|
| Status |
Public on Jun 08, 2020 |
| Title |
ATAC-Seq: ARID1A-WT1 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
endometrial epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endometrial epithelial cells
genotype: ARID1A WT
biological replicate: 1
technical replicate: 3
|
| Treatment protocol |
wo biological pairs of wild-type (ARID1AWT) and knockout (ARID1AKO) cells were used (PMID: 26953344). These pairs of isogenic ARID1A wildtype and knockout cell lines were established from human endometrial using a CRISPR/Cas9 genome editing method.
|
| Growth protocol |
The cell lines used in this study were maintained at 37°C and 5% CO2, and included immortalized isogenic human endometrial epithelial ARID1AWT and ARID1AKO cells. ARID1AWT and ARID1AKO cells were cultured in RPMI 1640 medium supplemented with 15% FBS, 1% MEM non-essential amino acids, and 1% penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq library construction was performed as previously described with minor modifications (PMID: 24097267) using 60,000 cells of two independent clones of human endometrial epithelial ARID1AWT and ARID1AKO cells. Transposed DNA was purified using a QIAgen MinElute PCR Purification kit, and was subsequently amplified using NEBNext High Fidelity 2x PCR master mix for 12 cycles. PCR products were purified using Agencourt AMPure XP, and sequencing was performed by JHMI Deep Sequencing and Microarray Core using a NextSeq500 platform with double-end reads of 75 bases.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ARID1A-WT1_ATAC.bedgraph
|
| Data processing |
For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2 (PMID: 20080505) under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (PMID: 18798982) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.
Genome_build: hg19
|
| |
|
| Submission date |
Jan 02, 2019 |
| Last update date |
Jun 08, 2020 |
| Contact name |
Yohan Suryo Rahmanto |
| E-mail(s) |
suryoysr@gmail.com
|
| Organization name |
Johns Hopkins School of Medicine
|
| Department |
Department of Pathology
|
| Street address |
CRB-2, Rm 376, 1550 Orleans St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE106658 |
Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [ATAC-Seq] |
| GSE106665 |
Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry |
|
| Relations |
| BioSample |
SAMN10686519 |
| SRA |
SRX5195743 |
