Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exome-seq of Jak2VF erythroid progenitors cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 17 weeks post transplantation

ABSTRACT: Exome sequencing of erythroid progenitors from Dnmt3a-Cas9-GFP+/- vs. emp-Cas9-GFP+/- controls.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Sebastien Jacquelin

PROVIDER: E-MTAB-7243 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls one week and five weeks post methylcellulose plating

Project description:Determination of differentially expressed genes in culture-derived hematopoietic stem cell progenitors (LSK) between Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-cas9.

2018-10-29 | E-MTAB-6635 | biostudies-arrayexpress

RNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation

Project description: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.

2018-10-29 | E-MTAB-6644 | biostudies-arrayexpress

ATAC-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation

Project description:Determination of chromatin accessibility in hematopoietic stem cell progenitors (LSK) of Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-Cas9 8 weeks post transplantation.

2018-10-29 | E-MTAB-6649 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run6)

Project description:Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish. Each loci has a control, where no Cas9/sgRNA were injected. This is amplicon sequencing with Illumina, after PCR amplification. Data was processed with ampliCan R package version 1.1.1.

2017-12-25 | E-MTAB-6310 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 9)

2017-12-15 | E-MTAB-6357 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 10)

2017-12-15 | E-MTAB-6358 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 8)

2017-12-15 | E-MTAB-6356 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 7)

2017-12-15 | E-MTAB-6355 | biostudies-arrayexpress

RNA-seq of engineered K562 cell line by CRISPR/Cas9 generation of t(7;12)(q36;p13) chromosomal translocation

Project description:We recreated the t(7;12) translocation in K562 cells by CRISPR/Cas9 to understand its effects on haematopoietic cells, which is of relevance to understand how this cytogenetic abnormalities causes and promotes acute leukaemia in infants. Wild-type K562 were edited by electroporation of ribonucleoprotein complexes consisting of Cas9 enzyme and two guide RNAs targeting patient-specific breakpoint loci. K562 electroporated with Cas9 enzyme only were used as control. Edited K562 harbouring the t(7;12) were single-cell cloned to obtain homogeneous populations (hereby referred to as K562-t(7;12)). We performed RNA sequencing analysis of K562-t(7;12) compared to K562 control to uncover transcriptional changes associated with the translocation.

2022-09-06 | E-MTAB-11851 | biostudies-arrayexpress

Cas9 target DNA specificity in vitro and in vivo (S. cerevisiae)

Project description: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, we compared mismatch tolerance for a specific Cas9::gRNA complex in vitro and in vivo (in Saccharomyces cerevisiae). A variety of truncated and full-length gRNAs (with 17, 18, and 20 nucleotides of complementarity sequence) were used. In each case, we observed notable differences between in vitro and in vivo Cas9 cleavage specificity profiles, with a more stringent effect of mismatches on activity seen in vivo. Increased specificity of the 18 nt complementarity truncated gRNA was evident in vivo, but not in vitro. Overall, this study highlights differences in the specificity of Cas9 cleavage between controlled in vitro conditions and complex and chromatinized in vivo conditions. We adapted a previous high throughput sequencing approach (doi: 10.1093/nar/gku1102) to assess the effects of single base variants in vivo. We used a polymorphic random variant library matched to a specific trigger sequence (for which we used a segment from the C. elegans unc-22 gene, previously designated âunc-22Aâ (doi: 10.1093/nar/gku1102). Cas9 in vivo and in vitro assays were carried out with four different gRNAs incorporating sequence from the unc-22A trigger segment. The four segments incorporate 17 nt, 18 nt, 20 nt, and 20+G nt of unc-22A complementarity respectively. The retention is calculated based on PMID: 25399416. File names denote the experiment-> gRNAname_gRNAlength_(invitro or invivo)_(incubation or induction time)_IlluminaRunID.dat The files contain all normalized sequences in column one with their calculated retentions in column 2.

2016-06-10 | E-GEOD-79667 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data