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Series GSE16552 Query DataSets for GSE16552
Status Public on Jun 11, 2009
Title Transcriptome of wild type N2 worms at embronic stage and starved L1 stage
Project modENCODE
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in C. elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and starvation stress response. We defined binding sites for PHA-4 during formation of the embryonic pharynx, and in starved larvae. PHA-4 binds to thousands of locations throughout the genome. These sites shift dramatically between embryos and larvae, from developmentally regulated genes to genes involved in metabolism. We acquired transcriptome of wild type N2 worms at embyonic and starved L1 stages using RNA-seq method in comparing to the ChIP-seq experiment to study transcription factor binding. The wild type worms were cultured the same as the transgenic worms for transcription factor binding experiment.

Keywords: Transcriptome Analysis

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 Two development stages embryo and starved larvae each contains 3 technical replicates are reported
Web link http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
 
Contributor(s) Zhong M, Raha D
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA168961
Submission date Jun 11, 2009
Last update date May 15, 2019
Contact name Flora Vaccarino
Organization name Yale University
Department Child Study Center
Lab Vaccarino
Street address 230 South Frontage Road
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL9309 Illumina Genome Analyzer (Caenorhabditis elegans)
Samples (6)
GSM415884 N2_emb_rep 1
GSM415885 N2_emb_rep 2
GSM415886 N2_emb_rep 3
Relations
SRA SRP001005

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
GSE16552_RAW.tar 1.9 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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