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| Status |
Public on Feb 22, 2022 |
| Title |
primary gastric cancer PT2 |
| Sample type |
SRA |
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| Source name |
primary gastric cancer
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| Organism |
Homo sapiens |
| Characteristics |
tissue: stomach
treatment: untreated
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| Treatment protocol |
We performed unbiased scRNA-seq analysis of 42,968 cells from 10 fresh human tissue samples from six patients. Primary tumor and adjacent non-tumoral samples and six metastases from different organs or tissues (liver, peritoneum, ovary, lymph node) were evaluated. Validation experiments were performed using histological assays and bulk transcriptomic datasets.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were washed twice by PBS supplied with 10% BSA (Sigma, USA), minced into small pieces with the size of 2–4 mm, and then dissociated by a Human Tumor Dissociation kit (Miltenyi Biotech, Germany). The only exception was the liver biopsy sample which was dissociated with the Mouse Tumor Dissociation kit (Miltenyi Biotech, Germany) based on the cell viability results of preliminary experiment. The cell suspension was further filtered through 70 μm SmarterStrainers (Miltenyi Biotech, Germany) to remove cell aggregates and re-suspended in PBS containing 10% BSA. Red blood cells were removed by a Red Blood Cell Lysis Solution (10×) (Miltenyi Biotech, Germany). Dead cells were eliminated by a Dead Cell Removal Kit (Miltenyi Biotech, Germany) to increase the efficiency of sorting robust, and the live cells were washed twice, re-suspended in PBS containing with 10% BSA, and then used for single-cell experiments.
The cell suspension was further filtered through 70 μm SmarterStrainers (Miltenyi Biotech, Germany) to remove cell aggregates and re-suspended in PBS containing 10% BSA. Red blood cells were removed by a Red Blood Cell Lysis Solution (10×) (Miltenyi Biotech, Germany). Dead cells were eliminated by a Dead Cell Removal Kit (Miltenyi Biotech, Germany) to increase the efficiency of sorting robust, and the live cells were washed twice, re-suspended in PBS containing with 10% BSA, and then used for single-cell experiments.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The raw sequencing data from 10X Genomics were aligned and quantified using the CellRanger (10X Genomics) suite (version 3.0.2). The human genome GRCh38 was used as the reference genome and the CellRanger count module was used to map reads. Raw gene expression matrices for each experimental condition were imported in R software (version 3.6.3) using Seurat R package (version 3.1.5).
We excluded the cells meeting the following criteria: less than 200 unique genes expressed, more than 5000 unique genes expressed or more than 20% of reads mapping to mitochondria.
The gene expression matrices of the remaining 42,968 cells were normalized through a global-scaling method with a default scale factor and natural-log transformed using log1p. Then the normalized expression was scaled through the function of ScaleData, aiming to remove the unwanted sources of variation.
Genome_build: GRCh38
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| Submission date |
Jan 04, 2021 |
| Last update date |
Feb 22, 2022 |
| Contact name |
penghui Yang |
| E-mail(s) |
yangph@zju.edu.cn
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| Phone |
18811381956
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| Organization name |
Pharmaceutical Informatics Institute
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310007 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE163558 |
Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing |
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| Relations |
| BioSample |
SAMN17210465 |
| SRA |
SRX9775388 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5004181_PT2_barcodes.tsv.gz |
46.0 Kb |
(ftp)(http) |
TSV |
| GSM5004181_PT2_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM5004181_PT2_matrix.mtx.gz |
69.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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