Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evidence for Antisense Transcription Associated with microRNAs in Arabidopsis

ABSTRACT: Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE15199 | GEO | 2009/04/10

SECONDARY ACCESSION(S): PRJNA114955

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Evidence for Antisense Transcription Associated with microRNAs in Arabidopsis

Project description:Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array. Two custom arrays were designed with 15,000 oligonucleotide (25-mer and 36-mer) probes in each array. The probes were selected tiling 200 base upstream and downstream (3 n.t. resolution) of miRNA target sites in Arabidopsis thaliana. The arrays were fabricated by Agilent Technologies, Santa Clara, CA. The 22 target genes on the arrays were chosen based on the abundance of associated smRNAs that mapped to the loci, the amplitude of the antisense transcription signals in published whole genome tiling microarray experiments and a representative cross section of miRNA families. For 15k arrays with 24 selected miRNA targets, a dye swap loop experiment design was utilized with 12 blocks for 7 genotypes on two chip arrays. The details of the experimental design are in Supplemental Table V of the manuscript. For the hen1-1 versus Ler-0 experiment, a dye swap with two versus three biological replicates and four array blocks was performed.

2009-04-10 | E-GEOD-15199 | biostudies-arrayexpress

MaTAR25 RNA Antisense Pulldown and Mass Spectrometry

Project description:It has been suggested that lncRNAs can interact with transcriptional regulators/co-factors to form ribonucleoprotein (RNP) complexes to regulate the expression of downstream genes in the cell nucleus. To identify potential interacting proteins of MaTAR25, we used two different paired sets of biotin-labeled antisense oligonucleotides targeting MaTAR25 for native RNA antisense oligonucleotide pull-down (RAP) in 4T1 cells followed by qRT-PCR to assess pull-down efficiency. Samples were also eluted from beads for mass spectrometry isobaric tags for relative and absolute quantitative (MS-iTRAQ) analysis to identify proteins that bind to MaTAR25, and PPIB as the corresponding control. We ranked the candidate interactors based on detectable peptides above background in both pair sets of oligonucleotide pull-downs, and selected candidates with at least 2-fold enrichment compared to corresponding PPIB oligo pull-down.

2020-12-23 | PXD017398 | Pride

Liver proteome upon in vivo N-acetylgalactosamine-conjugated antisense oligonucleotide silencing of ceramide synthase 2

Project description:Mouse liver proteome was investigated upon in vivo mouse treatment with a N-acetylgalactosamine-conjugated antisense oligonucleotide engineered to silence ceramide synthase 2 specifically in hepatocytes in vivo. The data is a part of a study on the involvement of ceramide enzymatic machinery in cardiovasular disorders and its potential as a target for the disease treatment.

2023-05-10 | PXD025957 | Pride

Exosomal natural antisense transcripts released from colorectal cancer SW480 cells into culture supernatants

Project description:In the present study, natural antisense transcripts (NATs), transcribed from reverse strand deoxynucleic acids (DNAs) of genes, into exosomes released from colorectal cancer SW480 cells were searched using an sense/antisense-custom microarray.

2015-05-19 | GSE68979 | GEO

Expression data from dosing an antisense oligonucleotide in mice

Project description:Expression data from dosing an antisense oligonucleotide in mice

| PRJNA392683 | ENA

Expression data from dosing an antisense oligonucleotide in mice I

Project description:We used microarrays to globally profile the gene expression changes observed in liver after 3 days when dosing an antisense oligonucleotide in mice

2018-04-30 | GSE100697 | GEO

Expression data from transfection of an antisense oligonucleotide in 518A2 cells

Project description:We used microarrays to globally profile the gene expression changes observed after 3 days when transfecting an antisense oligonucleotide in 518A2 cells

2017-04-21 | GSE93185 | GEO

Using pooled earthworm RNA to test 244K probes on TA-2 test array design 2520023 antisense 1

Project description:To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

2009-06-12 | GSE16548 | GEO

Using pooled earthworm RNA to test 244K probes on TA-4 test array design 2520025 antisense 2

Project description:To validate the 244K 60-mer or 40-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

2009-06-12 | GSE16550 | GEO

Alteration of target cleavage patterns and off-target reduction of antisense oligonucleotides incorporating 2-N-carbamoyl- or (2-pyridyl)guanine [Rluc]

Project description:We performed microarrays to evaluate the gene expression changes after 24 h of antisense oligonucleotide transfection.

2023-06-14 | GSE228741 | GEO