|
Status |
Public on Mar 22, 2017 |
Title |
Naïve (normoxia) control 1 |
Sample type |
SRA |
|
|
Source name |
Murine peripheral blood leukocytes (normoxia)
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 gender: Male genotype/variation: Wild type treatment: none
|
Extracted molecule |
total RNA |
Extraction protocol |
Murine peripheral blood leukocytes (1x106/condition) were lysed and RNA extracted using the mirVana™ total RNA isolation protocols (Ambion, Austin, USA). For RNA quantification, samples were treated with DNase (Ambion) and random hexamer cDNA synthesized by reverse transcription. Assays-on-demand gene expression TaqMan® MGB 6FAM dye-labeled products (Applied Biosystems) were used for relative quantification of cDNA. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out on a NextSeq-550 sequencer
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
|
|
Description |
Naïve_control_RNAseq_1 [RD04]
|
Data processing |
Paired ends aligned using FASTQ paired-end parser Quality control and Tophat 1.20 Alignment General sequence statistics calculated Quantitated Gene expression patterns Cuffdiff analysis to determine differentially expressed transcripts Genome_build: mm9 Supplementary_files_format_and_content: .txt file with FPKM expression values carried out using the Cufflinks tool.
|
|
|
Submission date |
Mar 22, 2016 |
Last update date |
May 15, 2019 |
Contact name |
John Paterson Thomson |
E-mail(s) |
john.thomson@igmm.ed.ac.uk
|
Organization name |
University of Edinburgh
|
Department |
MRC Human Genetics Unit
|
Lab |
Meehan
|
Street address |
Crewe Road
|
City |
Edinburgh |
ZIP/Postal code |
EH4 2XU |
Country |
United Kingdom |
|
|
Platform ID |
GPL21626 |
Series (1) |
GSE79484 |
RNAseq analysis in peripheral blood leukocytes between control (normoxia) and hypoxic mice +/- bacterial infection. |
|
Relations |
BioSample |
SAMN04572209 |
SRA |
SRX1653038 |