|
| Status |
Public on May 01, 2024 |
| Title |
MDA-MB-231, Control, 10 days, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
triple-negative breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: triple-negative breast cancer
cell line: MDA-MB-231
cell type: epithelial
treatment: untreated
|
| Treatment protocol |
Cells were first plated with a density of 1.5x10^6 cells into 100 mm dishes. After 4h of cell adherence, 100 uM of DETA/NO was added to the media and cells were allowed to grow for 48h. At this time, cells were collected with trypsin (Gibco), pooled according to each replicate, counted, and re-plated at the same starting density of 1.5x10^6 cells into new 100 mm dishes. This was repeated every 48 h for a total of 10 days of DETA/NO treatment.
|
| Growth protocol |
Cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% qualified fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco). All cells were cultured at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using the RNAqueous™-4PCR kit (Ambion) and treated with DNase I (Ambion) to avoid genomic DNA contaminations.
Libraries were prepared with KAPA RNA Hyper Prep kit (Roche).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
re-analysis of GSM7526964
|
| Data processing |
Reads were aligned to hg38 using STAR 2.5.2a (Gencode_human/release_22).
Bams were sorted using samtools.
Gene counts were generated using HTSeq (Gencode_human/release_22).
Differential expression analysis was completed using edgeR v3.40.2.
Gene Set Enrichment Analysis was completed using in-house OmicPath and edgeR.
Assembly: hg38
|
| |
|
| Submission date |
Nov 17, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Douglas David Thomas |
| E-mail(s) |
ddthomas@uic.edu
|
| Organization name |
University of Illinois Chicago
|
| Department |
Pharmaceutical Sciences
|
| Lab |
Thomas Lab
|
| Street address |
900 S Ashland Ave
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248150 |
Nitric oxide inhibits ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome [RNA-seq] |
| GSE248151 |
Nitric oxide inhibits Ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome |
|
| Relations |
| Reanalysis of |
GSM7526964 |
| BioSample |
SAMN36176576 |
| SRA |
SRX20852274 |
