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Sample GSM5404033 Query DataSets for GSM5404033
Status Public on Nov 07, 2022
Title pNF-2-003
Sample type SRA
 
Source name Peripheral nerve tumor
Organism Homo sapiens
Characteristics tissue: plexiform neurofibroma
Extracted molecule total RNA
Extraction protocol For human patient samples, tumor tissues were resected by surgery, cut into pieces of up to 2 mm and cryopreserved in 10% DMSO in liq N2. Tissues requested were shipped and transported to Lu lab in dry ice from Johns Hopkins NF repository. For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV), and single cells were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, up to 16,000 cells were loaded to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing For 10X Genomics data, CellRanger was used for 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: hg19
Supplementary_files_format_and_content: CellRanger output files
 
Submission date Jun 28, 2021
Last update date Nov 07, 2022
Contact name Lai Man (Natalie) Wu
E-mail(s) laiman.wu@cchmc.org
Organization name CCHMC
Street address 3333 Burnet Avenue, MLC7013,Lu lab, T6.525
City CINCINNATI
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL24676
Series (2)
GSE179033 Transcriptional programs dictating Schwann cell transformation in MPNST [10X scRNA-seq]
GSE179043 Transcriptional programs dictating Schwann cell transformation in MPNST
Relations
BioSample SAMN19919141
SRA SRX11243099

Supplementary file Size Download File type/resource
GSM5404033_NF-2-003-filtered_feature_bc_matrix.tar.gz 27.1 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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