YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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
- 21 samples: 6 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
- YTHDC1 m(6)A-dependent and m(6)A-independent functions converge to preserve the DNA damage responseThe EMBO journal · 2024
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 GSE239333_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 PRJNA998818 and SRA study SRP451557. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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.
- GSM7663234 A549 RNAseq, siYTHDC1, rep1 A549 RNAseq, siYTHDC1,
- GSM7663235 A549 RNAseq, siYTHDC1, rep2 A549 RNAseq, siYTHDC1,
- GSM7663236 A549 RNAseq, siYTHDC1, rep3 A549 RNAseq, siYTHDC1,
- GSM7663237 A549 RNAseq, siYTHDC1, rep4 A549 RNAseq, siYTHDC1,
- GSM7663238 A549 RNAseq, siYTHDC1, rep5 A549 RNAseq, siYTHDC1,
- GSM7663239 A549 RNAseq, siYTHDC1, rep6 A549 RNAseq, siYTHDC1,
- GSM7663240 A549 RNAseq, siSCR, rep1 A549 RNAseq, siSCR,
- GSM7663241 A549 RNAseq, siSCR, rep2 A549 RNAseq, siSCR,
- GSM7663242 A549 RNAseq, siSCR, rep3 A549 RNAseq, siSCR,
- GSM7663243 A549 RNAseq, siSCR, rep4 A549 RNAseq, siSCR,
- GSM7663244 A549 RNAseq, siSCR, rep5 A549 RNAseq, siSCR,
- GSM7663245 A549 RNAseq, siSCR, rep6 A549 RNAseq, siSCR,
- GSM7663246 A549 Ythdc1 ChIP, rep1 A549 Ythdc1 ChIP,
- GSM7663247 A549 Ythdc1 ChIP, rep2 A549 Ythdc1 ChIP,
- GSM7663248 A549 Ythdc1 ChIP, rep3 A549 Ythdc1 ChIP,
- GSM7663249 A549 PolII ChIP, siYTHDC1, rep1 A549 PolII ChIP, siYTHD…
- GSM7663250 A549 PolII ChIP, siYTHDC1, rep2 A549 PolII ChIP, siYTHD…
- GSM7663251 A549 PolII ChIP, siSCR, rep1 A549 PolII ChIP, siSCR,
- GSM7663252 A549 PolII ChIP, siSCR, rep2 A549 PolII ChIP, siSCR,
- GSM8170661 A549 cells, YTHDC1 CLIP-seq rep1 A549 cells, YTHDC1 CLIP…
- GSM8170662 A549 cells, YTHDC1 CLIP-seq rep2 A549 cells, YTHDC1 CLIP…
- GSE283317 YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks 30 samples shares ythdc1, damage
- GSE291973 HSF1 and YTHDC1 facilitate DNA damage repair upon heat stress by promoting the expressions of repair related genes 10 samples shares ythdc1, damage
- GSE252349 H3S10-phosphorylation spreading in mitosis stably preserves 3D chromatin structure and functions 27 samples shares functions, preserve
- GSE287825 The METTL3-YTHDC1 axis mediates architectural RNA m6A modification to modulate the integrity of chromatin TADs in MLLr+ AML genome 36 samples shares ythdc1
- GSE244402 The elevated YTHDC1 affects trophoblastic function and induces preterm birth in ART conception via augmenting RPL37 translation 20 samples shares ythdc1
- GSE245860 YTHDC1 affects the ubiquitination level of RAD51 by negatively regulating UBE3A expression and inhibits colorectal cancer cells apoptosis 12 samples shares ythdc1
- GSE317469 Gene Expression Changes Induced by YTHDC1 knockdown in triple-negative breast cancer cells 12 samples shares ythdc1
- GSE252982 Toggling of BRD4 functions is triggered through its phosphorylation by JNK. 52 samples shares functions
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.