Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A [RNA-seq]
RNA-seq (gene expression) · human · 36 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
- 36 samples: 18 conditions, mostly in duplicateGroups 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
- Dynamic control of RNA-DNA hybrid formation orchestrates DNA2 activation at stalled forks by RNAPII and DDX39AMolecular cell · 2025
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 GSE252171_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 PRJNA1058405 and SRA study SRP480457. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 18 replicated groups read from 36 sample titles; they account for 36 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.
- GSM7996180 rna_ctrl_1 rna_ctrl
- GSM7996181 rna_ctrl_2 rna_ctrl
- GSM7996182 rna_ctrl_hu_1 rna_ctrl_hu
- GSM7996183 rna_ctrl_hu_2 rna_ctrl_hu
- GSM7996186 rna_ko_hu_1 rna_ko_hu
- GSM7996187 rna_ko_hu_2 rna_ko_hu
- GSM8567591 batch2_rna_ko_hu_1 batch2_rna_ko_hu
- GSM8567592 batch2_rna_ko_hu_2 batch2_rna_ko_hu
- GSM8567593 rna_ko_hu_DRB_1 rna_ko_hu_DRB
- GSM8567594 rna_ko_hu_DRB_2 rna_ko_hu_DRB
- GSM8567595 rna_ko_hu_RH_1 rna_ko_hu_RH
- GSM8567596 rna_ko_hu_RH_2 rna_ko_hu_RH
- GSM8567597 rna_siCtrl_hu_1 rna_siCtrl_hu
- GSM8567598 rna_siCtrl_hu_2 rna_siCtrl_hu
- GSM8567599 rna_siRAD51_hu_1 rna_siRAD51_hu
- GSM8567600 rna_siRAD51_hu_2 rna_siRAD51_hu
- GSM8567601 rna_siSMARCAL1_hu_1 rna_siSMARCAL1_hu
- GSM8567602 rna_siSMARCAL1_hu_2 rna_siSMARCAL1_hu
- GSM8567603 rnaInput_ctrl_1 rnaInput_ctrl
- GSM8567604 rnaInput_ctrl_2 rnaInput_ctrl
- GSM8567605 rnaInput_ctrl_hu_1 rnaInput_ctrl_hu
- GSM8567606 rnaInput_ctrl_hu_2 rnaInput_ctrl_hu
- GSM8567607 rnaInput_ko_hu_1 rnaInput_ko_hu
- GSM8567608 rnaInput_ko_hu_2 rnaInput_ko_hu
- GSM8567609 batch2_rnaInput_ko_hu_1 batch2_rnaInput_ko_hu
- GSM8567610 batch2_rnaInput_ko_hu_2 batch2_rnaInput_ko_hu
- GSM8567611 rnaInput_ko_hu_DRB_1 rnaInput_ko_hu_DRB
- GSM8567612 rnaInput_ko_hu_DRB_2 rnaInput_ko_hu_DRB
- GSM8567613 rnaInput_ko_hu_RH_1 rnaInput_ko_hu_RH
- GSM8567614 rnaInput_ko_hu_RH_2 rnaInput_ko_hu_RH
- GSM8567615 rnaInput_siCtrl_hu_1 rnaInput_siCtrl_hu
- GSM8567616 rnaInput_siCtrl_hu_2 rnaInput_siCtrl_hu
- GSM8567617 rnaInput_siRAD51_hu_1 rnaInput_siRAD51_hu
- GSM8567618 rnaInput_siRAD51_hu_2 rnaInput_siRAD51_hu
- GSM8567619 rnaInput_siSMARCAL1_hu_1 rnaInput_siSMARCAL1_hu
- GSM8567620 rnaInput_siSMARCAL1_hu_2 rnaInput_siSMARCAL1_hu
- GSE252173 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A. 42 samples shares rna-dna, rnapii, ddx39a, dna2, orchestrates, activation, formation, dynamic
- GSE252172 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A [ChIP-seq] 6 samples shares rna-dna, rnapii, ddx39a, dna2, orchestrates, activation, formation, dynamic
- GSE254534 Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions [DNA2_MRE11_ChIPseq] 9 samples shares rna-dna, dna2
- GSE320287 NF-κB transcriptionally perturbs p53 dynamics hampering DNA2repair. 56 samples shares dna2, dynamic
- GSE324875 Elongin B orchestrates chromatin and transcriptional programs in H3K27M‑mutant diffuse midline glioma [XIII_ELOBKO_chIP_ELOB_RNAPII] 10 samples shares rnapii, orchestrates
- GSE261054 Bypass of blocking lesions by RNAPII reveals a novel stress induced by DNA damage [RNA-seq] 62 samples shares rnapii
- GSE307861 Maintenance of gene expression homeostasis by systems-level feedback loops in response to changes in RNA polymerase II dosage [RNAPII_levels_mRNAseq] 42 samples shares rnapii
- GSE269570 Nuclear speckles regulate functional programs in cancer (RNA SART1, DDX39A, SARNP, FIBP, TMEM259 kd) 26 samples shares ddx39a
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.