Single-nucleus single-nucleus assay for transposase-accessible chromatin with sequencing analysis of in vitro cardiac differentiations
Single-nucleus RNA-seq · human · 22 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Samples
- 22 samples: 11 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.
- Paper
- Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac developmentCell genomics · 2024
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 GSE245498_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1028608 and SRA study SRP466612. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 11 replicated groups read from 22 sample titles; they account for 22 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.
- GSM7843921 D0, rep1 D0,
- GSM7843922 D0, rep2 D0,
- GSM7843923 2D D2, rep1 2D D2,
- GSM7843924 2D D2, rep2 2D D2,
- GSM7843925 2D D5, rep1 2D D5,
- GSM7843926 2D D5, rep2 2D D5,
- GSM7843927 2D D7, rep1 2D D7,
- GSM7843928 2D D7, rep2 2D D7,
- GSM7843929 2D D15, rep1 2D D15,
- GSM7843930 2D D15, rep2 2D D15,
- GSM7843931 2D D25, rep1 2D D25,
- GSM7843932 2D D25, rep2 2D D25,
- GSM7843933 3D D3, rep1 3D D3,
- GSM7843934 3D D3, rep2 3D D3,
- GSM7843935 3D D5, rep1 3D D5,
- GSM7843936 3D D5, rep2 3D D5,
- GSM7843937 3D D7, rep1 3D D7,
- GSM7843938 3D D7, rep2 3D D7,
- GSM7843939 3D D15, rep1 3D D15,
- GSM7843940 3D D15, rep2 3D D15,
- GSM7843941 3D D25, rep1 3D D25,
- GSM7843942 3D D25, rep2 3D D25,
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares single-nucleus, chromatin
- GSE247455 Single-nucleus chromatin and gene expression profiling across hundreds of skeletal muscle samples reveals context-specific regulation 8 samples shares single-nucleus, chromatin
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
- GSE327821 Single-molecule, single-cell profiling of linked chromatin states [Single_cell_CoCUT&Tag] 200 samples shares chromatin
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares chromatin
- GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares chromatin
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares chromatin
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares 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.