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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
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
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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