|
| Status |
Public on Nov 28, 2019 |
| Title |
056_EOS |
| Sample type |
SRA |
| |
|
| Source name |
Overy
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: BRCA
tissue: Ovary
race: White
ethnicity: Non_Hispanic
sample.type: Tumor
reservation.type: FFPE
treatment.best.response: SD
brca.status: BRCA2
brca.study.entry: Carrier
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy FFPE kit is used for FFPE sample extraction.
Illumina library preparation for RNA-Seq is done using the TruSeq RNA Access library prep kit. The samples were sequenced on Illumina Nextseq 500 high output v2 platform (2x75).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of Homo sapiens: Ovarian cancer
|
| Data processing |
Quality Check: FASTQ file quality was checked using FASTQC v0.11.2. The summary reports showed no potential errors or warnings.
Alignment and Pre-processing: Reads were mapped using STAR Aligner tool v020201 to the human genome reference (Hg19) downloaded from UCSC genome browser.
Transcripts quantification: Gene expression levels were obtained from the RNA-seq dataset using RSEM v1.2.31 with Ensembl gene annotation database.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each Sample, obtained using RSEM V1.2.31.
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Sheida Nabavi |
| E-mail(s) |
sheida.nabavi@uconn.edu
|
| Organization name |
University of Connecticut
|
| Street address |
371 Fairfield Way
|
| City |
Storrs |
| ZIP/Postal code |
06269 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE141142 |
An immune-centric exploration of BRCA1 and BRCA2 germline mutation related breast and ovarian cancers |
|
| Relations |
| BioSample |
SAMN13415848 |
| SRA |
SRX7232483 |
