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Series GSE48744 Query DataSets for GSE48744
Status Public on Jul 11, 2013
Title Snyder_GEI-11_GFP_Emb
Project modENCODE
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary modENCODE_submission_4037
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: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: embryo; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
Web link http://www.modencode.org
 
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 missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA63455
Submission date Jul 10, 2013
Last update date Nov 03, 2017
Contact name DCC modENCODE
E-mail 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)
GSM1183805 Snyder_GEI-11_GFP_Emb_Input_Rep1
GSM1183806 Snyder_GEI-11_GFP_Emb_ChIP_Rep1
GSM1183807 Snyder_GEI-11_GFP_Emb_Input_Rep2
Relations
SRA SRP028473

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
GSE48744_RAW.tar 109.1 Mb (http)(custom) TAR (of BEDGRAPH, GFF3)
GSE48744_Snyder_GEI-11_GFP_Emb_GFP_combined.bedgraph.gz 32.0 Mb (ftp)(http) BEDGRAPH
GSE48744_Snyder_GEI-11_GFP_Emb_Input_combined.bedgraph.gz 74.5 Mb (ftp)(http) BEDGRAPH
GSE48744_Snyder_GEI-11_GFP_Emb_combined.GFF3.gz 24.8 Kb (ftp)(http) GFF3
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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