|
| Status |
Public on Jan 26, 2024 |
| Title |
EPEN_SPEPN_000UT_00002846_DR |
| Sample type |
SRA |
| |
|
| Source name |
Spinal ependymoma (FFPE tissue)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Spinal ependymoma (FFPE tissue)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of SP-EPN was isolated from FFPE tissues using the Maxwell® RSC RNA FFPE Kit (Promega). Concentrations were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was analyzed using the RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies).
Library preparation was conducted using the SMART-Seq Stranded Kit (Takara Bio)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Pre-processing was started by checking RNA sequencing read quality using FASTQC (v0.11.9) and subsequently aligned to the human reference genome assembly (GRCh38.106) using STAR aligner (v2.7.10a) in default 1-pass mode.
Mapped reads were quantified using featureCounts (v1.6.0) as part of the Subread software package. The “isPairedEnd” parameter was specified in default “unstranded” read counting mode.
Assembly: GRCh38.106
Supplementary files format and content: The count matrix is provided as non-normalized and unfiltered raw read counts.
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
Jan 26, 2024 |
| Contact name |
Karoline Hack |
| E-mail(s) |
hack@kinderkrebs-forschung.de
|
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Department |
Children's Cancer Center Hamburg
|
| Lab |
Schüller
|
| Street address |
Martinistraße 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE242992 |
Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [RNA-seq] |
| GSE242994 |
Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations |
|
| Relations |
| BioSample |
SAMN37366018 |
| SRA |
SRX21761896 |
