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| Status |
Public on Mar 16, 2022 |
| Title |
Patient1 |
| Sample type |
SRA |
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| Source name |
Patient1
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| Organism |
Homo sapiens |
| Characteristics |
patient: Patient1
disease state: esophageal squamous cell carcinoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Preparation: collect the tumor tissue from ESCC patients. The samples were washed by 0.04% PBS-BSA. After Golu's iodine solution spraying, the uncolored region of tissue was used to lysis with shearing. Then, PBS was used to wash the samples more than 20 times. After the tissue preparation, collagen I (0.5mgml-1) and collagen IV (50mgml-1) was combined to lysis the samples with 2 hours in 37℃. The 400g centrifuge was used with 5 minutes. After discarding the supernatant, 10 ml trypsin was used to resuspend with 1 hour in 37℃. The 10% FBS was added to medium, and filter the mixture through 70μm. Then 400g centrifuge was used. After discarding the supernatant, 3ml 1XACK was used to resuspend the cells on the ice with 3 minutes. And 200 μl 0.04%BSA-PBS was used to resuspend cells. After quantifying the cell number, adjusting the concentration to the 800-1200 cells/μl and ensuring the cell activity > 85%, we used the 10X genomics platform to construct the single cell library of samples.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform
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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 |
ScRNA-seq alignment process was completed by cellranger (version 3.0.0)
Seurat V3 workflow
Genome_build: hg19
Supplementary_files_format_and_content: txt files with gene counts for scRNA-seq
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| Submission date |
Nov 15, 2021 |
| Last update date |
Mar 16, 2022 |
| Contact name |
Xaingyu Pan |
| E-mail(s) |
pangxueyu233@outlook.com
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| Organization name |
Sichuan University
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| Department |
State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
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| Lab |
Chen & Liu Lab
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| Street address |
No.17 Renming road section3
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| City |
Chengdu, Cihna |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE188900 |
The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma [scRNA-Seq] |
| GSE188955 |
The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma |
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| Relations |
| BioSample |
SAMN23168283 |
| SRA |
SRX13144549 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5691642_Patient1.tar.gz |
23.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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