Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [RNA-seq]
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: 3 × mRNA-seq of Hek293 FLP-in cells with siNT, vs 3 × mRNA-seq of Hek293 FLP-in cells with siTAF5, vs 3 × mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, vs 3 × mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8,Groups 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
- Genome-scale exon perturbation screens uncover exons critical for cell fitnessMolecular cell · 2024
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 GSE244357_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 PRJNA1022470 and SRA study SRP463976. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7814161 mRNA-seq of Hek293 FLP-in cells with siNT, Replicate1 mRNA-seq of Hek293 FLP-…
- GSM7814162 mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate1 mRNA-seq of Hek293 FLP-…
- GSM7814163 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate1 mRNA-seq of Hek293 FLP-…
- GSM7814164 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate1 mRNA-seq of Hek293 FLP-…
- GSM7814165 mRNA-seq of Hek293 FLP-in cells with siNT, Replicate2 mRNA-seq of Hek293 FLP-…
- GSM7814166 mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate2 mRNA-seq of Hek293 FLP-…
- GSM7814167 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate2 mRNA-seq of Hek293 FLP-…
- GSM7814168 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate2 mRNA-seq of Hek293 FLP-…
- GSM7814169 mRNA-seq of Hek293 FLP-in cells with siNT, Replicate3 mRNA-seq of Hek293 FLP-…
- GSM7814170 mRNA-seq of Hek293 FLP-in cells with siTAF5, Replicate3 mRNA-seq of Hek293 FLP-…
- GSM7814171 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-FL, Replicate3 mRNA-seq of Hek293 FLP-…
- GSM7814172 mRNA-seq of Hek293 FLP-in cells with siTAF5+TAF5-DE8, Replicate3 mRNA-seq of Hek293 FLP-…
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares perturbation, rna-seq
- GSE305979 Perturbational single-cell RNA-seq time course of CD34+ HSPC megakaryocyte differentiation with CMO multiplexing (Days 0–7, 1 uM compounds) 34 samples shares perturbation, rna-seq
- GSE275778 AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer [RNA-seq: 22RV1] 20 samples shares critical, rna-seq
- GSE278135 Genome-scale DNA methylome and transcriptome profiles of early prostate cancer recurrence after prostatectomy [RNA-seq] 18 samples shares genome-scale, rna-seq
- GSE296115 The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCaP Bulk RNA-Seq] 16 samples shares critical, rna-seq
- GSE205613 Identification of Ephrin type-B receptor 4 (EphB4) as a critical mediator of tissue fibrosis [RNA-seq] 16 samples shares critical, rna-seq
- GSE281048 Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens 4 samples shares perturbation, screens
- GSE327727 D-SPIN constructs regulatory network models from scRNA-seq revealing organizing principles of perturbation response 194 samples shares perturbation, 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.