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Sample GSM4089151 Query DataSets for GSM4089151
Status Public on Sep 01, 2020
Title Patient #1-scRNA
Sample type SRA
Source name Castration resistant prostate cancer (CRPC) tissue
Organism Homo sapiens
Characteristics disease state: Castration resistant prostate cancer (CRPC)
Sex: Male
age: 82
tumor stage: T4
tissue: primary tumor
Extracted molecule total RNA
Extraction protocol Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell
Submission date Sep 23, 2019
Last update date Sep 02, 2020
Contact name Jia Wang
Phone 15821724825
Organization name SJTU CHINA
Street address Huashan Rd. 1940, build 3. Shanghai,
City Shanghai
State/province Shanghai China
ZIP/Postal code 200017
Country China
Platform ID GPL24676
Series (1)
GSE137829 Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
BioSample SAMN12818421
SRA SRX6887739

Supplementary file Size Download File type/resource
GSM4089151_P1_gene_cell_exprs_table.txt.gz 11.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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