|
| Status |
Public on Feb 28, 2022 |
| Title |
DMSO_8h_R1 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: DMSO 20 μM
treatment duration: 8 hours
|
| Treatment protocol |
Cells were treated with DMSO (control) or MKC8866 (IRE1 inhibitor) for the indicated time.
|
| Growth protocol |
MDA-MB-231 cells were seeded at density 2 × 104 cells per mm2 24 hours before treatment. Cultured in DMEM high glucose (Sigma-Aldrich, D6429) supplemented with 10% FBS and 2 mM L-glutamine at 37 °C, 5% CO2 in a humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Rneasy columns (Qiagen, 74104) according to the manufacturer’s protocol. RNA integrity was checked using the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols at EMBL Genomics Core facility in Heidelberg
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
control
|
| Data processing |
Sequenced reads were assessed in a quality control step with FastQC, MultiQC. Followed by adapter sequences trimming with TrimGalore.
Reads were aligned with reference genome using STAR. > 80% of uniquely mapped reads for each library.
Reads/counts per gene were summarized with FeatureCounts.
Genome_build: GRCh38 (Ensembl 99)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 09, 2021 |
| Last update date |
Feb 28, 2022 |
| Contact name |
Afshin Samali |
| E-mail(s) |
afshin.samali@nuigalway.ie
|
| Organization name |
NUIG Galway
|
| Department |
Apoptosis Research Centre
|
| Street address |
Newcastle Road, Biosciences Research Building
|
| City |
Galway |
| ZIP/Postal code |
H91 W2TY |
| Country |
Ireland |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE176454 |
Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer |
|
| Relations |
| BioSample |
SAMN19642121 |
| SRA |
SRX11099928 |
