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Sample GSM3039934 Query DataSets for GSM3039934
Status Public on Mar 01, 2020
Title CD69- replicate 1
Sample type SRA
 
Source name day 12 P14 T cells from LCMV infected kidney
Organism Mus musculus
Characteristics cell subtype: CD69-
background strain: C57BL/6
tissue: Virus-specific CD8+ T cells from the kidney
Treatment protocol Day 12 post infection, indicated cell subsets were FACS sorted from pooled kidneys
Growth protocol naïve P14 TCR transgenic CD8 T cells were adoptively transferred into C57BL/6 mice followed by LCMV Armstrong infection
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sorted cells using Quick-RNA miniprep kit from Zymo Research (Cat# 11-328)
Total RNA samples about 1-2 µg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
 
Submission date Mar 14, 2018
Last update date Mar 01, 2020
Contact name Yidong Chen
E-mail(s) cheny8@uthscsa.edu
Phone 2105629163
Organization name UT Health Science Center at San Antonio
Department Population Health Sciences
Street address 8403 Floyd Curl Drive, MSC 7784
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL21493
Series (1)
GSE111801 Kidney-resident CD8 T cells downregulate IL-18R during maturation
Relations
BioSample SAMN08707905
SRA SRX3787679

Supplementary file Size Download File type/resource
GSM3039934_CON_69neg1_Genes_ReadCount.txt.gz 93.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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