DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]
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 × HCT cells, WT, without hypoxicstress, vs 3 × HCT cells, DNA-PK KO, without hypoxicstress, vs 3 × HCT cells, WT, with hypoxicstress, vs 3 × HCT cells, DNA-PK KO, with hypoxicstress,Groups 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
- Epigenetic dysregulation of H19/IGF2 in hepatic cells exposed to toxic metal mixtures in vitroScientific reports · 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 GSE285698_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 PRJNA1205669 and SRA study SRP554899. 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.
- GSM8706908 HCT cells, WT, without hypoxicstress, rep1 HCT cells, WT, without …
- GSM8706909 HCT cells, WT, without hypoxicstress, rep2 HCT cells, WT, without …
- GSM8706910 HCT cells, WT, without hypoxicstress, rep3 HCT cells, WT, without …
- GSM8706911 HCT cells, DNA-PK KO, without hypoxicstress, rep1 HCT cells, DNA-PK KO, w…
- GSM8706912 HCT cells, DNA-PK KO, without hypoxicstress, rep2 HCT cells, DNA-PK KO, w…
- GSM8706913 HCT cells, DNA-PK KO, without hypoxicstress, rep3 HCT cells, DNA-PK KO, w…
- GSM8706914 HCT cells, WT, with hypoxicstress, rep1 HCT cells, WT, with hyp…
- GSM8706915 HCT cells, WT, with hypoxicstress, rep2 HCT cells, WT, with hyp…
- GSM8706916 HCT cells, WT, with hypoxicstress, rep3 HCT cells, WT, with hyp…
- GSM8706917 HCT cells, DNA-PK KO, with hypoxicstress, rep1 HCT cells, DNA-PK KO, w…
- GSM8706918 HCT cells, DNA-PK KO, with hypoxicstress, rep2 HCT cells, DNA-PK KO, w…
- GSM8706919 HCT cells, DNA-PK KO, with hypoxicstress, rep3 HCT cells, DNA-PK KO, w…
- GSE277501 Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (RNA-Seq) 4 samples shares topoisomerase, interaction, rna-seq
- GSE306599 DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [RNA-Seq] 6 samples shares dna-pk, rna-seq
- GSE293331 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [RNA-seq] 54 samples shares topological, rna-seq
- GSE275117 CRAMP1-dependent histone H1 biogenesis is essential for topoisomerase II inhibitor tolerance [RNA-seq] 20 samples shares topoisomerase, rna-seq
- GSE292860 Selective CDK7 Inhibition Sensitizes Tumors to Topoisomerase I Inhibitor-Antibody Drug Conjugates by Blocking The Transition of The RNA polymerase II Initiation Complex into Elongation [RNA-seq] 16 samples shares topoisomerase, rna-seq
- GSE268804 Effect of depletion of hypoxia-inducible factor (HIFs) on gene expression in MDA231-BrM2 breast cancer brain-selective metastatic cells with RNA-Seq. 12 samples shares hypoxia-inducible, rna-seq
- GSE246286 Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [RNA-Seq] 10 samples shares topological, rna-seq
- GSE240551 Hypoxia drives the formation of lung micropapillary adenocarcinoma through hypoxia-inducible factor-1a (RNA-seq) 4 samples shares hypoxia-inducible, rna-seq
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.