Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response [RNA-seq]
RNA-seq (gene expression) · human · 18 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
- 18 samples: 6 conditions, mostly in triplicateGroups 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
- Deubiquitinating enzyme mutagenesis screens identify a USP43-dependent HIF-1 transcriptional responseThe EMBO journal · 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 GSE252654_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 PRJNA1061575 and SRA study SRP482168. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8004861 Control hypoxia biol rep 1 Control hypoxia biol
- GSM8004862 Control hypoxia biol rep 2 Control hypoxia biol
- GSM8004863 Control hypoxia biol rep 3 Control hypoxia biol
- GSM8004864 Control normoxia biol rep 1 Control normoxia biol
- GSM8004865 Control normoxia biol rep 2 Control normoxia biol
- GSM8004866 Control normoxia biol rep 3 Control normoxia biol
- GSM8004867 HIF1B KO hypoxia biol rep 1 HIF1B KO hypoxia biol
- GSM8004868 HIF1B KO hypoxia biol rep 2 HIF1B KO hypoxia biol
- GSM8004869 HIF1B KO hypoxia biol rep 3 HIF1B KO hypoxia biol
- GSM8004870 HIF1B KO normoxia biol rep 1 HIF1B KO normoxia biol
- GSM8004871 HIF1B KO normoxia biol rep 2 HIF1B KO normoxia biol
- GSM8004872 HIF1B KO normoxia biol rep 3 HIF1B KO normoxia biol
- GSM8004873 USP43 KO hypoxia biol rep 1 USP43 KO hypoxia biol
- GSM8004874 USP43 KO hypoxia biol rep 2 USP43 KO hypoxia biol
- GSM8004875 USP43 KO hypoxia biol rep 3 USP43 KO hypoxia biol
- GSM8004876 USP43 KO normoxia biol rep 1 USP43 KO normoxia biol
- GSM8004877 USP43 KO normoxia biol rep 2 USP43 KO normoxia biol
- GSM8004878 USP43 KO normoxia biol rep 3 USP43 KO normoxia biol
- GSE252655 Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response 22 samples shares usp43, hif-1, deubiquitinating, mutagenesis, screens, enzyme, driven
- GSE324038 HIF-1α and HIF-2α regulate overlapping and distinct transcriptional programs in primary human T cells [RNA-Seq] 16 samples shares hif-1, rna-seq
- GSE315097 Lactylation of HIF-1α at K172 drives HIF1 complex assemble to promote hypoxia-induced immune evasion in esophageal squamous cell carcinoma [RNA-Seq] 8 samples shares hif-1, rna-seq
- GSE327855 Endothelial FGF13 impairs angiogenesis by accelerating oxygen-independent HIF-1α degradation [RNA-Seq] 6 samples shares hif-1, rna-seq
- GSE336140 mTORC2-HIF-1β signaling creates a targetable sphingolipid vulnerability in lung cancer [RNA-Seq] 6 samples shares hif-1, rna-seq
- GSE324430 Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects [RNA-seq] 88 samples shares mutagenesis, rna-seq
- GSE319526 Effect of HIF-1alpha and HIF-2alpha on hypoxic response in Panc1 cells 36 samples shares hif-1
- GSE302327 HIF-1alpha activity affects stem cell fate in patient-derived ileum organoids 29 samples shares hif-1
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.