|
| Status |
Public on Mar 06, 2013 |
| Title |
Solid1-GMCSF |
| Sample type |
SRA |
| |
|
| Source name |
Neutrophil
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
age: 29
treatment: incubated for 1h with GM-CSF (5 ng/mL)
|
| Treatment protocol |
Neutrophils were isolated from peripheral blood and incubated for 1h with TNF-alpha (10 ng/mL) or GM-CSF (5 ng/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol-chloroform precipitation, followed by clean-up with the Rneasy kit (Qiagen) including DNA digestion. RNAseq was carried out using standard SOLiD and Illumina protocols. mRNA was enriched by ribosomal depletion (SOLiD) or poly-A selection (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
RNA (ribosome-depleted)
|
| Data processing |
Reads were mapped to the human genome (hg19) using TopHat (v1.4.1).
Illumina libraries:default TopHat parameters were used with the addition of the -g / --max-multi-hits option set as 1, to report only uniquely mapping reads.
SOLiD libraries: preliminary analysis of read quality scores showed a decrease in quality of SOLiD reads towards the 3’ end of the read, and consequently reads were trimmed by 10 bases from the 3’ end and first mapped to the human genome using Bowtie (v0.12.7). Reads not uniquely mapped by Bowtie were then mapped using TopHat and the two datasets merged.
Gene annotation and calculation of RPKM values was carried out using Cufflinks (v1.3.0) with the provision of a GTF annotation file (hg19).
Genome_build: hg19
Supplementary_files_format_and_content: Files were created using cuffdiff applying a 5% false discovery rate and with the provision of a reference GTF (hg19)
|
| |
|
| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Helen Louise Wright |
| E-mail(s) |
hlwright@liverpool.ac.uk
|
| Organization name |
University of Liverpool
|
| Department |
Institute of Life Course and Medical Sciences
|
| Street address |
6 West Derby Street
|
| City |
Liverpool |
| ZIP/Postal code |
L7 8TX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE40548 |
RNAseq analysis of the human neutrophil transcriptome, with and without in vitro cytokine stimulation |
|
| Relations |
| SRA |
SRX182670 |
| BioSample |
SAMN01161893 |
