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| Status |
Public on Mar 31, 2023 |
| Title |
E12SCC |
| Sample type |
SRA |
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| Source name |
tumor tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: esophagus
collection method: surgery
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| Extracted molecule |
total RNA |
| Extraction protocol |
Esophagus were resected, and a part of resected tissue was made into sigle cells. RNA was extracted and barcorded using Chromium Single Cell 3' Reagent Kits v3.1 (PN- 1000121).
Same as above.
single cell RNA-sequence
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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 |
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Genome_build: GRCh38
Supplementary_files_format_and_content: 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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| Submission date |
Mar 01, 2022 |
| Last update date |
Mar 31, 2023 |
| Contact name |
Sho Okuda |
| E-mail(s) |
[email protected]
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| Phone |
0926425441
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| Organization name |
Kyushu University
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| Department |
Surgery and Oncology
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| Street address |
Maidashi 3-1-1
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| City |
Higashiku |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE197677 |
Single cell RNA-sequence reveals the effect of neoadjuvant chemotherapy on immune cells in human esophageal squamous cell carcinoma. |
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| Relations |
| Reanalyzed by |
GSE209524 |
| BioSample |
SAMN26453725 |
| SRA |
SRX14386944 |
| 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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