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| Status |
Public on Oct 06, 2024 |
| Title |
TF ChIP-seq Caenorhabditis elegans II |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies particular TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.
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| Overall design |
Peak calling of sequence files using ENCODE TF/Histone ChIP-Seq pipeline version 1.3.6 https://github.com/ENCODE-DCC/chip-seq-pipeline2
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| Contributor(s) |
Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Oct 02, 2024 |
| Last update date |
Oct 07, 2024 |
| Contact name |
Louis Gevirtzman |
| E-mail(s) |
gevirtzman@gmail.com
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| Organization name |
University of Washington
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| Department |
Genome Science
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| Lab |
Waterston
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platforms (1) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (24)
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| GSM8551291 |
ceh-37,OH16345,L1larva,Exp1,ChIP1 |
| GSM8551292 |
ceh-37,OH16345,L1larva,Exp1,ChIP2 |
| GSM8551293 |
ceh-37,OH16345,L1larva,Exp1,Input1 |
| GSM8551294 |
ceh-51,PHX1551,midembryonic,Exp1,ChIP1 |
| GSM8551295 |
ceh-51,PHX1551,midembryonic,Exp1,ChIP2 |
| GSM8551296 |
ceh-51,PHX1551,midembryonic,Exp1,Input1 |
| GSM8551297 |
ceh-5,PHX1592,lateembryonic,Exp1,ChIP1 |
| GSM8551298 |
ceh-5,PHX1592,lateembryonic,Exp1,ChIP2 |
| GSM8551299 |
ceh-5,PHX1592,lateembryonic,Exp1,Input1 |
| GSM8551300 |
fkh-7,PS9154,L1larva,Exp1,ChIP1 |
| GSM8551301 |
fkh-7,PS9154,L1larva,Exp1,ChIP2 |
| GSM8551302 |
fkh-7,PS9154,L1larva,Exp1,Input1 |
| GSM8551303 |
mec-3,OP55,lateembryonic,Exp1,ChIP1 |
| GSM8551304 |
mec-3,OP55,lateembryonic,Exp1,ChIP2 |
| GSM8551305 |
mec-3,OP55,lateembryonic,Exp1,Input1 |
| GSM8551306 |
pop-1,JIM531,earlyembryonic,Exp1,ChIP1 |
| GSM8551307 |
pop-1,JIM531,earlyembryonic,Exp1,ChIP2 |
| GSM8551308 |
pop-1,JIM531,earlyembryonic,Exp1,Input1 |
| GSM8551309 |
sma-3,CS152,L4larva,Exp1,ChIP1 |
| GSM8551310 |
sma-3,CS152,L4larva,Exp1,ChIP2 |
| GSM8551311 |
sma-3,CS152,L4larva,Exp1,Input1 |
| GSM8551312 |
sma-4,CS692,L4larva,Exp1,ChIP1 |
| GSM8551313 |
sma-4,CS692,L4larva,Exp1,ChIP2 |
| GSM8551314 |
sma-4,CS692,L4larva,Exp1,Input1 |
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| This SubSeries is part of SuperSeries: |
| GSE271850 |
Binding profiles for 602 Drosophila and 350 C. elegans transcription factors reveal tissue specific regulatory relationships |
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| Relations |
| BioProject |
PRJNA1169645 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE278617_denovo_ceh-37.tar.gz |
1.2 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_ceh-5.tar.gz |
1.5 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_ceh-51.tar.gz |
1.2 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_fkh-7.tar.gz |
1.3 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_mec-3.tar.gz |
1.4 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_pop-1.tar.gz |
1.1 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_sma-3.tar.gz |
1.2 Gb |
(ftp)(http) |
TAR |
| GSE278617_denovo_sma-4.tar.gz |
1003.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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