CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma.
RNA-seq (gene expression) · human · 9 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- MedulloblastomaThis series is part of our curated briefing on it.
- Samples
- 9 samples: 3 × shCtrl vs 3 × shHSPA5_2 vs 3 × shHSPA5_5Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE290496_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1228504 and SRA study SRP566385. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8815179 shCtrl_1 shCtrl
- GSM8815180 shHSPA5_2-1 shHSPA5_2
- GSM8815181 shHSPA5_5-1 shHSPA5_5
- GSM8815182 shCtrl_2 shCtrl
- GSM8815183 shHSPA5_2-2 shHSPA5_2
- GSM8815184 shHSPA5_5-2 shHSPA5_5
- GSM8815185 shCtrl_3 shCtrl
- GSM8815186 shHSPA5_2-3 shHSPA5_2
- GSM8815187 shHSPA5_5-3 shHSPA5_5
- GSE323995 CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [RNA-Seq 3] 48 samples same disease briefing · shares eif2a, phosphorylation, medulloblastoma, crep-mediated, high-risk, control, central, node
- GSE290626 CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [D458] 24 samples same disease briefing · shares eif2a, phosphorylation, medulloblastoma, crep-mediated, high-risk, control, central, node
- GSE222699 The OTX2-regulated alternative splicing landscape controls differentiation and reconstitutes the developmental origins of Group 3 medulloblastoma 8 samples same disease briefing · shares medulloblastoma, control
- GSE294901 Measles oncolytic virus as an immunotherapy for recurrent/refractory pediatric medulloblastoma and atypical teratoid rhabdoid tumor: results from PNOC005 84 samples same disease briefing · shares medulloblastoma
- GSE269909 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq] 50 samples same disease briefing · shares medulloblastoma
- GSE253557 Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq] 39 samples same disease briefing · shares medulloblastoma
- GSE318970 Metabolic Dependencies in Medulloblastoma Reflect Underlying Cellular Origins 33 samples same disease briefing · shares medulloblastoma
- GSE229150 The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma 30 samples same disease briefing · shares medulloblastoma
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.