Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids [CUT&Tag]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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
- 16 samples: 7 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.
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 GSE288046_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 PRJNA1215765 and SRA study SRP559921. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 16 sample titles; they account for 14 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.
- GSM8757911 ExpLBM_H3K27me3_rep1 ExpLBM_H3K27me3
- GSM8757912 ExpLBM_H3K27ac_rep1
- GSM8757917 414C2day0_H3K27me3_rep1 414C2day0_H3K27me3
- GSM8757918 414C2day0_H3K27ac_rep1 414C2day0_H3K27ac
- GSM8757919 LBM_H3K27me3_rep1 LBM_H3K27me3
- GSM8757920 LBM_H3K27ac_rep1 LBM_H3K27ac
- GSM8757921 LPM_H3K27me3_rep1 LPM_H3K27me3
- GSM8757922 LPM_H3K27ac_rep1 LPM_H3K27ac
- GSM8757927 ExpLBM_H3K27me3_rep2 ExpLBM_H3K27me3
- GSM8757928 ExpLBM_325_rep2
- GSM8757929 414C2day0_H3K27me3_rep2 414C2day0_H3K27me3
- GSM8757930 414C2day0_H3K27ac_rep2 414C2day0_H3K27ac
- GSM8757931 LBM_H3K27me3_rep2 LBM_H3K27me3
- GSM8757932 LBM_H3K27ac_rep2 LBM_H3K27ac
- GSM8757933 LPM_H3K27me3_rep2 LPM_H3K27me3
- GSM8757934 LPM_H3K27ac_rep2 LPM_H3K27ac
- GSE262419 Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes 4558 samples shares cell-derived, pluripotent, stem
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, stem
- GSE239775 Quantification of Systemic Inflammation by a Gene Score Uncovers Relevant Features on Acutely Decompensated Cirrhosis 1177 samples shares cut, stem
- GSE243299 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia 112 samples shares cut, modeling
- GSE130955 Global skin gene expression profile of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive immunity profile 91 samples shares cut, stem
- GSE300793 Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma [RNAseq] 57 samples shares cut, stem
- GSE243298 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C] 35 samples shares cut, modeling
- GSE248287 Remodeling of the immune microenvironment is linked to adverse outcome in pediatric T cell acute lymphoblastic leukemia 34 samples shares cut, modeling
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.