Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 6 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.
- Paper
- Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomicsCell stem cell · 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 GSE229024_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 PRJNA952584 and SRA study SRP431115. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 12 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.
- GSM7147964 ChIP_p300_mESCs_1 ChIP_p300_mESCs
- GSM7147965 ChIP_p300_mESCs_2 ChIP_p300_mESCs
- GSM7147966 input_mESCs
- GSM7147967 ChIP_p300_gastruloids_1 ChIP_p300_gastruloids
- GSM7147968 ChIP_p300_gastruloids_2 ChIP_p300_gastruloids
- GSM7147969 input_gastruloids
- GSM7147970 ChIP_Rxrα_mESCs_1 ChIP_Rxrα_mESCs
- GSM7147971 ChIP_Rxrα_mESCs_2 ChIP_Rxrα_mESCs
- GSM7147972 ChIP_Rxrα_gastruloids_1 ChIP_Rxrα_gastruloids
- GSM7147973 ChIP_Rxrα_gastruloids_2 ChIP_Rxrα_gastruloids
- GSM7147974 ChIP_Sp5_gastruloids_1 ChIP_Sp5_gastruloids
- GSM7147975 ChIP_Sp5_gastruloids_2 ChIP_Sp5_gastruloids
- GSM7147976 ChIP_Zeb2_gastruloids_1 ChIP_Zeb2_gastruloids
- GSM7147977 ChIP_Zeb2_gastruloids_2 ChIP_Zeb2_gastruloids
- GSE284146 Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [ChIP-seq] 15 samples shares specification, chip-seq, lineage
- GSE215177 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation 69 samples shares specification, lineage
- GSE250176 Chromatin Landscape Instructs Precise Transcription Factor Regulome during Embryonic Lineage Specification [CUT&RUN] 42 samples shares specification, lineage
- GSE274494 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [ChIP-Seq] 40 samples shares embryogenesis, chip-seq
- GSE254023 The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq) 12 samples shares embryogenesis, chip-seq
- GSE284145 Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [ATAC-seq] 12 samples shares specification, lineage
- GSE242000 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation [ATAC-Seq] 6 samples shares specification, lineage
- GSE215181 Selective requirement of 3D genomic organization for the Mdm1-Il22-Ifng locus regulation in initial Th1 cell lineage specification and differentiation 135 samples shares specification, lineage
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.