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Sample GSM3583644 Query DataSets for GSM3583644
Status Public on Jan 31, 2020
Title RNA-seq DKO2
Sample type SRA
 
Source name Naïve T cells
Organism Mus musculus
Characteristics cell type: naive T cells
surface marker: TCRb+CD4+CD25-CD62LhiCD44low
genotype: BTG1/2 double KO, Btg1f/f Btg2f/f-CD4-Cre
Treatment protocol n/a
Growth protocol Naive CD4 T cells (TCRb+CD4+CD25-CD62LhiCD44low) from two pairs of WT and DKO mice were isolated by FACS sorting.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated by RNeasy Micro Kit (QIAGEN, 74004).
RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description rRNA-depleted RNA-seq
Data processing The sequences were basecalled by Illumina RTA embedded in HiSeq X Control Software by the standard workflow.
Reads were mapped to the mouse transcriptome (ensembl release 89; cDNA and ncRNA) and quantified by Kallisto with a k-mer index 31 and 60 bootstrapping.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM
 
Submission date Jan 29, 2019
Last update date Jan 31, 2020
Contact name Jaechul Lim
E-mail(s) jaechul.lim@snu.ac.kr
Organization name Seoul National University
Street address 1 Gwanak-ro, 1 Gwanak-gu
City Seoul
State/province CT
ZIP/Postal code 08826
Country South Korea
 
Platform ID GPL21273
Series (2)
GSE125865 mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence [RNA-seq]
GSE125890 mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence
Relations
BioSample SAMN10842032
SRA SRX5307520

Supplementary file Size Download File type/resource
GSM3583644_DKO2.abundance.tsv.gz 1.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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