|
| Status |
Public on Jun 08, 2020 |
| Title |
ARID1A-KO FBS rep2 |
| Sample type |
SRA |
| |
|
| Source name |
endometrial epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endometrial epithelial cells
genotype: ARID1A KO
treatment: Complete Growth Media (15% FBS)
|
| 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 and mouse uterine tissues using the Qiagen RNeasy Plus Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA Nano Chip. RIN values ranged from 9.5 to 10.0. RNA-sequencing was performed by GeneWiz, Inc. on the Illumina HiSeq2500 platform, in a 2x100 bp paired-end high output V4 chemistry configuration.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FBS.tabular
|
| Data processing |
Bioinformatics analysis was performed using Galaxy, an open access web-based program that contains variety of next-generation sequencing analysis tools. Reads were processed 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
Supplementary_files_format_and_content: Cuffdiff output
|
| |
|
| Submission date |
Nov 08, 2017 |
| 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 |
SAMN07998907 |
| SRA |
SRX3373140 |
