|
| Status |
Public on Aug 07, 2023 |
| Title |
TAMR Decitabine Day 7 2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
TAMR cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tamoxifen-resistant (TAMR) MCF7 cells
treatment: Decitabine Day 7
replicate: 2
|
| Treatment protocol |
Cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control Early”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35. Matched control cells were cultured for 35 days in normal media and harvested at day 35 for “Control Late”.
|
| Growth protocol |
Tamoxifen-resistant MCF7 cells (TAMR) were previously generated by the long-term culture of MCF7 cells in phenol red-free RPMI medium containing 10% charcoal-stripped FBS (Gibco) and 4-OH-tamoxifen (1 × 10−7 M; TAM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from harvested cells using the Trizol.
RNA was prepared for sequencing using the TruSeq Stranded mRNA Library Prep kit (Illumina) and libraries were sequenced on Illumina NovaSeq S4 in paired-end mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TAMR_Aza_Day7_Rep2
|
| Data processing |
Sequence adaptors were trimmed using Trim Galore (v.0.11.2), reads were processed with Xenome v.10.1. (Conway et al., 2012) to remove mouse sequences and remaining reads were mapped with STAR (v.2.7.7a) (Dobin et al., 2013) to the hg38/GRCh38 human genome build with GENCODE v33 used as a reference transcriptome (parameter settings: –quantMode TranscriptomeSAM–outFilterMatchNmin 101 –outFilterMultimapNmax 20).
TPM counts for each sample were obtained from DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: normalized transcript abundance measurment
|
| |
|
| Submission date |
Nov 01, 2022 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
joanna.achinger@adelaide.edu.au
|
| Organization name |
South Australian Immunogenomics Cancer Institute
|
| Street address |
AHMS Building, North Terrace
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE216988 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [RNA-seq] |
| GSE216989 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions |
|
| Relations |
| BioSample |
SAMN31553297 |
| SRA |
SRX18108427 |
