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Series GSE198467

Query DataSets for GSE198467

Status

Public on Sep 20, 2022

Title

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Organism

Mus musculus

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Probing epigenomic marks such as histone modifications at a single cell level in thousands of cells has been recently enabled by technologies such as scCUT&Tag. Here we developed a multimodal and optimized iteration of scCUT&Tag called nano-CT (for nano-CUT&Tag) that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. nano-CT is compatible with starting materials as low as 25 000 cells and has significantly higher resolution than scCUT&Tag, with a 16-fold increase in the number of fragments per cells. We used nano-CT to simultaneously profile chromatin accessibility, H3K27ac and H3K27me3 in a complex tissue - juvenile mouse brain. The obtained multimodal dataset allowed for discrimination of more cell types/states that scCUT&Tag, and inference of chromatin velocity between ATAC and H3K27ac in the oligodendrocyte (OL) lineage. In addition, we used nano-CT to deconvolute H3K27me3 repressive states and infer two sequential waves of H3K27me3 repression at distinct gene modules during OL lineage progression. Thus, given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in different biological systems at single cell level.

Overall design

Multimodal profiling of two histone modifications and open chromatin in single cells by nano-CT technology

Web link

https://doi.org/10.1038/s41587-022-01535-4

Contributor(s)

Bartosovic M, Castelo-Branco G

Citation(s)

36536148

Submission date

Mar 11, 2022

Last update date

Jan 09, 2023

Contact name

Marek Bartosovic

E-mail(s)

bartosovic.marek@gmail.com

Organization name

Karolinska Institute

Lab

Goncalo Castelo-Branco

Street address

Solnavagen 9

City

Stockholm

ZIP/Postal code

12432

Country

Sweden

Platforms (1)

GPL24247

Illumina NovaSeq 6000 (Mus musculus)

Samples (5)

More...

GSM5949205	nanoCT H3K27me3
GSM5949206	nanoCT ATAC H3K27ac H3K27me3 rep 1
GSM5949207	nanoCT H3K27ac H3K27me3 rep 1

Relations

BioProject

PRJNA815344

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE198467_ATAC_Seurat_object_clustered_renamed.Rds.gz	280.6 Mb	(ftp)(http)	RDS
GSE198467_ATAC_Seurat_object_clustered_renamed.h5seurat	292.8 Mb	(ftp)(http)	H5SEURAT
GSE198467_ATAC_cluster_AST_NT.bw	28.7 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_AST_TE.bw	27.7 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_BG.bw	9.7 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_CHP-EPE.bw	7.3 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_EXC1.bw	25.9 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_INH1.bw	21.3 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_INH2.bw	15.2 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_INH3.bw	6.8 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_MGL.bw	46.7 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_MOL.bw	25.0 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_OEC.bw	9.4 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_OPC.bw	11.0 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_RGC.bw	7.0 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_VEC.bw	31.3 Mb	(ftp)(http)	BW
GSE198467_ATAC_cluster_VLMC.bw	12.6 Mb	(ftp)(http)	BW
GSE198467_ATAC_fragments.tsv.gz	473.1 Mb	(ftp)(http)	TSV
GSE198467_ATAC_markers.csv.gz	888.7 Kb	(ftp)(http)	CSV
GSE198467_H3K27ac_Seurat_object_clustered_renamed.Rds.gz	1.1 Gb	(ftp)(http)	RDS
GSE198467_H3K27ac_Seurat_object_clustered_renamed.h5seurat	1.1 Gb	(ftp)(http)	H5SEURAT
GSE198467_H3K27ac_cluster_ABC.bw	6.3 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_AST3.bw	21.4 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_AST4.bw	27.1 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_AST_NT.bw	160.8 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_AST_TE.bw	155.4 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_BG.bw	44.8 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_CHP.bw	19.1 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_EPE.bw	15.2 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_EXC1.bw	152.5 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_EXC2.bw	12.6 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_EXC3.bw	28.9 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_EXC4.bw	9.6 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_INH1.bw	86.1 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_INH2.bw	34.2 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_INH3.bw	35.5 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_INH4.bw	22.6 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_MAC.bw	15.0 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_MGL1.bw	92.6 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_MGL2.bw	7.4 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_MGL3.bw	9.2 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_MOL.bw	156.2 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_OEC.bw	30.5 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_OPC.bw	43.0 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_PER.bw	17.0 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_RGC.bw	35.2 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_VEC.bw	98.5 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_VLMC.bw	17.4 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_cluster_VSMC.bw	7.9 Mb	(ftp)(http)	BW
GSE198467_H3K27ac_fragments.tsv.gz	2.3 Gb	(ftp)(http)	TSV
GSE198467_H3K27ac_markers.csv.gz	4.8 Mb	(ftp)(http)	CSV
GSE198467_H3K27me3_Seurat_object_clustered_renamed.Rds.gz	472.8 Mb	(ftp)(http)	RDS
GSE198467_H3K27me3_Seurat_object_clustered_renamed.h5seurat	484.2 Mb	(ftp)(http)	H5SEURAT
GSE198467_H3K27me3_cluster_AST3.bw	8.8 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_AST_NT.bw	65.0 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_AST_TE.bw	55.6 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_BG.bw	18.9 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_CHP.bw	9.8 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_EPE.bw	5.7 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_EXC1.bw	8.0 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_EXC2.bw	28.5 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_EXC3.bw	31.3 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_EXC4.bw	3.6 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_INH1.bw	15.3 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_INH2.bw	13.3 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_INH3.bw	14.6 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_INH4.bw	11.0 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_MAC.bw	10.6 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_MGL1.bw	74.5 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_MGL2.bw	3.9 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_MOL.bw	84.0 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_OEC.bw	12.2 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_OPC.bw	10.0 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_PER.bw	6.7 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_RGC.bw	22.1 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_VEC.bw	52.2 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_cluster_VLMC.bw	10.1 Mb	(ftp)(http)	BW
GSE198467_H3K27me3_fragments.tsv.gz	965.5 Mb	(ftp)(http)	TSV
GSE198467_H3K27me3_markers.csv.gz	1.7 Mb	(ftp)(http)	CSV
GSE198467_single_modality_H3K27me3_01.clustering.Rds.gz	707.4 Mb	(ftp)(http)	RDS
GSE198467_single_modality_H3K27me3_01.clustering.h5seurat	806.3 Mb	(ftp)(http)	H5SEURAT
GSE198467_single_modality_H3K27me3_cluster_0.bw	30.9 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_1.bw	55.7 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_10.bw	9.1 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_11.bw	6.9 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_12.bw	8.4 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_2.bw	36.5 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_3.bw	32.5 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_4.bw	47.5 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_5.bw	25.4 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_6.bw	26.9 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_7.bw	9.8 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_8.bw	13.6 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_cluster_9.bw	15.3 Mb	(ftp)(http)	BW
GSE198467_single_modality_H3K27me3_fragments.tsv.gz	421.5 Mb	(ftp)(http)	TSV
GSE198467_single_modality_H3K27me3_markers.csv.gz	4.6 Mb	(ftp)(http)	CSV
GSE198467_single_modality_H3K27me3_markers_top.csv.gz	31.7 Kb	(ftp)(http)	CSV
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record