Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing analysis of pepper

ABSTRACT: To facilitate the functional annotation of the pepper genome, analysis of miRNAs was performed for the sequenced data from five small RNA libraries described above, representing five different tissues. Starting with a set of 5,436 plant mature miRNA sequences available in miRBase, we annotated with high confidence 176 pepper miRNAs from 64 families, of which 30 families are computationally predicted to target TFs, suggesting important roles of these miRNA families in post-transcriptional gene regulation and transcription networks consistent with previous findings.

ORGANISM(S): Capsicum annuum

PROVIDER: GSE45040 | GEO | 2014/03/14

SECONDARY ACCESSION(S): PRJNA193078

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Small RNA sequencing analysis of pepper

Project description:To facilitate the functional annotation of the pepper genome, analysis of miRNAs was performed for the sequenced data from five small RNA libraries described above, representing five different tissues. Starting with a set of 5,436 plant mature miRNA sequences available in miRBase, we annotated with high confidence 176 pepper miRNAs from 64 families, of which 30 families are computationally predicted to target TFs, suggesting important roles of these miRNA families in post-transcriptional gene regulation and transcription networks consistent with previous findings. To identify genomic regions generating small RNAs, we applied previously described analytical strategies to five small RNA libraries from different tissues. Developing roots, stems and mature leaves were collected from plants grown in soil in a green house at 22 °C with a 16 hr light cycle and harvested from plants at full-bloom stage. Mature plants were harvested for fully open flowers. Additional flowers were allowed to self-pollinate and fruit was harvested in the breaker stage (thirty days after pollination when the fruit was turning red). Total RNA for different tissues was isolated from the frozen root samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions, and libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as previously described, then sequenced on an Illumina HiSeq2000 system.

2014-03-14 | E-GEOD-45040 | biostudies-arrayexpress

A quantitative map of human primary microRNA processing sites

Project description:Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

2021-07-28 | PXD025767 | Pride

Pepper leaf transcriptome profiling during an incompatible and a compatible pepper-tobamovirus interaction

Project description:Upon virus infections, the transcriptomic profile of host plants markedly changes. The rapid and comprehensive transcriptional reprogramming is critical to ward off virus attack. To learn more about transcriptional reprogramming in tobamovirus-infected pepper leaves, we carried out transcriptome-wide RNA-Seq analyses of pepper leaves following Obuda pepper virus (ObPV) and Pepper mild mottle virus (PMMoV)-inoculations.

2021-07-23 | E-MTAB-10769 | biostudies-arrayexpress

Identification and comparison of miRNAs involved in cotton fiber elongation between sea-island and upland cotton

Project description:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.

2010-12-03 | GSE25773 | GEO

Identification and comparison of miRNAs involved in cotton fiber elongation between sea-island and upland cotton

2010-12-03 | E-GEOD-25773 | biostudies-arrayexpress

Graft junction transcriptome between tomato and pepper over time

Project description:We report transcripts from tomato:tomato and pepper:pepper self-grafts, and tomato:pepper and pepper:tomato hetergrafts over 4 time points: 24 hours after grafting, 3 days after grafting, 5 day after grafting, and 2 weeks after grafting Examination of 4 graft combinations over 4 time points

2021-08-02 | GSE131700 | GEO

Expression data in response to pepper leaf curl virus (PepLCV) infection in Chili pepper at three leaf stage

2012-10-11 | GSE41131 | GEO

Expression data in response to pepper leaf curl virus (PepLCV) infection in Chilli pepper at three leaf stage

Project description:A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage. To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage. Tomato microarrays consisting of 43,803 probes were used for whole genome expression analysis of chilli peppers for resistance against PepLCV. Transcripts from the leaves of resistant (BS-35) and susceptible plants (IVPBC-535) were compared in response to PepLCV inoculation at three leaf stage.

2012-10-11 | E-GEOD-41131 | biostudies-arrayexpress

Identification and characterization of conserved microRNAs in pepper by high-throughput sequencing

Project description:High-throughput sequencing was employed to identify conserved microRNAs in pepper. 1 sample examined: flower and root in pepper

2015-05-16 | E-GEOD-37999 | biostudies-arrayexpress

Microarray identification of conserved microRNAs in Pinellia pedatisecta

Project description:An in situ synthesized custom miRNA microarray was employed to detect miRNAs from P. pedatisecta, A total of 99 miRNAs belonging to 22 miRNA families were identified. in the study present here, the microarray design was based on 2521 well-characterized miRNAs from 43 plant species on Sanger miRBase Release 16, and Eighteen 5S rRNAs that served as internal reference were chosen from A. thaliana, C. reticulata, and O. sativa with an equal amount. Eight quality control probes were synthesized to perfect match (PM) or one nucleotide mismatch (MM) with eight external spiked-in synthetic RNA (20mer).

2014-01-01 | E-GEOD-33915 | biostudies-arrayexpress

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