|
| Status |
Public on Dec 12, 2024 |
| Title |
MDA-MB-231, untreated, rep 0 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: breast
genotype: WT
treatment: untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
kit from Qiagen “allprep DNA/RNA/miRNA Universal kit” (ref. 80224) was used. Before extraction, samples were cut with cryostat to obtain around 200µm of thickness of tissue. The homogenization step with lysis buffer were done with tissue lyzer system
Stranded mRNA prep Ligation-Illumina
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Input transcriptome assembly
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore software (RNAseq samples) or Cutadapt (ribosome profiling samples)
STAR-2.5.3a single-pass mode was used to alignment the reads (all samples)
STAR-2.5.3a with two-pass mode was used to alignment the reads (only samples for StringTie/transcriptome assembly)
Assembly: hg19 (Ensembl)
Supplementary files format and content: stringtie output transcriptome assembly gtf file
Supplementary files format and content: tab-delimited text files include featureCounts output (PTEN-WWOX differential expression)
Supplementary files format and content: gtf of ORF quantification (RiboSeq samples)
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Dec 12, 2024 |
| Contact name |
Yago A Arribas |
| E-mail(s) |
yago.arribas-de-sandoval@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE234223 |
Transposable element exonization by non-canonical splicing generates a diversity reservoir of functional protein isoforms |
|
| Relations |
| BioSample |
SAMN35639665 |
| SRA |
SRX20599774 |
