|
| Status |
Public on Jul 19, 2020 |
| Title |
HDA-1_input (dve-1) rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HDA-1_input (dve-1)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: hda-1p::hda-1::gfp;glp-4(bn2)
developmental stage: Day1 of adulthood
chip antibody: none
|
| Treatment protocol |
atp-2 RNAi bacterial culture solution was seeded after worms cultured on the first RNAi clones.
|
| Growth protocol |
Synchronized worms were raised on RNAi at 20°C. Synchronized from L1 to Day of adulthood stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were cross-linked by formaldehyde and homogenized by a glass homogenizer.Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared by DNA Sample Kit (NEB, E7370).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
HG-D2-input_TKD181002510
|
| Data processing |
Adaptor in reads were filtered using in-house script then Trim Galore was used to do the quality control with following parameters: -q 20 --fastqc --illumina --stringency 6 -e 0 --length 50 --trim-n –paired.
Processed reads were mapped to the C. elegans genome (ce11) using bwa (v0.7.13-r1126) with default parameters.
Only proper paired uniquely mapping reads with mapping quality ≥20 and mismatches <8 were retained. PCR duplicates were removed by picard-2.17.6 (http://broadinstitute.github.io/picard) MarkDuplicates command.
MACS2 (v2.1.1) was used to obtain peak regions with following parameter: -g ce -f BAMPE --broad --SPMR.
ChIP-seq signals were calculated using deeptools (v2.4.2) by normalizing the read coverage to 10 million reads then subtracting input coverage from the ChIP samples to get final ChIP-seq signals.
Genome_build: C. elegans genome (ce11)
Supplementary_files_format_and_content: Bed3 files contain called peaks of each sample.
|
| |
|
| Submission date |
May 25, 2020 |
| Last update date |
Jul 19, 2020 |
| Contact name |
Liwa Shao |
| E-mail(s) |
liwa@pku.edu.cn
|
| Organization name |
Peking University
|
| Street address |
No.5 Yiheyuan Road Haidian District
|
| City |
Beijing |
| State/province |
- |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL25147 |
| Series (1) |
| GSE141042 |
DVE-1_ChIP-seq and HDA-1_ChIP-seq of worms |
|
| Relations |
| BioSample |
SAMN15010715 |
| SRA |
SRX8392422 |
