Effect of USP10 knockout using CRISPR on gene expression in MCF7 breast cancer cells
RNA-seq (gene expression) · human · 10 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 10 samples: 5 × MCF7- WT vs 5 × MCF7-KOGroups 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
- USP10/GSK3β-mediated inhibition of PTEN drives resistance to PI3K inhibitors in breast cancerThe Journal of clinical investigation · 2025
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 GSE302500_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 PRJNA1291091 and SRA study SRP600745. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM9105198 MCF7- WT-1 MCF7- WT
- GSM9105199 MCF7- WT-2 MCF7- WT
- GSM9105200 MCF7- WT-3 MCF7- WT
- GSM9105201 MCF7- WT-4 MCF7- WT
- GSM9105202 MCF7- WT-5 MCF7- WT
- GSM9105203 MCF7-KO-1 MCF7-KO
- GSM9105204 MCF7-KO-2 MCF7-KO
- GSM9105205 MCF7-KO-3 MCF7-KO
- GSM9105206 MCF7-KO-4 MCF7-KO
- GSM9105207 MCF7-KO-5 MCF7-KO
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE224986 Single-cell CRISPRi screens of breast cancer associated enhancers 94 samples shares crispr, breast
- GSE210007 Estrogen Receptor alpha CUT&RUN analysis of estrogen receptor positive breast cancer cell lines MCF7 and UCD12 with 1h hormone E2 treatment 40 samples shares mcf7, breast
- GSE288118 An arrayed CRISPR screen identifies knockout combinations improving antibody productivity in HEK293 cells 28 samples shares crispr, knockout
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.