Establishment of Human Formative Pluripotent Stem Cell Like Cells Exhibiting Amniotic Differentiation Potentials
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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
- 21 samples: 5 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 GSE298432_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 PRJNA1269394 and SRA study SRP588755. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 5 replicated groups read from 21 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.
- GSM9014131 hfPSCs_1_ATAC
- GSM9014132 hfPSCs_2_ATAC
- GSM9014139 hESCs_H9
- GSM9014140 hESCs_MGT3
- GSM9014141 hfPSCs_H9
- GSM9014142 hfPSCs_MGT3
- GSM9014143 hifPSCs
- GSM9014144 hALSCs_1 hALSCs
- GSM9014145 hALSCs_2 hALSCs
- GSM9014146 hESCs_sus_1 hESCs_sus
- GSM9014147 hESCs_sus_2 hESCs_sus
- GSM9014148 3D_to_2D_P1_1 3D_to_2D_P1
- GSM9014149 3D_to_2D_P1_2 3D_to_2D_P1
- GSM9014150 3D_to_2D_P2_1 3D_to_2D_P2
- GSM9014151 3D_to_2D_P2_2 3D_to_2D_P2
- GSM9014152 hfPSCs_single cell_1 hfPSCs_single cell
- GSM9014153 hfPSCs_single cell_2 hfPSCs_single cell
- GSM9014154 hfPSCs_single cell_3 hfPSCs_single cell
- GSM9014155 hfPSCs_single cell_4 hfPSCs_single cell
- GSM9014156 hfPSCs_H9_DNA methylation
- GSM9014157 hfPSCs_MGT3_DNA methylation
- GSE298429 Establishment of Human Formative Pluripotent Stem Cell Like Cells Exhibiting Amniotic Differentiation Potentials [bulk RNA-seq] 13 samples shares establishment, pluripotent, exhibiting, potentials, formative, amniotic, stem, like
- GSE78116 Differentiation of human and murine induced pluripotent stem cells to microglia-like cells 45 samples shares pluripotent, stem, like
- GSE52824 Derivation of novel human ground state naïve pluripotent stem cells. 71 samples shares pluripotent, stem
- GSE52617 Derivation of novel human ground state naïve pluripotent stem cells [ChIP-seq; RRBS-seq] 59 samples shares pluripotent, stem
- GSE252590 Generation of mature epicardium derived from human-induced pluripotent stem cells via inhibition of mTOR signaling 23 samples shares pluripotent, stem
- GSE268632 Modulation of mitochondrial abundance in pluripotent stem cells and embryos 12 samples shares pluripotent, stem
- GSE282077 In vitro generation of a ureteral organoid from pluripotent stem cells 11 samples shares pluripotent, stem
- GSE89301 Genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells 10 samples shares pluripotent, stem
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.