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| Status |
Public on Apr 26, 2024 |
| Title |
MNG950 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
disease state: Meningioma tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Plus mini kit. Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). Samples with RIN < 5 were removed from further analysis. RNA was normalized to 50ng/ul and 500ng was submitted for library preparation.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Sequencing was performed using an Illumina NovaSeq 6000 employing a paired-end, 50 base read length (PE50) sequencing strategy. RNA extraction was performed by the Specimen Processing & Research Cell Bank at Fred Hutch. Library preparation and sequencing was performed by the Genomics and Bioinformatics Core Services at Fred Hutch.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
MNG950
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| Data processing |
RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly genome using STAR2 (v2.7.7a) and then using HTSeq (v0.11.0) reads were counted for each associated gene using the Gencode V39 primary assembly annotations
Gene expression values from combined datasets were batch corrected and normalized and converted to units of log2 transcripts per million (log2TPM)
Assembly: hg38
Supplementary files format and content: tab-delimited files contain log2 TPM values for each sample
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| Submission date |
Dec 30, 2023 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Eric Holland |
| E-mail(s) |
eholland@fredhutch.org
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| Organization name |
Fred Hutch Cancer Center
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| Department |
Human Biology
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| Lab |
Holland
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| Street address |
1100 Fairview Ave. N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE252291 |
Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome |
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| Relations |
| BioSample |
SAMN39203311 |
| SRA |
SRX23064904 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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