Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 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
- 36 samples: 36 samples, each with a distinct title — no replicated groupsGroups 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
- Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiationCell stem cell · 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 GSE241378_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 PRJNA1007772 and SRA study SRP456198. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 36 sample titles: 36 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.
- GSM7727926 ESC_WT-1 (rep-1)
- GSM7727927 ESC_WT-2 (rep-2)
- GSM7727928 ESC_WT-3 (rep-3)
- GSM7727929 ESC_E7KO-1 (rep-1)
- GSM7727930 ESC_E7KO-2 (rep-2)
- GSM7727931 ESC_E7KO-3 (rep-3)
- GSM7727932 ESC_E7KI-1 (rep-1)
- GSM7727933 ESC_E7KI-2 (rep-2)
- GSM7727934 ESC_E7KI-3 (rep-3)
- GSM7727935 NPC_WT-1 (rep-1)
- GSM7727936 NPC_WT-2 (rep-2)
- GSM7727937 NPC_WT-3 (rep-3)
- GSM7727938 NPC_E7KO-1 (rep-1)
- GSM7727939 NPC_E7KO-2 (rep-2)
- GSM7727940 NPC_E7KO-3 (rep-3)
- GSM7727941 NPC_E7KI-1 (rep-1)
- GSM7727942 NPC_E7KI-2 (rep-2)
- GSM7727943 NPC_E7KI-3 (rep-3)
- GSM7727944 ESC_WT-1 (RNA-seq rep-1)
- GSM7727945 ESC_WT-3 (RNA-seq rep-2)
- GSM7727946 ESC_E7KO-1 (RNA-seq rep-1)
- GSM7727947 ESC_E7KO-3 (RNA-seq rep-2)
- GSM7727948 ESC_E7KI-2 (RNA-seq rep-1)
- GSM7727949 ESC_E7KI-3 (RNA-seq rep-2)
- GSM7727950 NPC_WT-1 (RNA-seq rep-1)
- GSM7727951 NPC_WT-3 (RNA-seq rep-2)
- GSM7727952 NPC_E7KO-1 (RNA-seq rep-1)
- GSM7727953 NPC_E7KO-3 (RNA-seq rep-2)
- GSM7727954 NPC_E7KI-2 (RNA-seq rep-1)
- GSM7727955 NPC_E7KI-3 (RNA-seq rep-2)
- GSM7727956 GN_WT-1 (RNA-seq rep-1)
- GSM7727957 GN_WT-3 (RNA-seq rep-2)
- GSM7727958 GN_E7KO-1 (RNA-seq rep-1)
- GSM7727959 GN_E7KO-3 (RNA-seq rep-2)
- GSM7727960 GN_E7KI-2 (RNA-seq rep-1)
- GSM7727961 GN_E7KI-3 (RNA-seq rep-2)
- GSE322558 Physiologic variation in sperm miRNAs tunes embryonic gene regulatory programs and developmental outcomes 622 samples shares regulatory, embryonic, programs
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares maintenance, embryonic, programs
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares chromatin, programs
- GSE342312 T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics] 40 samples shares regulatory, chromatin
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares maintenance, modifier
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares chromatin, programs
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares chromatin, modifier
- GSE242179 Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification 40 samples shares alternative, splicing
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.