|
| Status |
Public on Oct 10, 2021 |
| Title |
hESC_HERVH KD_ATAC-seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hESCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
treatment: LNA-GapmeRs treated
genotype: wild type (CHD7-HA)
|
| Treatment protocol |
Cells were treated with 4-Thiouridine for 16 hours and with LNA-GapmeRs for 24 hours, respectively, before harvesting for further experiments.
|
| Growth protocol |
Human ES cell line H9 was cultured and maintained in mTesR1 medium (Stem Cell Technologies).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from cells using TRI Reagent (Molecular Research Center, Inc) and further purified using Zymo RNA clean and concentrator-5 kit (Zymo Research) with DNase I treatment. DNA was extracted using phenol/chloroform followed by ethanol precipitation.
Sequencing libraries were prepared as described previously in Bowman SK et al. (2013).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by deeptools bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Mar 30, 2021 |
| Last update date |
Oct 10, 2021 |
| Contact name |
Fei Ji |
| Organization name |
Massachusetts General Hospital
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE171135 |
The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [ATAC-seq] |
| GSE171139 |
The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 |
|
| Relations |
| BioSample |
SAMN18537549 |
| SRA |
SRX10478672 |
