Targeting branched-chain amino acids alleviates pulmonary fibrosis [CUT&Tag, histone_modification]
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: 10 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.
- Paper
- Dietary intake and BCAA metabolism regulate pulmonary fibrosis through KDM4A-mediated epigenetic remodeling in male miceNature communications · 2026
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 GSE295425_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 PRJNA1254654 and SRA study SRP580878. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 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.
- GSM8947683 BCAA_TGFb_H3K36me3_1 BCAA_TGFb_H3K36me3
- GSM8947684 BCAA_TGFb_H3K36me3_2 BCAA_TGFb_H3K36me3
- GSM8947685 Free_TGFb_H3K36me3_1 Free_TGFb_H3K36me3
- GSM8947686 Free_TGFb_H3K36me3_2 Free_TGFb_H3K36me3
- GSM8947687 BCAA_TGFb_H3K9me3_1 BCAA_TGFb_H3K9me3
- GSM8947688 BCAA_TGFb_H3K9me3_2 BCAA_TGFb_H3K9me3
- GSM8947689 Free_TGFb_H3K9me3_1 Free_TGFb_H3K9me3
- GSM8947690 Free_TGFb_H3K9me3_2 Free_TGFb_H3K9me3
- GSM8947691 BCAA_TGFb_H3K27me3_1 BCAA_TGFb_H3K27me3
- GSM8947692 BCAA_TGFb_H3K27me3_2 BCAA_TGFb_H3K27me3
- GSM8947693 Free_TGFb_H3K27me3_1 Free_TGFb_H3K27me3
- GSM8947694 Free_TGFb_H3K27me3_2 Free_TGFb_H3K27me3
- GSM8947695 BCAA_TGFb_H3K4me3_1 BCAA_TGFb_H3K4me3
- GSM8947696 BCAA_TGFb_H3K4me3_2 BCAA_TGFb_H3K4me3
- GSM8947697 Free_TGFb_H3K4me3_1 Free_TGFb_H3K4me3
- GSM8947698 Free_TGFb_H3K4me3_2 Free_TGFb_H3K4me3
- GSM8947699 BCAA_TGFb_H3K27ac_1 BCAA_TGFb_H3K27ac
- GSM8947700 BCAA_TGFb_H3K27ac_2 BCAA_TGFb_H3K27ac
- GSM8947701 Free_TGFb_H3K27ac_1 Free_TGFb_H3K27ac
- GSM8947702 Free_TGFb_H3K27ac_2 Free_TGFb_H3K27ac
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares cut, modification, histone
- GSE319420 Uncovering Critical Lysines in Mammalian Histone H3 with High-Throughput CRISPR Prime Editing [CUT&Tag] 26 samples shares cut, histone
- GSE252269 Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity [CUT&Tag/ATAC-seq] 18 samples shares cut, targeting
- GSE281926 Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&Tag] 18 samples shares cut, histone
- GSE291663 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_CUT&Tag] 10 samples shares cut, histone
- GSE326538 Aqueous Artemisia argyi extract mitigates acute lung injury by coordinating gut microbiota, metabolic homeostasis, and pulmonary inflammatory signaling 24 samples shares cut, pulmonary
- GSE297441 Development of CAR T cells Targeting U5 snRNP200 for the Treatment of Acute Myeloid and B-Lymphoid Leukemias 19 samples shares cut, targeting
- GSE196745 Changes in Ikaros binding and histone-modifications upon oncogenic β-catenin activation [ChIP-Seq] 30 samples shares modification, histone
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.