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Sample GSM435291 Query DataSets for GSM435291
Status Public on Jul 31, 2009
Title CEH-14 L2 replicate 1 GFP
Sample type SRA
 
Source name OP73, CEH-14:GFP:3xFLAG animals
Organism Caenorhabditis elegans
Characteristics strain: OP73
growth stage: L2
antibody: anti-GFP
Treatment protocol L2 animals were crossedliked in 2% formaldehyde solution for 30 minutes at room temperature, washed one time 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 and then stored at -80 oC.
Growth protocol CEH-14:GFP:3xFLAG animals were grown on NGM plates to obtain gravity adults with embryos and then bleached to obtain embryos. Embryos were hatched overnight in M9 Buffer to obtain snychronized L1animals. L1 animals were then transfered into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grew at 20 oC in an incubator shaking at 230 rpm. Concentrated E. Coli were added as necessary during growth. When reached at L2 stage, animals were collected, washed, and cross-linked.
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody and purified using Qiangen PCR purification kit. The protocol for library preparation was adapted from the protocol "Preparing Samples for sequencing genomic DNA" by Illumina.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against anti-GFP
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 Jul 31, 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)
GSE17454 Identification of transcription factor CEH-14 binding sites in C.elegans
Relations
SRA SRX015093
BioSample SAMN00007177

Supplementary file Size Download File type/resource
GSM435291_Snyder_CEH-14_Rep1_Peaks.gff.gz 32.7 Kb (ftp)(http) GFF
GSM435291_Snyder_CEH-14_Rep1_eland_result_FC314F1HM_20090306_ACGT_s_3.txt.gz 75.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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