Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production

ABSTRACT: In this study, we aim at understanding which RNA degradation pathways are involved in keeping the secondary siRNA production in check in Arabidopsis thaliana. We have sequenced small RNAs from various T-DNA insertation single mutants and compared their capability of producing ectopic secondary siRNAs from endogenous miRNA targets. The mutants used in the work stem from three library pools from three different experiments. Libraries from all three experiments are submitted together here. The experiments can be distinguished by their title and their tag:experiment. There is a matrix of normalized reads from each pool of library as well called normalizedExp1.txt, normalizedExp2.txt and normalizedExp3.txt

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE173426 | GEO | 2021/04/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production

Project description:Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production

| PRJNA725493 | ENA

Ruegeria pomeroyi transporter mutant substrate drawdown

Project description:The goal of this project was to identify bacterial transporters responsible for uptake of environmentally relevant marine metabolites. We used the model marine heterotrophic bacterium Ruegeria pomeroyi DSS-3, for which an arrayed library of single gene knockout mutants has been generated by selecting isolated from a barcoded transposon mutant library (BasSeq). Knockout mutants of putative transporters were grown on minimal medium with a single substrate as sole carbon source. Mutant defect was assessed by comparing the substrate drawdown of isolated mutants to drawdown by a pooled mutant library (BarSeq), a proxy for wildtype fitness.

2022-11-16 | ST002381 | MetabolomicsWorkbench

Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex

Project description:The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library. And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.

2022-05-12 | GSE198440 | GEO

Global profiling of B. subtilis comparing wild-type to mutants with altered cytoplasmic membrane composition

Project description:The Bacillus subtilis membrane contains diacylglycerol-based lipids with at least five distinct headgroups that impart distinct physical and chemical properties to the lipid bilayer. Here, we describe the phenotypic characterization of mutant strains lacking one or more of the following lipids: glycolipids (ugtP mutants), phosphatidylethanolamine (pssA and psd mutants), lysylphosphatidylglycerol (mprF), and cardiolipin (ywnE and ywjE). Alterations of membrane lipid headgroup composition are generally well tolerated by the cell and even severe alterations lead to only modest effects on growth proficiency. Mutants with decreased levels of positively charged lipids display an increased sensitivity to a cationic antimicrobial compounds and cells lacking glycolipids are sensitive to the lantibiotic sublancin and are defective in swarming motility. A quadruple mutant strain (ugtP pssA mprF ywnE), with a membrane comprised predominantly of phosphatidylglycerol, is viable and grows at near wild-type rates, although it forms long, coiled filaments. Transcriptome comparisons identify numerous regulons with altered expression in ugtP mutant cells, the pssA mprF ywnE triple mutant, and the uptP pssA mprF ywnE quadruple mutant. These effects include a general decrease in expression of the SigD and FapR regulons, and increased expression of cell envelope stress responses mediated by ?M and the YvrGHb two-component system. WT vs.ugtP single mutant (U), WT vs. mprFpssAywnE triple mutant (T) or WT vs. ugtPmprFpssAywnE quadruple mutant (Q). Each experiment (WT vs. mutant) was conducted four times using three independent total RNA preparations (3 independent experiement + dye swap). For the 3 datasets used for final analysis wild-type was labeled with Alexa Fluor 555 and mutants with Alexa Fluor 647. For dye swap experiments wild-type was labeled with Alexa Fluor 647 and mutants with Alexa Fluor 555.

2010-05-18 | E-GEOD-13036 | biostudies-arrayexpress

Adoptively transferred in vitro-generated MDSCs improve T cell function and antigen-specific immunity after blunt chest trauma-induced lung injury

Project description:Does the adoptive transfer of MDSCs modulate lymphocyte (T cell) functions? Microarray expression analysis of T cells from MDSC-treated mice after Blunt chest trauma (TxT)

2022-06-16 | GSE188171 | GEO

Transcription profiling of human macrophages and dendritic cells exposed to phylogenetically distinct parasites

Project description:Monocyte-derived dendritic cells (DC) and macrophages (MÎ¦) generated in vitro from the same individual blood donors were exposed to five different pathogens, and gene expression profiles were assessed by microarray analysis. Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, L. donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger.<br><br>Note that the following pairs of files as imported from GEO are identical: GSM5135.txt and GSM5144.txt; GSM5137.txt and GSM5138.txt; GSM5143.txt and GSM5150.txt; GSM5148.txt and GSM5155.txt

2007-12-13 | E-GEOD-360 | biostudies-arrayexpress

Transcription profiling of rat heart samples from animals with physiological or pathological cardiac hypertrophy

Project description:Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a; vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html<br><br>Note that files GSM11886.txt and GSM12308.txt, and files GSM11887.txt and GSM12309.txt as downloaded from GEO contain identical data.

2007-10-11 | E-GEOD-776 | biostudies-arrayexpress

Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase.

Project description: Not available

| S-EPMC4957061 | biostudies-literature

LD/DD time course of cn bw Drosophila

Project description:Mechanisms composing Drosophila's clock are conserved within the animal kingdom. To learn how such clocks influence behavioral and physiological rhythms, we determined the complement of circadian transcripts in adult Drosophila heads. High-density oligonucleotide arrays were used to collect data in the form of three 12-point time course experiments spanning a total of 6 days. Analyses of 24 hr Fourier components of the expression patterns revealed significant oscillations for 400 transcripts. Based on secondary filters and experimental verifications, a subset of 158 genes showed particularly robust cycling and many oscillatory phases. Circadian expression was associated with genes involved in diverse biological processes, including learning and memory/synapse function, vision, olfaction, locomotion, detoxification, and areas of metabolism. Data collected from three different clock mutants (per0, tim01, and ClkJrk), are consistent with both known and novel regulatory mechanisms controlling circadian transcription (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71). For more information see also http://biorhythm.rockefeller.edu Keywords: Time course

2006-02-03 | GSE3829 | GEO

LD/DD time course of y w Drosophila #2

2006-02-03 | GSE3828 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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