NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5880684 Query DataSets for GSM5880684
Status Public on May 26, 2022
Title PBS3 IEL
Sample type SRA
 
Source name Small intestine epithelium
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Small intestine epithelium
time: 10 days post treatment
infection status: PBS control
Extracted molecule total RNA
Extraction protocol For bulk RNAseq: Sorted cells (800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% b-mercaptoethanol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Raw fastq files were processed by using the mouse transcriptome with the kallisto (v0.46) software (Bray et al., 2016).
Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017)
We modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (LRT). To determine significantly expressed genes between group pairs, we used the wald-test function.
TCRa and TCRb CDR3 sequences were reconstructed in silico using MixCR software (Bolotin et al., 2015) and the extracted sequences were analyzed with the Immunarch package (v0.6.5) for R (10.5281/zenodo.3893991).
Genome_build: Gencode M23 GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files (Kallisto)
 
Submission date Feb 09, 2022
Last update date May 27, 2022
Contact name Roham Parsa
E-mail(s) Rohamparsa@gmail.com
Phone 2123277521
Organization name Rockefeller University
Lab Mucosal Immunology
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL19057
Series (1)
GSE196417 Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection
Relations
BioSample SAMN25810896
SRA SRX14113235

Supplementary file Size Download File type/resource
GSM5880684_abundance11.tsv.gz 1.8 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap