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Sample GSM389309 Query DataSets for GSM389309
Status Public on Apr 11, 2009
Title ama-1 L4/young adult replicate 1 POL II
Sample type SRA
 
Source name ama-1 transgenic worm OP34
Organism Caenorhabditis elegans
Characteristics strain: OP34
growth stage: L4/young adult
antibody: anti-POL II
Treatment protocol Resuspend L4/young adult 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. When worms reaches to L4/young adult stage, spin down worms at 3000 g for 3 minutes. Resuspend the worm pellet 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 and anti-POL II 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 Chromatin IP against anti-POL II
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 03, 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)
GSE15535 Genome-wide identification of the occupancy of RNA polymerase II (POL II) at L4/young adult stage in C. elegans
Relations
Reanalyzed by GSE53412
SRA SRX005626
BioSample SAMN02197813

Supplementary file Size Download File type/resource
GSM389309_Yale_AMA1_L4YA_POLII_rep1_eland_result_FC30P5JHM_20081205_s_8.bed.gz 135.5 Mb (ftp)(http) BED
GSM389309_Yale_AMA1_L4YA_POLII_rep1_peaks.bed.gz 100.6 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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