Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 56 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
- Mus musculus (mouse)
- Samples
- 56 samples: 26 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.
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 GSE273948_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 PRJNA1144138 and SRA study SRP524136. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 52 samples.
How we read this: 26 replicated groups read from 56 sample titles; they account for 52 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.
- GSM8440233 ConA-ChIP-seq-rep1 ConA-ChIP-seq
- GSM8440234 ConA-ChIP-seq-rep2 ConA-ChIP-seq
- GSM8440235 Buffer-ChIP-seq-rep1 Buffer-ChIP-seq
- GSM8440236 Buffer-ChIP-seq-rep2 Buffer-ChIP-seq
- GSM8440237 DMSO-ConA-ChIP-seq-rep1 DMSO-ConA-ChIP-seq
- GSM8440238 DMSO-ConA-ChIP-seq-rep2 DMSO-ConA-ChIP-seq
- GSM8440239 DMSO-Buffer-ChIP-seq-rep1 DMSO-Buffer-ChIP-seq
- GSM8440240 DMSO-Buffer-ChIP-seq-rep2 DMSO-Buffer-ChIP-seq
- GSM8440241 Inhibitor-ConA-ChIP-seq-rep1 Inhibitor-ConA-ChIP-seq
- GSM8440242 Inhibitor-ConA-ChIP-seq-rep2 Inhibitor-ConA-ChIP-seq
- GSM8440243 Inhibitor-Buffer-ChIP-seq-rep1 Inhibitor-Buffer-ChIP-s…
- GSM8440244 Inhibitor-Buffer-ChIP-seq-rep2 Inhibitor-Buffer-ChIP-s…
- GSM8440245 DMSO-H3K9me3-ChIP-seq-rep1 DMSO-H3K9me3-ChIP-seq
- GSM8440246 DMSO-H3K9me3-ChIP-seq-rep2 DMSO-H3K9me3-ChIP-seq
- GSM8440247 Inhibitor-H3K9me3-ChIP-seq-rep1 Inhibitor-H3K9me3-ChIP-…
- GSM8440248 Inhibitor-H3K9me3-ChIP-seq-rep2 Inhibitor-H3K9me3-ChIP-…
- GSM8440249 TMPO-WT-H3K9me3-ChIP-seq-rep1 TMPO-WT-H3K9me3-ChIP-seq
- GSM8440250 TMPO-WT-H3K9me3-ChIP-seq-rep2 TMPO-WT-H3K9me3-ChIP-seq
- GSM8440251 TMPO-MUT-H3K9me3-ChIP-seq-rep1 TMPO-MUT-H3K9me3-ChIP-s…
- GSM8440252 TMPO-MUT-H3K9me3-ChIP-seq-rep2 TMPO-MUT-H3K9me3-ChIP-s…
- GSM8440253 DMSO-SETDB1-ChIP-seq-rep1 DMSO-SETDB1-ChIP-seq
- GSM8440254 DMSO-SETDB1-ChIP-seq-rep2 DMSO-SETDB1-ChIP-seq
- GSM8440255 DMSO-SETDB1-ChIP-seq-input
- GSM8440256 Inhibitor-SETDB1-ChIP-seq-rep1 Inhibitor-SETDB1-ChIP-s…
- GSM8440257 Inhibitor-SETDB1-ChIP-seq-rep2 Inhibitor-SETDB1-ChIP-s…
- GSM8440258 Inhibitor-SETDB1-ChIP-seq-input
- GSM8440259 TMPO-WT-SETDB1-ChIP-seq-rep1 TMPO-WT-SETDB1-ChIP-seq
- GSM8440260 TMPO-WT-SETDB1-ChIP-seq-rep2 TMPO-WT-SETDB1-ChIP-seq
- GSM8440261 TMPO-WT-SETDB1-ChIP-seq-input
- GSM8440262 TMPO-MUT-SETDB1-ChIP-seq-rep1 TMPO-MUT-SETDB1-ChIP-seq
- GSM8440263 TMPO-MUT-SETDB1-ChIP-seq-rep2 TMPO-MUT-SETDB1-ChIP-seq
- GSM8440264 TMPO-MUT-SETDB1-ChIP-seq-input
- GSM9440133 DMSO-H3K9me3-CUT-RUN-rep1 DMSO-H3K9me3-CUT-RUN
- GSM9440134 DMSO-H3K9me3-CUT-RUN-rep2 DMSO-H3K9me3-CUT-RUN
- GSM9440135 Inhibitor-H3K9me3-CUT-RUN-rep1 Inhibitor-H3K9me3-CUT-R…
- GSM9440136 Inhibitor-H3K9me3-CUT-RUN-rep2 Inhibitor-H3K9me3-CUT-R…
- GSM9440137 DMSO-LADs-CUT-RUN-rep1 DMSO-LADs-CUT-RUN
- GSM9440138 DMSO-LADs-CUT-RUN-rep2 DMSO-LADs-CUT-RUN
- GSM9440139 Inhibitor-LADs-CUT-RUN-rep1 Inhibitor-LADs-CUT-RUN
- GSM9440140 Inhibitor-LADs-CUT-RUN-rep2 Inhibitor-LADs-CUT-RUN
+ 16 more — browse all 56 samples with per-sample file links →
- GSE297380 ER-resident CCDC134 safeguards TLR4 maturation by maintaining gp96 stability 16 samples shares stability, maintain
- GSE298935 Mettl3 maintains genome stability of erythroid cells via Mthfd1-mediated nucleotide biosynthesis 16 samples shares stability, maintain
- GSE269433 Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq] 18 samples shares maintain
- GSE278811 EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization [ChIP-Seq] 77 samples shares maintain
- GSE268146 Integrator complex bridges TFIID and RNA polymerase II to maintain pluripotency during development (ChIP-Seq) 38 samples shares maintain
- GSE314913 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture [CUT&TAG] 36 samples shares maintain
- GSE253692 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_CTCF_MBD3_ChIP_Seq] 36 samples shares maintain
- GSE271006 Stem cells tightly regulate dead cell clearance to maintain tissue fitness [ATAC-seq] 34 samples shares maintain
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.