|
| Status |
Public on Mar 09, 2022 |
| Title |
Untreated_T0_run2_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
endometrial adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: endometrial adenocarcinoma
cell line: Ishikawa
passages: 20-25
cell type: epithelial-like
growth mode: adherent
treatment: untreated Ishikawa cells
|
| Treatment protocol |
Adequate number of cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 12h.
|
| Growth protocol |
Ishikawa cells were routinely cultured in DMEM/F12 (1:1) supplemeted with 10% FCS and gentamycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed once in PBS and whole cell lysates were prepared using Trizol reagent (Invitrogen). Total RNA (>200bp) was obtain using RNeasy Plus Mini kit (Qiagen) according to manufacturer specifications.
Poly-A-enriched RNA was used to prepare libraries with TruSeq RNA Sample Preparation kit v2 y v4 (ref. RS-122-2001/2, Illumina) according to instructions from manufacturer followed by single-end (run1) and paired-end (run2) sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Good quality 50bp reads were aligned to the reference human genome (hg19, UCSC) using Tophat software keeping those that mapped uniquely to the reference with up to two mismatches and transcript assembly, abundance quantification and differential expression analyses were performed with the Cufflinks tool.
Genes under 200bp in length or with FPKM values below 0,1 were excluded from downstream analyses. Genes were classified into induced, repressed or non-regulated depending on log2FC value relative to untreated cells (T0). Threshold value was arbitrarily set at log2FC = +/- 0.8 and q<0.05 (FDR).
Genome_build: hg19
Supplementary_files_format_and_content: text file including fpkm values for all samples of two biological replicates (run1 and run2) and fold change versus untreated sample
|
| |
|
| Submission date |
Oct 25, 2019 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Patricia Saragüeta |
| E-mail(s) |
[email protected]
|
| Organization name |
IByME
|
| Street address |
Vuelta de Obligado 2490
|
| City |
buenos aires |
| State/province |
CABA |
| ZIP/Postal code |
1490 |
| Country |
Argentina |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE139393 |
Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (RNAseq) |
| GSE139398 |
Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression |
|
| Relations |
| BioSample |
SAMN13113628 |
| SRA |
SRX7057539 |
