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| Status |
Public on Aug 18, 2022 |
| Title |
RCC-PR3-PTumor3 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Homo sapiens |
| Characteristics |
condition: Tumor
Stage: ccRCC
treatment: No
metastasic sites: No
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| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Single cell 3' gene expression V2
Single cells from the tumor and the normal adjacent kidney samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.2.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv
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| Submission date |
Jun 18, 2021 |
| Last update date |
Aug 18, 2022 |
| Contact name |
Shenglin Mei |
| E-mail(s) |
samleomei@gmail.com
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| Organization name |
Harvard medical school (DMBI)
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| Street address |
10 Shattuck Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE178481 |
A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma |
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| Relations |
| BioSample |
SAMN19776117 |
| SRA |
SRX15391501 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5392423_RCC-PR3-PTumor3.count.csv.gz |
13.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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