scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells
Single-cell RNA-seq · mouse · 46 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
- 46 samples: 46 samples, each with a distinct title — no replicated groupsGroups 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
- scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cellsNature methods · 2024
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 GSE249799_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 PRJNA1042935 and SRA study SRP473783. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 46 sample titles: 46 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.
- GSM7964458 scNanoSeq-CUT&Tag_K562_H3K4me3_Millipore_04_745
- GSM7964459 scNanoSeq-CUT&Tag_K562_H3K27ac_Abcam_ab4729
- GSM7964460 scNanoSeq-CUT&Tag_K562_H3K36me3_Abcam_ab9050
- GSM7964461 scNanoSeq-CUT&Tag_K562_H3K27me3_CST_9733T
- GSM7964462 scNanoSeq-CUT&Tag_K562_H3K9me3_Abcam_ab8898
- GSM7964463 scNanoSeq-CUT&Tag_K562_CTCF_Millipore_07_729
- GSM7964464 scNanoSeq-CUT&Tag_K562_RAD21_GeneTex_GTX106012
- GSM7964465 scNanoSeq-CUT&Tag_293T_H3K4me3_Millipore_04_745
- GSM7964466 scNanoSeq-CUT&Tag_293T_H3K27ac_Abcam_ab4729
- GSM7964467 scNanoSeq-CUT&Tag_293T_H3K36me3_Abcam_ab9050
- GSM7964468 scNanoSeq-CUT&Tag_293T_H3K27me3_CST_9733T
- GSM7964469 scNanoSeq-CUT&Tag_293T_H3K9me3_Abcam_ab8898
- GSM7964470 scNanoSeq-CUT&Tag_293T_CTCF_Millipore_07_729
- GSM7964471 scNanoSeq-CUT&Tag_293T_RAD21_GeneTex_GTX106012
- GSM7964472 scNanoSeq-CUT&Tag_GM12878_H3K4me3_Millipore_04_745
- GSM7964473 scNanoSeq-CUT&Tag_GM12878_H3K27ac_Abcam_ab4729
- GSM7964474 scNanoSeq-CUT&Tag_GM12878_H3K36me3_Abcam_ab9050
- GSM7964475 scNanoSeq-CUT&Tag_GM12878_H3K27me3_CST_9733T
- GSM7964476 scNanoSeq-CUT&Tag_GM12878_H3K9me3_Abcam_ab8898
- GSM7964477 scNanoSeq-CUT&Tag_GM12878_CTCF_Millipore_07_729
- GSM7964478 scNanoSeq-CUT&Tag_GM12878_RAD21_GeneTex_GTX106012
- GSM7964479 scNanoSeq-CUT&Tag_HG002_H3K4me3_Millipore_04_745
- GSM7964480 scNanoSeq-CUT&Tag_HG002_H3K27ac_Abcam_ab4729
- GSM7964481 scNanoSeq-CUT&Tag_HG002_H3K36me3_Abcam_ab9050
- GSM7964482 scNanoSeq-CUT&Tag_HG002_H3K27me3_CST_9733T
- GSM7964483 scNanoSeq-CUT&Tag_HG002_H3K9me3_Abcam_ab8898
- GSM7964484 scNanoSeq-CUT&Tag_HG002_CTCF_Millipore_07_729
- GSM7964485 scNanoSeq-CUT&Tag_HG002_RAD21_GeneTex_GTX106012
- GSM7964486 scNanoSeq-CUT&Tag_H9_H3K4me3_Millipore_04_745
- GSM7964487 scNanoSeq-CUT&Tag_H9_H3K27ac_Abcam_ab4729
- GSM7964488 scNanoSeq-CUT&Tag_H9_H3K36me3_Abcam_ab9050
- GSM7964489 scNanoSeq-CUT&Tag_H9_H3K27me3_CST_9733T
- GSM7964490 scNanoSeq-CUT&Tag_H9_H3K9me3_Abcam_ab8898
- GSM7964491 scNanoSeq-CUT&Tag_H9_CTCF_Millipore_07_729
- GSM7964492 scNanoSeq-CUT&Tag_H9_RAD21_GeneTex_GTX106012
- GSM7964493 scNanoSeq-CUT&Tag_HFF1_H3K4me3_Millipore_04_745
- GSM7964494 scNanoSeq-CUT&Tag_HFF1_H3K27ac_Abcam_ab4729
- GSM7964495 scNanoSeq-CUT&Tag_HFF1_H3K36me3_Abcam_ab9050
- GSM7964496 scNanoSeq-CUT&Tag_HFF1_H3K27me3_CST_9733T
- GSM7964497 scNanoSeq-CUT&Tag_HFF1_H3K9me3_Abcam_ab8898
+ 6 more — browse all 46 samples with per-sample file links →
- GSE286290 Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [CUT&RUN] 81 samples shares cut, chromatin
- GSE261788 AMAR-seq: automated multimodal sequencing of DNA methylation, chromatin accessibility, and RNA expression with single-cell resolution 83 samples shares single-cell, chromatin
- GSE232637 Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenetic maintenance 42 samples shares modification, single-cell
- GSE290486 Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland 37 samples shares single-cell, chromatin
- GSE255572 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 34 samples shares modification, chromatin
- GSE246859 ChromaFold predicts the 3D contact map from single-cell chromatin accessibility 3 samples shares single-cell, chromatin
- GSE253161 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_without_blocking] 1 samples shares single-cell, chromatin
- GSE172296 A myeloid maturation program initiated by nucleotide depletion during S phase [Cut & Run] 47 samples shares cut
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.