|
| Status |
Public on Feb 17, 2025 |
| Title |
PE121410-RBM10 cells, cloneA, Replicate2, RBM10 re-expression |
| Sample type |
SRA |
| |
|
| Source name |
PE121410
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PE121410
cell type: Thyroid cancer cell line
genotype: RBM10WT-reexpression
|
| Growth protocol |
The biological replicates of RBM10 overexpressing or KD isogenic thyroid cancer cell lines were cultured in vitro, where applicable treated with doxycyclin to induce RBM10 expression for 72 hours prior to RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the 5 isogenic RBM10 overexpressing or KD thyroid cancer cell lines using the Qiagen RNeasy extraction kit
500 ng of total RNA with RQN values of 9.1-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq in a PE125 run, using the HiSeq 3000/4000 SBS Kit (Illumina). An average of 100 million paired reads was generated per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Library name: PE_Cl_A_Rep2_IGO_07389_10_S19
|
| Data processing |
Transcript counts were obtained using Partek Flow version 6.0.17.0614 (www.partek.com). Briefly, raw reads were aligned to human assembly hg19 using STAR aligner (STAR-2.5.3a) with default parameters. The aligned reads were quantified to Partek E/M annotation model using hg19 assembly generating gene and transcript counts.
Assembly: hg19
Supplementary files format and content: Matrix table with transcript counts for every gene and every sample
|
| |
|
| Submission date |
Dec 30, 2024 |
| Last update date |
Feb 17, 2025 |
| Contact name |
Gnana P Krishnamoorthy |
| Organization name |
Memorial Sloan Kettering cancer center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Fagin Lab
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE285560 |
RBM10 loss promotes metastases by aberrant splicing of cytoskeletal and extracellular matrix mRNAs. |
|
| Relations |
| BioSample |
SAMN46039984 |
| SRA |
SRX27217655 |
