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

Genome-wide miRNA turnover profile after transcription inhibition in HDMYZ cells with biological triplicate

ABSTRACT: HDMYZ cells were treated with 4ug/ml ActD for 0, 1, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina). Measure miRNA expression level at 0, 1, 4, 12 hours post ActinomycinD treatment to examine miRNA turnover pattern.

ORGANISM(S): Homo sapiens

SUBMITTER: Mei Zhong

PROVIDER: E-GEOD-60036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide miRNA profile of MCF7 cells overexpressing wild-type and mutant miR-222

Project description:MCF7 cells were infected with retrovirus to overexpress wild-type and mutant miR-222 Measure miRNA expression level in MCF7 cells after overexpressing wild-type and mutant miR-222

2015-02-05 | E-GEOD-64363 | biostudies-arrayexpress

Comparative analysis of the small RNA transcriptome of four developmental stages of the Citrus red mite (Panonychus citri)

Project description:Total RNAs from the Citrus red mite at the embryo, larva, nymph and adult stages were used to construct small RNA libraries for Solexa sequencing. Several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the Citrus red mite. The total RNAs from embryo, larva, nymph and adult stages of Panonychus citri were used to construct small RNA libraries for Solexa sequencing. The data from Solexa sequencer (Illumina) was compared to identify small RNAs in different stages of Panonychus citri.

2014-05-01 | E-GEOD-48985 | biostudies-arrayexpress

Small RNAs in tgh-1 mutant

Project description:miRNAs are regulators of gene expression in plants and animals. Their biogenesis is precisely controlled to secure normal development of organisms. Here we report that TOUGH (TGH) is a novel component of DCL1-HYL1-SE complex that processes of primary transcripts of miRNAs (pri-miRNAs) into miRNAs in Arabidopsis. Lack of TGH impairs multiple DCL activities in vitro and reduces the accumulation of miRNAs and siRNAs in vivo. TGH is an RNA binding protein, binds with pri-miRNAs in vivo and contributes to pri-miRNA-HYL1interaction. These results indicate that TGH might regulate abundance of miRNAs through promoting the DCL1 cleavage efficiency and/or recruitment of pri-miRNAs. Because TGH is a conserved protein in plants and animals, our study shall have implications on miRNA pathway in other organisms tgh-1 mutant vs. wild type

2012-08-02 | E-GEOD-38600 | biostudies-arrayexpress

Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria

Project description:To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs. Sequencing of small RNAs from Arabidopsis infected by control and 3 bacterias in 6h and 14h.

2010-07-23 | E-GEOD-19694 | biostudies-arrayexpress

Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing

Project description:The present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile of M. amblycephala with different growth performance. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes in fish and the study of miRNA function and phenotype-associated miRNA identification in fish. To investigate the functions of miRNAs associated with growth of M. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) of M. amblycephala using individuals with relatively high and low growth rates.

2014-05-25 | E-GEOD-51638 | biostudies-arrayexpress

miRNA high-throughput sequencing of follicular thyroid tumors

Project description:We report data obtaibed from high-throughput sequencing of small RNAs in 20 samples of follicular thyroid tumors. We analyzed a total of 4.7±1.5million reads per sample with 3 different pipelines. The main goal was to evaluate the usefulness of next generation sequencing in small RNA profiling and the concordance of its results with microarrays and qPCR. Additionally we verified published follicular thyroid tumor biomarkers in the set of our samples. Small RNA expression profiling with High Throughput Sequencing of 20 thyroid tumor samples, performed on an Illumina HiScan-SQ.

2014-03-07 | E-GEOD-39112 | biostudies-arrayexpress

Genome-wide profiling of small RNAs in Arabidopsis under abiotic stresses

Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in Arabidopsis, we generated small RNA sequences from adult Arabidopsis plants under control and under dought, salt, and cold stress treatments. Over 23 million reads were generated. Sequencing of small RNAs in Arabidopsis under control, drought, salt, and cold stress conditions.

2012-03-12 | E-GEOD-26356 | biostudies-arrayexpress

Genome-wide profiling of small RNAs in rice under abiotic stresses

Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated. sequencing of small RNAs in rice under control, drought, salt, and cold stress conditions.

2012-03-12 | E-GEOD-26357 | biostudies-arrayexpress

Nucleosome maps in skeletal muscle in response to diet in vivo

Project description:The nucleosome signature reflects the cellular epigenetic memory and contributes to the cellular phenotype and function. Obesity and type 2 diabetes pathogenesis is largely dependent on environmentally-induced epigenetic modifications and is marked by skeletal muscle insulin resistance; however, no in vivo skeletal muscle nucleosome maps exist to date. Herein, whole genome nucleosome maps via MNase-seq in skeletal muscle of mice on a low fat, high fat or high fat diet with the chromatin modifier sodium butyrate show that complex interactions among mitochondrial function, the tissue microenvironment, cellular phenotype and nucleosome landscape determine whole body phenotype and insulin resistance. Skeletal muscle samples (n=5 per group) were pooled after homogenization under liquid nitrogen with a motar and pestle to give one sample per group for MNase-seq

2012-05-11 | E-GEOD-37913 | biostudies-arrayexpress

MicroRNA expression during cell cycle arrest

Project description:The miR-16 family, which targets genes important for the G1-S transition, is a known modulator of the cell cycle, and members of this family are often deleted or down-regulated in many types of cancers. Here we report the reciprocal relationship - that of the cell cycle controlling the miR-16 family. Levels of this family increase rapidly as cells are arrested in G0. Conversely, as cells are released from G0 arrest, levels of the miR-16 family rapidly decrease. Such rapid changes are made possible by the unusual instabilities of several family members. The repression mediated by the miR-16 family is sensitive to these cell cycle changes, which suggests that the rapid up-regulation of the miR-16 family reinforces cell cycle arrest in G0. Upon cell cycle re-entry, the rapid decay of several members allows levels of the family to decrease, alleviating repression of target genes and allowing proper resumption of the cell cycle. Small RNAs were profiled by high-throughput sequencing either during synchronous release after serum starvation or during cell-cycle arrest by contact inhibition.

2011-09-15 | E-GEOD-31225 | 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