Pax8 regulates proximal-tubule-specific identity via distal enhancer elements
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 32 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
- 32 samples: 8 conditions, mostly with about 4 replicates eachGroups 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 GSE300117_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 PRJNA1279059 and SRA study SRP592861. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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.
- GSM9053936 TAMnegH3K4me1_rep1 TAMnegH3K4me1
- GSM9053937 TAMnegH3K4me1_rep2 TAMnegH3K4me1
- GSM9053938 TAMnegH3K4me1_rep3 TAMnegH3K4me1
- GSM9053939 TAMnegH3K4me1_rep4 TAMnegH3K4me1
- GSM9053940 TAMposH3K4me1_rep1 TAMposH3K4me1
- GSM9053941 TAMposH3K4me1_rep2 TAMposH3K4me1
- GSM9053942 TAMposH3K4me1_rep3 TAMposH3K4me1
- GSM9053943 TAMposH3K4me1_rep4 TAMposH3K4me1
- GSM9053944 TAMnegH3K4me3_rep1 TAMnegH3K4me3
- GSM9053945 TAMnegH3K4me3_rep2 TAMnegH3K4me3
- GSM9053946 TAMnegH3K4me3_rep3 TAMnegH3K4me3
- GSM9053947 TAMnegH3K4me3_rep4 TAMnegH3K4me3
- GSM9053948 TAMposH3K4me3_rep1 TAMposH3K4me3
- GSM9053949 TAMposH3K4me3_rep2 TAMposH3K4me3
- GSM9053950 TAMposH3K4me3_rep3 TAMposH3K4me3
- GSM9053951 TAMposH3K4me3_rep4 TAMposH3K4me3
- GSM9053952 TAMnegH3K27ac_rep1 TAMnegH3K27ac
- GSM9053953 TAMnegH3K27ac_rep2 TAMnegH3K27ac
- GSM9053954 TAMnegH3K27ac_rep3 TAMnegH3K27ac
- GSM9053955 TAMnegH3K27ac_rep4 TAMnegH3K27ac
- GSM9053956 TAMposH3K27ac_rep1 TAMposH3K27ac
- GSM9053957 TAMposH3K27ac_rep2 TAMposH3K27ac
- GSM9053958 TAMposH3K27ac_rep3 TAMposH3K27ac
- GSM9053959 TAMposH3K27ac_rep4 TAMposH3K27ac
- GSM9053960 TAMnegH3K27me3_rep1 TAMnegH3K27me3
- GSM9053961 TAMnegH3K27me3_rep2 TAMnegH3K27me3
- GSM9053962 TAMnegH3K27me3_rep3 TAMnegH3K27me3
- GSM9053963 TAMnegH3K27me3_rep4 TAMnegH3K27me3
- GSM9053964 TAMposH3K27me3_rep1 TAMposH3K27me3
- GSM9053965 TAMposH3K27me3_rep2 TAMposH3K27me3
- GSM9053966 TAMposH3K27me3_rep3 TAMposH3K27me3
- GSM9053967 TAMposH3K27me3_rep4 TAMposH3K27me3
- GSE277236 Synergy between regulatory elements can render cohesin dispensable for distal enhancer function 118 samples shares enhancer, elements, distal
- GSE293129 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN] 36 samples shares identity, enhancer
- GSE293139 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging 90 samples shares identity, enhancer
- GSE306301 Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer. 81 samples shares enhancer, distal
- GSE326309 Cohesin complex cooperates with PU.1 at super-enhancers to regulate the differentiation and identity of conventional dendritic cells 34 samples shares identity, enhancer
- GSE283392 Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function 25 samples shares enhancer, elements
- GSE293130 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [RNA-seq] 23 samples shares identity, enhancer
- GSE336091 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [CUT&Tag] 48 samples shares enhancer
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.