|
| Status |
Public on Apr 17, 2019 |
| Title |
Tumor_8472 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Human breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
8p11-p12 amplification: Amplified
age: 83
pt status: pT3
lymph node status: NA
er status: pos
pgr status: pos
her2 status: neg
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer and RNA quantification with Nanodrop and Qubit.
Illumina TruSeq strand-specific RNA libraries (Ribosomal depletion using RiboZero human) containing 125 bp pair-end reads were obtained for each sample on a HiSeq2000 sequencer (Illumina) using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Quality control of raw RNA-seq reads was performed prior to assembly using FastQC (0.11.5), followed by trimming and filtering of the reads with TrimGalore (0.3.3) to remove adapter sequences and reads with Phred quality scores below 20.
Counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using HtSeq (0.6.1)(60) and Cufflinks (2.2.1)(61).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshima Z. Parris |
| E-mail(s) |
toshima.parris@oncology.gu.se
|
| Organization name |
University of Gothenburg
|
| Department |
Department of Oncology
|
| Lab |
Sahlgrenska Cancer Center
|
| Street address |
Medicinaregatan 1G, 6th floor
|
| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE97293 |
Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas |
| GSE100799 |
Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [RNA-seq] |
|
| Relations |
| BioSample |
SAMN07316000 |
| SRA |
SRX2984072 |
