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Sample GSM5251691 Query DataSets for GSM5251691
Status Public on Jun 28, 2021
Title 4M Tcirc 3
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics mosue strain: C57BL/6
pathogen: Influenza
treatment: IV- CD69-/CD103-
tissue: Spleen
Treatment protocol B6 mice containing CD90.1 congenic Primary (1M) or Quarternary (4M) Memory P14 cells at 23-30 days post Intranasal Influenza (PR8-GP33) infection were IV labeled with CD45.2-BV450 3 minutes prior to sacrifice. Pooled splenocytes (6-10 samples/sort) or Mediastinal Lymph Nodes (15-25 samples/sort) were isolated, processed through a 70uM cell strainer, stained with APC-labeled -CD19, -NK1.1 and -CD4 and CD103-PE, CD69-PE-CY7, CD90.1-PerCP-eFluor710, Live/Dead-e780. Samples were negatively enriched with aAPC-beads and Macs columns, resuspended in MACS buffer with DNAse for subsequent sorting. Populations of IV- CD69-/CD103- (Tcirculating) and IV- CD69+/CD103+ (Tms) were sort purified and resuspended in TRIzol.
Extracted molecule total RNA
Extraction protocol Freshly sorted 1M or 4M P14s were (as indicated above) were re-suspended in TRIzol and RNA was 757 purified using a RNAeasy kit (Qiagen) according to the manufacturer’s protocol. RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer.
RNA seq was performed using the single cell/low input library kit (NEB), full-length cDNAs were sequenced on the Illumina HiSeq 2500 High760 output platform using 2x150 Paired-end Libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 19092FL-07-01-06_S6_L004
Data processing The sequence reads quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and were aligned to the mouse genome version mm10 using STAR aligner.
Differentially expressed genes were identified using Partek GS software and genes with significant changes were filtered using adjusted p- value of 0.05 as threshold
Genome_build: mm10
Supplementary_files_format_and_content: ANOVA All genes SMA RNASeq.csv
 
Submission date Apr 18, 2021
Last update date Jun 28, 2021
Contact name John Harty
E-mail(s) john-harty@uiowa.edu
Phone 3193359720
Organization name University of Iowa
Street address 25 S. Grand Ave, 1020 ML, University of Iowa
City Iowa City
State/province Iowa
ZIP/Postal code 52242
Country USA
 
Platform ID GPL17021
Series (1)
GSE172279 Bulk RNAseq of Sort-purified IV- Primary (1M) or Quaternary (4M) Tcirc (IV- CD69-/CD103-) or Trm (IV- CD69+/CD103+) Memory P14 cells isolated from Spleen or Mediastinal Lymph Nodes
Relations
BioSample SAMN18791091
SRA SRX10629466

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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