CDK12 prevents MYC-induced transcription-replication conflicts [EdU-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 3 × EdU_HU_seq_shNT vs 3 × EdU_HU_seq_shNT_OHT vs 3 × EdU_HU_seq_shCDK12 vs 3 × EdU_HU_seq_shCDK12_OHTGroups 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
- CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflictsNature communications · 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 GSE236550_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA991567 and SRA study SRP447495. 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.
- GSM7549808 EdU_HU_seq_shNT_rep1 EdU_HU_seq_shNT
- GSM7549809 EdU_HU_seq_shNT_rep2 EdU_HU_seq_shNT
- GSM7549810 EdU_HU_seq_shNT_rep3 EdU_HU_seq_shNT
- GSM7549811 EdU_HU_seq_shNT_OHT_rep1 EdU_HU_seq_shNT_OHT
- GSM7549812 EdU_HU_seq_shNT_OHT_rep2 EdU_HU_seq_shNT_OHT
- GSM7549813 EdU_HU_seq_shNT_OHT_rep3 EdU_HU_seq_shNT_OHT
- GSM7549814 EdU_HU_seq_shCDK12_rep1 EdU_HU_seq_shCDK12
- GSM7549815 EdU_HU_seq_shCDK12_rep2 EdU_HU_seq_shCDK12
- GSM7549817 EdU_HU_seq_shCDK12_rep3 EdU_HU_seq_shCDK12
- GSM7549819 EdU_HU_seq_shCDK12_OHT_rep1 EdU_HU_seq_shCDK12_OHT
- GSM7549822 EdU_HU_seq_shCDK12_OHT_rep2 EdU_HU_seq_shCDK12_OHT
- GSM7549825 EdU_HU_seq_shCDK12_OHT_rep3 EdU_HU_seq_shCDK12_OHT
- GSE236546 CDK12 prevents MYC-induced transcription-replication conflicts [ChIP-seq] 2 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE236553 CDK12 prevents MYC-induced transcription-replication conflicts 48 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE236545 CDK12 prevents MYC-induced transcription-replication conflicts [RNA-seq] 14 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE236549 CDK12 prevents MYC-induced transcription-replication conflicts [EU-seq] 12 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE267495 Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq] 16 samples shares transcription-replication, conflicts
- GSE269841 Genome-wide Mapping of Topoisomerase Binding Sites Suggests Topoisomerase 3a (TOP3A) as a Reader of Transcription-Replication Conflicts (TRC) 15 samples shares transcription-replication, conflicts
- GSE292585 Mechanism of SETX-BRCA1-BARD1 complex in resolution of R-loops and transcription-replication conflicts 10 samples shares transcription-replication, conflicts
- GSE295262 KCTD10 is a sensor for co-directional transcription-replication conflicts 5 samples shares transcription-replication, conflicts
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.