|
| Status |
Public on Feb 09, 2017 |
| Title |
G401-sg1-HOXB13 |
| Sample type |
SRA |
| |
|
| Source name |
rhabdoid tumor of the kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
tumor type: rhabdoid
cell line: G401
|
| Growth protocol |
G401 cells were grown in RPMI + 15% FBS and harvested at 80% confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit
Extracted RNA was enriched using the Ribominus™ Eukaryote Kit (Invitrogen). The Ion PI™ Template OT2 200 Kit (Invitrogen) was used to prepare the RNA library for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Torrent Suite™ Software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie
Fragments Per Kilobase of exon per Million reads (FPKM) were calculated using TopHAT and Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: Excel files contain FPKM counts of each cell line
|
| |
|
| Submission date |
Feb 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul-Joseph P Aspuria |
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Women's Cancer Program
|
| Lab |
Sandra Orsulic
|
| Street address |
8400 Beverly Blvd.
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE65655 |
The effect of HOXB13 CRISPR knockout on the transcriptome in G401 cells |
|
| Relations |
| BioSample |
SAMN03329689 |
| SRA |
SRX866292 |
