METTL3-mediated chromatin contacts promote phase separation during senescence.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 22 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
- 22 samples: 18 distinct titles, 4 of them repeatedGroups 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.
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 GSE243047_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 PRJNA1016270 and SRA study SRP460167. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 8 as controls.
How we read this: Read from 22 sample titles: 18 distinct titles with little repetition. 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.
- GSM7777857 control, KAS-seq, input
- GSM7777858 control, KAS-seq, IP
- GSM7777859 senescent, shcontrol, KAS-seq, input
- GSM7777860 senescent, shcontrol, KAS-seq, IP
- GSM7777861 senescent, shMETTL3, KAS-seq, input
- GSM7777862 senescent, shMETTL3, KAS-seq, IP
- GSM7777863 senescent, shMETTL14, KAS-seq, input
- GSM7777864 senescent, shMETTL14, KAS-seq, IP
- GSM7777865 control, H3K27Ac, HiChIP-seq
- GSM7777866 senescent, control knockdown, H3K27Ac, HiChIP-seq
- GSM7777867 senescent, METTL3 knockdown, H3K27Ac, HiChIP-seq
- GSM7777868 senescent, METTL14 knockdown, H3K27Ac, HiChIP-seq
- GSM7777869 control, METTL3, HiChIP
- GSM7777870 senescent, METTL3, HiChIP
- GSM7777882 control_fastGRO-seq_replicate 1
- GSM7777883 control_fastGRO-seq_replicate 2
- GSM7777884 senescent_fastGRO-seq_shcontrol_knockdown_ replicate 1
- GSM7777885 senescent_fastGRO-seq_shcontrol_knockdown_ replicate 2
- GSM7777886 senescent_fastGRO-seq_shMETTL3_knockdown_ replicate 1
- GSM7777887 senescent_fastGRO-seq_shMETTL3_knockdown_ replicate 2
- GSM7777888 senescent_fastGRO-seq_shMETTL14_knockdown_ replicate 1
- GSM7777889 senescent_fastGRO-seq_shMETTL14_knockdown_ replicate 2
- GSE278512 Phase separation of chimeric antigen receptor promotes immunological synapse maturation and persistent cytotoxicity 45 samples shares separation, promote, phase
- GSE262518 Acute multi-level response to defective de novo chromatin assembly in S-phase 72 samples shares chromatin, phase
- GSE324154 Therapy Induced Senescence Promotes Immunogenicity in Acute Myeloid Leukemia through Reduced EZH2 Activity 22 samples shares senescence, promote
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
- GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares chromatin
- GSE325835 BATF3 regulates chromatin accessibility during CD8+ T lymphocyte differentiation 36 samples shares chromatin
- GSE146585 Functional genomics assays, including ChIP-seq, ATAC-seq, RNA-seq, GRO-seq, and in situ Hi-C, in the context of replicative senescence 223 samples shares senescence
- GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples shares chromatin
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.