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Hepatic gene expression changes following antisense oligonucleotide-based inhibition of miR-29a

ABSTRACT: Adult BALB/c female mice were injected intraperitoneally with a single dose at 20 mg per kg of antisense oligonucleotide either against miR-29a (5’-TAACCGATTTCAGATGGTGCTA-3’) or against a scrambled sequence (5’-TCATTGGCATGTACCATGCAGCT-3’ Antisense oligonucleotides contained 2’-O-methoxyethyl (2’-MOE), 2’-flouro (2’-F) 2'-alpha-flouro units with a phosphorothioate backbone (Regulus Therapeutics). Six days following the injection, liver was isolated, total RNA was prepared as described above, and the RNA was amplified and biotinylated using the MessageAmp Premier kit (Ambion). Samples (n=4 each experimental and control) were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays in the Children’s Hospital of Philadelphia Nucleic Acids Core Facility and analyzed with the assistance of the Penn Bioinformatics Core. Probe intensities were normalized using the GCRMA method and the significance of the log2-transformed, GCRMA-normalized signal intensities was determined using SAM

ORGANISM(S): Mus musculus

PROVIDER: GSE40261 | GEO | 2012/08/22

SECONDARY ACCESSION(S): PRJNA173361

REPOSITORIES: GEO

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Hepatic gene expression changes following antisense oligonucleotide-based inhibition of miR-29a

Project description:Adult BALB/c female mice were injected intraperitoneally with a single dose at 20 mg per kg of antisense oligonucleotide either against miR-29a (5’-TAACCGATTTCAGATGGTGCTA-3’) or against a scrambled sequence (5’-TCATTGGCATGTACCATGCAGCT-3’ Antisense oligonucleotides contained 2’-O-methoxyethyl (2’-MOE), 2’-flouro (2’-F) 2'-alpha-flouro units with a phosphorothioate backbone (Regulus Therapeutics). Six days following the injection, liver was isolated, total RNA was prepared as described above, and the RNA was amplified and biotinylated using the MessageAmp Premier kit (Ambion). Samples (n=4 each experimental and control) were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays in the Children’s Hospital of Philadelphia Nucleic Acids Core Facility and analyzed with the assistance of the Penn Bioinformatics Core. Probe intensities were normalized using the GCRMA method and the significance of the log2-transformed, GCRMA-normalized signal intensities was determined using SAM Adult mice injected with anti-miR-29a or scrambled control ASO, n=4 per group

2012-08-22 | E-GEOD-40261 | biostudies-arrayexpress

A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics

Project description:Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes bear great potential in the fight against antimicrobial resistance and for precision microbiome editing. The development of such antisense antibiotics has primarily focused on using phosphoramidite morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based therapy in general. Here, we compare seven chemically distinct 10mer-ASOs, all designed to target the same essential acpP mRNA upon delivery with a KFF-peptide carrier into Salmonella, comparing PNA, PMO, phosphorothioate modified-DNA (PTO), 2’-methoxylated RNA (RNA-OMe), 2’-methoxyethylated RNA (RNA-MOE), 2’-fluorinated RNA (RNA-F) and 2’-locked RNA (LNA). Our systematic analysis using a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and bacterial killing suggests that only PNA and PMO make it into Salmonella to cause bacterial growth inhibition. However, given their high target binding and translational repression activity in vitro, ASOs based on LNA and RNA-MOE appear to be promising candidates for antisense antibiotics that will require the identification of an efficient carrier.

2023-07-11 | GSE232819 | GEO

Human breast tumor expression

Project description:Gene expression for 47 human breast tumor cases; (* normalized by GCRMA for global expression analysis) Keywords: Type

2006-02-09 | GSE3744 | GEO

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing

Project description:Oligonucleotides and nucleic acid analogues that alter gene expression are showing therapeutic promise for selected human diseases. The modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, however, such modifications may also confer unexpected physicochemical and biological properties. Here we report backbone-specific effects of modified oligonucleotides on subnuclear organelles, altered distribution of nuclear proteins, the appearance of novel structured nuclear inclusions, and modification of RNA processing in cultured cells transfected with antisense oligonucleotides on a phosphorothioate backbone. Phosphodiester and phosphorodiamidate morpholino oligomers elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of fibroblasts exhibiting such disruption. These data suggest that the toxic effects and adverse events reported after clinical evaluation of phosphorothioate nucleic acid drugs may be mediated, at least in part, by non-specific interaction of nuclear components with the phosphorothioate backbone. The effects of antisense oligonucleotide transfection on morphology of subnuclear organelles, localisation of nuclear proteins and impact on RNA processing were examined in primary human cells.

2022-03-23 | GSE121713 | GEO

WT and php mutants

Project description:Transcriptional profiling for wild-type and php mutants Expression of >22,600 genes was analyzed in aerial tissues from 14 day old soil grown wild type and php mutant plants using Affymetrix ATH1 GeneChip, and two independent biological replicates. Data from CEL files were adjusted for background and normalized using the Bioconductor GCRMA package (http://www.bioconductor.org).

2010-04-01 | GSE13913 | GEO

Transcription profiling of rat liver after 13 weeks of subchronic exposure to TCDD, PeCDF, PCB126, PCB153 and PCB126/PCB153

Project description:This study investigates the effects of the aryl hydrocarbon receptor (AhR) ligands TCDD, PCB126 and PeCDF; the non-AhR ligand PCB153 and the binary mixture PCB126/PCB153 on hepatic gene expression in female sprague dawley rats. Rats were treated with toxicological equivalent doses of TCDD (100ng/kg), PeCDF (200ng/kg), PCB126 (1000ng/kg) and PCB153 (1000ug/kg) 5 days a week for 13 weeks. Experiment Overall Design: There are 6 control chips and representing animals treated with vehicle control. There are 3 biological replicates (3 chips) for each treatment group (eg. TCDD, PCB126), each biological replicate is derived from 2 individual animals. A total of 21 chips were analyzed. Intensities were normalized using the GC-Robust Multiarray (GCRMA) method through Genetraffic software package.

2008-06-14 | E-GEOD-5789 | biostudies-arrayexpress

Neuroblastoma Neuro2A Cell Differentiation induced by retinoic acid-treatment

Project description:To investigate a role of mKIAA genes in early stage of neurite outgrowth, in vitro time course experiment was performed using the mouse neuroblastoma Neuro2A cells and all-trans-retinoic acid. Six time points of 8 biological replicates were performed.These data were normalized by median intensities and subtracted background intensities. NOTE: Outlier involved several data were not deposited. Keywords: time-course

2005-04-28 | GSE2570 | GEO

Transcription profiling of 47 human breast tumor cases

Project description:Gene expression for 47 human breast tumor cases (normalized by GCRMA for global expression analysis)

2007-06-25 | E-GEOD-3744 | biostudies-arrayexpress

Long Non-Coding RNA MEG3 Promotes Angiogenesis by directly regulating integrin signaling impairing endothelial cell function [ChIP-seq]

Project description:We immunoprecipitated EZH2, together with associated chromatin isolated from the HUVECs (2 x 10^6) that were transfected with MEG3 GapmeRs (10 nM, 48 h) or a scrambled control GapmeRs (Ctr). For transfection, we used 10 nM scrambled LNA (locked nucleic acids) GapmeR control (Cat. No. 339515) or phosphorothioate antisense standard GapmeRs MEG3-lncRNA (Cat No. 339511, Qiagen). On beads crosslinked chromatin complexes were reversed, and DNA purified using QIAquick® PCR Purification Kit and quantified by Qubit HS assay (Q33230)

2024-04-12 | GSE234543 | GEO

Consensus Preprocessing of GEO and ArrayExpress Normal and Diseased Lung Tissue Microarray Data

Project description:The Affymetrix oligonucleotide microarrays measure gene expression by quantifying intensity of fluorescently labeled gene fragments that bind to sets of 25-mer oligonucleotide probes on the chip with specific sequences tailored to be complementary to the target genes. Each gene is associated with a "probe set" containing several pairs (usually 11) of "perfect match" (perfectly complementary to target sequence) and "mismatch" (different base at position 13 of 25) probes. The raw measurements of each probe set consist of a set of intensities from the probes, which require in silico preprocessing by (1) correcting for background variability, (2) normalizing intensities across samples, and (3) summarizing intensities across the probe set into a single expression value. The output of the summarization step corresponds to the background-adjusted value for the mRNA of interest. We preprocess using GCRMA, which corrects for background variability by accounting for optical noise, probe affinity, and mismatch probe adjustment; normalizes intensities by quantile normalization; and summarizes intensities using a median polish method. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the dataset together. However, preprocessing across multple platforms requires a consolidation of probes with identical sequences, precluding global preprocessing on datasets with multiple platforms using the standard preprocessing pipelines. To address this problem, we have developed and applied a custom preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets.

2014-09-18 | GSE60486 | GEO

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