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| Status |
Public on Nov 30, 2021 |
| Title |
18-38 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
meningioma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: meningioma tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
FFPE fixed tumor samples were sent, along with whole blood, to Tempus (Tempus Labs | 600 West Chicago Ave, Suite 510 | Chicago, IL 60654) for whole exome RNA-sequencing according to their protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and in-house pipeline for expression count.
The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of the raw counts data for the entire cohort of 110 primary meningiomas.
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| Submission date |
Nov 27, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
James Cushing Bayley |
| E-mail(s) |
James.Bayley@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Neurosurgery
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| Lab |
Patel
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| Street address |
One Baylor Plaza
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE189672 |
Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [RNA-Seq] |
| GSE189673 |
Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies |
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| Relations |
| Reanalysis of |
GSM4054963 |
| BioSample |
SAMN23470363 |
| SRA |
SRX13242341 |
| 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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