Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing
Single-cell RNA-seq · mouse · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × Control Experiments vs 3 × GM12878 RNA-seq vs 3 × HL-60 RNA-seqGroups 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 GSE68103_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 PRJNA281742 and SRA study SRP057508. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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.
- GSM1647121 GM12878 and Patski Mixture
- GSM1647122 GM12878 and HEK293T Mixture
- GSM1647123 GM12878 and HL-60 Mixture
- GSM1647124 Control Experiments Set 1 Control Experiments
- GSM1647125 Control Experiments Set 2 Control Experiments
- GSM1647126 Control Experiments Set 3 Control Experiments
- GSM1663002 GM12878 RNA-seq Replicate 1 GM12878 RNA-seq
- GSM1663003 GM12878 RNA-seq Replicate 2 GM12878 RNA-seq
- GSM1663004 GM12878 RNA-seq Replicate 3 GM12878 RNA-seq
- GSM1663005 HL-60 RNA-seq Replicate 1 HL-60 RNA-seq
- GSM1663006 HL-60 RNA-seq Replicate 2 HL-60 RNA-seq
- GSM1663007 HL-60 RNA-seq Replicate 3 HL-60 RNA-seq
- GSE278068 Nanobody-tethered transposition for dual profiling of chromatin accessibility and DNA methylation 201 samples shares accessibility, chromatin
- GSE261788 AMAR-seq: automated multimodal sequencing of DNA methylation, chromatin accessibility, and RNA expression with single-cell resolution 83 samples shares accessibility, chromatin
- GSE291229 Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC 19 samples shares accessibility, chromatin
- GSE278007 Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues 18 samples shares accessibility, chromatin
- GSE248813 MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility 52 samples shares accessibility, chromatin
- GSE255572 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 34 samples shares accessibility, chromatin
- GSE246859 ChromaFold predicts the 3D contact map from single-cell chromatin accessibility 3 samples shares accessibility, chromatin
- GSE274324 Thymic epithelia amplify noise in chromatin accessibility via p53 repression to impose immune tolerance 8 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.