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Sample GSM3348319 Query DataSets for GSM3348319
Status Public on Nov 02, 2018
Title HG1-P
Sample type SRA
 
Source name serous epithelial ovarian cancer
Organism Homo sapiens
Characteristics sample id: HG1-P
diagnosis: HGSOC
site: Primary
subject id: 349
Growth protocol Pathological discard tissue, from women who were scheduled for surgery to evaluate a suspicious pelvic mass, primary tumor and metastatic lesions (when available), were obtained at time of surgery and frozen for later analysis. Tissue was minced and frozen in 40% FBS, 40% RPMI and 20% DMSO.
Extracted molecule polyA RNA
Extraction protocol Thawed tissue samples were digested and dissociated into single-cell suspensions using Miltenyi’s gentleMACS Octo dissociator and tumor dissociation kit following manufacturer’s instructions. Single cells were collected by straining digested tissue through a MACS Smart strainer (70um), washed, then layered over a Ficoll gradient to remove red blood cells and debris. To enrich the tumor cell fraction for live cells, dead cells were excluded using Dead Cell Removal kit and MS columns (Miltenyi Biotec) and remaining viable cells were prepared for scRNA-seq.
Using the BioRad droplet digital SEQ Single-cell Isolator and the Illumina SureCell Whole Transcriptome Analysis 3’ library prep kit, scRNA-seq was performed on isolated cells from ovarian tumor tissue samples following the manufacturer’s instructions. Briefly single-cells were encapsulated, lysed then barcoded within each droplet. Following first and second strand cDNA synthesis, Illumina’s Nextera technology was used to generate a library for NGS. Final libraries were assessed and quantified using a High Sensitivity DNA chip and a 2100 BioAnalyzer (Agilent Technologies) prior to sequencing on a NexSeq 500 high output flow cell.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sample data was demultiplexed and raw sequence files generated using bcl2fastq2 app in Illumina’s cloud application, Basespace.
SureCell RNA Single-Cell application to extract the cell barcodes and the Unique Molecular Identifiers (UMIs). The raw sequence files were aligned to the hg19 human reference genome and gene expression was quantified.
A knee plot of the genic UMIs per cell barcode was used to set thresholds for cells for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: umicount table with genes as columns and cell barcodes as rows
 
Submission date Aug 21, 2018
Last update date Nov 03, 2018
Contact name Andrew Shih
E-mail(s) ashih@northwell.edu
Phone 516-562-2960
Organization name Feinstein Institute - Northwell Health
Street address 350 Community Dirive
City Mahasset
State/province NY
ZIP/Postal code 11030
Country USA
 
Platform ID GPL18573
Series (1)
GSE118828 Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq
Relations
BioSample SAMN09869249
SRA SRX4582172

Supplementary file Size Download File type/resource
GSM3348319_V00331081_Primary_S1.counts.umiCounts.aboveBackground.table.csv.gz 613.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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