Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [II]
RNA-seq (gene expression) · human · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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.
- Paper
- Functional screening reveals genetic dependencies and diverging cell cycle control in atypical teratoid rhabdoid tumorsGenome biology · 2024
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 GSE231286_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 PRJNA963052 and SRA study SRP435119. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM7256258 BT16_DMSO_REP_A
- GSM7256259 BT16_DMSO_REP_B
- GSM7256260 BT16_DMSO_REP_C
- GSM7256261 BT16_Abema_REP_A
- GSM7256262 BT16_Abema_REP_B
- GSM7256263 BT16_Abema_REP_C
- GSM7256264 CHLA06_DMSO_REP_A
- GSM7256265 CHLA06_DMSO_REP_B
- GSM7256266 CHLA06_DMSO_REP_C
- GSM7256267 CHLA06_Abema_REP_A
- GSM7256268 CHLA06_Abema_REP_B
- GSM7256269 CHLA06_Abema_REP_C
- GSE230742 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I] 21 samples shares investigation, dependencies, atypical, teratoid, rhabdoid, genetic, atrts
- GSE231287 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors 40 samples shares investigation, dependencies, atypical, teratoid, rhabdoid, genetic
- GSE282972 An in vitro pharmacogenomic approach reveals subtype-specific therapeutic vulnerabilities in atypical teratoid/rhabdoid tumors (AT/RT) [RNASeq] 13 samples shares atypical, teratoid, rhabdoid
- GSE197569 Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors 31 samples shares atypical, teratoid, rhabdoid
- GSE276501 Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy 18 samples shares atypical, teratoid, rhabdoid
- GSE283833 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq] 16 samples shares atypical, teratoid, rhabdoid
- GSE213249 Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [RNA-Seq] 12 samples shares atypical, teratoid, rhabdoid
- GSE283839 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snRNA_10Xv3] 12 samples shares atypical, teratoid, rhabdoid
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.