CDK12 prevents MYC-induced transcription-replication conflicts [EU-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 × EU_seq_shNT vs 3 × EU_seq_shCDK12 vs 3 × EU_seq_shNT_OHT vs 3 × EU_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 GSE236549_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 PRJNA991554 and SRA study SRP447496. 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.
- GSM7549796 EU_seq_shNT_rep1 EU_seq_shNT
- GSM7549797 EU_seq_shNT_rep2 EU_seq_shNT
- GSM7549798 EU_seq_shNT_rep3 EU_seq_shNT
- GSM7549799 EU_seq_shCDK12_rep1 EU_seq_shCDK12
- GSM7549800 EU_seq_shCDK12_rep2 EU_seq_shCDK12
- GSM7549801 EU_seq_shCDK12_rep3 EU_seq_shCDK12
- GSM7549802 EU_seq_shNT_OHT_rep1 EU_seq_shNT_OHT
- GSM7549803 EU_seq_shNT_OHT_rep2 EU_seq_shNT_OHT
- GSM7549804 EU_seq_shNT_OHT_rep3 EU_seq_shNT_OHT
- GSM7549805 EU_seq_shCDK12_OHT_rep1 EU_seq_shCDK12_OHT
- GSM7549806 EU_seq_shCDK12_OHT_rep2 EU_seq_shCDK12_OHT
- GSM7549807 EU_seq_shCDK12_OHT_rep3 EU_seq_shCDK12_OHT
- GSE236545 CDK12 prevents MYC-induced transcription-replication conflicts [RNA-seq] 14 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
- GSE236550 CDK12 prevents MYC-induced transcription-replication conflicts [EdU-seq] 12 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE236546 CDK12 prevents MYC-induced transcription-replication conflicts [ChIP-seq] 2 samples shares cdk12, transcription-replication, myc-induced, conflicts, prevents
- GSE239857 BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [RNA-seq] 8 samples shares transcription-replication, conflicts
- GSE289452 ABL Kinase Inactivation Promotes Transcription-Replication Conflicts and Compromises Replication Forks Revealing a Therapeutic Vulnerability in Metastatic Small Cell Lung Cancer 6 samples shares transcription-replication, conflicts
- GSE268017 Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction 37 samples shares transcription-replication, conflicts
- GSE267495 Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq] 16 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.