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Sample GSM5184299 Query DataSets for GSM5184299
Status Public on May 10, 2021
Title S4: CNS03DKO
Sample type SRA
 
Source name Lymphocytes of male mice
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: nTreg
genotype: CNS03DKO
Sex: male
Extracted molecule total RNA
Extraction protocol CD4+Foxp3-GFP+ nTreg cells were sorted from the spleen, skin draining LN, and mLN of individual WT GFP, CNS3, CNS0, and CNS3,0 mice at 16 days of age. Total RNA was extracted by TRIzol according to the manufacturer’s instructions. cDNA was synthesized by SMARTScribe Reverse Transcriptase with primers targeting the constant regions of mouse TCRa (5’-AGTCAAAGTCGGTGAAC-3’) or TCRb (5’-ATCTCTGCTTTTGATG-3’) chains and template switch adapter (5’-AAGCAGUGGTAUCAACGCAGAGUNNNNUNNNNUNNNNUCTTrGrGrGrG-3’).
TCRa and TCRb chains were further amplified by a two-step protocol. Sequencing adaptors were then added by Kapa Hyper Prep Kit (Kapa Biosystems). Samples were pooled and sequenced by Nova Seq with at least 10x coverage relative to the numbers of Treg cell used.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Library strategy: TCR-seq
VDJ gene assignments were calculated and filtered with MIGEC software. VDJtools v1.2.1 software was applied for filtering non-functional TCR and decontaminate samples
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contains CDR3 nucleotide sequence, CDR3 amino acid sequence, V gene usage, D gene usage and J gene usage. And different TCR counts and frequency.
 
Submission date Mar 19, 2021
Last update date May 10, 2021
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL24247
Series (2)
GSE158223 Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity
GSE169228 Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [TCR-seq]
Relations
BioSample SAMN18379000
SRA SRX10386451

Supplementary file Size Download File type/resource
GSM5184299_TRA_S4.txt.gz 23.5 Kb (ftp)(http) TXT
GSM5184299_TRB_S4.txt.gz 20.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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