|
| Status |
Public on Dec 07, 2020 |
| Title |
Input_cco-1 |
| Sample type |
SRA |
| |
|
| Source name |
input
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Wild-type N2
RNAi clone: E. coli HT115, cco-1 RNAi
stage at harvesting: L4/young adult
|
| Treatment protocol |
RNAi treatment was started from the egg phase and treated until worms reached L4/young adult phase and then collected in 15 mL tubes
|
| Growth protocol |
Worms were synchronized by bleaching. Synchronized worm eggs were plated in NGM plates under the described conditions and raised at 20 ̊C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were harvested and washed with M9 buffer for three times. Worms were then fixed with 1% formaldehyde in PBS for 30 min, and quenched by glycine. Immunoprecipitaion were carried by using the antibodies against H3K18Ac (Cat. 07-354, Merck) or H3K27Ac (Ab4729, abcam).
Libraries were prepared for sequencing using standard BGISeq500 protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Input sample
|
| Data processing |
After sequencing on the BGIseq-500 platform, FastQC was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
Alignment was performed against C. elegans genome (WBcel235 ce11 top-level and Ensembl release 89 annotation) following the bowtie2 (version 2.3.5) manual guidelines with default parameters.
SAMtools (version 1.4.1) was used to sort, filter and index the obtained alignments.Peak calling was performed using MACS2 (version 2.1.2) against default Poisson distribution to generate raw counts for each sample, or between samples of interest for comparison.
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with peak counts identified for each group
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Terytty Yang Li |
| E-mail(s) |
[email protected]
|
| Organization name |
EPFL
|
| Street address |
EPFL SV IBI-SV LISP AI 1145
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL25145 |
| Series (2) |
| GSE131616 |
The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress |
| GSE148328 |
The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN14995913 |
| SRA |
SRX8379808 |
