|
| Status |
Public on Jun 08, 2020 |
| Title |
ARID1A-WT2 Starved rep2 |
| Sample type |
SRA |
| |
|
| Source name |
endometrial epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endometrial epithelial cells
genotype: ARID1A WT
biological replicate: 2
technical replicate: 2
treatment: Serum Starved (0% FBS, 24h)
|
| Treatment protocol |
Two 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 |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured human endometrial epithelial cells using the Qiagen RNeasy Plus Mini Kit.
RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA Nano Chip. RIN values ranged from 9.2 to 10.0 for human endometrial epithelial cells. RNA-sequencing was performed by GeneWiz, Inc. on the Illumina HiSeq2500 platform, in a 2x150 bp paired-end high output V4 chemistry configuration.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Clone2_Starved.tabular.txt
|
| Data processing |
Bioinformatics analysis was performed using Galaxy, an open access web-based program that contains a variety of next-generation sequencing analysis tools. Reads were processed, trimmed to 101 bp, and aligned to Homo sapiens reference genome build hg19 using TopHat gapped-read mapper (ver. 2.1.0). The aligned reads were processed with Cufflinks transcript assembly (ver. 2.2.1.0), and output of the resulting GTF files was amalgamated to UCSC hg19 RefSeq genes annotation files using Cuffmerge (ver. 2.2.1.0). Differential expression analysis was performed using Cuffdiff (ver. 2.2.1.3) to produce a list of genes whose expression changes were significant (FDR < 0.05) between the groups tested.
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 |
GPL16791 |
| Series (2) |
| GSE106661 |
Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [RNA-Seq] |
| GSE106665 |
Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry |
|
| Relations |
| BioSample |
SAMN10686867 |
| SRA |
SRX5195754 |
