Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

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 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

ORGANISM(S): Homo sapiens

SUBMITTER: masayuki nashimoto

PROVIDER: E-GEOD-49578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

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 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.

2014-06-30 | GSE49578 | GEO

Identification of differentially expressed genes upon treatment with Eltrombopag in HL60 cells

Project description:Identification of differentially expressed genes upon treatment with Eltrombopag in HL60 cells. HL60 cells were untreated, or treated with 3ug/ml of Eltrombopag for 36 hrs in RPMI with 10% FBS HL60 cells were untreated, or treated with 3ug/ml of Eltrombopag for 36 hrs in RPMI with 10% FBS

2012-06-24 | E-GEOD-37580 | biostudies-arrayexpress

Nuclear proteomics of induced granulocytic differentiation

Project description:The nuclear proteome harbors a sheer number of regulatory proteins, including transcription factors (TFs). Profiling of nuclear proteome during all-trans-retinoid acid(ATRA)-induced differentiation of HL60 cells allows to unveil molecular mechanisms of granulocytic maturation. It is especially important to have an understanding of molecular perturbations at the early stages of the differentiation process. Applying proteomic profiling using isobaric labeling coupled with alkaline fractionation (TMT/2D) we identified 1860 nuclear proteins with high confidence (FDR<0.01, at least 2 unique peptides per protein). Among them 136, 226, 280, 312 and 241 proteins were found to be altered at 3, 6, 9, 12, and 72 h in HL60 cell nuclear fraction under ATRA treatment.

2023-03-11 | PXD035281 | Pride

Gene expression analysis of human microRNA-150 expression in PL21 and HL60 cells

Project description:Analysis of gene expression changes associated with lentiviral vector mediated expression of pre-microRNA-150 expression in the AML cell lines PL21 and HL60 cells. To identify genes, direct putative miRNA-150 targets, biological and molecular functions and pathways that distinguish cells that express miR-150 from those that do not. Total RNA isolated from HL60 or PL21 cells transduced with pre-microRNA-150 or empty vector control and assayed by gene expresssion analysis 20 days post transduction. Two replicates were performed for each condition (miR-150 and control) in each of two cell lines (HL60 and PL21).

2013-01-15 | E-GEOD-40147 | biostudies-arrayexpress

Transcription profiling by array of human HL60 cells treated with eicosapantaenoic acid (EPA) to investigate the effect on the signalling pathways involved in growth arrest/apoptosis

Project description:We investigated the effect of EPA on the signalling pathways involved in growth arrest/apoptosis in HL60 cells. EPA inhibited cell proliferation in HL60 cells in a dose dependent manner. Gene expression profiling of HL60 cells treated with EPA was performed by Affymetrix GeneChip. System and key markers of relevant pathways were verified at protein level by western blotting.

2008-11-11 | E-MEXP-1389 | biostudies-arrayexpress

Effects of gene scilencing of USP2 on expression profiles of HL60 cells

Project description:So far, we have found PMA induced USP2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937. To explore molecular function of USP2 in the cells, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA. HL60 derivatives continuously expressing shRNA for USP2 and control shRNA were treated with PMA (30nM) for 0, 1, 2, and 3 days. Total RNA was extracted from the cells and subjected to microarray experiments using Human Genome U133 GeneChips.

2013-08-27 | E-GEOD-20476 | 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

Gene regulation by phosphomimetic Myc and retinoic acid

Project description:We aimed to investigate the E-box and Max-independent functions of the oncogene Myc in gene regulation and differentiation of leukemic cells. Expression in HL60 leukemic cells of a mutant form of Myc with impaired Max and E-box interaction by replacing the phosphorylation sites of Pak2 kinase to aspartic acid (MycD), resulted in downregulation of 235 genes and, interestingly, upregulation of 586 genes. Eleven percent of the genes upregulated by MycD coincided with those stimulated by a short treatment of retinoic acid (RA) alone. When leukemic cells expressing MycD were stimulated with RA, the overlap with the RA-alone signature increased to 32% (492/1556 genes). Importantly, 320 of these 492 bona-fide direct RA target genes were specifically superactivated in presence of MycD (MycD+RA>RA), and not by MycA (MycD+RA>MycA+RA), further suggesting a synergy between the two pathways. The list of superactivated genes included important regulators of development and differentiation such as GATA6, ICAM1 and HOX genes, whose expression was validated in independent experiments by RT-qPCR. Induced gene expression in HL60 cells was measured after a short-treatment of retinoic acid (100nM, 4 hours). Cells were either wild-type or expressing ER-tagged MycD or MycA. Four biologically independent experiments were performed at each time.

2012-01-05 | E-GEOD-24731 | biostudies-arrayexpress

Genome wide (GW) and validation CRISPR screens on encephalitogenic CD4+ T cell migration into the CNS

Project description:To identify genes driving encephalitogenic CD4+ T cell migration into the CNS, we performed a genome-wide CRISPR screen and a subsequent validation screen For the genome-wide CRISPR screen, up to 4 sgRNA per gene and 800 non targeted controls were included, for a total of 87690 individual sgRNAs, and for the validation screen, up to 6 sgRNA per gene and 241 non targeted controls for a total of 12000 individual sgRNAs

2023-08-01 | GSE232340 | GEO

Genome-wide identification of CRISPR/Cas9 off-targets in human genome

Project description:By a robust unbiased ChIP-seq approach, we demonstrated that CRISPR/Cas9 had crRNA-specific off-target binding activities in human genome. However, most of those binding off-targets could not be efficiently cleaved both in vivo and in vitro which suggested the cleavage off-target activity of CRISPR/Cas9 in human genome is very limited. We provided a valuable tool to further investigate the molecular mechanism of CRISPR/Cas9 and to optimize its in vivo targeting sgRNA binding sites were identified with ChipSeq by using GFP antibody (there are 2 replicates for egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in Hek293T cells, one egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in HeLaS3 cells)

2014-06-18 | E-GEOD-58511 | 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