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| Status |
Public on Dec 07, 2022 |
| Title |
CM_WT_3 [ATAC-seq] |
| Sample type |
SRA |
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| Source name |
H1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: Cardiomyocytes
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected and respended in ATAC-seq buffer, and proceeded with transposase reaction. Tagmented DNA was purified by Zymo columns.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Sequencing reads were trimmed to remove adapter sequences and low-quality bases using Cutadapt v3.4.
The trimmed reads were aligned to the human GRCh37 reference genome using bowtie2 v2.4.4 with parameters '-X 2000 --very-sensitive -k 5'.
Duplicate reads were discarded using picard v2.26.2.
Peaks were identified for each replicate sample using Genrich v0.6.1 with parameters '-j -q 0.05 -a 200.0' and '-e' to remove mitochondrial genome and regions not assembled into chromosomes, and '-E' to exclude 'N' homopolymers or high mappability regions in the genome.
Coverage tracks in bigwig format were generated using the deepTools package v3.5.1.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
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| Submission date |
May 13, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
|
| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE202965 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [ATAC-seq] |
| GSE202967 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection. |
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| Relations |
| BioSample |
SAMN28233780 |
| SRA |
SRX15262378 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6139350_CM_WT_3.bw |
242.9 Mb |
(ftp)(http) |
BW |
| GSM6139350_CM_WT_3.narrowPeak.gz |
453.4 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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