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| Status |
Public on Sep 01, 2022 |
| Title |
HAP1_ATAC-seq_ARID1A_shControl_Testosterone_r6 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
library: ATAC-seq
cell line: HAP1
replicate: 6
knockout: ARID1A
knockdown: Control
drug_treatment: Testosterone
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| Growth protocol |
HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
ATAC-seq for HAP1 cell line with ARID1A knockout and control shRNA, treated with Testosterone, replicate 6
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| Data processing |
Sequenced reads were trimmed for adaptor sequences with Skewer
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
ATAC-seq read coverage at every reference genome position using BEDTools coverage and divided by the total number of reads, converted into bedgraph files and subsequently to bigwig format using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peak files have MACS2 peak calls, BigWig files have read counts per million mapped reads
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| Submission date |
Jan 17, 2019 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
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| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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| Street address |
Lazarettgasse 14
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE125220 |
Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies [ATAC-Seq] |
| GSE125221 |
Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies |
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| Relations |
| BioSample |
SAMN10764575 |
| SRA |
SRX5258429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3566549_HAP1_ATAC-seq_ARID1A_shControl_Testosterone_r6.bigWig |
447.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM3566549_HAP1_ATAC-seq_ARID1A_shControl_Testosterone_r6.peaks.narrowPeak.gz |
433.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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