 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 22, 2024 |
| Title |
SHH MB13 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Medulloblastomas
tissue: brain
main molecular_subgroup: SHH
proteome subtype_voss: sSHH
|
| Treatment protocol |
NA
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Maxwell RSC RNA FFPE Kit
400 ng total per sample, rRNA depletion (Lexogen RiboCop rRNA Depletion with prob mix HMR V2, according to manufacture protocol), followed by the Lexogen CORALL total RNA-Seq V2 Library Prep Kit with UDIs (according to manufacture protocol, short insert size version).
Illumina NextSeq2000 machine using the P3 Reagents / 100 cycle kit as paired-end sequencing 2x 57 bp (+ 2x index read 12bp)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
M_featureCounts_data13
|
| Data processing |
usegalaxy and rstudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (reads with quality < 20 were trimmed)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (length of genome sequence around annotated junction = 100, using basic 2 pass-mapping,excluding alignements with indels or soft clippings, MAPQ value for unique mapper filter = 60, number of genome bins for coordinate-sorting = 50 and maximum number of loci anchor allowed to map to = 50)
Read count extraction and normalization using featureCount and VST normalized files from DESeq2 were used for downstream analysis
Batch effect correction was performed with the HarmonizR algorithm using combat mode in order to combine data with a previously published dataset (obtained from the European Genome-phenome Archive: EGAS00001001953)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include featureCount files for each sample, and a VST-file from DESeq2
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Julia Elisabeth Neumann |
| Organization name |
University Hospital Hamburg Eppendorf
|
| Department |
ZMNH
|
| Street address |
Martinistrasse 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE243795 |
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [RNA-Seq] |
| GSE243796 |
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level |
|
| Relations |
| BioSample |
SAMN37514011 |
| SRA |
SRX21859695 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
