ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma [PDX RNA-seq]
RNA-seq (gene expression) · human · 10 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)
- Samples
- 10 samples
- 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 GSE275636_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 PRJNA1152352 and SRA study SRP528578. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run sampleno1 … sampleno5 and carry no group information.
- GSM8481416 sampleno1
- GSM8481417 sampleno27
- GSM8481418 sampleno28
- GSM8481419 sampleno29
- GSM8481420 sampleno2
- GSM8481421 sampleno30
- GSM8481422 sampleno31
- GSM8481423 sampleno33
- GSM8481424 sampleno3
- GSM8481425 sampleno5
- GSE275637 ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma 50 samples shares atf4-mediated, vulnerability, therapeutic, chordoma, stress
- GSE293843 Targeting the ferritinophagy-lysosome axis as a therapeutic vulnerability in gastroenteropancreatic neuroendocrine tumors [RNA-Seq] 10 samples shares vulnerability, therapeutic, rna-seq
- GSE222774 A Novel Humanized Immune Stroma PDX Model for Therapeutic Studies 36 samples shares pdx, therapeutic
- GSE247690 Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: PDX] 17 samples shares pdx, rna-seq
- GSE271134 Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML PDX Bulk RNA-seq] 14 samples shares pdx, rna-seq
- GSE292538 KRAS-Dependent Metabolic Reprogramming of Endothelial Cells as a Therapeutic Vulnerability in Brain Arteriovenous Malformations 18 samples shares vulnerability, therapeutic
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares therapeutic, rna-seq
- GSE294016 A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [bulk RNA-seq] 95 samples shares therapeutic, rna-seq
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.