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Sample GSM4912031 Query DataSets for GSM4912031
Status Public on Nov 01, 2022
Title WT 2
Sample type SRA
 
Source name Spleen and lymph nodes
Organism Mus musculus
Characteristics cell type: CD4+ T cells
strain: C57BL/6j
genotype: WT
Treatment protocol stimulated for 48 hours in vitro with CD3, CD28 and IL-2.
Growth protocol naïve CD4+ T cells sorted by MACS cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
 
Submission date Nov 17, 2020
Last update date Nov 01, 2022
Contact name Hoyul Lee
E-mail(s) hoyul.lee@outlook.kr
Organization name Kyungpook Nationatl University Hospital
Department Bio-medical Research Institute
Street address 807, Hoguk-ro, Buk-gu
City Daegu
ZIP/Postal code 41404
Country South Korea
 
Platform ID GPL19057
Series (1)
GSE161653 Gene expression in activated WT or PDK4 -/- CD4+ T cells
Relations
BioSample SAMN16821885
SRA SRX9522332

Supplementary file Size Download File type/resource
GSM4912031_WT2.txt.gz 116.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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