|
| Status |
Public on Jun 11, 2023 |
| Title |
A-3_IgG |
| Sample type |
SRA |
| |
|
| Source name |
hESCs H9 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: hESCs
antibody: Rabbit (DA1E) mAb IgG XP® Isotype Control #3900, Cell signaling technology
|
| Treatment protocol |
Briefly, hESCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with anti-ARID1A antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies)
|
| Growth protocol |
H9 hESCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
50
genomic DNA
|
| Data processing |
Base calling and quality scoring were performed in Illumina NextSeq/HiSeq
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using rabbit IgG as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks
|
| |
|
| Submission date |
Jun 11, 2020 |
| Last update date |
Jun 11, 2023 |
| Contact name |
Lei Yang |
| E-mail(s) |
lyang7@iu.edu
|
| Phone |
(317) 278-5233
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Department of Pediatrics
|
| Street address |
1044 W. Walnut St.
|
| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE152324 |
Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN15217780 |
| SRA |
SRX8533205 |
