|
| Status |
Public on Feb 01, 2019 |
| Title |
qd328_PA14_2 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
genotype: atf-7(qd328[atf-7::2xTY1::GFP])
bacterial exposure: PA14
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_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_PA14.tdf
D17-4714
|
| 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 |
SAMN09939142 |
| SRA |
SRX4626833 |
