Networks
Regions
Maps
- D. melanogaster
- C. elegans
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Histone Variants
Genome-wide Chromatin Profiling in Drosophila
Pi: Steven HenikoffLabs: Kamran AhmadSubmissions: 6Experimental factors: biochemical fraction, cell line, extraction time, sodium chloride concentrationGBrowse Tracks: 6 -
Histone Variants
Genome-wide Chromatin Profiling
Pi: Steven HenikoffLabs: Kamran Ahmad, Steven HenikoffSubmissions: 32Experimental factors: developmental stage, biochemical fraction, cell line, extraction time, sodium chloride concentrationGBrowse Tracks: 32
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- Jason Lieb
- Steven Henikoff
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Chromatin Function
Nucleosome mapping
Pi: Jason LiebLabs: Jason LiebSubmissions: 3Experimental factors: developmental stage, strain, temperatureGBrowse Tracks: 3 -
Histone Variants
Genome wide chromatin profiling in C. elegans
Pi: Steven HenikoffLabs: Steven HenikoffSubmissions: 8Experimental factors: developmental stage, biochemical fraction, extraction time, sodium chloride concentration, strainGBrowse Tracks: 8
- D. melanogaster
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Origins of Replication
CGH drosophila cell lines
Pi: David MacAlpineLabs: David MacAlpineSubmissions: 1Experimental factors: cell lineGBrowse Tracks: 1 -
Origins of Replication
CNV in Drosophila cell lines
Pi: David MacAlpineLabs: David MacAlpineSubmissions: 4Experimental factors: cell lineGBrowse Tracks: 4 -
Origins of Replication
Differential Replication of Polytene Chromosomes
Pi: David MacAlpineLabs: Terry Orr-WeaverSubmissions: 4Experimental factors: developmental stage, strain, tissueFeatures: CopyNumberVariation: 149GBrowse Tracks: 4
- D. melanogaster
- C. elegans
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- Brian Oliver
- Sue Celniker
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Comparative Genomics
Annotation of the developmental transcriptome of Drosophila melanogaster
Pi: Brian OliverLabs: Brian OliverSubmissions: 1 -
The Drosophila Transcriptome
RT-PCR
Pi: Sue CelnikerLabs: Michael BrentSubmissions: 5Experimental factors: developmental stageGBrowse Tracks: 8 -
The Drosophila Transcriptome
Analysis of TSS using stranded RACE products
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 1Experimental factors: developmental stageGBrowse Tracks: 1 -
The Drosophila Transcriptome
5' RACE
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 8Experimental factors: developmental stageGBrowse Tracks: 5 -
The Drosophila Transcriptome
Validation of Drosophila transcripts by full-length cDNA screening and sequencing
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 1Experimental factors: cDNA libraryFeatures: CDNAMatch: 17294GBrowse Tracks: 1 -
The Drosophila Transcriptome
Confirmation of Drosophila transcripts by full-length cDNA screening
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 1Experimental factors: cDNA libraryFeatures: CDNAMatch: 1706 -
The Drosophila Transcriptome
Annotation of Drosophila splice junctions by RNA-seq
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 30Experimental factors: developmental stageGBrowse Tracks: 30 -
The Drosophila Transcriptome
Cap Analysis of Gene Expression
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 1Experimental factors: developmental stageGBrowse Tracks: 2 -
The Drosophila Transcriptome
Drosophila Cell Line and Developmental Stage Gene and Exon Scores
Pi: Sue CelnikerLabs: Peter CherbasSubmissions: 1Experimental factors: developmental stage -
The Drosophila Transcriptome
Gene Model Prediction
Pi: Sue CelnikerLabs: Michael BrentSubmissions: 2Features: Gene: 14654, Exon: 368834, MRNA: 43846, OverlappingESTSet: 72572, ExonRegion: 97494, CDS: 219985, TranscriptionEndSite: 10836, FivePrimeUTR: 60186, StartCodon: 39549, ThreePrimeUTR: 40998, TSS: 22656, StopCodon: 39424, TranscriptRegion: 105560, EST: 354287GBrowse Tracks: 1
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- Fabio Piano
- Robert Waterston
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The 3' UTRome
Encyclopedia of C. elegans 3'UTRs and their regulatory elements
Pi: Fabio PianoLabs: Fabio Piano, John KimSubmissions: 41Experimental factors: developmental stage, strain, temperature, tissueFeatures: Exon: 21355, Gene: 20220, MRNA: 3720, PolyASignalSequence: 27135, Transcript: 27417, ThreePrimeRACEClone: 2700, PolyASite: 35382, CDS: 23792, EST: 2694, ThreePrimeRST: 2700, ThreePrimeUST: 2700, ThreePrimeUTR: 24055GBrowse Tracks: 103 -
The C. elegans Transcriptome
SL Acceptor Site Confirmation in C. elegans
Pi: Robert WaterstonLabs: Phil GreenSubmissions: 2Experimental factors: developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer, strainGBrowse Tracks: 3 -
The C. elegans Transcriptome
Reanalysis of comprehensive set of C. elegans transcripts and expression for various stages and conditions
Pi: Robert WaterstonLabs: Robert WaterstonSubmissions: 18Experimental factors: developmental stage, strainFeatures: TSS: 95411, Exon: 1833553, OverlappingESTSet: 157570, SL1AcceptorSite: 144581, Transcript: 614816, Intron: 1309480, PolyASite: 123763, CDS: 391265, TranscriptionEndSite: 62159, SL2AcceptorSite: 43020GBrowse Tracks: 65 -
The C. elegans Transcriptome
Intron Confirmation in C. elegans
Pi: Robert WaterstonLabs: Phil GreenSubmissions: 6Experimental factors: developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer, reverse primer, strainGBrowse Tracks: 23 -
The C. elegans Transcriptome
Mass spectrometric validation of short ORFs
Pi: Robert WaterstonLabs: Michael MacCossSubmissions: 1Experimental factors: developmental stage, strain, temperatureGBrowse Tracks: 1 -
The C. elegans Transcriptome
Genelet Gap Closing
Pi: Robert WaterstonLabs: Phil GreenSubmissions: 1Experimental factors: developmental stage, forward primer, reverse primer, strain -
The C. elegans Transcriptome
Identification of small RNAs in C. elegans
Pi: Robert WaterstonLabs: Frank SlackSubmissions: 7Experimental factors: developmental stage, strainGBrowse Tracks: 7 -
The C. elegans Transcriptome
Transcription Start Site Confirmation in C. elegans
Pi: Robert WaterstonLabs: Phil GreenSubmissions: 1Experimental factors: developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer, strain
- D. melanogaster
- C. elegans
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- Gary Karpen
- Kevin White
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Chromosomal Proteins
HMM Prediction of D. melanogaster Chromatin States
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Chromosomal Proteins
Genomic Distributions of Histone Modifications
Pi: Gary KarpenLabs: Gary Karpen, Mitzi Kuroda, Sarah Elgin, Vincent PirrottaSubmissions: 182Experimental factors: developmental stage, antibody, cell line, strain, tissueFeatures: BindingSite: 1290477GBrowse Tracks: 181 -
Regulatory Elements in Drosophila
Chromatin Binding Site Mapping of Modified Histone Proteins in D. melanogaster
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 6Experimental factors: developmental stage, antibody, strainFeatures: ProteinBindingSite: 15926GBrowse Tracks: 6
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Chromatin Function
Chromatin ChIP-chip of Modified Histones in C. elegans
Pi: Jason LiebLabs: Jason Lieb, Julie Ahringer, Susan StromeSubmissions: 10Experimental factors: developmental stage, antibody, strain, temperatureFeatures: BindingSite: 57588GBrowse Tracks: 10 -
Chromatin Function
Chromatin ChIP-seq
Pi: Jason LiebLabs: Jason Lieb, Julie AhringerSubmissions: 16Experimental factors: developmental stage, antibody, strain, temperatureFeatures: BindingSite: 134277GBrowse Tracks: 22
- D. melanogaster
- C. elegans
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The Drosophila Transcriptome
RNA made in Bloomington
Pi: Sue CelnikerLabs: Peter Cherbas, Tom GingerasSubmissions: 14Experimental factors: developmental stage, cell line, compartment, compound, strain, tissueGBrowse Tracks: 114
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The C. elegans Transcriptome
Validation of C. elegans miRNAs by qRT-PCR
Pi: Robert WaterstonLabs: Frank SlackSubmissions: 1Experimental factors: developmental stage, strain, temperature
- D. melanogaster
- C. elegans
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- Gary Karpen
- Kevin White
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Chromosomal Proteins
RNAi of non-Histone Chromosomal Proteins in D. melanogaster
Pi: Gary KarpenLabs: Sarah Elgin, Vincent PirrottaSubmissions: 30Experimental factors: antibody, RNAi reagent, cell lineFeatures: BindingSite: 145163GBrowse Tracks: 30 -
Chromosomal Proteins
Genomic Distributions of non-Histone Chromosomal Proteins in D. melanogaster
Pi: Gary KarpenLabs: Gary Karpen, Mitzi Kuroda, Sarah Elgin, Vincent PirrottaSubmissions: 94Experimental factors: developmental stage, antibody, cell line, strainFeatures: BindingSite: 337010GBrowse Tracks: 96 -
Regulatory Elements in Drosophila
Chromatin Binding Site Mapping of non-Histone Chromosomal Proteins in D. melanogaster
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 13Experimental factors: developmental stage, antibody, strainFeatures: ProteinBindingSite: 94040 -
Regulatory Elements in Drosophila
Classification of D. melanogaster Insulator Binding Sequences
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 1Features: InsulatorBindingSite: 7685GBrowse Tracks: 1
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Chromatin Function
Chromatin ChIP-chip
Pi: Jason LiebLabs: Arshad Desai, Jason Lieb, Julie Ahringer, Susan StromeSubmissions: 106Experimental factors: developmental stage, antibody, strain, temperatureFeatures: BindingSite: 306823GBrowse Tracks: 106 -
Chromatin Function
Chromatin ChIP-chip of non-Histone Chromosomal Proteins in C. elegans
Pi: Jason LiebLabs: Jason LiebSubmissions: 7Experimental factors: developmental stage, antibody, strain, temperatureFeatures: BindingSite: 25280GBrowse Tracks: 7
- D. melanogaster
- C. elegans
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- Brian Oliver
- Steven Henikoff
- Kevin White
- Eric Lai
- Sue Celniker
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Comparative Genomics
Transcriptional Profiling of additional Drosophila species with RNA-Seq
Pi: Brian OliverLabs: Brian OliverSubmissions: 27Experimental factors: developmental stage, strain, tissueGBrowse Tracks: 4 -
Histone Variants
Transcriptional profiling of Drosophila cell lines
Pi: Steven HenikoffLabs: Kamran AhmadSubmissions: 3Experimental factors: RNAi reagent, cell lineGBrowse Tracks: 3 -
Regulatory Elements in Drosophila
RNA-seq support of the ChIP data
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 12Experimental factors: developmental stage, strainGBrowse Tracks: 12 -
Small and microRNAs
Small RNA identification
Pi: Eric LaiLabs: Eric Lai, Gregory HannonSubmissions: 80Experimental factors: developmental stage, cell line, strain, tissueGBrowse Tracks: 160 -
The Drosophila Transcriptome
Short read sequencing of fly mRNA
Pi: Sue CelnikerLabs: Michael BrentSubmissions: 1Experimental factors: developmental stageGBrowse Tracks: 1 -
The Drosophila Transcriptome
Paired End RNA-Seq of Drosophila Cell Lines
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 8Experimental factors: developmental stageGBrowse Tracks: 8 -
The Drosophila Transcriptome
Developmental Time Course Transcriptional Profiling of D. melanogaster Embryo Using SOLiD Stranded Total RNA-Seq
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 12Experimental factors: developmental stageGBrowse Tracks: 12 -
The Drosophila Transcriptome
Identification of transcribed sequences with expression profile maps
Pi: Sue CelnikerLabs: Tom GingerasSubmissions: 80Experimental factors: developmental stageFeatures: TranscriptRegion: 3665935GBrowse Tracks: 80 -
The Drosophila Transcriptome
Transcriptional Profiling of D. melanogaster cell lines using Illumina poly(A)+ RNA-Seq
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 21Experimental factors: developmental stageGBrowse Tracks: 21 -
The Drosophila Transcriptome
Tissue-specific Transcriptional Profiling of D. melanogaster using Illumina poly(A)+ RNA-Seq
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 29Experimental factors: developmental stageGBrowse Tracks: 29 -
The Drosophila Transcriptome
Stranded Cell Line Transcriptional Profiling Using Illumina poly(A)+ RNA-seq
Pi: Sue CelnikerLabs: Sue CelnikerSubmissions: 19Experimental factors: developmental stageGBrowse Tracks: 19 -
The Drosophila Transcriptome
Capped and uncapped short RNAs
Pi: Sue CelnikerLabs: Tom GingerasSubmissions: 6Experimental factors: developmental stageGBrowse Tracks: 4 -
The Drosophila Transcriptome
Transcriptional Profiling of Compound-based treatments of D. melanogaster using Illumina poly(A)+ RNA-Seq uniquely aligned
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 21Experimental factors: developmental stageGBrowse Tracks: 21 -
The Drosophila Transcriptome
C-tailed RNA-Seq of Drosophila Cell lines and stages
Pi: Sue CelnikerLabs: Tom GingerasSubmissions: 6Experimental factors: developmental stageGBrowse Tracks: 6 -
The Drosophila Transcriptome
Developmental Stage Timecourse Transcriptional Profiling with RNA-Seq
Pi: Sue CelnikerLabs: Brenton Graveley, Sue CelnikerSubmissions: 61Experimental factors: developmental stageGBrowse Tracks: 69 -
The Drosophila Transcriptome
Tissue-specific Transcriptional Profiling of D. melanogaster using Illumina poly(A)+ RNA-Seq multiply TopHat analysis
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 29Experimental factors: developmental stageGBrowse Tracks: 29 -
The Drosophila Transcriptome
RNAi of RNA splicing factors in D. melanogaster
Pi: Sue CelnikerLabs: Brenton GraveleySubmissions: 60Experimental factors: RNAi reagent, cell lineGBrowse Tracks: 59
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- Jason Lieb
- Steven Henikoff
- Fabio Piano
- Robert Waterston
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Chromatin Function
Assaying RNA Expression in C. elegans
Pi: Jason LiebLabs: Jason LiebSubmissions: 1Experimental factors: developmental stage, strain, temperature -
Histone Variants
Transcriptional profiling of C. elegans N2 embryos
Pi: Steven HenikoffLabs: Kamran AhmadSubmissions: 1Experimental factors: developmental stage, strainGBrowse Tracks: 1 -
The 3' UTRome
Small RNA expression in C. elegans embryos
Pi: Fabio PianoLabs: Nikolaus RajewskySubmissions: 6Experimental factors: developmental stage, fixation state, fixative, strain, temperature -
The C. elegans Transcriptome
Identification of tissue and stage-specific transcribed sequences with expression profile maps
Pi: Robert WaterstonLabs: David Miller, Valerie ReinkeSubmissions: 47Experimental factors: developmental stage, antibody, strain, temperature, tissueFeatures: TranscriptRegion: 1907147GBrowse Tracks: 47 -
The C. elegans Transcriptome
Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions
Pi: Robert WaterstonLabs: Robert WaterstonSubmissions: 122Experimental factors: developmental stage, strain, temperatureFeatures: TSS: 146834, Exon: 2312679, OverlappingESTSet: 453994, SL1AcceptorSite: 140869, Transcript: 823605, Chromosome: 6, MatureTranscript: 12316, PolyASite: 257625, Intron: 1487784, CDS: 201632, TranscriptionEndSite: 127164, SL2AcceptorSite: 38664GBrowse Tracks: 125 -
The C. elegans Transcriptome
Definition of comprehensive set of C. briggsae transcripts and expression for various stages and conditions
Pi: Robert WaterstonLabs: Robert WaterstonSubmissions: 3Experimental factors: developmental stage, strain, temperature -
The C. elegans Transcriptome
Changes in expression of small RNAs under stress conditions in C. elegans
Pi: Robert WaterstonLabs: Frank SlackSubmissions: 4Experimental factors: developmental stage, strain, temperature -
The C. elegans Transcriptome
Identification of transcribed sequences under pathogenic bacterial growth conditions with expression profile maps
Pi: Robert WaterstonLabs: Valerie ReinkeSubmissions: 6Experimental factors: developmental stage, exposure time, food, strainFeatures: TranscriptRegion: 261696GBrowse Tracks: 6 -
The C. elegans Transcriptome
Changes in expression of small RNAs during aging in C. elegans
Pi: Robert WaterstonLabs: Frank SlackSubmissions: 15Experimental factors: developmental stage, days post-L4, strain, temperatureFeatures: MiRNA: 1705GBrowse Tracks: 15
- D. melanogaster
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Origins of Replication
Replication Timing Characterization
Pi: David MacAlpineLabs: David MacAlpineSubmissions: 3Experimental factors: cell lineGBrowse Tracks: 3 -
Origins of Replication
MacAlpine Early Origin of Replication Identification
Pi: David MacAlpineLabs: David MacAlpineSubmissions: 3Experimental factors: cell lineFeatures: OriginOfReplication: 1520GBrowse Tracks: 3 -
Origins of Replication
Genome-wide localization of essential replication initiators
Pi: David MacAlpineLabs: David MacAlpine, Terry Orr-WeaverSubmissions: 12Experimental factors: developmental stage, antibody, cell line, read length, strain, tissueGBrowse Tracks: 12 -
Origins of Replication
Replication Timing Characterization Repliseq
Pi: David MacAlpineLabs: David MacAlpineSubmissions: 1Experimental factors: cell lineGBrowse Tracks: 3 -
Origins of Replication
Genome-wide localization of essential replication initiators by ChIP-chip
Pi: David MacAlpineLabs: David MacAlpine, Terry Orr-WeaverSubmissions: 4Experimental factors: antibodyGBrowse Tracks: 2
- D. melanogaster
- C. elegans
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Regulatory Elements in Drosophila
Chromatin Binding Site Mapping
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 259Experimental factors: developmental stage, antibody, cell line, strain, thresholdFeatures: BindingSite: 10456, ProteinBindingSite: 901790, HistoneBindingSite: 12968, TFBindingSite: 31284GBrowse Tracks: 154 -
Regulatory Elements in Drosophila
Chromatin Binding Site Mapping of Transcription Factors in D. melanogaster by ChIP-seq
Pi: Kevin WhiteLabs: Kevin WhiteSubmissions: 25Experimental factors: developmental stage, antibody, strainFeatures: ProteinBindingSite: 52694GBrowse Tracks: 6
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Regulatory Elements in C. elegans
ChIP-Seq Identification of C. elegans TF Binding Sites
Pi: Michael SnyderLabs: Gerstein, Michael SnyderSubmissions: 108Experimental factors: developmental stage, strain, target gene, temperatureGBrowse Tracks: 162
