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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
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
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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