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| Status |
Public on Aug 31, 2023 |
| Title |
Enhancement of anti-tumor immunity by tertiary lymphoid structures in esophageal squamous cell carcinoma |
| Sample organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Our study showed that TLS enhanced anti-tumor immunity in ESCC.
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| Overall design |
We used droplet-based single cell RNA sequencing (scRNA-seq) data of 14 samples, including 10 tumor samples, 4 normal samples.
***14 Samples were re-analyzed from Series GSE197677. The ESCC.integrated.rds processed data includes the re-analyzed 14 Sample data***
data processing step:
The sequence data were quantified and mapped to human reference genome (GRCh38) using the Cell Ranger toolkit by 10x Genomics.
The matrix data were imported using the Seurat R package (version 3.6.3).
To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.
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| Contributor(s) |
Nakamura S, Ohuchida K |
| Citation(s) |
37604932 |
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| Submission date |
Jul 22, 2022 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Shoichi Nakamura |
| Organization name |
Kyushu University
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| Street address |
3-1-1
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| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
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| Relations |
| Reanalysis of |
GSM5928062 |
| Reanalysis of |
GSM5928064 |
| Reanalysis of |
GSM5928066 |
| Reanalysis of |
GSM5928068 |
| Reanalysis of |
GSM5928069 |
| Reanalysis of |
GSM5928070 |
| Reanalysis of |
GSM5928071 |
| Reanalysis of |
GSM5928072 |
| Reanalysis of |
GSM5928075 |
| Reanalysis of |
GSM5928076 |
| Reanalysis of |
GSM5928077 |
| Reanalysis of |
GSM5928079 |
| Reanalysis of |
GSM5928081 |
| Reanalysis of |
GSM5928086 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE209524_ESCC.integrated.rds.gz |
5.8 Gb |
(ftp)(http) |
RDS |
| Processed data are available on Series record |
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