Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network [RNA-Seq]
RNA-seq (gene expression) · human · 18 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
- 18 samples: 6 conditions, mostly in triplicateGroups 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.
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 GSE245297_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 PRJNA1027795 and SRA study SRP466186. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM7840408 HME, WT, replicate 1 HME, WT,
- GSM7840409 HME, WT, replicate 2 HME, WT,
- GSM7840410 HME, WT, replicate 3 HME, WT,
- GSM7840411 HME, ARID1A-KO, replicate 1 HME, ARID1A-KO,
- GSM7840412 HME, ARID1A-KO, replicate 2 HME, ARID1A-KO,
- GSM7840413 HME, ARID1A-KO, replicate 3 HME, ARID1A-KO,
- GSM7840414 HME, CREBBP-KO, replicate 1 HME, CREBBP-KO,
- GSM7840415 HME, CREBBP-KO, replicate 2 HME, CREBBP-KO,
- GSM7840416 HME, CREBBP-KO, replicate 3 HME, CREBBP-KO,
- GSM7840417 HCEC, WT, replicate 1 HCEC, WT,
- GSM7840418 HCEC, WT, replicate 2 HCEC, WT,
- GSM7840419 HCEC, WT, replicate 3 HCEC, WT,
- GSM7840420 HCEC, ARID1A-KO, replicate 1 HCEC, ARID1A-KO,
- GSM7840421 HCEC, ARID1A-KO, replicate 2 HCEC, ARID1A-KO,
- GSM7840422 HCEC, ARID1A-KO, replicate 3 HCEC, ARID1A-KO,
- GSM7840423 HCEC, CREBBP-KO, replicate 1 HCEC, CREBBP-KO,
- GSM7840424 HCEC, CREBBP-KO, replicate 2 HCEC, CREBBP-KO,
- GSM7840425 HCEC, CREBBP-KO, replicate 3 HCEC, CREBBP-KO,
- GSE277002 Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network 26 samples shares perturbation, underpinning, systematic, principles, robustness, epigenetic, regulatory, genetic
- GSE324132 Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenetic vulnerability 24 samples shares systematic, epigenetic, genetic
- GSE327727 D-SPIN constructs regulatory network models from scRNA-seq revealing organizing principles of perturbation response 194 samples shares perturbation, principles, regulatory
- GSE266127 Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation 56 samples shares principles, epigenetic, genetic
- GSE264667 Transcriptome-wide characterization of genetic perturbations 224 samples shares perturbation, genetic
- GSE252005 Cryptic splicing mediates genetic and therapeutic perturbation of human gene expression levels [naRNA_LCLs] 86 samples shares perturbation, genetic
- GSE296341 The genetic landscape of a human cell reveals conserved topology and principles of genetic networks 61 samples shares principles, genetic
- GSE281048 Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens 4 samples shares perturbation, systematic
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.