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Status |
Public on Nov 07, 2022 |
Title |
MPNST-6 |
Sample type |
SRA |
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Source name |
Peripheral nerve tumor
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Organism |
Homo sapiens |
Characteristics |
tissue: Peripheral nerve tumor age: 16 gender: M tumor type: MPNST
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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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
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Submission date |
Jun 27, 2021 |
Last update date |
Nov 07, 2022 |
Contact name |
Lai Man (Natalie) Wu |
E-mail(s) |
laiman.wu@cchmc.org
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Organization name |
CCHMC
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Street address |
3333 Burnet Avenue, MLC7013,Lu lab, T6.525
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City |
CINCINNATI |
State/province |
OH |
ZIP/Postal code |
45229 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN19904561 |
SRA |
SRX11237963 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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