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| Status |
Public on Mar 13, 2024 |
| Title |
WT_R3 (ATAC-seq) |
| Sample type |
SRA |
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| Source name |
UPS (3672-3)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: UPS (3672-3)
cell type: undifferentiated pleomorphic sarcoma cell line
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and then washed by PBS. Lysis with ATAC resuspension buffer(TRIS-HCl-pH7.4, 10mM; NaCl,10mM;MgCl2,3mM) plus 0.1% NP40, 0.1%Twwen-20,0.01%Digitonin.
Libraries were generated using NEBNext Ultra II kits.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ATACseq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: hg38
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: narrowPeak files generated by MACS2
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| Submission date |
Jan 04, 2024 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Douglas Barrows |
| E-mail(s) |
dbarrows@rockefeller.edu
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| Phone |
7749940981
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| Organization name |
Rockefeller University
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| Street address |
1230 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE240030 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells |
| GSE252530 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells [ATAC-seq] |
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| Relations |
| BioSample |
SAMN39255869 |
| SRA |
SRX23095737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8002624_Sorted_WT_R3Normalised.bw |
384.7 Mb |
(ftp)(http) |
BW |
| GSM8002624_WT_R3_withInput_WT_R3_peaks.narrowPeak.gz |
3.2 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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