BMAL1 represses transposable elements independently of CLOCK in pluripotent cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
- 20 samples: 16 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.
- Paper
- BMAL1-TRIM28 represses transposable elements independently of CLOCK in pluripotent cellsNature communications · 2025
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 GSE263285_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 PRJNA1096622 and SRA study SRP499900. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 20 sample titles: 16 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.
- GSM8189133 BMAL1-ChIPseq-JM8
- GSM8189134 BMAL1-ChIPseq-BMAL1KO
- GSM8189135 TRIM28-ChIPseq-JM8
- GSM8189136 TRIM28-ChIPseq-BMAL1KO
- GSM8189137 H3K9me3-ChIPseq-JM8
- GSM8189138 H3K9me3-ChIPseq-BMAL1KO
- GSM8189139 BMAL1-TRIM28-ChIPseq-JM8-Input
- GSM8189140 BMAL1-TRIM28-ChIPseq-BMAL1KO-Input
- GSM8189141 H3K9me3-ChIPseq-JM8-Input
- GSM8189142 H3K9me3-ChIPseq-BMAL1KO-Input
- GSM8189143 FLAG-ChIPSeq-FLAG-BMAL1-JM8
- GSM8189144 FLAG-BMAL1-JM8-Input
- GSM8189164 HiC-JM8-Exp1
- GSM8189165 HiC-JM8-Exp2
- GSM8189166 HiC-BMAL1KO-Exp1
- GSM8189167 HiC-BMAL1KO-Exp2
- GSM8189168 RNA-JM8-R1
- GSM8189169 RNA-JM8-R2
- GSM8189170 RNA-CLOCK-KO-R1
- GSM8189171 RNA-CLOCK-KO-R2
- GSE263279 BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [ChIP-seq] 12 samples shares bmal1, clock, independently, transposable, pluripotent, represses, elements
- GSE262714 The Core Circadian Clock Factor, Bmal1, Transduces Sex-specific Differences in Both Rhythmic and Nonrhythmic Gene Expression in the Mouse Heart 96 samples shares bmal1, clock
- GSE297376 A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration [Bmal1-KO] 25 samples shares bmal1, clock
- GSE279310 The circadian clock gene BMAL1 modulates autoimmunity features in lupus 20 samples shares bmal1, clock
- GSE294558 Derepression of transposable elements in mouse prefrontal cortex disrupts social behavior 74 samples shares transposable, elements
- GSE297796 Cartography and mechanism of enhanced transcriptome plasticity by transposable elements 24 samples shares transposable, elements
- GSE252760 OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide 16 samples shares transposable, elements
- GSE296397 Transposable elements are dynamically expressed within medium spiny neurons and associated with molecular and behavioral adaptations to cocaine 12 samples shares transposable, elements
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.