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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 28, 2022 |
| Title |
Con, ACT, scTCR-seq |
| Sample type |
SRA |
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| Source name |
colon tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon tumor
cell type: CD45.2+CD45.1-CD8+ transfered T cells
treatment: Control
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| Treatment protocol |
MC38-OVA tumor-bearing mice were treated with either PBS (Control group), decitabine (0.2 mg/kg/day) intraperitoneally for three consecutive days (DAC group), anti-PD-1 (200 μg per mouse) every three days (anti-P group), or decitabine-plus-anti-PD-1 (DP group). For the ACT assay, PBS or decitabine (10nM)-pretreated CD45.2+CD8+ T cells were transfered into MC38-OVA tumor-bearing CD45.1+ mice, followed by anti-PD-1 treatment 12 days after T cell transfer.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The tumor tissues were minced and dissociated into single-cell suspensions using a tissue dissociation kit (Miltenyi Biotec). Cells were washed and re-suspended in PBS and stained with a Viability Dye, CD45 and CD3, the alive CD45+CD3+ TILs were sorted on a BD Bioscience cell sorter. Sorted cells were collected into cold PBS plus 2% FBS, and used for the scRNA-seq or ATAC-seq. For the ACT assay, the alive CD45.2+CD45.1-CD8+ transfered T cells were sorted and used for the scRNA-seq. For the WGBS assay, CD8+ naive T cells were treated with PBS or decitabine (10nM) in vitro.
(scRNA-seq with paired scTCR-seq) Cells were loaded between 10,000 and 15,000 cells/chip position using the 10x Chromium Single Cell V(D)J Reagent Kits v1.1. Library was performed according to the manufacter's instructions (single cell 5' v1+TCR protocol).
(ATAC-seq) ATAC-seq DNA library was constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina.
(WGBS) The C-T transformation was Bisufile processed according to EZ DNA Methylation-GoldTM Kit (D5006) process, and then WGBS library was constructed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The scRNA-seq reads were aligned to the mm10 reference genome and quantified using cellranger count (10x Genomics, v6.0.1).
TCR reads were aligned to the mm10 reference genome and consensus TCR annotation was performed using cellranger vdj (10x Genomics, v6.0.1).
The quality control of ATAC-seq data was performed by FastQC (v0.11.9). Raw reads were trimmed using trim_galore (v0.6.6) and aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1). Duplicate reads were removed using picard MarkDuplicates(v2.25.5) and only primary alignments with mapping quality greater than 30 were retained. ATAC-seq peaks were called using MACS2 (v 2.2.7.1) on each individual sample. Peaks that present in both replicates are preserved for downstream analysis.
The quality control of WGBS (Whole Genome Bisulfite Sequencing) was performed by FastQC (v0.11.9) . Raw reads were trimmed using trim_galore (v0.6.6) and aligned to the mouse reference genome (mm10) using bsmap (v2.90). Duplicate reads were removed using sambamba (v.0.6.8).
Assembly: mm10
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| Submission date |
Jul 28, 2022 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Jing Nie |
| E-mail(s) |
niejing@301hospital.com.cn
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| Organization name |
Chinese PLA General Hospital
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| Street address |
No.28, Fuxing Road
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100853 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE209965 |
Decitabine-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ progenitor exhausted T cells |
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| Relations |
| BioSample |
SAMN30024323 |
| SRA |
SRX16716039 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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