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Transcriptome network analysis of Smug1 knock-out cells by using CRISPR/Cas9 system

ABSTRACT: Transcriptome network analysis of Smug1 knock-out cells by using CRISPR/Cas9 system

PROVIDER: PRJNA606327 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11075220_1.fastq.gz	Fastqsanger.gz
	SRR11075220_2.fastq.gz	Fastqsanger.gz
	SRR11075221_1.fastq.gz	Fastqsanger.gz
	SRR11075221_2.fastq.gz	Fastqsanger.gz
	SRR11075222_1.fastq.gz	Fastqsanger.gz

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Transcriptome network analysis of Smug1 knock-out cells by using CRISPR/Cas9 system

Project description:Purpose: To build a differential transcriptome network in Smug1 knock-out HepG2 hepatocarcinoma cells. Methods: Transcriptome analysis by the RNA-seq via mRNA pull-down. Results: We constructed transcriptome from Smug1 knock-out cells by using RNA-seq analysis. Nucleosome and miRNA related genes were highly enriched in Smug1 KO HepG2 cells. Conclusions: Smug1 regulate the gene expression related with nucleosome assembly and histone function.

2020-06-30 | GSE145210 | GEO

METTL21B is a novel human lysine methyltransferase of translation elongation factor 1A: discovery by CRISPR/Cas9 knock out

Project description:Lysine methylation is widespread on human proteins, however the enzymes that catalyse its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we report that human METTL21B is a protein methyltransferase, which methylates lysine 165 of eukaryotic translation elongation factor 1A (eEF1A). The CRISPR/Cas9 system was used to knock out putative protein methyltransferases METTL21B and METTL23 in K562 cells. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knock out of METTL21B, and the expected loss of lysine 79 methylation on knock out of EEF1AKMT1. No loss of eEF1A methylation was seen in the METTL23 knock out. Recombinant METTL21B was then shown to catalyse methylation on lysine 165 in eEF1A1 and eEF1A2 in vitro, confirming it as the methyltransferase responsible for this methylation site. Stable isotope labelling by amino acids in cell culture (SILAC) proteomic analysis revealed dysregulation of processes related to eEF1A function in knock outs of METTL21B and EEF1AKMT1, but specific dysregulation of ribosomal proteins in the knock out of METTL21B. This indicates a specific function for lysine 165 methylation of eEF1A in human. METTL21B is specific to vertebrates, with its target lysine showing similar evolutionary conservation. We suggest METTL21B be renamed eEF1A-KMT3. This is the first study to specifically generate CRISPR/Cas9 knock outs of the genes encoding putative protein methyltransferases, for the purpose of substrate discovery and site mapping. Our approach should prove useful for the discovery of further novel methyltransferases, and more generally for the discovery of sites for other protein-modifying enzymes.

2017-07-03 | PXD005497 | Pride

CRISPR/Cas9 knock down line

Project description:CRISPR/Cas9 knock down line

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Transcriptomic changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [RNA-seq]

Project description:Long non-coding RNAs (lncRNAs) are molecular switches in cellular differentiation, movement and in the reprogramming of cell states by altering gene expression patterns. However, in endothelial cells their role is not well understood. LINC00607 is an endothelial-enriched lncRNA. In order to uncover the functional relevance of LINC00607, an endothelial lentiCRISPR/Cas9-mediated knock-out was created and subjected to RNA- and ATAC-Seq, which revealed that LINC00607 is important for many pathways, among them VEGF- and TGF-beta-signalling.

2023-01-09 | GSE199877 | GEO

Chromatin accessibility changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [ATAC-seq]

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Leaf transcriptome of apple knock-out transgenic lines of MdAGG by CRISPR/Cas9 strategy

Project description:Leaf transcriptome of apple knock-out transgenic lines of MdAGG by CRISPR/Cas9 strategy

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Transcriptome changes in response to dDAVP stimulation in CRISPR/Cas9 mediated Camk2d knock-out mpkCCD cells

Project description:The Ca2+/CaM-dependent protein kinase 2-delta (CAMK2D) has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. RNA sequancing and quantitative proteomics analyses identified the expression of multiple CAMK2 isoforms, with CAMK2D being the most abundant in collecting duct cells. To investigate the role of CAMK2D in regulating RNA expression in response to vasopressin signaling, the transcriptome of CRISPR/Cas9-mediated Camk2d knock-out mpkCCD cells was profiled using RNA-Seq in the presence of vasopressin analogue dDAVP.

2023-06-01 | GSE228762 | GEO

Generation of VDR Knock-Out Mice via Zygote Injection of CRISPR/Cas9 System.

Project description:CRISPR/Cas9 system has become a new versatile technology for genome engineering in various species. To achieve targeted modifications at the same site in both human and mice genomes by a CRISPR/Cas9 nuclease, we designed two target sites in conserved regions of vitamin D receptor (VDR) gene, which cover more than 17 kb of chromosome region depending on the species. We first validated the efficacy of single sgRNA mediated gene specific modifications were 36% and 31% in HEK293T cells. Concurrently, targeted of the intervening genomic segments deletions were generated in chromosomes when two sgRNAs worked simultaneously. The large genomic DNA segments up to 23.4 Kb could be precisely deleted in human chromosomes. Subsequently, Cas9 mRNA and sgRNAs targeting VDRT1 and VDRT2 were co-microinjected into one-cell-stage embryos of C57BL/6 mice. Verified by T7E1 assay and DNA sequencing analysis, 12 mice showed VDR targeted disruption and 8 of which were biallelic knock-out, which demonstrated obvious phenotype of hair thinning. Furthermore, expression changes of Vitamin D metabolism genes in VDR-/-mice were detected. These results indicated that CRISPR/Cas9 mediated knock-out of VDR diminished its gene function in vivo. The off-target effects of CRISPR/Cas9 in VDR-/- founder mice were analyzed. Our results showed that CRISPR/Cas9 system could be employed to target the same sites in different species, when sgRNAs are designed within conserved regions, and therefore will be critically important and applicable for human disease model.

| S-EPMC5042489 | biostudies-literature

Transcriptomic changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [RNA-seq]

Project description:Transcriptomic changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [RNA-seq]

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Leaf transcriptome of apple knock-out transgenic lines of MdAGG by CRISPR/Cas9 strategy

Project description:Investigation of whole genome gene expression level changes in Acibenzolar-S-methyl-treated leaves of three MdAGG-knock-out transgenic lines (mdagg-2, mdagg-3 and mdagg-4) versus treated but non-transformed plants (wild-type)

2025-08-12 | GSE305162 | GEO

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