|
| Status |
Public on Sep 07, 2024 |
| Title |
rep1_L1-ChIRP-DNA |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: Human embryonic stem cells
fraction: L1
|
| Treatment protocol |
no treatment
|
| Growth protocol |
H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA for 48 hours then collected for the ChIRP pulldown experiment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIRP-DNAs after reverse crosslinking were purified using the MinElute PCR Purification Kit (QIAGEN #28004) following the instruction manuals. 40 ul of ChIRP-DNAs were eluted for each sample.
5 ul of purified ChIP-DNAs of each sample was used to prepare sequencing library. The library was prepared with NEBNextUltra II DNA Library Prep Kit for Illumina (NEB # E7645L), following the manual instruction. Library DNA were equally pooled at 8 nM for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
the raw sequencing data were processed using bowtie2, then filtered using samtools to generate bam files.
The bam files were processed with deeptools bamCoverage to generate RPKM normalized, and blacklist filtered BigWigs with default 50bp bins.
The merged bam files were processed with macs3 to call LINE1 ChIRP peaks in BED files.
Assembly: hg38
Supplementary files format and content: bw
Library strategy: ChIRP-seq
|
| |
|
| Submission date |
Apr 05, 2024 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Juan Zhang |
| E-mail(s) |
tzzhangjuan@gmail.com
|
| Organization name |
LTRI
|
| Street address |
25 Orde Street, Room 6-1001 MRS
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3H7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL34281 |
| Series (2) |
| GSE232939 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs |
| GSE263289 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [ChIRP-seq,RSeT+DT H9] |
|
| Relations |
| BioSample |
SAMN40759694 |
| SRA |
SRX24164760 |
