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| Status |
Public on May 29, 2024 |
| Title |
Ctrl replicate1 scRNA-seq |
| Sample type |
SRA |
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| Source name |
Tumor cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor cells
cell line: Hepa1-6
cell type: HCC cell line
genotype: WT
treatment: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissue was incubated in dissociation buffer containing 2 mg/ml Collagenase Ⅳ(sigma,C5138), 2 mg/ml Collagenase II sigma C6885， 10 mg/ml Dispase II (corning,354235) and 50,000U/ml DNase I (sigma, DN25) for 30 min at 37 °C. Enzymatic digestion was quenched with Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, 10270106, Gibco). Cells were resuspended at a concentration of 1 million cells per ml and stained with PBST containing 1% FCS. Then 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000–9000 cells.
The Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following the manufacturer’s instructions according to the Single Cell 3′ Reagent Kits User Guide Version 3.
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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 CellRanger (6.1.2) pipeline was used for demultiplexing, barcode processing, alignment, and initial clustering of the raw scRNA-seq profiles. Raw sequencing reads were then aligned to the human genome (GRCh38, ENSEMBL). We then used Seurat (V4.3.0) to process the unique molecular identifier (UMI) count matrix and integrate all cells according to sample ID by using Harmony
Assembly: mm10
Supplementary files format and content: molecular info files and matrixs files
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| Submission date |
Dec 12, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Yunxing Shi |
| E-mail(s) |
shiyx5@mail3.sysu.edu.cn
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| Organization name |
sun-yat sen university
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| Street address |
Erheng Road, Member Village, Tianhe District
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| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE249999 |
Targeting PRMT3 Impairs Methylation and Oligomerization of HSP60 to Boost Anti-Tumor Immunity by Activating cGAS/STING Signaling |
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| Relations |
| BioSample |
SAMN38790896 |
| SRA |
SRX22868109 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7968898_433filtered_feature_bc_matrix.h5 |
47.9 Mb |
(ftp)(http) |
H5 |
| GSM7968898_433molecule_info.h5 |
628.5 Mb |
(ftp)(http) |
H5 |
| GSM7968898_433raw_feature_bc_matrix.h5 |
93.5 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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