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| Status |
Public on Apr 04, 2020 |
| Title |
Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.
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| Overall design |
Ten batches of single cell RNA sequencing data were obtained from 2 patients, with 5 different sample preparations for primary colorectal cancer or matched normal mucosa respectively. For one patient, 3 different tissue dissociation protocols were applied for cancer and matched normal mucosa. For another freshly prepared or frozen-thawed cell stocks were tested for cancer and matched normal mucosa. After sequencing, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes to eliminate low-quality cells and 18,409 cells passed the filtering criteria.
****raw data files have not been provided due to patient privacy issues and will be available in EGA as controlled access****
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| Contributor(s) |
Lee H, Cho Y, Park W |
| Citation(s) |
32451460 |
| Submission date |
Jun 05, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Yourae Hong |
| Organization name |
Samsung Medical Center
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| Department |
Samsung Genome Institute
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| Street address |
81, Irwon-ro
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| City |
Seoul |
| ZIP/Postal code |
06351 |
| Country |
South Korea |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA546616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132257_GEO_processed_protocol_and_fresh_frozen_natural_log_TPM_matrix.txt.gz |
255.8 Mb |
(ftp)(http) |
TXT |
| GSE132257_GEO_processed_protocol_and_fresh_frozen_raw_UMI_count_matrix.txt.gz |
35.5 Mb |
(ftp)(http) |
TXT |
| GSE132257_processed_protocol_and_fresh_frozen_cell_annotation.txt.gz |
119.2 Kb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data are available on Series record |
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