|
| Status |
Public on Nov 20, 2017 |
| Title |
RAG1x3163 |
| Sample type |
SRA |
| |
|
| Source name |
terminal illeum
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: RAG1 -/-
|
| Treatment protocol |
All mice were maintained in specific-pathogen-free conditions at an Association for Assessment and Accreditation of Laboratory Animal Care-accredited animal facility at the NIAID and were used under a study protocol approved by NIAID Animal Care and Use Committee (National Institutes of Health).
|
| Growth protocol |
C57BL/6, Rag1-/-, Tcra-/- mice were obtained from Taconic Laboratories through a special NIAID contract.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol isolation from terminal illeum
Illumina mRNA Stranded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
genes.counts
rlogMat.csv
|
| Data processing |
bcl2fastq2.15.04 to demultiplex
tophat2.011 (Tophat version: 2.0.11, Bowtie version: 2.2.2.0) mapping using UCSC mm9 genome annotation
featureCounts from subread package v1.4.5-p1 to generate counts matrix
DESeq2 R package (Version: 1.12.3) to calculate differential expression and regularized log transform of counts matrix
Genome_build: UCSC mm9
Supplementary_files_format_and_content: rlogMat.csv: comma seperated table with regularized log transform output of Deseq for all genes different between RAG1 knockout and WT or TCRa knockout co-housed vs separately-housed (1% FDR), used to generate plots shown in manuscript. All genes with "Rik" at the end of their GeneID were further filtered from this list. gene.counts.txt: Tab-delimited tablewith output of featureCounts, used as input for DEseq2.
|
| |
|
| Submission date |
Sep 09, 2016 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Andrew Martins |
| E-mail(s) |
andrew.martins@yale.edu
|
| Organization name |
Yale School of Medicine
|
| Department |
Immunobiology
|
| Street address |
100 College Street Rm 1155
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE86780 |
Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism |
|
| Relations |
| BioSample |
SAMN05761457 |
| SRA |
SRX2155729 |
