|
| Status |
Public on May 02, 2024 |
| Title |
ctrlCyto3 |
| Sample type |
SRA |
| |
|
| Source name |
ATCC MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast adenocarcinoma
morphology: Epithelial-like
rna: cytosolic
treatment: DMSO
replicate: 3
|
| Treatment protocol |
MCF7 cells were serum starved for 12h prior treatment and treated with 4.2nM DMSO or 4.2nM insulin or 4.2nM insulin + 250nM torin1
|
| Growth protocol |
MCF7 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% L-glutamine (all from Wisent Bio Products).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Polysome-profiling
RNAseq libraries were obtained according to the strand specific TruSeq protocol including ribosomal RNA depletion (Ribo Zero)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P551_103mergedSort.bam
|
| Data processing |
Read alignment using HISAT default settings
Alignment to reference genome using rpkmForGenes.py (version 11 April 2013)
Genes mapping to multiple places in genome removed
Gene annotation using RefSeq database
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a .txt file containing rpkms and raw read counts for each sample obtained by the rpkmForGenes.py script
|
| |
|
| Submission date |
Dec 14, 2016 |
| Last update date |
May 02, 2024 |
| Contact name |
Christian Oertlin |
| E-mail(s) |
christian.oertlin@ki.se
|
| Organization name |
Karolinska Institutet
|
| Street address |
Tomtebodavägen 23A
|
| City |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE92402 |
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq |
|
| Relations |
| BioSample |
SAMN06141835 |
| SRA |
SRX2423045 |
