12_BEAF 32 ChIP-chip 21
- E0-12_CP190 ChIP-chip 22
- E0-12_dCTCF C-term ChIP-chip 769
- Kc167_CTCF-N ChIP-chip 908
- E0-12_dCTCF N-term ChIP-chip 770
- CTCF-N_S2 ChIP-chip 913
- Embryo 0-12h GAF ChIP-chip 23
- Embryo 0-12h Mod(mdg4) ChIP-chip 24
- Embryo 0-12h SuHw ChIP-chip 27
- E0-12_Su(Hw)PG 901
- E4-8_GFP-sens 979
- E0-12_H3K27me3 ChIP-chip 919
- E4-8h_sens 2577
- H3K4me3_Kc167 ChIP-chip 912
- H3K4me3_S2 ChIP-chip 914
- E0-8_Kr-D2 ChIP-chip 898
- TotalRNA_E0-12h 918
- E0-12_PolII 899
- E0-4_CBP 900
- E0-4_GFP_7T ChIP-chip 902
- E0-12_HDAC-492_ChIP-seq 2627
- E0-12_HDAC-493_ChIP-seq 2628
- E0-12_HDAC-494_ChIP-seq 2629
- E0-12_HDAC-495_ChIP-seq 2630
- E0-12_HDAC-496_ChIP-seq 2631
- E0-12_HDAC-497_ChIP-seq 2632
- E0-12_HDAC-498_ChIP-seq 2633
- E0-12_HDAC-499_ChIP-seq 2634
- E0-12_HDAC-500_ChIP-seq 2635
- E0-12_HDAC-501_ChIP-seq 2636
- E0-4h_cad 2570
- E4-8h_7T_ChIP-seq 2637
- E0-8_D 2571
- E-0-4h_bks 2569
- Kc167_Trl 2568
- Kc_Kr failed validation 2579
- E0-8h_GATAe 2573
- E0-8h_disco 2572
- E0-8h_h 2574
- E0-8h_hkb 2575
- E0-8h_jumu 2576
- R13_1-6_eve-GFP 2603
- ISO1_8-16_Ez 2585
- E4-8_sens 978
- ISO1_8-16_mod_mdg4 2602
Figure 8: Gene function prediction from co-expression and co-regulation patterns
- Dev Timecourse Adult Female Eclosure+1d RNA-Seq multimapped reads 2794
- Dev Timecourse Adult Female Eclosion+30d RNA-Seq multimapped reads 2793
- Dev Timecourse Adult Female Eclosion+5d RNA-Seq multimapped reads 2795
- Dev Timecourse Adult Male Eclosion+1d RNA-Seq multimapped reads 2790
- Dev Timecourse Adult Male Eclosion+30d RNA-Seq multimapped reads 2792
- Dev Timecourse Adult Male Eclosion+5d RNA-Seq multimapped reads 2791
- Dev Timecourse Embryo 0-2h RNA-Seq multimapped reads 2796
- Dev Timecourse Embryo 10-12h RNA-Seq multimapped reads 2797
- Dev Timecourse Embryo 12-14h RNA-Seq multimapped reads 2798
- Dev Timecourse Embryo 14-16h RNA-Seq multimapped reads 2799
- Dev Timecourse Embryo 16-18h RNA-Seq multimapped reads 2780
- Dev Timecourse Embryo 18-20h RNA-Seq multimapped reads 2801
- Dev Timecourse Embryo 2-4h RNA-Seq multimapped reads 2804
- Dev Timecourse Embryo 20-22h RNA-Seq multimapped reads 2802
- Dev Timecourse Embryo 22-24h RNA-Seq multimapped reads 2803
- Dev Timecourse Embryo 4-6h RNA-Seq multimapped reads 2805
- Dev Timecourse Embryo 6-8h RNA-Seq multimapped reads 2806
- Dev Timecourse Embryo 8-10h RNA-Seq multimapped reads 2807
- Dev Timecourse Larvae L1 RNA-Seq multimapped reads 2808
- Dev Timecourse Larvae L2 RNA-Seq multimapped reads 2809
- Dev Timecourse Larvae L3 12hr RNA-Seq multimapped reads 2810
- Dev Timecourse Larvae L3 PS7-9 RNA-Seq multimapped reads 2813
- Dev Timecourse Larvae L3 PS1-2 RNA-Seq multimapped reads 2811
- Dev Timecourse Larvae L3 PS3-6 RNA-Seq multimapped reads 2812
- Dev Timecourse White Pre-pupae 2 days RNA-Seq multimapped reads 2817
- Dev Timecourse White Pre-pupae 3 days RNA-Seq multimapped reads 2818
- Dev Timecourse White Pre-pupae 4 days RNA-Seq multimapped reads 2819
- Dev Timecourse White Pre-pupae RNA-Seq multimapped reads 2814
- Dev Timecourse White Pre-pupae 12hr RNA-Seq multimapped reads 2815
- Dev Timecourse White Pre-pupae 24hr RNA-Seq multimapped reads 2816
- BEAF-HB.S2 274
- CTCF-VC.BG3 282
- CTCF-VC.S2 283
- Chro(Chriz)BR.BG3 275
- Chro(Chriz)BR.Clone_8 276
- Chro(Chriz)BR.Kc 277
- Chro(Chriz)BR.S2 278
- Chro(Chriz)WR.S2 279
- CP190-VC.S2 280
- Ez.S2 284
- H2B-ubiq (NRO3).BG3 288
- H2B-ubiq (NRO3).Kc 289
- H2B-ubiq (NRO3).S2 290
- H3K18ac.BG3 291
- H3K18ac.S2 292
- H3K23ac.BG3 293
- H3K23ac.S2 294
- H3K27Ac.BG3 295
- H3K27Ac.S2 296
- H3K27Me3 (Abcam2).BG3 297
- H3K27me3 (Abcam2).S2 298
- H3K36me1.BG3 299
- H3K36me3.BG3 301
- H3K36me3.Kc 302
- H3K36me3.S2 303
- H3K4me1.S2 304
- H3K4Me3(LP).S2 305
- H3K79Me2.BG3 306
- H3K79Me2.S2 307
- H3K9ac.S2 309
- H3K9me2-Ab2 (new lot).BG3 310
- H3K9me2 antibody2.S2 311
- H3K9me3 (new lot).BG3 312
- H3K9me3.S2 313
- H4K16ac(L).BG3 316
- H4K16ac(L).Clone_8 317
- H4K16ac(L).Kc 318
- H4K16ac(L).S2 319
- H4K16ac(M).S2 320
- H4K5ac.S2 321
- H4K8ac.S2 322
- H4AcTetra.S2 201
- Pc.BG3 325
- Pc.S2 326
- RNA pol II (ALG).Clone_8 327
- RNA pol II (ALG).Kc 328
- RNA pol II (ALG).S2 329
- GAF.S2 285
- mod2.2-VC.BG3 324
- SU(HW)-HB.S2 330
- Su(Hw)-VC.S2 331
- Trx-C.S2 332
- GAF.BG3 2651
- H3K36me1.S2 3170
Figure 9:Predictive models of regulator, region, and gene activity
- E0-12h-CNC 627
- E0-12h-bab1 628
- pupae-brm ChIP-chip 602
- Embryo 0-12h chinmo ChIP-chip 608
- E-0-12h-dCtBP7667 607
- E0-12h-D 626
- E-0-12h-dll 606
- E0-12h-ENserum 625
- Embryo 7-24h end300 ChIP-chip 611
- E0-12h-FTZ-F1 624
- E0-12 GROAviva ChIP-chip 597
- E0-12h-Gro3 623
- Embryo 7-24h gsbnpurif ChIP-chip 610
- E0-12h-H3K36me3 620
- E0-12h-H3K4me3 622
- E0-12h-H3K9me3 621
- E-0-12h-INV7657 605
- Embryo 0-12h INV-GFP ChIP-chip 619
- E0-12h-KN 618
- E0-12h-RUN7659 617
- E-0-12h-bks 609
- Pupae-snr1 ChIP-chip 601
- E0-12h-Stat92E 616
- E0-12h-TTK 615
- E0-12h-UBX7701 614
- Embryo 3-8h UBX7701 ChIP-chip 603
- Embryo 3-8h UBX1 ChIP-chip 613
- Embryo 3-8h UBX2 ChIP-chip 612
- Embryo 0-12h ZFH1 ChIP-chip 604
- E0-12_BEAF 32 ChIP-chip 21
- E0-12_CP190 ChIP-chip 22
- E0-12_dCTCF C-term ChIP-chip 769
- Kc167_CTCF-N ChIP-chip 908
- E0-12_dCTCF N-term ChIP-chip 770
- CTCF-N_S2 ChIP-chip 913
- Embryo 0-12h GAF ChIP-chip 23
- Embryo 0-12h Mod(mdg4) ChIP-chip 24
- Embryo 0-12h SuHw ChIP-chip 27
- E0-12_Su(Hw)PG 901
- E4-8_GFP-sens 979
- E0-12_H3K27me3 ChIP-chip 919
- E4-8h_sens 2577
- H3K4me3_Kc167 ChIP-chip 912
- H3K4me3_S2 ChIP-chip 914
- E0-8_Kr-D2 ChIP-chip 898
- TotalRNA_E0-12h 918
- E0-12_PolII 899
- E0-4_CBP 900
- E0-4_GFP_7T ChIP-chip 902
- E0-12_HDAC-492_ChIP-seq 2627
- E0-12_HDAC-493_ChIP-seq 2628
- E0-12_HDAC-494_ChIP-seq 2629
- E0-12_HDAC-495_ChIP-seq 2630
- E0-12_HDAC-496_ChIP-seq 2631
- E0-12_HDAC-497_ChIP-seq 2632
- E0-12_HDAC-498_ChIP-seq 2633
- E0-12_HDAC-499_ChIP-seq 2634
- E0-12_HDAC-500_ChIP-seq 2635
- E0-12_HDAC-501_ChIP-seq 2636
- E0-4h_cad 2570
- E4-8h_7T_ChIP-seq 2637
- E0-8_D 2571
- E-0-4h_bks 2569
- Kc167_Trl 2568
- Kc_Kr failed validation 2579
- E0-8h_GATAe 2573
- E0-8h_disco 2572
- E0-8h_h 2574
- E0-8h_hkb 2575
- E0-8h_jumu 2576
- R13_1-6_eve-GFP 2603
- ISO1_8-16_Ez 2585
- E4-8_sens 978
- ISO1_8-16_mod_mdg4 2602
- Chro(Chriz)BR.BG3 275
- Chro(Chriz)BR.Clone_8 276
- Chro(Chriz)BR.Kc 277
- Chro(Chriz)BR.S2 278
- Chro(Chriz)WR.S2 279
- H2B-ubiq (NRO3).BG3 288
- H2B-ubiq (NRO3).Kc 289
- H2B-ubiq (NRO3).S2 290
- H3K18ac.BG3 291
- H3K18ac.S2 292
- H3K23ac.BG3 293
- H3K23ac.S2 294
- H3K27Ac.BG3 295
- H3K27Ac.S2 296
- H3K27Me3 (Abcam2).BG3 297
- H3K27me3 (Abcam2).S2 298
- H3K36me1.BG3 299
- H3K36me3.BG3 301
- H3K36me3.Kc 302
- H3K36me3.S2 303
- H3K4me1.S2 304
- H3K4Me3(LP).S2 305
- H3K79Me2.BG3 306
- H3K79Me2.S2 307
- H3K9ac.S2 309
- H3K9me2-Ab2 (new lot).BG3 310
- H3K9me2 antibody2.S2 311
- H3K9me3 (new lot).BG3 312
- H3K9me3.S2 313
- H4K16ac(L).BG3 316
- H4K16ac(L).Clone_8 317
- H4K16ac(L).Kc 318
- H4K16ac(L).S2 319
- H4K16ac(M).S2 320
- Pc.BG3 325
- Pc.S2 326
- SU(HW)-HB.S2 330
- Su(Hw)-VC.S2 331
SUPPLEMENTARY FIGURES
- All Supp figures in a single PDF
- All Supp tables in a single PDF
- Figure S1: Conserved RNA secondary structures.
- Figure S2: Genome-wide correlation of chromatin marks with patterns of physical properties.
- Figure S3: Detecting transcribed regions based on enrichment of histone marks.
- Figure S4: Predictive model of active promoters in S2 cells.
- Figure S5: Early origin activity, replication timing and cohesin binding in >10 kb H3K36me1 intergenic regions.
- Figure S6. Data analysis used for annotation of chromatin states.
- Figure S7: ORC is enriched at HOT spots.
- Figure S8: Fraction of constrained and unconstrained bases in modENCODE datasets.
- Figure S9: Density correlation amongst broadly grouped modENCODE datasets
- Figure S10: Chromatin State Recovery with Increasing Subsets of Marks.
- Figure S11: Heatmap of TF-TF and miR-TF interactions.
- Figure S12: Heatmaps showing expression, motif-enrichment and GO-enrichment for each cluster.
- Figure S13: Precision-recall curves of feature specific and functional regulatory network.
- Figure S14: Fold-enrichment of tissues among novel and known members of a GO process category.
- Figure S15: Information on Developmental Time Course Expression Splits Identified by DREM.
- Figure S16: Squared error, correlation coefficients and Regulators of 1487 predictable genes.
- Figure S17: Squared error, correlation coefficients and Regulators of 324 unpredictable genes.
- Figure S18: Cumulative distribution of correlations of individual gene time courses obtained from the two developmental RNAseq datasets.
TABLES
- Table S1: Drosophila cell lines characterized by modENCODE.
- Table S2: Protein symbols used in the paper.
- Table S3. cis-NAT-siRNA production in Drosophila melanogaster.
- Table S4. ChIP data sources used to create the pRN.
- Table S5: Number of genes and GO process terms at different FDRs.
- Table S6: Relative performance of different networks for predicting expression of target genes.
DATASETS
- DataS1: Listing of all modENCODE data sets and accession numbers
- DataS2: Novel transcripts with complete or incomplete conserved ORFs
- DataS3: Noncoding RNA-seq transcripts with conserved RNA secondary structure
- DataS4: Novel promoter predictions based on chromatin signatures
- DataS5: Genome annotated using the 9-state chromatin model
- DataS6: Genome annotated using the 30-state chromatin model
- DataS7: Predicted TFBS
- DataS8: HOT regions
- DataS9: Machine-parseable version of ChIP-based physical regulatory network (pRN) combined with miRNA regulations
- DataS10: Summary of connectivity properties of pRN
- DataS11: Lists of all motif instances for the 8 motifs shown in Figure 7B
- DataS12: Feature-specific data sets for functional network reconstruction
- DataS13: Functional regulatory network
- DataS14: Gene co-expression clusters
- DataS15: Function prediction of all genes
- DataS16: Genes predicted as regulators of key developmental events
- DataS17: Gene expression model based on regulator binding