Synthetic Introns Identify GPATCH8 as Required for Mis-splicing by SF3B1 Mutations [RNA-Seq 2]
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: 6 conditions, mostly in duplicateGroups 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
- GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignanciesMolecular 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 GSE262021_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 PRJNA1090048 and SRA study SRP496696. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM8156126 K700E,AAVS1-KO,non-differentiated,rep1 K700E,AAVS1-KO,non-diff…
- GSM8156127 K700E,AAVS1-KO,non-differentiated,rep2 K700E,AAVS1-KO,non-diff…
- GSM8156128 K700E,AAVS1-KO,erythroid-differentiated,rep1 K700E,AAVS1-KO,erythroi…
- GSM8156129 K700E,AAVS1-KO,erythroid-differentiated,rep2 K700E,AAVS1-KO,erythroi…
- GSM8156130 K700E,GPATCH8-KO,non-differentiated,rep1 K700E,GPATCH8-KO,non-di…
- GSM8156131 K700E,GPATCH8-KO,non-differentiated,rep2 K700E,GPATCH8-KO,non-di…
- GSM8156132 K700E,GPATCH8-KO,erythroid-differentiated,rep1 K700E,GPATCH8-KO,erythr…
- GSM8156133 K700E,GPATCH8-KO,erythroid-differentiated,rep2 K700E,GPATCH8-KO,erythr…
- GSM8156134 K700K,AAVS1-KO,non-differentiated,rep1 K700K,AAVS1-KO,non-diff…
- GSM8156135 K700K,AAVS1-KO,non-differentiated,rep2 K700K,AAVS1-KO,non-diff…
- GSM8156136 K700K,AAVS1-KO,erythroid-differentiated,rep1 K700K,AAVS1-KO,erythroi…
- GSM8156137 K700K,AAVS1-KO,erythroid-differentiated,rep2 K700K,AAVS1-KO,erythroi…
- GSE263299 Mis-splicing of mitotic regulators sensitizes SF3B1-mutated human HSCs to CHK1 inhibition [RNA-seq] 10 samples shares sf3b1, mis-splicing, rna-seq
- GSE263300 Mis-splicing of mitotic regulators sensitizes SF3B1-mutated human HSCs to CHK1 inhibition [scRNA-seq] 2 samples shares sf3b1, mis-splicing, rna-seq
- GSE280581 Intragenic Epigenetic Deregulation by IDH2 Mutations Synergizes with SRSF2 Mutations Causing Mis-splicing of Key Transcriptional Regulators [RNA-seq] 20 samples shares mis-splicing, mutations, rna-seq
- GSE304350 Distinct and convergent effects of SF3B1 mutations in human breast cancer 30 samples shares sf3b1, mutations
- GSE268355 Cancer-associated SF3B1 Mutations Inhibit mRNA Nuclear Export by Disrupting SF3B1–THOC5 Interactions 12 samples shares sf3b1, mutations
- GSE278363 SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [RNA-seq] 12 samples shares sf3b1, rna-seq
- GSE231387 Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis 12 samples shares sf3b1, mutations
- GSE236535 Mutations in the splicing factor SF3B1 are linked to frequent emergence of HLA-DRlow/neg monocytes in lower-risk myelodysplastic neoplasms 9 samples shares sf3b1, mutations
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.