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Status |
Public on Jul 18, 2024 |
Title |
Tumor5 |
Sample type |
SRA |
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Source name |
colon
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Organism |
Mus musculus |
Characteristics |
tissue: colon strain: C57BL/6 cell type: regulatory T cell genotype: Apc Min/+ Sex: male age: 16 weeks old
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Extracted molecule |
total RNA |
Extraction protocol |
Tregs (CD45+CD3+CD4+CD25+) were sort-purified from normal colons or tumors from WT and ApcMin/+ mice, respectively. Cells were collected into tubes with lysis buffer and ribonuclease inhibitor. Total RNA was extracted and reverse transcribed into cDNA using the Smart-Seq2 protocol. In order to remove contamination from primers from the previous step, VAHTS DNA Clean Beads (Vazyme, N411) were used to purify the products after each round of PCR. A two-round nested PCR was then performed using primers specific for TCRα and TCRβ. For the first round of PCR, 4.4 μL of reverse-transcribed product was used as a template, and the TCRα primer (5’-ctggttgctccaggcaatgg-3’) and TCRβ primer (5’-tgtaggcctgagggtccgt-3’) were used to specifically amplify TCRα and TCRβ. Subsequently, all product was used in the second round of PCR and the primers (TCRα: 5’- agtcaaagtcggtgaacaggca-3’, TCRβ: 5’-ggccaagcacacgagggta-3’) were used. The amplicons were purified using VAHTS DNA Clean Beads and subjected to paired-end sequencing (2 × 150 bp) on an Illumina platform (NovaSeq X Plus-PE150) according to standard protocols.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq X Plus |
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Description |
Smart-seq2
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Data processing |
The sequencing data was obtained after filtering low-quality sequences using a standard procedure. Alignment was performed using the RNA-seq pipeline in MIXCR. The CDR3 ratio was calculated based on read counts associated with each CDR3. Assembly: mm10 Supplementary files format and content: Comma-delimited csv files include each CDR3 count values and frequency.
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Submission date |
Jul 08, 2024 |
Last update date |
Jul 18, 2024 |
Contact name |
Shuqin Li |
E-mail(s) |
shuqin@stu.xmu.edu.cn
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Organization name |
Xiamen University
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Department |
Life Science
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Lab |
Kairui Mao Lab
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Street address |
Xiang'an south rd, Xiang'an district
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City |
Xiamen |
State/province |
Fujian Province |
ZIP/Postal code |
361000 |
Country |
China |
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Platform ID |
GPL34290 |
Series (2) |
GSE234186 |
Lymphatic-localized Treg-mregDC crosstalk limits antigen trafficking and restrains anti-tumor immunity |
GSE271765 |
Lymphatic-localized Treg-mregDC crosstalk limits antigen trafficking and restrains anti-tumor immunity [TCR-Seq] |
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Relations |
BioSample |
SAMN42377805 |
SRA |
SRX25244586 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8384804_TCRa_tumor5.csv.gz |
46.2 Kb |
(ftp)(http) |
CSV |
GSM8384804_TCRb_tumor5.csv.gz |
41.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
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