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Cut&Tag of GLI3 binding during early organoid development

ABSTRACT: Cut&Tag of GLI3 binding during early organoid development

PROVIDER: PRJEB55465 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10092480_1.fastq.gz	Fastqsanger.gz
	ERR10092480_2.fastq.gz	Fastqsanger.gz
	ERR10092481_1.fastq.gz	Fastqsanger.gz
	ERR10092481_2.fastq.gz	Fastqsanger.gz
	ERR10092482_1.fastq.gz	Fastqsanger.gz

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Cut&Tag of GLI3 binding during early organoid development

Project description:To investigate GLI3 TF targets during organoid fate decisions, we performed Cut&Tag of GLI3 binding

2022-08-28 | E-MTAB-12006 | biostudies-arrayexpress

The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

Project description:Purpose: This study seeks to determine whether GLI3 is required to recruit the SMARCC1 complex to GLI enhancers in the limb. Methods: To determine if Gli3 is required to recruit SMARCC1 to its anhancers, we performed differential chromatin binding to compare SMARCC1 binding in control and Gli3 mutants. We performed Cut&Run for SMARCC1 binding on individually genotyped E11.5 (40-43s) anterior forelimb pairs from control (Gli3+/+; 3 replicates) and Gli3 mutant (Gli3-/-; 4 replicates) embryos. Results: We found that there is no major difference in SMARCC1 binding in Gli3-mutants compared to controls.

2024-02-03 | GSE224508 | GEO

HCT116_SMARCA4 CUT&Tag

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CUT&TAG of OE19 cell line

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CUT&TAG of OE19 cell line

Project description:To map the chromatin binding sites for various factors in OE19 cells, we performed CUT&TAG.

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Multiome experiment from GLI3 KO brain organoids

Project description:To study the effect of GLI3 knockout on early brain organoid development, we collected single-cell multiome data from 18 day old brain organoids

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Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

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scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

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HCT116_SMARCA4 CUT&Tag

Project description:To investigate the enrichment of SMARCA4-R1157W mutation on downstream target gene promoters, we performed CUT&Tag experiments in HCT116 cells.

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CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding sites in HEK293 cells

Project description:To reveal the role of MCM8 in suppressing R-loop accumulation, we performed the CUT&TAG assay using the S9.6 antibody to map genome-wide R-loops in Mcm8 wildtype MEFs and Mcm8 knockout MEFs. We also conducted the CUT&TAG assay to detect genome-wide R-loops in Ddx5 downregulated MEFs by adenovirus infection and in control MEFs. To investigate the underlying molecular mechanism of MCM8 suppressing R-loops, we conducted the DNA sequencing of libraries from CUT&TAG assay using the antibody against FLAG in HEK293 cells transfected with FLAG-MCM8 plasmid and using the S9.6 antibody in HEK293 cells. Besides, an IgG control and control of RNH1 overexpression were included.

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