Single-cell mapping of regulatory DNA:Protein interactions
Single-cell RNA-seq · human · 14 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 14 samples: 13 distinct titles, 1 of them repeatedGroups 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 GSE296495_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 PRJNA1259498 and SRA study SRP583390. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 14 sample titles: 13 distinct titles with little repetition. 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.
- GSM8971607 K562 CTCF bulk D&D-seq
- GSM8971608 K562 GATA1 bulk D&D-seq
- GSM8971609 K562 GATA2 bulk D&D-seq
- GSM8971610 K562 JUN bulk D&D-seq
- GSM8971611 K562 P300 bulk D&D-seq
- GSM8971612 K562 SP1 bulk D&D-seq
- GSM8971613 K562 TAL1 bulk D&D-seq
- GSM8971656 K562 bulk CTCF D&D with WGS, primary template amplification (PTA)
- GSM8971657 single-cell D&D-seq, CA46 (CTCF) and K562 (GATA1) mixed
- GSM9381626 K562 CTCF bulk D&D-seq
- GSM9381627 K562 CTCF bulk D&D-seq primary Ab
- GSM9381628 K562 CTCF bulk D&D-seq secondary Ab
- GSM9381629 K562 GATA1 bulk D&D-seq primary Ab
- GSM9381630 K562 GATA1 bulk D&D-seq secondary Ab
- GSE327101 Single-Cell Multimodal Atlas Reveals Regulatory Programs in the Human Brain 220 samples shares single-cell, regulatory
- GSE299348 Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut 117 samples shares single-cell, protein
- GSE317257 Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Respons 35 samples shares interactions, mapping
- GSE277165 Single-cell transcriptomics and epigenomics point to CD58/CD59-CD2 interactions in controlling primary melanoma growth and immunity 20 samples shares interactions, single-cell
- GSE279180 Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [snRNA-seq] 16 samples shares interactions, mapping
- GSE253355 Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics 12 samples shares single-cell, mapping
- GSE305971 Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma 2105 samples shares single-cell
- GSE243013 A single-cell atlas of immune heterogeneity in anti-PD1-treated non-small cell lung cancer 243 samples shares single-cell
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.