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Series GSE25810 Query DataSets for GSE25810
Status Public on Feb 18, 2011
Title Identification of Transcription Factor SKN-1::GFP Binding Regions in L1
Project modENCODE
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary modENCODE_submission_2622
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
 
Overall design EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene skn-1; Strain OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq
Web link http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
 
Contributor(s) Zhong M, Snyder M, Slightam C, Kim S, Murray J, Waterston R, Gerstein M, Niu W, Janette J, Raha D, Agarwal A, Reinke V, Sarov M, Hyman A
Citation(s) 21177976, 21177963
BioProject PRJNA63461
Submission date Dec 02, 2010
Last update date May 15, 2019
Contact name DCC modENCODE
E-mail(s) help@modencode.org
Phone 416-673-8579
Organization name Ontario Institute for Cancer Research
Lab modENCODE DCC
Street address MaRS Centre, South Tower, 101 College Street, Suite 800
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platforms (1)
GPL9309 Illumina Genome Analyzer (Caenorhabditis elegans)
Samples (4)
GSM677691 Snyder_SKN-1_GFP_L1_rep1 extraction1_seq1 aliquote 1
GSM677692 Snyder_SKN-1_GFP_L1_rep1 extraction1_seq1 aliquote 2
GSM677693 Snyder_SKN-1_GFP_L1_rep2 extraction2_seq1 aliquote 1
Relations
SRA SRP005888

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25810_RAW.tar 119.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE25810_Snyder_SKN-1_GFP_L1_combined_peaks.GFF3.gz 165.5 Kb (ftp)(http) GFF3
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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