Effect of depletion of HIF-1α, FACT or RNF20/40 on gene expression in hypoxia of MCF7 breast cancer cells
RNA-seq (gene expression) · human · 24 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
- 24 samples: 24 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.
- Paper
- Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genesCell reports · 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 GSE217204_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 PRJNA897909 and SRA study SRP406129. 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 24 sample titles: 24 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.
- GSM6706532 MCF7 cells, shNTC, 20% O2 (biol rep 1)
- GSM6706533 MCF7 cells, shNTC, 20% O2 (biol rep 2)
- GSM6706534 MCF7 cells, shNTC, 20% O2 (biol rep 3)
- GSM6706535 MCF7 cells, shNTC, 1% O2 (biol rep 1)
- GSM6706536 MCF7 cells, shNTC, 1% O2 (biol rep 2)
- GSM6706537 MCF7 cells, shNTC, 1% O2 (biol rep 3)
- GSM6706538 MCF7 cells, shHIF-1α, 20% O2 (biol rep 1)
- GSM6706539 MCF7 cells, shHIF-1α, 20% O2 (biol rep 2)
- GSM6706540 MCF7 cells, shHIF-1α, 20% O2 (biol rep 3)
- GSM6706541 MCF7 cells, shHIF-1α, 1% O2 (biol rep 1)
- GSM6706542 MCF7 cells, shHIF-1α, 1% O2 (biol rep 2)
- GSM6706543 MCF7 cells, shHIF-1α, 1% O2 (biol rep 3)
- GSM6706544 MCF7 cells, shFACT, 20% O2 (biol rep 1)
- GSM6706545 MCF7 cells, shFACT, 20% O2 (biol rep 2)
- GSM6706546 MCF7 cells, shFACT, 20% O2 (biol rep 3)
- GSM6706547 MCF7 cells, shFACT, 1% O2 (biol rep 1)
- GSM6706548 MCF7 cells, shFACT, 1% O2 (biol rep 2)
- GSM6706549 MCF7 cells, shFACT, 1% O2 (biol rep 3)
- GSM6706550 MCF7 cells, shRNF20-40, 20% O2 (biol rep 1)
- GSM6706551 MCF7 cells, shRNF20-40, 20% O2 (biol rep 2)
- GSM6706552 MCF7 cells, shRNF20-40, 20% O2 (biol rep 3)
- GSM6706553 MCF7 cells, shRNF20-40, 1% O2 (biol rep 1)
- GSM6706554 MCF7 cells, shRNF20-40, 1% O2 (biol rep 2)
- GSM6706555 MCF7 cells, shRNF20-40, 1% O2 (biol rep 3)
- 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 hypoxia, 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
- GSE285077 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq] 76 samples shares fact, hypoxia
- GSE249319 Single-cell profiling reveals a critical role for hypoxia-inducible factor-1a signaling in leukocytes during human craniotomy infection 14 samples shares fact, hypoxia
- GSE264084 Depletion of ribosome biogenesis factors in NPM1-mutant acute myeloid leukemia: Insights into direct consequences of the mutation and implications for treatment 12 samples shares fact, depletion
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.