|
| Status |
Public on Oct 16, 2020 |
| Title |
sample_5_1: MVA.Ad |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole blood
strain: C57BL/6
Sex: Female
batch: 1
condition: Test
vaccine/antigen: MVA prime, adenovirus boost
min_noise: 6.5
|
| Treatment protocol |
Groups of 3-6 female C57BL/6 mice (6-8 weeks old) were immunised intramuscularly with 1/5 of the human dose (1e7 viral particles of MVA or 1e9 viral particles of adenovirus) of one of the listed vaccines. Mice were given a second dose of vaccine 3 weeks later (8 weeks for viral vectored vaccines) and cardiac bled to obtain whole blood 24h ours after this second dose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mouse whole blood samples using a Mouse RiboPure(TM)-Blood RNA Isolation Kit (Life Technologies) and depleted for glibin mRNA using a GLOBINclear(TM) mouse/rat Kit (Life Technologies)
Polyadenylated transcripts were oligo (dT) bead-selected, reverse transcribed, amplified and labelled with an Illumina TotalPrep(TM)-96 RNA Amplification Kit (Life Technologies)
Sample fragments were 75 bp size-selected and multiplexed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
sample_5_1
|
| Data processing |
RNA was sequenced (75 bp, paired end) using an Illumina HISeq 4000
Raw fastq files were analysed for sequence quality using fastqc software
Reads were aligned to the Mus musculus reference genome (GRCm38) and genes were quantified using STAR with the --quantMode GeneCounts function
Resultant count matrices were filtered to include only genes with counts per million of greater than 1 million in 5 or more samples (smallest group size)
Count matrices were analysed for differential gene expression using the limma/voom pipeline
Genome_build: GRCm38, release 95
Supplementary_files_format_and_content: Tab-delimited files (.tab) were generated using STAR –quantMode GeneCounts and each value represent the number of reads incident to a gene in a given sample
|
| |
|
| Submission date |
Oct 29, 2019 |
| Last update date |
Oct 30, 2019 |
| Contact name |
Dylan Sheerin |
| E-mail(s) |
dylan.sheerin@stx.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Street address |
Churchill Hospital, Old Road
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE139529 |
Comparison of whole blood transcriptional changes induced by menignoccocal capsular group B vaccines in mice |
|
| Relations |
| BioSample |
SAMN13152078 |
| SRA |
SRX7068040 |
