|
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
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|
|
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 |