|
| Status |
Public on May 04, 2019 |
| Title |
P2-1-RNA-FF |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
time point: pre-treatment biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used
All samples were processed and libraries constructed following the manufacturer's.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Patient 2 pre-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 1
|
| Data processing |
For RNASeq samples the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used and sequencing was performed on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.
Probes were mapped to Ensembl gene annotations using BioMart.
Data were log2 transformed and quantile normalised using R/Bioconductor software and packages.
Genome_build: Human genome version GRCh38.77
Supplementary_files_format_and_content: The processed data files contain expression data for each sample mapped to Ensemble gene IDS.
|
| |
|
| Submission date |
May 03, 2019 |
| Last update date |
May 04, 2019 |
| Contact name |
Carlos Martinez-Perez |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Edinburgh
|
| Department |
Institute of Genetics and Molecular Medicine
|
| Street address |
Western General Hospital, Crewe Road South
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE130645 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches |
| GSE130660 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN11567995 |
| SRA |
SRX5784027 |
