|
| Status |
Public on Sep 01, 2016 |
| Title |
Patient20 |
| Sample type |
SRA |
| |
|
| Source name |
HNSCC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HNSCC tumour
tumour site: Larynx
tumour stage: T4
hpv status: Negative
til status: Moderate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HNSCC tissues were collected and snap frozen within 60 seconds. Cryosections (10µm) were cut and RNA was harvested using Rneasy Mini Kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyser before library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
bcl2fastq 1.8.4 was used for base calling
Reads were aligned to hg19 genome using TopHat v2.0.9 with parameters -p 6 --library-type fr-firststrand --no-coverage-search
DUST wcores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads( DUSC >4) were removed from the BAM files
After removing multi mapped reads with low-complexity reads, SAM files were generated from BAM files with SAMtools (v 1.1). Gene specific read counts were obtained with HTSeq-count v.0.5.4 using 'union" option.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq anntated read counts per each gene.
|
| |
|
| Submission date |
Aug 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Woelk |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Southampton
|
| Department |
Faculty of Medicine
|
| Lab |
LE74A
|
| Street address |
Southampton General Hospital
|
| City |
Southampton |
| State/province |
Hampshire |
| ZIP/Postal code |
SO16 6YD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE72536 |
Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours. |
|
| Relations |
| BioSample |
SAMN04019078 |
| SRA |
SRX1175087 |
