Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids [RNA-seq]
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 6 × RNA-seq-H9_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.
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 GSE277920_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1164758 and SRA study SRP534477. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 11 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
- GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares accessibility, hesc-derived, regulatory, chromatin, organoids, dynamics, kidney
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares chromatin, organoids, rna-seq
- GSE316391 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq] 32 samples shares accessibility, chromatin, rna-seq
- GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares regulatory, chromatin, dynamics
- GSE341753 Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis [RNA-Seq] 12 samples shares regulatory, rna-seq
- GSE327727 D-SPIN constructs regulatory network models from scRNA-seq revealing organizing principles of perturbation response 194 samples shares regulatory, rna-seq
- 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
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.