|
| Status |
Public on May 31, 2021 |
| Title |
EB2 |
| Sample type |
SRA |
| |
|
| Source name |
cortical brain tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cortical brain tissue
group: Malnourished_Microbes (MALBG)
strain: C57BL/6J
cell type: CD11b+ cells
|
| Treatment protocol |
After weaning, mice were fed a standard chow diet (CON), or an isocaloric low fat/protein diet (MAL) for one month, with a malnourished subset exposued to a mix of E. coli/Bacteroidales species (MAL-BG)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cortical brain tissue was harvested and stored in RPMI media on ice before cell isolation and CD11b+ enrichment using Miltenyi Biotec murine kits
Standard Illumina protocols prepared by BRC-Seq (Sequencing core at the University of British Columbia, Vancouver, Canada)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment: STAR (Mus musculus mm10 reference sequence)
gene counts were generated from bam files using htseq-count v.2.5
DESeq2: Prefilter remove low counts (sum less than 10 in samples in the smallest group, CON n=4)
DESeq2: DEGs (padj <0.05, FC > |1.5|
Genome_build: mm10 (GRCm38.94)
|
| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Kylynda C Bauer |
| E-mail(s) |
Kylynda.c.bauer@gmail.com
|
| Organization name |
Michael Smith Laboratories
|
| Lab |
Finlay Lab
|
| Street address |
#301 – 2185 East Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6N2Y8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN12873960 |
| SRA |
SRX6923968 |
