|
| Status |
Public on May 07, 2019 |
| Title |
P2-2-Ampli-FFPE |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
time point: early on-treatment biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 2x20µm FFPE tissue sections using the RNeasy FFPE kit.
All samples were processed and libraries constructed following the manufacturer's guidelines in the Edinburgh Clinical Research Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Sample 1
Patient 2 early on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.
|
| Data processing |
Samples were analysed in an Ion Proton instrument.
Data were generated using the AmpliSeq RNA plugin in the Torrent Suite Software and normalised using RPM (reads assigned per million mapped reads) method.
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 06, 2019 |
| Last update date |
May 07, 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 |
GPL17303 |
| Series (2) |
| GSE130645 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches |
| GSE130762 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [AmpliSeq] |
|
| Relations |
| BioSample |
SAMN11582081 |
| SRA |
SRX5796633 |
