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Sample GSM2363316 Query DataSets for GSM2363316
Status Public on Oct 28, 2016
Title Nexabiotic#2
Sample type SRA
 
Source name SI-LP
Organism Mus musculus
Characteristics cell type: CD4+ T cells
bacterial species: Nexabiotic
strain: C57BL/6
age: 6 weeks
Sex: Male
phenotype markers: CD4+ TCRb+ CD45+ DAPI-
Treatment protocol Germ-free mice were left unmanipulated or colonized with different bacterial species for 2 weeks prior to sacrifice
Extracted molecule total RNA
Extraction protocol Cells were sorted into TCL buffer (Qiagen #1031576) + 2-Mercaptoethanol (Sigma-Aldrich# M6250) and then processed according to the Smart-Seq2 protocol by the Broad Technology Labs
The Smart-Seq2 protocol was performed by the Broad Technology Labs
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Data was separated by barcode and aligned using Tophat version 2.0.10 with default settings.
Transcripts were quantified using the Cufflinks suite version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
 
Submission date Oct 27, 2016
Last update date May 15, 2019
Contact name CBDM Lab
E-mail(s) cbdm@hms.harvard.edu
Phone 617-432-7747
Organization name Harvard Medical School
Department Microbiology and Immunobiology
Lab CBDM
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL19057
Series (1)
GSE89261 Transcriptional response of small-intestinal lamina propria CD4+ T cells to bacterial colonization
Relations
BioSample SAMN05949065
SRA SRX2276612

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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