Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis
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 × HG-3 SF3B1 K700E vs 3 × HG-3 SF3B1 WT vs 3 × MEC-1 SF3B1 K700E vs 3 × MEC-1 SF3B1 WTGroups 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
- Engineering Oncogenic Hotspot Mutations on SF3B1 via CRISPR-Directed PRECIS MutagenesisCancer research communications · 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 GSE231387_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 PRJNA964746 and SRA study SRP435420. 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.
- GSM7268144 HG-3 SF3B1 K700E rep1 HG-3 SF3B1 K700E
- GSM7268146 HG-3 SF3B1 K700E rep2 HG-3 SF3B1 K700E
- GSM7268147 HG-3 SF3B1 K700E rep3 HG-3 SF3B1 K700E
- GSM7268148 HG-3 SF3B1 WT rep1 HG-3 SF3B1 WT
- GSM7268149 HG-3 SF3B1 WT rep2 HG-3 SF3B1 WT
- GSM7268150 HG-3 SF3B1 WT rep3 HG-3 SF3B1 WT
- GSM7268151 MEC-1 SF3B1 K700E rep1 MEC-1 SF3B1 K700E
- GSM7268152 MEC-1 SF3B1 K700E rep2 MEC-1 SF3B1 K700E
- GSM7268154 MEC-1 SF3B1 K700E rep3 MEC-1 SF3B1 K700E
- GSM7268155 MEC-1 SF3B1 WT rep1 MEC-1 SF3B1 WT
- GSM7268156 MEC-1 SF3B1 WT rep2 MEC-1 SF3B1 WT
- GSM7268157 MEC-1 SF3B1 WT rep3 MEC-1 SF3B1 WT
- 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
- GSE262021 Synthetic Introns Identify GPATCH8 as Required for Mis-splicing by SF3B1 Mutations [RNA-Seq 2] 12 samples shares sf3b1, mutations
- GSE305128 PreciCE: Precision engineering of cell fates via data-driven multi-gene control of transcriptional networks 3 samples shares precis, engineering
- GSE295447 On target: Transcriptomic analysis of 12 human iPSC-derived cell phenotypes shows precision in an extensive pharmacological investigation [set 2] 840 samples shares precis
- GSE295444 On target: Transcriptomic analysis of 12 human iPSC-derived cell phenotypes shows precision in an extensive pharmacological investigation [set 1] 840 samples shares precis
- GSE214129 Precisely controlled cell-cell interactions with single-cell transcriptome readout identify a time-demand threshold response of human oncolytic NK cells 447 samples shares precis
- GSE245473 Precise hourly personalized embryo transfer significantly improves clinical outcomes in patients with repeated implantation failure 115 samples shares precis
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.