The circadian clock gene BMAL1 modulates autoimmunity features in lupus
RNA-seq (gene expression) · mouse · 20 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 20 samples: 5 × Untreated, WT # vs 5 × Untreated, KO # vs 5 × IMQ treated, WT # vs 5 × IMQ treated, KO #Groups 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
- The circadian clock gene BMAL1 modulates autoimmunity features in lupusFrontiers in immunology · 2024
Read the full summary ↓
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 GSE279310_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1171840 and SRA study SRP537982. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8566418 Untreated, WT #1 Untreated, WT #
- GSM8566419 Untreated, WT #2 Untreated, WT #
- GSM8566420 Untreated, WT #3 Untreated, WT #
- GSM8566421 Untreated, WT #4 Untreated, WT #
- GSM8566422 Untreated, WT #5 Untreated, WT #
- GSM8566423 Untreated, KO #1 Untreated, KO #
- GSM8566424 Untreated, KO #2 Untreated, KO #
- GSM8566425 Untreated, KO #3 Untreated, KO #
- GSM8566426 Untreated, KO #4 Untreated, KO #
- GSM8566427 Untreated, KO #5 Untreated, KO #
- GSM8566428 IMQ treated, WT #1 IMQ treated, WT #
- GSM8566429 IMQ treated, WT #2 IMQ treated, WT #
- GSM8566430 IMQ treated, WT #3 IMQ treated, WT #
- GSM8566431 IMQ treated, WT #4 IMQ treated, WT #
- GSM8566432 IMQ treated, WT #5 IMQ treated, WT #
- GSM8566433 IMQ treated, KO #1 IMQ treated, KO #
- GSM8566434 IMQ treated, KO #2 IMQ treated, KO #
- GSM8566435 IMQ treated, KO #3 IMQ treated, KO #
- GSM8566436 IMQ treated, KO #4 IMQ treated, KO #
- GSM8566437 IMQ treated, KO #5 IMQ treated, KO #
- 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, circadian, clock
- GSE255357 Pharmacological Modulation of BMAL1 Alters Circadian Dynamics and the Macrophage Immune Response 36 samples shares bmal1, circadian
- GSE284165 Reorganization of PBAF/cBAF remodelers on H3.3 chromatin regulates BMAL1 activity in the absence of circadian negative feedback 47 samples shares bmal1, circadian
- GSE266472 Transcriptomic Plasticity of the Circadian Clock in Response to Photoperiod: A Study in Male Melatonin-Competent Mice 123 samples shares circadian, clock
- GSE248462 Hepatic Vagal Afferents Convey Clock-Dependent Signals to Regulate Circadian Food Intake Patterns 48 samples shares circadian, clock
- GSE288748 The liver clock drives circadian rhythms in white adipose tissue [AML12] 48 samples shares circadian, clock
- GSE295306 Autonomous circadian bladder capacity rhythm independent of the central clock 36 samples shares circadian, clock
- GSE304692 Hepatocyte Circadian Clocks Control Cholesterol Metabolism and Protect From Metabolic Dysfunction-Associated Steatohepatitis (MASH) [RNAseq_palmitate_silencing] 24 samples shares circadian, clock
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.