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| Status |
Public on Nov 07, 2022 |
| Title |
MPNST-3 |
| 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: 27
gender: F
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 |
SAMN19904564 |
| SRA |
SRX11237960 |
| 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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