modENCODE blog
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modMine 18 contains the 15 February 2010 data freeze
modMine release 17 erratum: Waterston CDS/mRNA data.

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Gene structure mRNA expression profiling ncRNA expression profiling Transcription factor binding sites Histone modification and replacement Chromatin structure DNA replication Copy number variation
 

Gene structure

 

Annotation of Drosophila splice junctions by RNA-seq

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Graveley
This experiment has 30 data submissions. 		ExonRegion: 3005431
Intron: 1745570
TranscriptRegion: 1745570
with 5236710 expression levels.

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Cap Analysis of Gene Expression

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 1 data submission. It has produced 1 entry in public repositories. The experimental factors are developmental stage and strain.

1 entry in SRA

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SL Acceptor Site Confirmation in C. elegans

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Green
This experiment has 1 data submission. It has produced 1207 entries in public repositories. The experimental factors are developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer and strain. 		SL1AcceptorSite: 933
TranscriptRegion: 1453
SL2AcceptorSite: 43
EST: 1405

1 GBrowse track

1207 entries in Trace Archive

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RT-PCR

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Brent
This experiment has 5 data submissions. It has produced 3680 entries in public repositories. The experimental factor is cell line. 		MRNA: 1691
EST: 2352

295 entries in dbEST

3385 entries in Trace Archive

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Gene Model Prediction

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Brent
This experiment has 1 data submission. 		Exon: 308394
Gene: 14659
MRNA: 43857
OverlappingESTSet: 47162
ExonRegion: 48747
CDS: 220003
FivePrimeUTR: 60196
StartCodon: 39559
ThreePrimeUTR: 41005
CDNA: 16678
StopCodon: 39433
TranscriptRegion: 80157
EST: 348440

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5' RACE

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 6 data submissions. It has produced 2507 entries in public repositories. The experimental factors are developmental stage and strain. 		MRNA: 7707
EST: 1188488

2500 entries in dbEST

7 entries in SRA

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Encyclopedia of C. elegans 3'UTRs and their regulatory elements

Project:The 3' UTRome   (Fabio Piano)   Labs: Kim, Piano
This experiment has 40 data submissions. It has produced 3099 entries in public repositories. The experimental factors are developmental stage, strain, temperature and tissue. 		Gene: 20220
Exon: 21355
PolyASignalSequence: 27135
MRNA: 31137
ThreePrimeRACEClone: 2700
PolyASite: 35382
CDS: 23792
EST: 2694
ThreePrimeRST: 2700
ThreePrimeUST: 2700
ThreePrimeUTR: 24055

379 entries in dbEST

26 entries in GEO

2694 entries in Trace Archive

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Intron Confirmation in C. elegans

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Green
This experiment has 6 data submissions. It has produced 3426 entries in public repositories. The experimental factors are developmental stage, inner forward primer, inner reverse primer, outer forward primer, outer reverse primer, reverse primer and strain. 		Intron: 10284
EST: 6855

11 GBrowse tracks

884 entries in dbEST

2542 entries in Trace Archive

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Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Waterston
This experiment has 53 data submissions. It has produced 20 entries in public repositories. The experimental factors are developmental stage, exposure time, food, strain and temperature. 		TSS: 314286
Exon: 4458116
OverlappingESTSet: 1611337
MRNA: 25028
Transcript: 1071311
SL1AcceptorSite: 253226
PolyASite: 238179
Intron: 2859156
CDS: 387696
TranscriptionEndSite: 258882
SL2AcceptorSite: 66411
with 6826759 expression levels.

38 GBrowse tracks

20 entries in SRA

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mRNA expression profiling

 

Short read sequencing of fly mRNA

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Brent
This experiment has 1 data submission. It has produced 4 entries in public repositories. The experimental factors are developmental stage and strain.

4 entries in GEO

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Identification of transcribed sequences under pathogenic bacterial growth conditions with expression profile maps

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Reinke
This experiment has 6 data submissions. The experimental factors are developmental stage, exposure time, food and strain. 		TranscriptRegion: 261696

6 GBrowse tracks

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Developmental Time Course Transcriptional Profiling of D. melanogaster Embryo Using SOLiD Stranded Total RNA-Seq

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 12 data submissions. It has produced 12 entries in public repositories. The experimental factors are developmental stage and strain.

12 GBrowse tracks

12 entries in SRA

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Identification of tissue and stage-specific transcribed sequences with expression profile maps

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Miller, Reinke
This experiment has 40 data submissions. The experimental factors are developmental stage, antibody, strain, temperature and tissue. 		TranscriptRegion: 1630565

40 GBrowse tracks

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Transcriptional Profiling of additional Drosophila species with RNA-Seq

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Oliver
This experiment has 2 data submissions. It has produced 1 entry in public repositories. The experimental factors are developmental stage, strain and tissue.

1 entry in GEO

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C-tailed RNA-Seq of Drosophila Cell lines and stages

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Gingeras
This experiment has 6 data submissions. It has produced 18 entries in public repositories. The experimental factors are developmental stage, cell line and strain.

18 entries in GEO

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Developmental Stage Timecourse Transcriptional Profiling with RNA-Seq

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 31 data submissions. It has produced 101 entries in public repositories. The experimental factors are developmental stage and strain.

101 entries in SRA

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Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Waterston
This experiment has 53 data submissions. It has produced 20 entries in public repositories. The experimental factors are developmental stage, exposure time, food, strain and temperature. 		TSS: 314286
Exon: 4458116
OverlappingESTSet: 1611337
MRNA: 25028
Transcript: 1071311
SL1AcceptorSite: 253226
PolyASite: 238179
Intron: 2859156
CDS: 387696
TranscriptionEndSite: 258882
SL2AcceptorSite: 66411
with 6826759 expression levels.

38 GBrowse tracks

20 entries in SRA

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Confirmation of Drosophila transcripts by full-length cDNA screening

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 1 data submission. The experimental factor is cDNA library. 		CDNA: 1055

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RNA made in Bloomington

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Cherbas
This experiment has 4 data submissions. The experimental factors are developmental stage, cell line, strain and tissue.

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Identification of transcribed sequences with expression profile maps

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Cherbas, Gingeras
This experiment has 78 data submissions. The experimental factors are developmental stage, cell line, strain and tissue. 		TranscriptRegion: 3425616

76 GBrowse tracks

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RNAi of RNA splicing factors in D. melanogaster

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Graveley
This experiment has 27 data submissions. It has produced 27 entries in public repositories. The experimental factors are RNAi reagent and cell line.

27 entries in GEO

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ncRNA expression profiling

 

Identification of small RNAs in C. elegans

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Slack
This experiment has 7 data submissions. It has produced 7 entries in public repositories. The experimental factors are developmental stage and strain.

7 entries in GEO

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Paired End RNA-Seq of Drosophila Cell Lines

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Graveley
This experiment has 8 data submissions. It has produced 12 entries in public repositories. The experimental factor is cell line.

6 entries in GEO

6 entries in SRA

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Changes in expression of small RNAs during aging in C. elegans

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Slack
This experiment has 15 data submissions. It has produced 5 entries in public repositories. The experimental factors are developmental stage, days post-L4, strain and temperature. 		MiRNA: 1705
with 1342 expression levels.

5 entries in GEO

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Small RNA identification

Project:Small and microRNAs   (Eric Lai)   Labs: Hannon, Lai
This experiment has 62 data submissions. It has produced 64 entries in public repositories. The experimental factors are developmental stage, cell line, strain and tissue.

62 GBrowse tracks

64 entries in GEO

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Small RNA expression in C. elegans embryos

Project:The 3' UTRome   (Fabio Piano)   Labs: Rajewsky
This experiment has 6 data submissions. It has produced 6 entries in public repositories. The experimental factors are developmental stage, fixation state, fixative, strain and temperature.

6 entries in GEO

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Transcription factor binding sites

 

Chromatin Binding Site Mapping

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 278 data submissions. It has produced 297 entries in public repositories. The experimental factors are developmental stage, antibody, cell line, strain and threshold. 		BindingSite: 10456
ProteinBindingSite: 1011756
HistoneBindingSite: 12968
TFBindingSite: 31284

272 GBrowse tracks

297 entries in GEO

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ChIP-Seq Identification of C. elegans TF Binding Sites

Project:Regulatory Elements in C. elegans   (Michael Snyder)   Labs: Snyder
This experiment has 49 data submissions. It has produced 65 entries in public repositories. The experimental factors are developmental stage, strain, target gene and temperature. 		BindingSite: 275520

114 GBrowse tracks

65 entries in GEO

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RNA-seq support of the ChIP data

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 12 data submissions. It has produced 12 entries in public repositories. The experimental factors are developmental stage and strain.

12 entries in GEO

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Histone modification and replacement

 

Chromatin Binding Site Mapping

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 278 data submissions. It has produced 297 entries in public repositories. The experimental factors are developmental stage, antibody, cell line, strain and threshold. 		BindingSite: 10456
ProteinBindingSite: 1011756
HistoneBindingSite: 12968
TFBindingSite: 31284

272 GBrowse tracks

297 entries in GEO

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Chromatin ChIP-chip

Project:Chromatin Function   (Jason Lieb)   Labs: Ahringer, Desai, Lieb, Strome
This experiment has 78 data submissions. It has produced 84 entries in public repositories. The experimental factors are developmental stage, antibody, strain and temperature. 		BindingSite: 48517

69 GBrowse tracks

1 entry in ArrayExpress

83 entries in GEO

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Genomic Distributions of Histone Modifications

Project:Chromosomal Proteins   (Gary Karpen)   Labs: Elgin, Karpen, Kuroda, Pirrotta
This experiment has 116 data submissions. It has produced 116 entries in public repositories. The experimental factors are developmental stage, antibody, cell line, strain and tissue. 		BindingSite: 761178

115 GBrowse tracks

116 entries in GEO

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RNA-seq support of the ChIP data

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 12 data submissions. It has produced 12 entries in public repositories. The experimental factors are developmental stage and strain.

12 entries in GEO

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Chromatin structure

 

Nucleosome mapping

Project:Chromatin Function   (Jason Lieb)   Labs: Lieb
This experiment has 2 data submissions. It has produced 1 entry in public repositories. The experimental factors are developmental stage, strain and temperature.

2 GBrowse tracks

1 entry in GEO

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Genome-wide Chromatin Profiling

Project:Histone Variants   (Steven Henikoff)   Labs: Henikoff
This experiment has 36 data submissions. It has produced 47 entries in public repositories. The experimental factors are developmental stage, biochemical fraction, cell line, extraction time, sodium chloride concentration and strain.

34 GBrowse tracks

47 entries in GEO

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DNA replication

 

Replication Timing Characterization

Project:Origins of Replication   (David MacAlpine)   Labs: MacAlpine
This experiment has 3 data submissions. The experimental factor is cell line.

3 GBrowse tracks

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MacAlpine Early Origin of Replication Identification

Project:Origins of Replication   (David MacAlpine)   Labs: MacAlpine
This experiment has 3 data submissions. The experimental factor is cell line. 		OriginOfReplication: 1520

3 GBrowse tracks

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Genome-wide localization of essential replication initiators

Project:Origins of Replication   (David MacAlpine)   Labs: MacAlpine
This experiment has 6 data submissions. The experimental factor is antibody. 		BindingSite: 8927
ProteinBindingSite: 84312

13 GBrowse tracks

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Copy number variation

 

CGH drosophila cell lines

Project:Origins of Replication   (David MacAlpine)   Labs: MacAlpine
This experiment has 1 data submission. The experimental factor is cell line.

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CNV in Drosophila cell lines

Project:Origins of Replication   (David MacAlpine)   Labs: MacAlpine
This experiment has 3 data submissions. The experimental factor is cell line.

3 GBrowse tracks

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Differential Replication of Polytene Chromosomes

Project:Origins of Replication   (David MacAlpine)   Labs: Orr-Weaver
This experiment has 4 data submissions. The experimental factors are developmental stage, strain and tissue. 		CopyNumberVariation: 149

4 GBrowse tracks

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Fly Worm All submissions




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