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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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In vivo transcriptional activation using CRISPR-Cas9 in Drosophila

ABSTRACT: Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together. RNA from Drosophila cells following CRISPR/Cas9-based activation of Twist, Snail, or Twist and Snail together, compared with non-targeting sgRNA. Two biological replicates for each experiment

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Norbert Perrimon

PROVIDER: E-GEOD-71430 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila.

Lin Shuailiang S Ewen-Campen Ben B Ni Xiaochun X Housden Benjamin E BE Perrimon Norbert N

Genetics 20150805 2

A number of approaches for Cas9-mediated transcriptional activation have recently been developed, allowing target genes to be overexpressed from their endogenous genomic loci. However, these approaches have thus far been limited to cell culture, and this technique has not been demonstrated in vivo in any animal. The technique involving the fewest separate components, and therefore the most amenable to in vivo applications, is the dCas9-VPR system, where a nuclease-dead Cas9 is fused to a highly ...[more]

PMID: 26245833

Similar Datasets

In vivo transcriptional activation using CRISPR-Cas9 in Drosophila

Project description:Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together.

2015-08-10 | GSE71430 | GEO

Genome-wide analysis of gene expression in normal and fibrotic mouse kidneys with and without Twist1 or with and without Snai1(Snail) expression in proximal tubular epithelial cells

Project description:In this study mice were engineered to specifically delete Twist1 or Snail expression in proximal tubular epithelial cells of the kidney (ggt-cre+;Twist flox/flox and ggt-cre+;Snail flox/flox ). These mice and control mice (ggtcre-;Twist flox/flox: these express Twist1, and ggtcre-;Snail flox/flox:these express Snail) were subjected to unilaterial ureteric obstruction. This experiment allows for the collection and analysis of expression in contralateral healthy (HK) kidney adn obstructed disease (DK) kidney. Total RNA was isolated from the contralateral healthy (HK) and obstructed disease (DK) kidneys of 3 mice with ggt-cre-;Twist flox/flox genotype (Wildtype like) and 4 mice with ggt-cre+;Twist flox/flox genotype (loss of Twist1 in proximal tubular epithelial cells), 3 mice with ggt-cre-;Snail flox/flox genotype (Wildtype like) and 3 mice with ggt-cre+;Snail flox/flox genotype (loss of Snail in proximal tubular epithelial cells). Total RNA was also isolated from kidneys of completely healthy mice: 3 mice ggt-cre-;WT, 3 mice ggt-cre+;WT, 3 mice ggt-cre+;Twist flox/flox and 3 ggt-cre+;Snail flox/flox

2015-08-03 | E-GEOD-60685 | biostudies-arrayexpress

Genome-wide analysis of gene expression in mouse pancreas tumors

Project description:Genetically engineered mice developed spontaneous pancreas cancer (Pdx-Cre;LSL-KRASG12D;P53Mut). Mice were also engineered to develop similar spontaneous pancreas cancer without Twist or Snail (conditional gene knockout). The pancreas tumors were harvested and analysed for gene expression profiles comparisons. Total RNA was isolated from the pancreas tumors of 2 mice with wild-type Twist and Snail, from 2 mice without Twist expression in the pancreas, and from 2 mice without Snail expression in the pancreas.

2015-11-20 | E-GEOD-66981 | biostudies-arrayexpress

Snail and Twist expression in HMLE and MCF10A cells

Project description:Snail and Twist are two EMT inducer, expression of Snail or Twist will induce EMT in HMLE and MCF10A cells. By introducing Snail or Twist in HMLE and MCF10A cells, which lack the expression of these two proteins, will identify the genes are induced during EMT. We used microarray analysis to compare the gene expression profiles between the mammamry epithleial cells and the cells undergone EMT.

2020-01-10 | GSE143349 | GEO

Genome-wide analysis of gene expression in normal and fibrotic mouse kidneys with and without Twist1 or with and without Snai1(Snail) expression in proximal tubular epithelial cells

2015-08-03 | GSE60685 | GEO

ChIP-chip mapping of twist, dorsal, snail, weckle in Drosophila embryos

Project description:We performed ChIP-chip analysis using sheared chromatin isolated from Drosophila embryos of 1-3 hours in age. Keywords: high-resolution tiling array, drosophila, twist, dorsal, snail, weckle ChIP-chip of twist, dorsal, snail, and weckle

2011-02-28 | E-GEOD-26285 | biostudies-arrayexpress

Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. RNA-seq was performed to observe the effects of MED1 deletion on gene expression in 697.

2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress

Genome-wide profiling of MED1 and RUNX1 binding in MED1 wild-type and knockout human pre-B ALL cell line 697 (ChIP-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. ChIP-seq was performed to identify genomic regions responsible for recruitment of MED1 and RUNX1.

2020-05-13 | E-MTAB-8177 | biostudies-arrayexpress

RNA-Seq of WT Flp-In T-REx 293 and UPF3B knockout cell lines with additional siRNA-mediated control or UPF3A knockdowns

Project description:UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an exon-exon junction activates NMD and leads to the degradation of the mRNA. To investigate the role of UPF3B and UPF3A in NMD, we have generated UPF3B knockout human Flp-In T-REx 293 cells using CRISPR-Cas9. We generated RNA-Sequencing data for wildtype and UPF3B KO cells with additional siRNA-mediated knockdown of Luciferase (Luc) as control or UPF3A.

2022-04-25 | E-MTAB-10711 | biostudies-arrayexpress

Twist, Snail and Zeb1 targets in the context of TrkB

Project description:RK3E cells expressing TrkB and BDNF: comparison control (sh-EGFP) and sh-Twist, sh-Snail or sh-Zeb1

2011-10-12 | E-MTAB-456 | biostudies-arrayexpress