Gene expression profiling of Triple Negative Breast Cancer MB157 cells and GSI-resistant MB157R cells upon induction of Notch1 or Sox2 signaling.
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 × EV vs 3 × N vs 3 × Px vs 3 × SOXGroups 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
- Reciprocal inhibition of NOTCH and SOX2 shapes tumor cell plasticity and therapeutic escape in triple-negative breast cancerEMBO molecular medicine · 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 GSE262001_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 PRJNA1090014 and SRA study SRP496659. 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.
- GSM8155782 EV_REP1 EV
- GSM8155783 EV_REP2 EV
- GSM8155784 EV_REP3 EV
- GSM8155785 N_REP1 N
- GSM8155786 N_REP2 N
- GSM8155787 N_REP3 N
- GSM8155788 Px_REP1 Px
- GSM8155789 Px_REP2 Px
- GSM8155790 Px_REP3 Px
- GSM8155791 SOX_REP1 SOX
- GSM8155792 SOX_REP2 SOX
- GSM8155793 SOX_REP3 SOX
- GSE262007 Chromatine immunoprecipitation (ChIP-seq) for RBPJ and SOX2 in Triple negative breast cancer MB157 cells and GSI-resistant MB157R cells upon induction of Notch1 or Sox2 signaling. 34 samples shares mb157r, notch1, mb157, sox2, gsi-resistant, induction, negative, triple
- GSE262009 Reciprocal inhibition of NOTCH and SOX2 shapes tumor cell plasticity and therapeutic escape in triple negative breast cancer. 54 samples shares sox2, negative, triple
- GSE335924 RNA-seq Identifies FOS as a Potential Therapeutic Target Activating Neural Stem Cells via miR-21/SOX2 Pathway in Hypertensive Intracerebral Hemorrhage 53 samples shares sox2
- GSE72409 NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence 48 samples shares notch1
- GSE292924 Effects of Normoxia, Hypoxia, Oscillatory Hypoxia, and Lactate on Wild-Type, NOTCH1-Knockdown, and TP53-Knockdown MDA-MB-231 Cells 36 samples shares notch1
- GSE264191 Secreted factors from M1 macrophages drive prostate cancer stem cell plasticity by upregulating NANOG, SOX2 and CD44 through NFκB signaling 30 samples shares sox2
- GSE293100 Modulation of NOTCH1 signaling in CLL and MCL cell lines 30 samples shares notch1
- GSE72407 NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence [CSM] 24 samples shares notch1
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.