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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 10, 2021 |
| Title |
S5: CNS0KO |
| Sample type |
SRA |
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| Source name |
Lymphocytes of male mice
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: nTreg
genotype: CNS0KO
Sex: male
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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.
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| Submission date |
Mar 19, 2021 |
| Last update date |
May 10, 2021 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN18378999 |
| SRA |
SRX10386452 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5184300_TRA_S5.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSM5184300_TRB_S5.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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