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Sample GSM3368739 Query DataSets for GSM3368739
Status Public on Feb 01, 2019
Title qd328_OP50_1
Sample type SRA
 
Source name whole animal
Organism Caenorhabditis elegans
Characteristics tissue: whole animal
genotype: atf-7(qd328[atf-7::2xTY1::GFP])
bacterial exposure: OP50
exposure length: 4 hours
age: L4
antibody: Ab290 (ChIP-grade polyclonal antibody from Abcam)
Treatment protocol L4 animals were washed to agar plates seeded with non-pathogenic (OP50) or pathogenic (PA14) bacteria for a period of 4 hours at 25 degrees C before animals were harvested for ChIP
Growth protocol Animals were synchronized by bleach prep. Arrested L1s dropped onto agar plates seeded with OP50 and grown at 20 degrees C until the L4 larval stage.
Extracted molecule genomic DNA
Extraction protocol After three washes in M9 buffer, animal pellets were resuspended in an equal volume of PBS + complete ULTRA protease inhibitor tablets (Roche) and flash frozen in liquid nitrogen and stored at -80°C until chromatin immunoprecipitation (ChIP). ChIP was preformed using Abcam antibody Ab290.
Libraries were prepared using the SPRIworks Fragment Library System (Beckman Coulter) and single-end sequenced on an Illumina HiSeq2000 sequencer with v3 chemistry in high-output mode.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description qd328_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_OP50.tdf
D17-4489
Data processing Base-calling was performed using Illumina's HiSeq control software, v. 2.2.58.
Quality control: Reads were aligned against C. elegans (ws258/WBPS9) using bwa aln/ samse v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads and number of unique 20-mers at the 5’ end of the reads were calculated using dedicated perl scripts and bedtools v. 2.25.0.64. The resulting bam files were sorted and indexed using samtools v. 1.5.
For each replicate, tdf and wig files were generated using IGVtools v. 2.1.24 with parameters count -e 150 ce_ws258_WBPS9 on the bam files. In addition, replicates were pooled by condition for downstream analysis using samtools merge.
Peaks were called using MACS2 v. 2.1.1.20160309 in callpeak mode with flags -g ce --keep-dup all --call-summits --extsize 150 -p 1e-3 --nomodel -B against the pooled N2_PA14_control samples.
Genome_build: ws258/WBPS9
Supplementary_files_format_and_content: For each replicate, tdf and wig files are provided (generated with IGV tools), and for the pooled replicates, ENCODE narrowPeak and tdf files that were used for the analysis are included.
 
Submission date Aug 30, 2018
Last update date Feb 03, 2019
Contact name Dennis Kim
Organization name MIT
Street address 31 Ames Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL13657
Series (2)
GSE119293 Binding profile of the bZIP transcription factor, ATF-7, in C. elegans on pathogenic Pseudomonas aeruginosa
GSE119294 C. elegans on pathogenic Pseudomonas aeruginosa
Relations
BioSample SAMN09939146
SRA SRX4626829

Supplementary file Size Download File type/resource
GSM3368739_D17-4489_bwa_ws258_bwaaln_mapped.sorted.tdf 18.2 Mb (ftp)(http) TDF
GSM3368739_D17-4489_bwa_ws258_bwaaln_mapped.sorted.wig.gz 15.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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