Origin of extra-embryonic mesenchyme points to evolutionary novelty in primate early development [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- Samples
- 20 samples: 8 conditions, mostly in triplicateGroups 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
- HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCsCell reports · 2025
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 GSE219291_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 PRJNA907861 and SRA study SRP411109. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 8 replicated groups read from 20 sample titles; they account for 20 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.
- GSM6782199 KOLF2_WT_BSA_HAND1_R1 KOLF2_WT_BSA_HAND1
- GSM6782200 KOLF2_WT_BSA_HAND1_R2 KOLF2_WT_BSA_HAND1
- GSM6782201 KOLF2_WT_BSA_HAND1_R3 KOLF2_WT_BSA_HAND1
- GSM6782202 KOLF2_WT_BSA_H3K4me3_R1 KOLF2_WT_BSA_H3K4me3
- GSM6782203 KOLF2_WT_BSA_H3K4me3_R2 KOLF2_WT_BSA_H3K4me3
- GSM6782204 KOLF2_WT_BSA_H3K4me3_R3 KOLF2_WT_BSA_H3K4me3
- GSM6782205 KOLF2_HAND1_KO_BSA_HAND1_R1 KOLF2_HAND1_KO_BSA_HAND1
- GSM6782206 KOLF2_HAND1_KO_BSA_HAND1_R2 KOLF2_HAND1_KO_BSA_HAND1
- GSM6782207 KOLF2_HAND1_KO_BSA_H3K4me3_R1 KOLF2_HAND1_KO_BSA_H3K4…
- GSM6782208 KOLF2_HAND1_KO_BSA_H3K4me3_R2 KOLF2_HAND1_KO_BSA_H3K4…
- GSM6782209 KOLF2_WT_BSA_input_R1 KOLF2_WT_BSA_input
- GSM6782210 KOLF2_WT_BSA_input_R2 KOLF2_WT_BSA_input
- GSM6782211 KOLF2_WT_BSA_input_R3 KOLF2_WT_BSA_input
- GSM6782212 KOLF2_HAND1_KO_BSA_input_R1 KOLF2_HAND1_KO_BSA_input
- GSM6782213 KOLF2_HAND1_KO_BSA_input_R2 KOLF2_HAND1_KO_BSA_input
- GSM6782214 KOLF2_WT_BSA_IgG_R1 KOLF2_WT_BSA_IgG
- GSM6782215 KOLF2_WT_BSA_IgG_R2 KOLF2_WT_BSA_IgG
- GSM6782216 KOLF2_WT_BSA_IgG_R3 KOLF2_WT_BSA_IgG
- GSM6782217 KOLF2_HAND1_KO_BSA_IgG_R1 KOLF2_HAND1_KO_BSA_IgG
- GSM6782218 KOLF2_HAND1_KO_BSA_IgG_R2 KOLF2_HAND1_KO_BSA_IgG
- GSE220844 Origin of extra-embryonic mesenchyme points to evolutionary novelty in primate early development 59 samples shares extra-embryonic, evolutionary, mesenchyme, novelty, primate, origin, points
- GSE335058 Evolutionary guided transcription factor design programs novel T cell states [ChIP-Seq] 66 samples shares evolutionary, chip-seq
- GSE280574 mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer 576 samples shares chip-seq
- GSE271752 Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq] 194 samples shares chip-seq
- GSE277608 Characterization of induced cohesin loop extrusion trajectories in living cells [ChIP-seq] 147 samples shares chip-seq
- GSE299672 PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers [ChIP-seq] 132 samples shares chip-seq
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares chip-seq
- GSE297914 PU.1-Activated Genomic Regions Define Low-risk MDS Subsets Characterized by Immune Dysregulation and Disease Progression [ChIP-seq] 112 samples shares chip-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.