Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 25 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
- 25 samples: 6 × RNA-seq-H9_D vs 6 × ATAC-seq-H9_D vs 6 × ATAC-seq-H9_DOT1L_KO_D vs 5 × RNA-seq-H9_DOT1L_KO-DGroups 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 GSE277922_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 PRJNA1164746 and SRA study SRP534473. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 23 samples.
How we read this: 4 replicated groups read from 25 sample titles; they account for 23 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.
- GSM8534705 RNA-seq-H9
- GSM8534706 RNA-seq-H9_D14 RNA-seq-H9_D
- GSM8534707 RNA-seq-H9_D16 RNA-seq-H9_D
- GSM8534708 RNA-seq-H9_D3 RNA-seq-H9_D
- GSM8534709 RNA-seq-H9_D6 RNA-seq-H9_D
- GSM8534710 RNA-seq-H9_D8 RNA-seq-H9_D
- GSM8534711 RNA-seq-H9_D9 RNA-seq-H9_D
- GSM8534712 RNA-seq-H9_DOT1L_KO-D16 RNA-seq-H9_DOT1L_KO-D
- GSM8534713 RNA-seq-H9_DOT1L_KO-D19 RNA-seq-H9_DOT1L_KO-D
- GSM8534714 RNA-seq-H9_DOT1L_KO-D6 RNA-seq-H9_DOT1L_KO-D
- GSM8534715 RNA-seq-H9_DOT1L_KO-D8 RNA-seq-H9_DOT1L_KO-D
- GSM8534716 RNA-seq-H9_DOT1L_KO-D9 RNA-seq-H9_DOT1L_KO-D
- GSM8534717 ATAC-seq-H9
- GSM8534718 ATAC-seq-H9_D14 ATAC-seq-H9_D
- GSM8534719 ATAC-seq-H9_D16 ATAC-seq-H9_D
- GSM8534720 ATAC-seq-H9_D3 ATAC-seq-H9_D
- GSM8534721 ATAC-seq-H9_D6 ATAC-seq-H9_D
- GSM8534722 ATAC-seq-H9_D8 ATAC-seq-H9_D
- GSM8534723 ATAC-seq-H9_D9 ATAC-seq-H9_D
- GSM8534724 ATAC-seq-H9_DOT1L_KO_D12 ATAC-seq-H9_DOT1L_KO_D
- GSM8534725 ATAC-seq-H9_DOT1L_KO_D16 ATAC-seq-H9_DOT1L_KO_D
- GSM8534726 ATAC-seq-H9_DOT1L_KO_D19 ATAC-seq-H9_DOT1L_KO_D
- GSM8534727 ATAC-seq-H9_DOT1L_KO_D6 ATAC-seq-H9_DOT1L_KO_D
- GSM8534728 ATAC-seq-H9_DOT1L_KO_D8 ATAC-seq-H9_DOT1L_KO_D
- GSM8534729 ATAC-seq-H9_DOT1L_KO_D9 ATAC-seq-H9_DOT1L_KO_D
- GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares regulatory, chromatin, dynamics
- GSE270602 Comparative analysis of chromatin accessibility during chondrogenesis and in osteoarthritis 26 samples shares accessibility, chromatin
- GSE204912 Mapping genotypes to chromatin accessibility profiles in single cells 55 samples shares accessibility, chromatin
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares accessibility, chromatin
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares accessibility, chromatin
- GSE325835 BATF3 regulates chromatin accessibility during CD8+ T lymphocyte differentiation 36 samples shares accessibility, chromatin
- GSE282760 Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [ChIP-seq] 36 samples shares chromatin, dynamics
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares chromatin, organoids
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.