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Sample GSM3330559 Query DataSets for GSM3330559
Status Public on Sep 01, 2018
Title Tumor Disc Pre
Sample type SRA
Source name Tumor
Organism Homo sapiens
Characteristics tissue: Merkel Cell Carcinoma Tumor
time point: PreRx
chromium index: SI-GA-A2
Growth protocol N/A - ex vivo
Extracted molecule total RNA
Extraction protocol PBMC were isolated with standard FICOLL, tumor tissues were digested in RPMI with DNAse, Collagenase, and hyaluronidase, strained and frozen. All samples were thawed on same day and immediately processed
10x Genomics Gene Expression 3' Chromium V 2.0 per manufacturer's instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description PreRx MCC Tumor Digest
Data processing Guide barcode reads - Read length: Read 1: 26 (cell-barcode, UMI), Index read 2 (i5): 8, Read 2: 98 (RNA read)
Raw base BCL files were demultiplexed using the Cell Ranger mkfastq pipeline into sample-specific FASTQ files.
FASTQ files were processed individually using the Cell Ranger count pipeline, which made use of the STAR software to align cDNA reads to the GRCh38 and the Merkel cell polyomavirus sequence (HM011556.1).
Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads.
Tumor and PBMC samples were respectively aggregated together using the Cell Ranger aggr pipeline resulting in two gene-barcode count matrices (tumor and PBMC) to be used for downstream analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for tumor and PBMC
Submission date Aug 13, 2018
Last update date Sep 01, 2018
Contact name Kelly Garneski Paulson
Organization name Fred Hutchinson Cancer Research Center
Lab Chapuis Lab, Thomas D3-235
Street address 1100 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platform ID GPL16791
Series (1)
GSE117988 scRNAseq reveals mechanisms of Merkel cell carcinoma acquired immunotherapy resistance [1]
BioSample SAMN09813394
SRA SRX4579479

Supplementary data files not provided
Raw data are available in SRA
Processed data are available on Series record

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