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Sample GSM5402785 Query DataSets for GSM5402785
Status Public on Nov 07, 2022
Title MPNST-6
Sample type SRA
 
Source name Peripheral nerve tumor
Organism Homo sapiens
Characteristics tissue: Peripheral nerve tumor
age: 16
gender: M
tumor type: MPNST
Extracted molecule total RNA
Extraction protocol RNA of frozen neurofibroma and MPNST patient samples were extracted using TRIZOL (Life Technologies) followed by purification using a Direct-zol RNA MiniPrep Kit (Zymo Research). RNA-seq libraries were prepared and sequenced by a BGISEQ-500 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Jun 27, 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 GPL23227
Series (2)
GSE178989 Transcriptional programs dictating Schwann cell transformation in MPNST [bulk RNA-seq]
GSE179043 Transcriptional programs dictating Schwann cell transformation in MPNST
Relations
BioSample SAMN19904561
SRA SRX11237963

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

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