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ABSTRACT: CUT&-Tag assay on wheat 4 DAP seeds

PROVIDER: PRJNA956711 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24201346_1.fastq.gz	Fastqsanger.gz
	SRR24201346_2.fastq.gz	Fastqsanger.gz
	SRR24201347_1.fastq.gz	Fastqsanger.gz
	SRR24201347_2.fastq.gz	Fastqsanger.gz
	SRR24201348_1.fastq.gz	Fastqsanger.gz

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Project description:CUT&Tag assay

| PRJNA1243281 | ENA

CUT&TAG analysis of H3K27ac in granulosa cells from control and POI patients

Project description:To reveal the role of NCOA7 in cellular senescence, we performed the CUT&TAG assay using the H3K27ac antibody to map acetylation in granulosa cells from control and POI patients. We conducted the DNA sequencing of libraries from CUT&TAG assay using the H3K27ac antibody in human primary granulosa cells.

2023-12-25 | GSE250222 | GEO

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.

2024-05-30 | GSE254352 | GEO

Investigation of potential targets of TaSPL6-D in wheat

Project description:Here, we performed the cleavage under targets and tagmentation (CUT&Tag) assay, a recently developed technology for protein-DNA interaction, in protoplasts extracted from wheat root tissues to genome-widely identity the potential targets of TaSPL6-D. Using CUT-Tag-seq, we obtained 7,403 confidential peaks from two biological replicates, with which 2688 genes was associated. Zooming in the promoter region, GTAC motif was significantly enriched in the peaks. Gene Ontology analysis of genes with binding peaks in the promoter region revealed that, the most enriched gene term is ‘response to temperature/heat stimuli’, which is consistent with previous studies on the functions of TaSPL6-D orthologs in rice and Arabidopsis. The following enriched terms are genes of ‘regulation of response to salt stress’, ‘regulation of response to osmotic stress’, and particularly ‘positive regulation of response to salt stress’, implying TaSPL6-D is an upstream regulator of salt stress response.

2024-03-10 | GSE245464 | GEO

CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line

Project description:To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to DON treatment. we performed CUT&Tag sequencing in murine PDAC cells. sgPaxip1 cells were treated in Cont group or DON group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

2025-03-05 | GSE246545 | GEO

CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line

Project description:To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to glutamine starvation. we performed CUT&Tag sequencing in murine PDAC cells. KPC1199 cells were treated in Cont group or Low Gln group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

2024-12-31 | GSE229903 | GEO

proteome sequencing of Triticum aestivum L

Project description:The 15 DAP and 20 DAP endosperm samples from WT and lgp1 seeds were used for tandem mass tag (TMT) proteasome analysis. Three biological replicates were used for each genotype

2021-08-01 | PXD027683 |

Gene expression profiling via LongSAGE in a non-model plant species: A case study in seeds of Brassica napus

Project description:Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression in about 10 % of all matched genes, with a total abundance of 44 %, showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6 % of A. thaliana genes were matched by Brassica ESTs detected by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development. Seeds from 2 developmental stages of B. napus were used to construct 2 LongSAGE libraries, 23 days after pollination (23 DAP) and 35 days after pollination (35 DAP). Biological replicates and confirmation: Cloning of tag-amplified RT-PCR products, Real-time RT-PCR

2009-02-15 | E-GEOD-14313 | biostudies-arrayexpress

Genome-wide mapping of MEF2A binding sites by CUT&Tag-seq in chicken primary myoblasts

Project description:In this study, CUT&Tag-seq technology was employed to investigate MEF2A binding sites across the entire genome of chicken primary myoblasts. CUT&Tag was performed using CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. Antibody targeting MEF2A as well as IgG were used.The final DNA library on a HiSeq PE150 platform was subjected for the analyses. This study provides a wide landscape of MEF2A target genes from chicken primary myoblasts, which supports the active role of MEF2A in avian muscle development.

2023-12-05 | GSE249097 | GEO

CUT&Tag of mouse primary B cells transduced Pbx1 overexpression plasmid.

Project description:We performed the cleavage under targets and tagmentation (Cut & tag) assay followed by sequencing enriched DNA fragments to reveal the direct downstream targets of Pbx1. Firstly, we overexpressed Pbx1b with Pbx1b-IRES-GFP retrovirus in murine peripheral B cells to ensure the yields of DNA fragments. CUT & tag libraries were generated following instructions of the manufacturer’s protocol (Vazyme; cat TD901-01) and the Pbx1 antibody (CST; cat 4342) was used for signal enrichment.

2023-03-26 | E-MTAB-12769 | biostudies-arrayexpress

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