|
| Status |
Public on May 20, 2015 |
| Title |
K0504Sr |
| Sample type |
SRA |
| |
|
| Source name |
Renal Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: S
pretreatment: Sutent
grade: Sarcomatoid
Stage: IV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was isolated from core punches using the Epicentre MasterPure™ Complete DNA and RNA Purification Kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol following de-paraffinization and proteinase K treatment. RNA was quantified using the Picogreen assay.
cDNA was made from total RNA using the NuGEN Ovation RNA-Seq FFPE System (Part # 7150-08). Libraries were prepared for sequencing using cDNA into the Illumina TruSeq DNA-seq protocol (Part #: FC-121-2001). Both parts followed the standard NuGEN and Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were trimmed for adaptor sequence, and aligned to hg19 using TopHat v2.0.8b
HTSeq-0.5.3p9 was used to generate counts for each gene and edgeR Bioconductor package was used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for all samples
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Horatiu Voicu |
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE59066 |
RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN02902375 |
| SRA |
SRX645348 |
