BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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 GSE263279_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 PRJNA1096625 and SRA study SRP499933. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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
- GSE263285 BMAL1 represses transposable elements independently of CLOCK in pluripotent cells 20 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
- GSE39977 Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [ChIP-seq] 138 samples shares clock, chip-seq
- GSE242901 An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq] 45 samples shares clock, chip-seq
- GSE294069 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [ChIP-Seq 1] 20 samples shares bmal1, chip-seq
- GSE294070 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [ChIP-Seq 2] 15 samples shares bmal1, chip-seq
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.