|
| Status |
Public on Sep 07, 2020 |
| Title |
Uninfected control - lung #15 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
infection: Control
stimulation: Iso
|
| Treatment protocol |
C57Bl/6 female mice were infected with Mycobacterium tuberculosis strain HN878 and treated with anti-GM-CSF monoconal antibody (aGM-CSF) or isotype control (iso) the day prior to infection and then twice a week during the course of the experiment. Uninfected mice were also treated and used as uninfected controls. Three weeks post-infection, whole blood and lungs from each individual mouse were harvested and processed for RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the Tempus™ Spin RNA isolation kit (Thermo Fisher Scientific). Globin RNA was depleted from total RNA (1.5–2 µg) using the GLOBINclear™-Mouse/Rat Globin mRNA removal kit (Thermo Fisher Scientific). Lungs were collected in TRI-Reagent (Sigma-Aldrich). Total RNA was extracted using the RiboPure™ Kit (Ambion).
KAPA mRNA polyA HyperPrep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data header: TEI448A35
GEO_lung_DESEQ2_normalised_values.txt.gz
|
| Data processing |
Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.
|
| |
|
| Submission date |
Nov 29, 2019 |
| Last update date |
Sep 07, 2020 |
| Contact name |
Anne OGarra |
| E-mail(s) |
Anne.OGarra@crick.ac.uk
|
| Organization name |
Francis Crick Insititue
|
| Lab |
IMMUNOREGULATION AND INFECTION LABORATORY
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE141205 |
GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation [Lung] |
| GSE141207 |
GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation |
|
| Relations |
| BioSample |
SAMN13429860 |
| SRA |
SRX7242320 |
