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Series GSE224579

Query DataSets for GSE224579

Status

Public on Jul 13, 2023

Title

Scalable single-cell profiling of chromatin modifications with sciCUT&Tag

Organisms

Homo sapiens; Mus musculus

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing precipitation-based methods. The efficiency of the method enabled chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution high-throughput single-cell chromatin profiling. We describe a pipeline for single-cell indexed CUT&Tag (sciCUT&Tag) that uses SNPs to facilitate doublet-cell removal and minimize batch effects. We illustrate the optimized protocol by analysis of mouse and human cell lines, as well as human peripheral blood mononuclear cells. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.

Overall design

We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

Contributor(s)

Greene J, Janssens DH, Wu SJ, Codomo CA, Minot S, Furlan SN, Ahmad K, Henikoff S

Citation(s)

Submission date

Feb 06, 2023

Last update date

Dec 06, 2023

Contact name

Jorja Henikoff

E-mail(s)

jorja@fhcrc.org

Phone

206-667-4850

Organization name

Fred Hutchinson Cancer Research Center

Department

Basic Sciences

Lab

Henikoff

Street address

1100 Fairview AV N, A1-162

City

Seattle

State/province

WA

ZIP/Postal code

98109-1024

Country

USA

Platforms (2)

GPL30173	NextSeq 2000 (Homo sapiens)
GPL30202	NextSeq 2000 (Homo sapiens; Mus musculus)

Samples (34)

More...

GSM7026602	BY_K27me3_KHRM3_10cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_10cpw_220802)
GSM7026603	BY_K27me3_KHRM3_20cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_20cpw_220802)
GSM7026604	BY_K27me3_KHRM3_40cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_40cpw_220802)

GSM7026605	BY_K27me3_KHRM3_5cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_5cpw_220802)
GSM7026606	PBMC_K27me3_A_0.125X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.125X_220527)
GSM7026607	PBMC_K27me3_A_0.25X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.25X_220527)
GSM7026608	PBMC_K27me3_A_0.5X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.5X_220527)
GSM7026609	PBMC_K27me3_A_1X_(220826_DJ_Hs_PBMC_K27me3_DJ_1X_220527)
GSM7026610	PBMC_K27me3_A_PE79_(220901_DJ_Hs_PBMC_K27me3_DJ_PE79_220523)
GSM7026611	PBMC_K27me3_AnB_0.125X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.125X_220527)
GSM7026612	PBMC_K27me3_AnB_0.25X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.25X_220527)
GSM7026613	PBMC_K27me3_AnB_0.5X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.5X_220527)
GSM7026614	PBMC_K27me3_AnB_1X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_1X_220527)
GSM7026615	PBMC_K27me3_AnB_PE79_(220901_DJ_Hs_PBMC_K27me3_DJnMM_PE79_220523)
GSM7026616	PBMC_K27me3_B_0.125X_(220826_DJ_Hs_PBMC_K27me3_MM_0.125X_220527)
GSM7026617	PBMC_K27me3_B_0.25X_(220826_DJ_Hs_PBMC_K27me3_MM_0.25X_220527)
GSM7026618	PBMC_K27me3_B_0.5X_(220826_DJ_Hs_PBMC_K27me3_MM_0.5X_220527)
GSM7026619	PBMC_K27me3_B_1X_(220826_DJ_Hs_PBMC_K27me3_MM_1X_220527)
GSM7026620	PBMC_K27me3_B_PE79_(220901_DJ_Hs_PBMC_K27me3_MM_PE79_220523)
GSM7026621	PBMC_K4me123_A_0.125X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.125X_220527)
GSM7026622	PBMC_K4me123_A_0.25X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.25X_220527)
GSM7026623	PBMC_K4me123_A_0.5X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.5X_220527)
GSM7026624	PBMC_K4me123_A_1X_(220826_DJ_Hs_PBMC_K4me123_DJ_1X_220527)
GSM7026625	PBMC_K4me123_A_PE79_(220901_DJ_Hs_PBMC_K4me123_DJ_PE79_220523)
GSM7026626	PBMC_K4me123_AnB_0.125X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.125X_220527)
GSM7026627	PBMC_K4me123_AnB_0.25X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.25X_220527)
GSM7026628	PBMC_K4me123_AnB_0.5X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.5X_220527)
GSM7026629	PBMC_K4me123_AnB_1X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_1X_220527)
GSM7026630	PBMC_K4me123_AnB_PE79_(220901_DJ_Hs_PBMC_K4me123_DJnMM_PE79_220523)
GSM7026631	PBMC_K4me123_B_0.125X_(220826_DJ_Hs_PBMC_K4me123_MM_0.125X_220527)
GSM7026632	PBMC_K4me123_B_0.25X_(220826_DJ_Hs_PBMC_K4me123_MM_0.25X_220527)
GSM7026633	PBMC_K4me123_B_0.5X_(220826_DJ_Hs_PBMC_K4me123_MM_0.5X_220527)
GSM7026634	PBMC_K4me123_B_1X_(220826_DJ_Hs_PBMC_K4me123_MM_1X_220527)
GSM7026635	PBMC_K4me123_B_PE79_(220901_DJ_Hs_PBMC_K4me123_MM_PE79_220523)

Relations

BioProject

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
GSE224579_RAW.tar	1.7 Gb	(http)(custom)	TAR (of BW)
GSE224579_scCUTnTag_protocol.pdf	7.3 Mb	(ftp)(http)	PDF
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file

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