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TranscriptomicsCas9 target DNA specificity in vitro and in vivo (S. cerevisiae)
Cas9, a CRISPR RNA-guided nuclease, has been rapidly adopted as a tool for biochemical and genetic manipulation of DNA. Although Cas9 offers remarkable specificity and versatility for genome manipulation, mis-targeted events occur. To extend the understanding of Cas9 target::homology requirements, w...
ORGANISM(S): synthetic construct 
2016-06-10 | E-GEOD-79667 | biostudies-arrayexpress
TranscriptomicsWeaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome
RNA-seq profiling of HeLa GFP cells treated with a Cas9 bearing either a scramble or a GFP guide to study the activation of inflammatory pathways 3 days after Cas9 delivery
ORGANISM(S): Homo sapiens 
2025-05-06 | E-MTAB-14730 | biostudies-arrayexpress
GenomicsCovalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Based on the hypothesis that, enhancing the local concentration of donor oligos could increase the correction rates, we generated and tested novel CRISPR-Cas9 systems, in which the DNA repair template is covalently conjugated to Cas9 (RNPD system). To validate our results from the HEK293T reporter c...
ORGANISM(S): Mus musculus 
2018-06-04 | E-MTAB-6808 | biostudies-arrayexpress
GenomicsRNA-guided Location and Function of the Cas9 CRISPR Endonuclease in Mammalian Cells
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated enzyme Cas9 is an RNA-guided nuclease that has been widely adapted for genome editing in eukaryotic cells. However, the in vivo target specificity of Cas9 is poorly understood and most studies rely on in silico predicti...
ORGANISM(S): Mus musculus 
2014-08-29 | E-GEOD-57650 | biostudies-arrayexpress
TranscriptomicsIn vivo transcriptional activation using CRISPR-Cas9 in Drosophila
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 activatio...
ORGANISM(S): Drosophila melanogaster 
2015-08-10 | E-GEOD-71430 | biostudies-arrayexpress
GenomicsA genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most previous studies have examined predicted off-target bi...
ORGANISM(S): Homo sapiens 
2015-03-04 | E-GEOD-61099 | biostudies-arrayexpress
ProteomicsCas9 immunoprecipatation-mass spectrometry (IP-MS)
In this study, we conducted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify Cas9-interacting proteins specific to the autophagic condition.
ORGANISM(S): Homo sapiens (Human) 
2025-03-20 | PXD054207 | Pride
Mass spectrometry Immunoprecipitation Cas9 
TranscriptomicsRNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls one week and five weeks post methylcellulose plating
Determination of differentially expressed genes in culture-derived hematopoietic stem cell progenitors (LSK) between Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-cas9.
ORGANISM(S): Mus musculus 
2018-10-29 | E-MTAB-6635 | biostudies-arrayexpress
TranscriptomicsRNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation
Determination of differentially expressed genes from in vivo hematopoietic stem cell progenitors (LSK) in Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-Cas9 8 weeks post transplantation.
ORGANISM(S): Mus musculus 
2018-10-29 | E-MTAB-6644 | biostudies-arrayexpress
TranscriptomicsATAC-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation
Determination of chromatin accessibility in hematopoietic stem cell progenitors (LSK) of Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-Cas9 8 weeks post transplantation.
ORGANISM(S): Mus musculus 
2018-10-29 | E-MTAB-6649 | biostudies-arrayexpress
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