Transcriptome analysis of triple-negative breast cancer cells HCC1937 and MDA-MB-231 treated with Kalanchoe pinnata (Bryophyllum pinnata) reveals regulation of migration and invasion by downregulation of genes JAK2, ROCK1, ROCK2 and PIK3CA.
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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE287572_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 PRJNA1213762 and SRA study SRP558721. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM8748189 MDA-MB-231 cells, E1 control
- GSM8748190 MDA-MB-231 cells, E2 control
- GSM8748191 MDA-MB-231 cells, E3 control
- GSM8748192 MDA-MB-231 cells, E7 extract
- GSM8748193 MDA-MB-231 cells, E8 extract
- GSM8748194 MDA-MB-231 cells, E9 extract
- GSM8748195 HCC1937 cells, E25 control
- GSM8748196 HCC1937 cells, E26 control
- GSM8748197 HCC1937 cells, E27 control
- GSM8748198 HCC1937 cells, E31 extract
- GSM8748199 HCC1937 cells, E32 extract
- GSM8748200 HCC1937 cells, E33 extract
- 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
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE185760 RNA-Seq of MDA-MB-231 human triple-negative breast cancer cells treated with a copper chelator 9 samples shares mda-mb-231, triple-negative
- GSE316771 RNA-seq analysis of MDA-MB-231 triple-negative breast cancer cells treated with CIr2 for 24 h 6 samples shares mda-mb-231, triple-negative
- GSE325029 METTL3 modulates cell viability and motility in HCC1143 and MDA-MB-231 triple-negative breast cancer cell lines 4 samples shares mda-mb-231, triple-negative
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.