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Homo sapiens

ABSTRACT: H3K27me3 CUT&Tag in keloid derived fibroblasts with or without LSP1P5 knocked down

PROVIDER: PRJNA972833 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24556774_1.fastq.gz	Fastqsanger.gz
	SRR24556774_2.fastq.gz	Fastqsanger.gz
	SRR24556775_1.fastq.gz	Fastqsanger.gz
	SRR24556775_2.fastq.gz	Fastqsanger.gz
	SRR24556776_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:RNA-sequencing of keloid derived fibroblasts with or without LSP1P5 knocked down

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Decoding the Genomic regions that R-loop distributed associated with A3B expression

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Project description:In order to study the mechanism of nuclear PD-L1 in uveal melanoma, we knocked down PD-L1 and applied RNA-seq and CUT&Tag to identify its target genes in uveal melanoma.

2023-04-04 | GSE202884 | GEO

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

Project description:We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis in chemical reprogramming, we construct Flag-Rxra-OE cells. We performed Flag-Rxra CUT&Tag with reprogramming intermediate, also we performed CUT&Tag with or without CD treatment for reprogramming intermediates.

2023-05-03 | GSE208767 | GEO

YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, CUT&TAG sequencing for YAP, H3K27ac, and H3K27me3

Project description:Cleavave Under Targets and Tagmentation (CUT&TAG) sequencing for YAP, H3K27ac, and H3K27me3 of tongue epithelia-derived, transgene-selected primarily cultured cells from control mice or transgenic mice expressing HPV16E6-E7 and YAP1S127A

2024-09-09 | GSE276779 | GEO

A microarray of circular RNAs in human keloid dermal fibroblasts

Project description:To further explore the expression of circular RNAs in keloid，we have completed the Arraystar Human circRNA Array V2 analysis of the 8 samples，including 4 patients-derived keloid dermal fibroblasts and 4 normal dermal fibroblasts.

2022-02-23 | GSE184097 | GEO

Effect of LINC00899 depletion on histone mark enrichment in HeLa cells

Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.

2019-03-29 | E-MTAB-7419 | biostudies-arrayexpress

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

Project description:We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

2022-03-31 | GSE199611 | GEO

Cut&Run in Drosophila melanogaster control, mutant and knockdown ovaries

Project description:H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.

2021-12-10 | GSE174250 | GEO

Transcriptomic analysis of keloid fibroblasts demonstrates reduced expression of vitamin D binding partner Retinoid-X receptor α: Implications for clinical treatment

Project description:Keloids are benign fibroproliferative tumours resulting from skin damage such as trauma, burns or surgery. Keloids are more prevalent in populations with darkly pigmented skin. Links between skin pigmentation and vitamin D production have been established and some studies indicate involvement of vitamin D signalling in keloid pathology. This study assessed the impact of paricalcitol (a selective vitamin D signalling activator) on fibroblasts derived from keloid and normal skin, to further investigate the role and potential clinical relevance of vitamin D signalling in keloid pathology. Analysis of keloid and normal skin tissue using immunohistochemistry demonstrated a significant reduction of nuclear vitamin D receptor (VDR) in keloid tissue. After treatment with paricalcitol, nuclear VDR was increased in both keloid and normal fibroblasts. RNA sequencing of normal fibroblasts treated with paricalcitol demonstrated significant changes in gene expression, with many upregulated genes identified to have anti-fibrotic effects. However, paricalcitol failed to alter gene expression in Keloid fibroblasts. To investigate this further, we performed RNA sequencing of normal and keloid fibroblasts and found that retinoid-X receptor α (RXRα), a key binding partner of VDR required for downstream transcriptional activation, is significantly downregulated in keloid fibroblasts. Our results indicate that paricalcitol can effectively activate VDR translocation to the nucleus but is unable to effect change at the transcriptional level in keloid fibroblasts, most likely due to the reduced expression of RXRα. This suggests Vitamin D signalling may be aberrant in keloids, and that supplementation with Vitamin D alone would likely be ineffective in restoring signalling. Keywords: Keloid, Vitamin D receptor, Paricalcitol, Retinoid-X receptor α

2024-12-03 | GSE282479 | GEO

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