|
Status |
Public on Nov 20, 2017 |
Title |
TCRaCox3155 |
Sample type |
SRA |
|
|
Source name |
terminal illeum
|
Organism |
Mus musculus |
Characteristics |
genotype/variation: TCRa -/-
|
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 |
Wild-type age matched male mice were ear-tagged and housed in the same cage with equal number of respective knockout mice for 4 to 8 weeks. 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 |
SAMN05761454 |
SRA |
SRX2155732 |