Unraveling Epigenetic and Immune Mechanisms Underlying Cystogenesis in Autosomal Dominant Polycystic Kidney Disease [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
- 15 samples: 13 distinct titles, 2 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
- Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cellsJournal of biological methods · 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 GSE244998_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 PRJNA1026595 and SRA study SRP465466. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 15 sample titles: 13 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.
- GSM7833993 ADPKD_H3K27ac
- GSM7833994 ADPKD_H3K27me3
- GSM7833995 ADPKD_H3K36me3
- GSM7833996 ADPKD_H3K4me1
- GSM7833997 ADPKD_H3K4me3
- GSM7833998 ADPKD_H3K9ac
- GSM7833999 ADPKD_H3K9me3
- GSM7834000 ADPKD_H3K4me3_MR
- GSM7834001 WT_H3K27ac
- GSM7834002 WT_H3K27me3
- GSM7834003 WT_H3K36me3
- GSM7834004 WT_H3K4me1
- GSM7834005 WT_H3K4me3
- GSM7834006 WT_H3K9ac
- GSM7834007 WT_H3K9me3
- GSE244450 Unraveling Epigenetic and Immune Mechanisms Underlying Cystogenesis in Autosomal Dominant Polycystic Kidney Disease 19 samples shares cystogenesis, unraveling, epigenetic, underlying, polycystic, autosomal, dominant
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares epigenetic, chip-seq
- GSE289108 Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ChIP-Seq] 57 samples shares epigenetic, chip-seq
- GSE275917 Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation [ChIP-seq] 17 samples shares epigenetic, chip-seq
- GSE299381 KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [ChIP-Seq] 13 samples shares epigenetic, chip-seq
- GSE244496 Establishment of nuclear organization in mouse embryos is regulated by multiple and redundant epigenetic pathways. 183 samples shares epigenetic
- GSE313359 Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [Cut & Run] 45 samples shares epigenetic
- GSE298002 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run] 38 samples shares epigenetic
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.