Phf6 truncating mutation drives leukemogenesis via disrupted epigenetic regulation in mice
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
- 27 samples: 11 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.
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 GSE198504_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 PRJNA815648 and SRA study SRP363783. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 27 samples.
How we read this: 11 replicated groups read from 27 sample titles; they account for 27 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.
- GSM5949623 RNA-seq_WT_rep1 RNA-seq_WT
- GSM5949624 RNA-seq_WT_rep2 RNA-seq_WT
- GSM5949625 RNA-seq_WT_rep3 RNA-seq_WT
- GSM5949626 RNA-seq_WT_rep4 RNA-seq_WT
- GSM5949627 RNA-seq_Phf6 KO_rep1 RNA-seq_Phf6 KO
- GSM5949628 RNA-seq_Phf6 KO_rep2 RNA-seq_Phf6 KO
- GSM5949629 RNA-seq_Phf6 KO_rep3 RNA-seq_Phf6 KO
- GSM5949630 RNA-seq_Phf6 Tg_rep1 RNA-seq_Phf6 Tg
- GSM5949631 RNA-seq_Phf6 Tg_rep2 RNA-seq_Phf6 Tg
- GSM5949632 RNA-seq_Phf6 Tg_rep3 RNA-seq_Phf6 Tg
- GSM5949633 RNA-seq_Phf6 Tg_rep4 RNA-seq_Phf6 Tg
- GSM5949634 ChIP_H3K27ac_WT_rep1 ChIP_H3K27ac_WT
- GSM5949635 ChIP_H3K27ac_WT_rep2 ChIP_H3K27ac_WT
- GSM5949636 ChIP_H3K27ac_Phf6 Tg_rep1 ChIP_H3K27ac_Phf6 Tg
- GSM5949637 ChIP_H3K27ac_Phf6 Tg_rep2 ChIP_H3K27ac_Phf6 Tg
- GSM5949638 ChIP_H3K4me1_WT_rep1 ChIP_H3K4me1_WT
- GSM5949639 ChIP_H3K4me1_WT_rep2 ChIP_H3K4me1_WT
- GSM5949640 ChIP_H3K4me1_Phf6 Tg_rep1 ChIP_H3K4me1_Phf6 Tg
- GSM5949641 ChIP_H3K4me1_Phf6 Tg_rep2 ChIP_H3K4me1_Phf6 Tg
- GSM5949642 ChIP_H3K4me3_WT_rep1 ChIP_H3K4me3_WT
- GSM5949643 ChIP_H3K4me3_WT_rep2 ChIP_H3K4me3_WT
- GSM5949644 ChIP_H3K4me3_Phf6 Tg_rep1 ChIP_H3K4me3_Phf6 Tg
- GSM5949645 ChIP_H3K4me3_Phf6 Tg_rep2 ChIP_H3K4me3_Phf6 Tg
- GSM5949646 scRNA-seq_WT_rep1 scRNA-seq_WT
- GSM5949647 scRNA-seq_WT_rep2 scRNA-seq_WT
- GSM5949648 scRNA-seq_Phf6 Tg_rep1 scRNA-seq_Phf6 Tg
- GSM5949649 scRNA-seq_Phf6 Tg_rep2 scRNA-seq_Phf6 Tg
- GSE247970 Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation 76 samples shares epigenetic, mutation
- GSE327604 Epigenetic control of microglial mitochondrial immunity by KAT7 drives Alzheimer’s disease pathogenesis [RNA-Seq] 12 samples shares epigenetic, drives
- GSE270456 PHF6 regulates stress susceptibility in the pituitary intermediate lobe [RNA-seq] 24 samples shares phf6
- GSE266584 Epigenetic and transcriptional regulation of dendritic cell development and anti-tumor function by HDAC1 34 samples shares epigenetic
- GSE279810 Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8 18 samples shares epigenetic
- GSE236580 Adipose tissue retains an epigenetic memory of obesity after weight loss 135 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
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.