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Sample GSM388729 Query DataSets for GSM388729
Status Public on Apr 03, 2009
Title DPY-27 emb replicate 2 input
Sample type SRA
Source name dpy-27 transgenic worm OP32
Organism Caenorhabditis elegans
Characteristics strain: OP32
growth stage: embryo
antibody: none
Treatment protocol Resuspend embryo or Lava stage samples in 2% formaldehyde solution. Place on a shaker (50-100 rpm) and incubate for 30 minutes at room temperature. Wash samples once with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors.
Growth protocol Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. Continue with the same wash and cross-linking steps.
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody, purified for the DNA fragments bound by transcription factor, and sequenced it using Illumina Genome Analyzers.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description No ChIP just input DNA from the same preparation
Data processing Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200 bp.
Submission date Apr 01, 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
Platform ID GPL9309
Series (1)
GSE15501 Identification of transcription factor DPY-27 binding sites
SRA SRX003833
BioSample SAMN02197811

Supplementary file Size Download File type/resource
GSM388729_Yale_DPY27_emb_Input_rep2_eland_result_FC30V3HHM_20090120_s_6.bed.gz 73.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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