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| Status |
Public on Oct 29, 2020 |
| Title |
Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Esophageal squamous-cell carcinoma (ESCC), one of the most prevalent and lethal malignant disease, has a complex but unknown tumor ecosystem. Here, we decipher for the first time the full compositions of ESCC tumor based on analyzing 208,659 single-cell transcriptomes in ESCC derived from 60 individuals. We identify 8 essential expression programs from malignant epithelial cells and discovered 43 cell types including 26 immune cell and 17 nonimmune stromal cell subtypes in the tumor microenvironment (TME), and also explicate the interactions between cancer cells and other cells and the interactions among different cell types in the TME. Moreover, we have linked the cancer cell transcriptomes to the somatic mutations and identified several markers significantly associated with survival time in patients, which may be relevant to precision cares of ESCC patients. These results renew our understanding of ESCC and provide a valuable example and resource for investigating other types of solid tumor.
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| Overall design |
We performed scRNA-seq on 60 ESCC tumor and 4 adjacent normal tissue samples obtained from 60 individuals using 10X Genomics platform.
Raw data is available at https://bigd.big.ac.cn/gsa-human/ under the accession ID of HRA000195.
For the details or customized demand of Raw and Processed data, please feel free to contact Prof Zhang (xiannian@ccmu.edu.cn). We are glad to help.
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| Contributor(s) |
Zhang X, Peng L, Guo Y, Guo W, Yao J, Shao M, Fan W, Chen Y, Cui Q, Xi Y, Sun Y, Niu X, Zhao X, Chen L, Wang Y, liu Y, Wang J, Wu C, Lin D |
| Citation(s) |
34489433, 38097539 |
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| Submission date |
Oct 28, 2020 |
| Last update date |
Jan 02, 2024 |
| Contact name |
Xiannian Zhang |
| E-mail(s) |
xiannian@ccmu.edu.cn
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| Organization name |
Captital Medical University
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| Department |
Department of neurology
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| Street address |
10 YouAnMen Xitoutiao, Fengtai District
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| City |
Beijing |
| ZIP/Postal code |
100086 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (128)
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| Relations |
| BioProject |
PRJNA672851 |
| SRA |
SRP327758 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE160269_CD45neg_UMIs.txt.gz |
269.4 Mb |
(ftp)(http) |
TXT |
| GSE160269_CD45neg_cells.txt.gz |
529.7 Kb |
(ftp)(http) |
TXT |
| GSE160269_CD45pos_UMIs.txt.gz |
215.4 Mb |
(ftp)(http) |
TXT |
| GSE160269_CD45pos_cells.txt.gz |
595.0 Kb |
(ftp)(http) |
TXT |
| GSE160269_TCR_contig_annotations.csv.gz |
8.6 Mb |
(ftp)(http) |
CSV |
| GSE160269_UMI_matrix_Bcell.txt.gz |
42.0 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Endothelial.txt.gz |
26.2 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Epithelia.txt.gz |
139.6 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_FRC.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Fibroblast.txt.gz |
94.7 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Myeloid.txt.gz |
47.4 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Pericytes.txt.gz |
7.8 Mb |
(ftp)(http) |
TXT |
| GSE160269_UMI_matrix_Tcell.txt.gz |
128.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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