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| Status |
Public on Jul 18, 2024 |
| Title |
Colon4 |
| 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: WT
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 |
SAMN42377800 |
| SRA |
SRX25244591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8384809_TCRa_colon4.csv.gz |
50.7 Kb |
(ftp)(http) |
CSV |
| GSM8384809_TCRb_colon4.csv.gz |
51.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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