GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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) 37935964
Submission date Feb 06, 2023
Last update date Dec 06, 2023
Contact name Jorja Henikoff
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)
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)
BioProject PRJNA931915

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap