|
Status |
Public on Oct 10, 2021 |
Title |
hESC_CHD7 KO_p300 CnR_rep2 |
Sample type |
SRA |
|
|
Source name |
hESCs
|
Organism |
Homo sapiens |
Characteristics |
cell line: H9 treatment: Untreated genotype: CHD7 -/- chip antibody: p300
|
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).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Library strategy: CUT&RUN-seq 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
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|
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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) |
GSE171136 |
The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [CUT&RUN] |
GSE171139 |
The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 |
|
Relations |
BioSample |
SAMN18537597 |
SRA |
SRX10478715 |