|
| 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 |
