Unraveling Epigenetic and Immune Mechanisms Underlying Cystogenesis in Autosomal Dominant Polycystic Kidney Disease
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 19 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
- 19 samples: 15 distinct titles, 4 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
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 GSE244450_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 PRJNA1023185 and SRA study SRP465466. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 19 sample titles: 15 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.
- GSM7833989 WT_ATAC_rep1
- GSM7833990 WT_ATAC_rep2
- GSM7833991 ADPKD_ATAC_rep1
- GSM7833992 ADPKD_ATAC_rep2
- 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
- GSE236580 Adipose tissue retains an epigenetic memory of obesity after weight loss 135 samples shares epigenetic
- GSE247970 Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation 76 samples shares epigenetic
- GSE294258 Intracellular iron homeostasis-regulated epigenetic reprogramming contributes to -7/del(7q) leukemia 71 samples shares epigenetic
- GSE207943 Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas 59 samples shares epigenetic
- GSE272888 Dynamic transcriptional and epigenetic changes define postnatal tendon growth 54 samples shares epigenetic
- GSE247454 Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer 38 samples shares epigenetic
- GSE266584 Epigenetic and transcriptional regulation of dendritic cell development and anti-tumor function by HDAC1 34 samples shares epigenetic
- GSE157232 The CD8+ T cell tolerance checkpoint triggers a transcriptionally and epigenetically distinct differentiation state defined by protein translation defects 30 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.