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

Small RNA and High Molecular Weight RNA Deep Sequencing Analysis of miR-17~92 Mimics Transfected HeLa cells

ABSTRACT: Transient transfection of miRNA mimics are widely used to alter microRNA expression in cells. The goal of this study is to perform small RNA deep sequencing analysis of HeLa cells transfected with miR-17~92 cluster and address potential source of non-specific effects caused by this approach. HeLa cells were cultured as adherent cells. Equal molar concentration of miRNA mimics of miR-17~92 (100nM, 16.7nM each) were transfected and harvedsted at 6h post-transfection for small RNA deep sequencing analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Changchun Xiao

PROVIDER: E-GEOD-73099 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Impact of miR-132 and miR-381 on endogenous forskolin responsive CREB targets in HEK293T cells

Project description:Expression profiling of HEK293T cells transfected with miR-neg (negative control), miR-132 or miR-381 mimics and treated with forskolin for 0, 1 or 4hrs. HEK293T cells were reverse transfected with the respective miRNA mimics. 72hrs post-transfection, cells were treated with forskolin for 0, 1 or 4hrs. Total RNA was then extracted. Expression profiling was carried out with Affymetrix arrays. Experiment was performed in duplicate. Total of 18 samples.

2011-07-01 | E-GEOD-24812 | biostudies-arrayexpress

Analysis of DNA methylation dynamics at Alu elements during human B cell activation

Project description:Paired-end sequencing of methylated DNA fragments in B cell subsets revealed widespread loss of methylation at Alu elements upon B cell activation. DNA methylation pattern was analyzed in purified naïve and germinal-center B cells derived from 1 patient

2013-03-01 | E-GEOD-42386 | biostudies-arrayexpress

Sequencing random oligonucleotides using standard GA II protocol

Project description:Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina protocol or HD protocol

2012-07-23 | E-GEOD-36540 | biostudies-arrayexpress

MiSeq 2x300 paired-end sequencing of HEK293T cells stably expressing eGFP-PPP2R5A transduced with a HIV-1 Vif mutant library

Project description:The goal of this experiment was to map the binding surface between the HIV-1 Vif protein and the cellular phospho-regulator PPP2R5A. Previous studies had shown that Vif can target PPP2R5A for proteasomal degradation but the binding surface required had yet to be elucidated. For this experiment, HEK293T cells stably expressing eGFP-PPP2R5A were transduced with virus containing a Vif mutant library. The transduction was done at a low multiplicity of infection so that, on average, each cell only received a single Vif variant. The Vif library was built using a mCherry-T2A-Vif expression cassette so transduced cells could be monitored via mCherry fluorescence. Once the library had been introduced into the eGFP-PPP2R5A cells, fluorescence-activated cell sorting was used to separate out transduced cells that could, and could not, degrade eGFP-PPP2R5A. For example, if a cell received a functional variant, it would lose eGFP fluorescence (PPP2R5A degradation) but retain mCherry fluorescence. On the other hand, if a variant was non-functional, eGFP fluorescence would persist (no PPP2R5A degradation). The unsorted transduced population, mCherry+/eGFP-, and mCherry+/eGFP+ populations were subjected to a 2x300 bp MiSeq run to comprehensively identify mutants that were functional and non-functional.

2019-10-01 | E-MTAB-8357 | biostudies-arrayexpress

Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation

Project description:The Arabidopsis ARGONAUTE (AGO) protein AGO1 associates with microRNA (miRNA) and specific classes of short-interfering RNA (siRNA). AGO1-small RNA complexes recognize target RNA transcripts through base-pairing interactions and inhibit translation of target RNAs through endonucleolytic cleavage (slicing) or non-degradative mechanisms. The PIWI domain of AGO1 contains a metal-coordinating triad [Asp-Asp-His] (DDH) that is required for slicer activity. Here, we compared the activities of wild type (DDH) and slicer active-site defective (DAH) forms of AGO1 by sequencing small RNA and target transcript RNAs that co-immunoprecipitated with hemagglutinin (HA)-tagged AGO1 proteins. We found that the population of miRNA that associated with both AGO1-DDH and AGO1-DAH proteins largely overlapped, suggesting that cleavage activity does not affect miRNA maturation. In contrast, slicer-defective AGO1-miRNA complexes associated with target RNA more effectively than did wild type AGO1-miRNA. These data indicate that slicer-defective AGO proteins can be used as an approach to capture AGO-small RNA-target RNA ternary complexes more efficiently for genome-wide analyses. AGO1-DDH (wild type) AGO1-DAH (slicer mutant) proteins were immunoprecipitated (N-terminal 3xHA) from Arabidopsis (Columbia) flower (stages 1-12) lysate. Immunoprecipitations were also done from control plants transformed with vector only. Small RNA from immunoprecipitate fractions of vector, AGO1-DDH and AGO1-DAH were sequenced.

2012-09-28 | E-GEOD-40258 | biostudies-arrayexpress

Survival and Diversity of Human Homologous Dietary MicroRNAs in Conventionally Cooked Top Sirloin and Dried Bovine Tissue Extracts

Project description:We report the human homologous microRNA profiles in food-grade, bovine-sourced sirloin, heart and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts) Deep miRNA sequencing of sirloin (raw and cooked), heart tissue (raw, cooked, and pastuerized, freeze-dried extracts) and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts), 3 replicates each process group

2015-09-02 | E-GEOD-69874 | biostudies-arrayexpress

A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo

Project description:Argonaute/Piwi proteins associate with small RNAs that typically provide sequence specificity for RNP function in gene and genome regulation. Here we show that Twi12, a Tetrahymena Piwi protein essential for growth, is loaded with mature tRNA fragments. The tightly bound ~18-22 nt tRNA 3M-bM-^@M-^Y fragments are biochemically distinct from the tRNA halves produced transiently in response to stress. Notably, the end positions of Twi12-bound tRNA 3' fragments precisely match RNAs detected in total small RNA of mouse embryonic stem cells and human cancer cells. Our studies demonstrate unanticipated evolutionary conservation of mature tRNA processing to tRNA-fragment small RNAs. Two libraries are analyzed here: sRNAs associated with slightly overexpressed ZZ-tagged Twi12 purified under native conditions (size range 15-34nt), and those associated after formaldehyde crosslinking (15-22nt).

2010-10-26 | E-GEOD-24916 | biostudies-arrayexpress

Salmonella 14028s AraC ChIP-Seq

Project description:We mapped the genome-wide binding of C-terminally FLAG-tagged AraC in S. enterica subsp. enterica serovar Typhimurium strain 14028s using ChIP coupled with deep sequencing (ChIP-seq). We identified five putative target loci for AraC: upstream of araB/araC, araE, araJ, STM14_0178, and within sseD.

2013-10-09 | E-MTAB-1915 | biostudies-arrayexpress

ChIP-seq of sigma 70 in wild-type and hns mutant Escherichia coli K-12 MG1655

Project description:We mapped the genome-wide binding of sigma 70 in E. coli K-12 MG1655 and an hns mutant that is otherwise isogenic using ChIP coupled with deep sequencing (ChIP-seq). We show that intragenic binding of sigma 70 is increased in the hns mutant.

2013-12-15 | E-MTAB-2148 | biostudies-arrayexpress

Mapping ONECUT1 TF binding with ChIP-exo

Project description:The aim of this project is to locate the precise binding of the ONECUT1 transcription factor. NOTE: This study was updated on 7th May 2014. All samples, experiments, runs and files were replaced. This was due to an incorrect reagent being used in the earlier version.

2014-05-10 | E-MTAB-2060 | 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