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modMine 17 contains the 15 February 2010 data freeze

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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

 

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 27 entries in public repositories. The experimental factors are developmental stage, strain, temperature and tissue. 		Gene: 20220
Exon: 21355
MRNA: 31137
ThreePrimeRACEClone: 2700
PolyASite: 35382
CDS: 23792
EST: 2694
ThreePrimeRST: 2700
ThreePrimeUST: 2700
ThreePrimeUTR: 24055

27 entries in GEO

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Intron Confirmation in C. elegans

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Green
This experiment has 6 data submissions. 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

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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
ExperimentalFeature: 6826759
Exon: 4458116
OverlappingESTSet: 1611337
MRNA: 25028
Transcript: 1071311
SL1AcceptorSite: 253226
PolyASite: 238179
Intron: 2859156
CDS: 387696
TranscriptionEndSite: 258882
SL2AcceptorSite: 66411

20 entries in SRA

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Annotation of Drosophila splice junctions by RNA-seq

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

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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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RT-PCR

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Brent
This experiment has 5 data submissions. The experimental factor is cell line. 		MRNA: 1688
EST: 1360

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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: 346679

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5' RACE

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Celniker
This experiment has 6 data submissions. It has produced 7 entries in public repositories. The experimental factors are developmental stage and strain. 		MRNA: 7707
EST: 1187953

7 entries in SRA

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mRNA expression profiling

 

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

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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

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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
ExperimentalFeature: 6826759
Exon: 4458116
OverlappingESTSet: 1611337
MRNA: 25028
Transcript: 1071311
SL1AcceptorSite: 253226
PolyASite: 238179
Intron: 2859156
CDS: 387696
TranscriptionEndSite: 258882
SL2AcceptorSite: 66411

20 entries in SRA

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Short read sequencing of fly mRNA

Project:The Drosophila Transcriptome   (Sue Celniker)   Labs: Brent
This experiment has 1 data submission. It has produced 2 entries in public repositories. The experimental factors are developmental stage and strain.

2 entries in GEO

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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 entries in SRA

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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 19 entries in public repositories. The experimental factors are developmental stage, cell line and strain.

19 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 112 entries in public repositories. The experimental factors are developmental stage and strain.

112 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

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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

 

Small RNA identification

Project:Small and microRNAs   (Eric Lai)   Labs: Hannon, Lai
This experiment has 62 data submissions. It has produced 50 entries in public repositories. The experimental factors are developmental stage, cell line, strain and tissue.

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

Project:The C. elegans Transcriptome   (Robert Waterston)   Labs: Slack
This experiment has 7 data submissions. It has produced 5 entries in public repositories. The experimental factors are developmental stage, days post-L4, strain and temperature. 		ExperimentalFeature: 465

5 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 11 entries in public repositories. The experimental factor is cell line.

5 entries in GEO

6 entries in SRA

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Transcription factor binding sites

 

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 63 entries in public repositories. The experimental factors are developmental stage, strain, target gene and temperature. 		BindingSite: 275520

63 entries in GEO

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Chromatin Binding Site Mapping

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 278 data submissions. It has produced 276 entries in public repositories. The experimental factors are developmental stage, antibody, cell line, strain and threshold. 		BindingSite: 10456
ProteinBindingSite: 1011756
HistoneBindingSite: 12968
TFBindingSite: 31284

276 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 ChIP-chip

Project:Chromatin Function   (Jason Lieb)   Labs: Ahringer, Desai, Lieb, Strome
This experiment has 78 data submissions. It has produced 82 entries in public repositories. The experimental factors are developmental stage, antibody, strain and temperature. 		BindingSite: 48517

1 entry in ArrayExpress

81 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

116 entries in GEO

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Chromatin Binding Site Mapping

Project:Regulatory Elements in Drosophila   (Kevin White)   Labs: White
This experiment has 278 data submissions. It has produced 276 entries in public repositories. The experimental factors are developmental stage, antibody, cell line, strain and threshold. 		BindingSite: 10456
ProteinBindingSite: 1011756
HistoneBindingSite: 12968
TFBindingSite: 31284

276 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.

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 50 entries in public repositories. The experimental factors are developmental stage, biochemical fraction, cell line, extraction time, sodium chloride concentration and strain.

50 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.

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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

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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

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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.

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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

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Fly Worm All submissions




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