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PROJECTS	PI	LABS		EXPERIMENTS	GBrowse Tracks & Submissions to Repositories		FEATURES export formats:
The Drosophila Transcriptome	Celniker [ALL submissions]	Graveley [ALL submissions]	fly	Annotation of Drosophila splice junctions by RNA-seq Gene structure 30 Data submissions.			3005431 ExonRegion 1745570 Intron 1745570 TranscriptRegion
The Drosophila Transcriptome	Celniker [ALL submissions]	Celniker [ALL submissions]	fly	Cap Analysis of Gene Expression Gene structure 1 Data submission. Experimental factors: developmental stage and strain.		SRA: 1 entry
Origins of Replication	MacAlpine [ALL submissions]	MacAlpine [ALL submissions]	fly	CGH drosophila cell lines Copy number variation 1 Data submission. Experimental factor: cell line.
The C. elegans Transcriptome	Waterston [ALL submissions]	Slack [ALL submissions]	worm	Identification of small RNAs in C. elegans ncRNA expression profiling 7 Data submissions. Experimental factors: developmental stage and strain.		GEO: 7 entries
Regulatory Elements in Drosophila	White [ALL submissions]	White [ALL submissions]	fly	Chromatin Binding Site Mapping ·Histone modification and replacement ·Transcription factor binding sites 278 Data submissions. Experimental factors: developmental stage, antibody, cell line, strain and threshold.	544	GEO: 297 entries	10456 BindingSite 1011756 ProteinBindingSite 12968 HistoneBindingSite 31284 TFBindingSite
Origins of Replication	MacAlpine [ALL submissions]	MacAlpine [ALL submissions]	fly	CNV in Drosophila cell lines Copy number variation 3 Data submissions. Experimental factor: cell line.	3
Regulatory Elements in C. elegans	Snyder [ALL submissions]	Snyder [ALL submissions]	worm	ChIP-Seq Identification of C. elegans TF Binding Sites Transcription factor binding sites 49 Data submissions. Experimental factors: developmental stage, strain, target gene and temperature.		GEO: 65 entries	275520 BindingSite
The C. elegans Transcriptome	Waterston [ALL submissions]	Green [ALL submissions]	worm	SL Acceptor Site Confirmation in C. elegans Gene structure 1 Data submission. Experimental factors: developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer and strain.		Trace Archive: 1207 entries	933 SL1AcceptorSite 1453 TranscriptRegion 43 SL2AcceptorSite 1405 EST
The Drosophila Transcriptome	Celniker [ALL submissions]	Brent [ALL submissions]	fly	Short read sequencing of fly mRNA mRNA expression profiling 1 Data submission. Experimental factors: developmental stage and strain.		GEO: 4 entries
The Drosophila Transcriptome	Celniker [ALL submissions]	Brent [ALL submissions]	fly	RT-PCR Gene structure 5 Data submissions. Experimental factor: cell line.		dbEST: 295 entries Trace Archive: 3385 entries	1691 MRNA 2352 EST
The Drosophila Transcriptome	Celniker [ALL submissions]	Graveley [ALL submissions]	fly	Paired End RNA-Seq of Drosophila Cell Lines ncRNA expression profiling 8 Data submissions. Experimental factor: cell line.		GEO: 6 entries SRA: 6 entries
The C. elegans Transcriptome	Waterston [ALL submissions]	Reinke [ALL submissions]	worm	Identification of transcribed sequences under pathogenic bacterial growth conditions with expression profile maps mRNA expression profiling 6 Data submissions. Experimental factors: developmental stage, exposure time, food and strain.			261696 TranscriptRegion
The C. elegans Transcriptome	Waterston [ALL submissions]	Slack [ALL submissions]	worm	Changes in expression of small RNAs during aging in C. elegans ncRNA expression profiling 15 Data submissions. Experimental factors: developmental stage, days post-L4, strain and temperature.		GEO: 5 entries	1705 MiRNA
Chromatin Function	Lieb [ALL submissions]	Lieb [ALL submissions]	worm	Nucleosome mapping Chromatin structure 2 Data submissions. Experimental factors: developmental stage, strain and temperature.		GEO: 1 entry
The Drosophila Transcriptome	Celniker [ALL submissions]	Brent [ALL submissions]	fly	Gene Model Prediction Gene structure 1 Data submission.			308394 Exon 14659 Gene 43857 MRNA 47162 OverlappingESTSet 48747 ExonRegion 220003 CDS 60196 FivePrimeUTR 39559 StartCodon 41005 ThreePrimeUTR 16678 CDNA 39433 StopCodon 80157 TranscriptRegion 348440 EST
The Drosophila Transcriptome	Celniker [ALL submissions]	Celniker [ALL submissions]	fly	5' RACE Gene structure 6 Data submissions. Experimental factors: developmental stage and strain.		dbEST: 2500 entries SRA: 7 entries	7707 MRNA 1188488 EST
Origins of Replication	MacAlpine [ALL submissions]	MacAlpine [ALL submissions]	fly	Replication Timing Characterization DNA replication 3 Data submissions. Experimental factor: cell line.	3
Origins of Replication	MacAlpine [ALL submissions]	MacAlpine [ALL submissions]	fly	MacAlpine Early Origin of Replication Identification DNA replication 3 Data submissions. Experimental factor: cell line.	6		1520 OriginOfReplication
The 3' UTRome	Piano [ALL submissions]	Kim [ALL submissions] Piano [ALL submissions]	worm	Encyclopedia of C. elegans 3'UTRs and their regulatory elements Gene structure 40 Data submissions. Experimental factors: developmental stage, strain, temperature and tissue.		dbEST: 379 entries GEO: 26 entries Trace Archive: 2694 entries	20220 Gene 21355 Exon 27135 PolyASignalSequence 31137 MRNA 2700 ThreePrimeRACEClone 35382 PolyASite 23792 CDS 2694 EST 2700 ThreePrimeRST 2700 ThreePrimeUST 24055 ThreePrimeUTR
The Drosophila Transcriptome	Celniker [ALL submissions]	Celniker [ALL submissions]	fly	Developmental Time Course Transcriptional Profiling of D. melanogaster Embryo Using SOLiD Stranded Total RNA-Seq mRNA expression profiling 12 Data submissions. Experimental factors: developmental stage and strain.		SRA: 12 entries
Chromatin Function	Lieb [ALL submissions]	Ahringer [ALL submissions] Desai [ALL submissions] Lieb [ALL submissions] Strome [ALL submissions]	worm	Chromatin ChIP-chip Histone modification and replacement 78 Data submissions. Experimental factors: developmental stage, antibody, strain and temperature.		ArrayExpress: 1 entry GEO: 83 entries	48517 BindingSite
Origins of Replication	MacAlpine [ALL submissions]	Orr-Weaver [ALL submissions]	fly	Differential Replication of Polytene Chromosomes Copy number variation 4 Data submissions. Experimental factors: developmental stage, strain and tissue.			149 CopyNumberVariation
Small and microRNAs	Lai [ALL submissions]	Hannon [ALL submissions] Lai [ALL submissions]	fly	Small RNA identification ncRNA expression profiling 62 Data submissions. Experimental factors: developmental stage, cell line, strain and tissue.		GEO: 64 entries
The C. elegans Transcriptome	Waterston [ALL submissions]	Miller [ALL submissions] Reinke [ALL submissions]	worm	Identification of tissue and stage-specific transcribed sequences with expression profile maps mRNA expression profiling 40 Data submissions. Experimental factors: developmental stage, antibody, strain, temperature and tissue.			1630565 TranscriptRegion
The C. elegans Transcriptome	Waterston [ALL submissions]	Green [ALL submissions]	worm	Intron Confirmation in C. elegans Gene structure 6 Data submissions. Experimental factors: developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer, reverse primer and strain.		dbEST: 884 entries Trace Archive: 2542 entries	10284 Intron 6855 EST
Chromosomal Proteins	Karpen [ALL submissions]	Elgin [ALL submissions] Karpen [ALL submissions] Kuroda [ALL submissions] Pirrotta [ALL submissions]	fly	Genomic Distributions of Histone Modifications Histone modification and replacement 116 Data submissions. Experimental factors: developmental stage, antibody, cell line, strain and tissue.		GEO: 116 entries	761178 BindingSite
The Drosophila Transcriptome	Celniker [ALL submissions]	Oliver [ALL submissions]	fly	Transcriptional Profiling of additional Drosophila species with RNA-Seq mRNA expression profiling 2 Data submissions. Experimental factors: developmental stage, strain and tissue.		GEO: 1 entry
Origins of Replication	MacAlpine [ALL submissions]	MacAlpine [ALL submissions]	fly	Genome-wide localization of essential replication initiators DNA replication 6 Data submissions. Experimental factor: antibody.	25		8927 BindingSite 84312 ProteinBindingSite
The Drosophila Transcriptome	Celniker [ALL submissions]	Gingeras [ALL submissions]	fly	C-tailed RNA-Seq of Drosophila Cell lines and stages mRNA expression profiling 6 Data submissions. Experimental factors: developmental stage, cell line and strain.		GEO: 18 entries
Histone Variants	Henikoff [ALL submissions]	Henikoff [ALL submissions]	fly worm	Genome-wide Chromatin Profiling Chromatin structure 36 Data submissions. Experimental factors: developmental stage, biochemical fraction, cell line, extraction time, sodium chloride concentration and strain.		GEO: 47 entries
The Drosophila Transcriptome	Celniker [ALL submissions]	Celniker [ALL submissions]	fly	Developmental Stage Timecourse Transcriptional Profiling with RNA-Seq mRNA expression profiling 31 Data submissions. Experimental factors: developmental stage and strain.		SRA: 101 entries
Regulatory Elements in Drosophila	White [ALL submissions]	White [ALL submissions]	fly	RNA-seq support of the ChIP data ·Histone modification and replacement ·Transcription factor binding sites 12 Data submissions. Experimental factors: developmental stage and strain.		GEO: 12 entries
The C. elegans Transcriptome	Waterston [ALL submissions]	Waterston [ALL submissions]	worm	Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions ·Gene structure ·mRNA expression profiling 53 Data submissions. Experimental factors: developmental stage, exposure time, food, strain and temperature.		SRA: 20 entries	314286 TSS 4458116 Exon 1611337 OverlappingESTSet 25028 MRNA 1071311 Transcript 253226 SL1AcceptorSite 238179 PolyASite 2859156 Intron 387696 CDS 258882 TranscriptionEndSite 66411 SL2AcceptorSite
The Drosophila Transcriptome	Celniker [ALL submissions]	Celniker [ALL submissions]	fly	Confirmation of Drosophila transcripts by full-length cDNA screening mRNA expression profiling 1 Data submission. Experimental factor: cDNA library.			1055 CDNA
The Drosophila Transcriptome	Celniker [ALL submissions]	Cherbas [ALL submissions]	fly	RNA made in Bloomington mRNA expression profiling 4 Data submissions. Experimental factors: developmental stage, cell line, strain and tissue.
The 3' UTRome	Piano [ALL submissions]	Rajewsky [ALL submissions]	worm	Small RNA expression in C. elegans embryos ncRNA expression profiling 6 Data submissions. Experimental factors: developmental stage, fixation state, fixative, strain and temperature.		GEO: 6 entries
The Drosophila Transcriptome	Celniker [ALL submissions]	Cherbas [ALL submissions] Gingeras [ALL submissions]	fly	Identification of transcribed sequences with expression profile maps mRNA expression profiling 78 Data submissions. Experimental factors: developmental stage, cell line, strain and tissue.			3425616 TranscriptRegion
The Drosophila Transcriptome	Celniker [ALL submissions]	Graveley [ALL submissions]	fly	RNAi of RNA splicing factors in D. melanogaster mRNA expression profiling 27 Data submissions. Experimental factors: RNAi reagent and cell line.		GEO: 27 entries

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