Rational cell fate engineering through chromatin dynamics [ATAC-Seq]
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: 8 × Nanog+Oct4, Day vs 8 × NanogN70+Oct4, Day vs 3 × ESCGroups 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
- Engineering mouse cell fate controller by rational designNature communications · 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 GSE243513_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 PRJNA1018833 and SRA study SRP461617. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 3 replicated groups read from 20 sample titles; they account for 19 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.
- GSM7789740 MEF
- GSM7789741 ESC_rep1 ESC
- GSM7789742 ESC_rep2 ESC
- GSM7789743 ESC_rep3 ESC
- GSM7789744 Nanog+Oct4, Day0 Nanog+Oct4, Day
- GSM7789745 Nanog+Oct4, Day1 Nanog+Oct4, Day
- GSM7789746 Nanog+Oct4, Day3 Nanog+Oct4, Day
- GSM7789747 Nanog+Oct4, Day5 Nanog+Oct4, Day
- GSM7789748 Nanog+Oct4, Day7 Nanog+Oct4, Day
- GSM7789749 Nanog+Oct4, Day8 Nanog+Oct4, Day
- GSM7789750 Nanog+Oct4, Day10 Nanog+Oct4, Day
- GSM7789751 Nanog+Oct4, Day12 Nanog+Oct4, Day
- GSM7789752 NanogN70+Oct4, Day0 NanogN70+Oct4, Day
- GSM7789753 NanogN70+Oct4, Day1 NanogN70+Oct4, Day
- GSM7789754 NanogN70+Oct4, Day3 NanogN70+Oct4, Day
- GSM7789755 NanogN70+Oct4, Day5 NanogN70+Oct4, Day
- GSM7789756 NanogN70+Oct4, Day7 NanogN70+Oct4, Day
- GSM7789757 NanogN70+Oct4, Day8 NanogN70+Oct4, Day
- GSM7789758 NanogN70+Oct4, Day10 NanogN70+Oct4, Day
- GSM7789759 NanogN70+Oct4, Day12 NanogN70+Oct4, Day
- GSE310322 Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate 37 samples shares chromatin, fate
- GSE279088 Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis [ATAC-Seq] 74 samples shares dynamics, atac-seq
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares chromatin, atac-seq
- GSE294103 SIRT6 Overexpression Counteracts Chromatin Aging [ATAC-Seq_tg] 28 samples shares chromatin, atac-seq
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples shares chromatin, dynamics
- GSE249077 Mapping the female mouse chromatin accessibility landscape by UUATAC-seq 23 samples shares chromatin, atac-seq
- GSE342565 Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq 2 samples shares chromatin, atac-seq
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares chromatin, atac-seq
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.