Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening of a heptamer-type sgRNA library for therapeutic agents against hematological malignancies.

ABSTRACT: tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5′-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49578 | GEO | 2014/06/30

SECONDARY ACCESSION(S): PRJNA214325

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Screening of a heptamer-type sgRNA library for therapeutic agents against hematological malignancies.

Project description:tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5M-bM-^@M-2-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA. Changes in gene expression in HL60 cells were measured after 18-hour incubation in the absence or presence of one of five different heptamer-type sgRNAs. *Heptamer sequences requested but not provided by submitter

2014-06-30 | E-GEOD-49578 | biostudies-arrayexpress

Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease [sgRNA]

Project description:To identify potential single-guide RNA (sgRNAs) contaminants in the GMP HBG-sgRNA, we performed SMARTer smRNA-sequencing (Takara). 80.79% of the 5' spacer sequence perfectly matched the targeting sgRNA sequence and no evidence of contaminants sgRNAs that could target other genomic regions.

2024-08-21 | GSE275157 | GEO

Transcription profiling of human 293 cells

Project description:A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets. Experiment Overall Design: In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid.

2009-06-23 | E-GEOD-12524 | biostudies-arrayexpress

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

Project description:RNA-guided genome editing with the CRISPR-Cas9 system has great potential for basic and clinical research, but the determinants of targeting specificity and the extent of off-target cleavage remain insufficiently understood. Using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we mapped genome-wide binding sites of catalytically inactive Cas9 (dCas9) in HEK293T cells, in combination with 12 different single guide RNAs (sgRNAs). The number of off-target sites bound by dCas9 varied from ~10 to >1,000 depending on the sgRNA. Analysis of off-target binding sites showed the importance of the PAM-proximal region of the sgRNA guiding sequence and that dCas9 binding sites are enriched in open chromatin regions. When targeted with catalytically active Cas9, some off-target binding sites had indels above background levels in a region around the ChIP-seq peak, but generally at lower rates than the on-target sites. Our results elucidate major determinants of Cas9 targeting, and we show that ChIP-seq allows unbiased detection of Cas9 binding sites genome-wide 1.sgRNA1-6 binding sites were identified with ChipSeq by using HA antibody (there are 2 replicates for sgRNA1-3, one sample for sgRNA4-6,one control without sgRNA) 2.PCR products which amplifies " off-target genomic sites" were deep sequenced in the presence of WT Cas9+sgRNA or WT Cas9 alone( unique adaptor was used for each sgRNA and mixed for multiplex run)

2014-05-18 | E-GEOD-55887 | biostudies-arrayexpress

Expression data from human 293 cells

2009-06-15 | GSE12524 | GEO

TRIM28 controls the expression of the G2/M gene program and is required for mitosis execution in malignant pleural mesothelioma.

Project description:The goal of this experiment was to get deep into TRIM28 biological function in malignant pleural mesothelioma. To this end MSTO-211H cell line was infected by two different sgRNAs targeting TRIM28 and a non-targeting sgRNA as control. Two independent experiments were performed.RNA was collected 7 days after infection and changes in gene expression were analyzed by mRNA-seq.

2023-09-16 | E-MTAB-10942 | biostudies-arrayexpress

RNA-guided Location and Function of the Cas9 CRISPR Endonuclease in Mammalian Cells

Project description: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 predictions to define the potential off-target editing spectrum. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we delineate the genome-wide binding panorama of catalytically inactive Cas9 directed by two different single guide (sg) RNAs targeting the Trp53 locus. Cas9:sgRNA complexes are able to load onto multiple sites with short seed regions adjacent to 5’NGG3’ protospacer adjacent motifs (PAM). Examination of dmCas9 binding sites using two Trp53 targeting sgRNAs in Arf -/- MEF cell line (mouse).

2014-08-29 | E-GEOD-57650 | biostudies-arrayexpress

Potent and targeted activation of HIV-1 using the CRISPR/Cas9 activator Complex

Project description:Integration of the HIV-1 provirus in the host genome ensures a persistent supply of latently infected cells. This latent reservoir is recalcitrant to antiretroviral therapy (ART) making lifelong treatment the only option for patients. The â??shock and killâ?? strategy aims to eradicate latent HIV by reactivating proviral gene expression followed by ART treatment. Gene specific transcriptional activation can be achieved using the RNA-guided CRISPR-Cas9 system comprising small guide RNAs (sgRNAs) with a nuclease deficient Cas9 mutant (dCas9) fused to the VP64 transactivation domain (dCas9-VP64). Â We engineered this system to target 23 sites within the LTR promoter of HIV-1 and identified a â??hotspotâ?? for activation. We studied the functionality of activating sgRNAs to transcriptionally modulate the latent proviral genome across multiple differentÂ in vitroÂ latency cell models including several J-Lat, ACH2 J1.1 and the CEM T cell model comprising a single clonal population of integrated mCherry-IRES-Tat from a full-length HIV LTR (LChIT).Â While we observed variable responses of latent cell models to well-characterized chemical stimuli, we detected consistent efficient activation of latent virus mediated by activator sgRNAs.Â In addition, transcriptome analysis of chemically treated cells revealed massive non-specific gene dysregulation whereas by comparison, dCas9-VP64/sgRNAs induced specific activation of the integrated provirus.Â In conclusion, we show the potential for CRISPR-mediated gene activation systems to provide enhanced efficiency and specificity in a targeted latency reactivation strategy. This represents a promising approach to a â??functional cureâ?? of HIV/AIDS. Three experimental conditions (sgRNA control, TNF treated and sgRNA against the LTR of HIV-1) were analyzed in triplicate using two sequencing lanes

2016-08-20 | E-GEOD-72259 | biostudies-arrayexpress

Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches

Project description:We conducted a two-vector CRISPR/Cas13d proliferation screening experiment. The screening library contains 10,830 sgRNAs targeting 192 protein-coding genes and 234 lncRNAs, and the screening experiment was performed using a melanoma cell line A375. It provides a unique dataset to model Cas13d sgRNA efficiency and specificity. We designed a deep learning model, named DeepCas13, to predict the sgRNA on-target activity with high accuracy from sgRNA sequences and RNA secondary structures.

2023-01-16 | GSE183256 | GEO

Functional CRISPR Screen Identifies AP1-associated Enhancer regulating FOXF1 to modulate Oncogene-Induced Senescence

Project description:We carried out CRISPR-Cas9 functional screen focused on AP-1 bound enhancers that are activated upon oncogenic stress. The screen discovered Enh.AP1.OIS1 - an enhancer bound by AP1 that is required for activation of oncogene-induced senescence (OIS) response. We applied RNA-seq analysis to RASG12V-activated BJ cells transduced with either sgRNAs targeting AP-1 bound enhancer (sgRNA-69 or sgRNA71), or sgRNA targeting the target gene FOXF1 or non-targeting control sgRNA (sgNT)

2018-07-15 | GSE112458 | GEO

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