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Profiling of small RNA populations in tricellular pollen of rice

ABSTRACT: To investigate the potential function of miRNAs during male gametogenesis in rice, 13-40 nt RNA were extrected from tricellular pollen (TCP) for high-throughput sequencing. We identified 104 unique miRNAs from TCP library, 57 of which are novel derived from 39 pre-miRNAs. This subseries contain one small RNA sequencing data in tricellular pollen (TCP) stage.

ORGANISM(S): Oryza sativa Indica Group

SUBMITTER: Sheng-hua Wang

PROVIDER: E-GEOD-29178 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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MicroRNA profiles and their control of male gametophyte development in rice.

Peng Hua H Chun Jun J Ai Tao-bo TB Tong Yong-ao YA Zhang Rong R Zhao Ming-ming MM Chen Fang F Wang Sheng-hua SH

Plant molecular biology 20120309 1

Plant microRNAs (miRNAs) act as negative regulators of gene expression by slicing target transcripts or inhibiting translation. A number of miRNAs play important roles in development. In order to investigate the potential function of miRNAs during male gametogenesis in rice, we obtained both gene and small RNA expression profiles by combining microarray and high-throughput sequencing technologies. From the microarray datasets, 2,925 male gametophyte-specific genes were identified, including 107 ...[more]

PMID: 22403030

Similar Datasets

MicroRNA Profiles and Their Control of Male Gametophyte Development in Rice

Project description:Plant microRNAs (miRNAs) act as negative regulators of gene expression by slicing target transcripts or inhibiting the translation, and a number of miRNAs play important roles in development. In order to investigate the potential function of miRNAs during male gametogenesis in rice, we obtained both gene and small RNA expression profiles by combining Affymetrix microarray and high-throughput sequencing technologies. In genome-scale, we compared arrays and sRNA-Seq datasets in different stages/organs of rice by applying computational and statistical approaches. Subsequently, we identified 13363 expressed genes and 104 expressed unique miRNAs in pollen, thus, we constructed an interaction network of miRNA-target basing on two datasets. By employing enrichment analysis, we found miRNA-regulated targets involved in both up and down pathways, but predominantly in down pathways including 30 GO biological processes and 34 KEGG pathways. Our findings indicated that miRNAs plays a broad regulatory role during male gametophyte development in rice. This SuperSeries is composed of the following subset Series: GSE29080: Gene Expression Profiling during Male Gametophyte Development in Rice GSE29178: Profiling of small RNA populations in tricellular pollen of rice

2012-03-15 | E-GEOD-29212 | biostudies-arrayexpress

Gene Expression Profiling during Male Gametophyte Development in Rice

Project description:To investigate the potential function of miRNAs during male gametogenesis in rice, we first obtained gene expression profiles by using Affymetrix microarray technologies. In genome-scale, we found a common characteristic shared by rice and Arabidopsis, which vast of genes are down regulated from Pb to Pc stage. next, a total of 13363 genes were detected during the gametophyte development in rice, which contains 2925 pollen-enriched/-specific genes including 107 transcription factors. We also analyzed the microarray-based expression patterns of genes in miRNA pathways, and found 3 pollen-specific AGO genes (AGO12, AGO13 and AGO17). This subseries contains three datasets of gene expression in pollen development stages: uninucleate microspore (UNM/Pa), bicellular pollen (BCP/Pb) and tricellular pollen (TCP/Pc)

2012-03-15 | E-GEOD-29080 | biostudies-arrayexpress

Profiling of small RNA populations in tricellular pollen of rice

Project description:To investigate the potential function of miRNAs during male gametogenesis in rice, 13-40 nt RNA were extrected from tricellular pollen (TCP) for high-throughput sequencing. We identified 104 unique miRNAs from TCP library, 57 of which are novel derived from 39 pre-miRNAs.

2012-03-15 | GSE29178 | GEO

Tricellular pollen and pollen mother cells (11447)

Project description:We isolated tricellular pollen (TCP) and pollen mother cells (PMC) of rice using laser microdissection, and did microarray analysis with Agilent 44k rice array.

2010-07-31 | GSE17098 | GEO

Profiling of small RNA populations in uninucleate microspores and bicellular pollen of rice

Project description:There are multiple types of small RNAs that may affect rice pollen’s development. To investigate the small RNA populations’ change during rice pollen development, 13-40 nt RNA were extracted from uninucleate microspores (UNM) and bicellular pollen (BCP) for high throughput sequencing. Together with our laboratory’s previous published rice tricellular pollen (TCP) small RNA sequencing data (GSM722128), sharp increase of tRNA fragments (tRFs) in BCP stage and a slightly decreased tRFs in TCP were found. Among which, new lengths of tRFs were also discovered. Our work accomplished the knowledge about tRFs in rice pollen development.

2017-09-01 | GSE101998 | GEO

Characterization of the small RNA populations of developing Arabidopsis thaliana pollen.

Project description:Small RNA diversity and function has been widely characterized in various tissues of the sporophytic generation of the angiosperm model Arabidopsis thaliana. In contrast, there is limited knowledge about small RNA diversity and their roles in developing male gametophytes. We thus carried out small RNA sequencing on RNA isolated from four stages of developing Arabidopsis thaliana pollen. Spores from 4 stages of pollen development (UNM: Uninucleate microspore M-bM-^@M-^S BCP: Bicellular pollen M-bM-^@M-^S TCP: Tricellular pollen M-bM-^@M-^S MP: Mature pollen) were isolated using a percoll gradient-based method (Honys and Twell, 2004) and the small RNA fraction for each sample was isolated and sequenced by Illumina technology. Reference: Honys, D. and Twell, D. (2004) Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 5/11/R85.

2014-07-01 | E-GEOD-34190 | biostudies-arrayexpress

Small RNA profiles of the rice non-pollen male sterile line Wuxiang S reveal miRNAs involved in the fertility transition

Project description:Illumina sequencing was employed to examine the expression profiles of rice anther miRNAs from the a non-pollen male sterile line Wuxiang S (WXS), one of photo-thermo sensitive genical male sterile (PTGMS) line rice, during in the fertility transition stage. A total of 493 known miRNAs and 273 novel miRNAs were identified during rice anther development. Based on the number of sequencing reads, a total of 26 miRNAs were discovered to be significant difference expression between WXS(S, Sterility) and WXS(F, Fertility), and the results were partially validated by qRT-PCR. Among these, 11 miRNAs were decreased and 15 miRNAs were increased in WXS(S) compared with WXS(F). The expression patterns for targets of osa-miR156a-j, osa-miR3879, osa-miR159c/d/e, osa-miR171a/c/e/i, osa-miR398b, osa-miR164d, osa-miR528 and osa-miR408 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. These targets have previously been reported to be related with pollen development and male sterility, suggesting that miRNAs might act as regulators of rice anthers. Furthermore, miRNA editing events were observed. The U-to-C and U-to-A editing phenomenon was validated by molecular cloning and sequencing. Examine small RNA profiles change of four tissues of the rice non-pollen male sterile line Wuxiang S under two different environments.

2016-02-14 | E-GEOD-74003 | biostudies-arrayexpress

Oryza sativa

Project description:Tricellular pollen and pollen mother cells (11447)

| PRJNA117817 | ENA

microRNA expression profile in mouse lung development

Project description:We performed miRNA and mRNA profiling over a 7-point time course, encompassing all recognized stages of lung development and explore dynamically regulated miRNAs and potential miRNA-mRNA interaction networks specific to mouse lung development replicated time course of mouse lung development in 7 time points

2010-08-17 | E-GEOD-21052 | biostudies-arrayexpress

RNA sequencing of Oryza sativa japonica control and OsRALF17/19 knockout mutant in mature rice anthers

Project description:Pollen tube growth is essential for successful fertilization and stable crop yields. We constructed loss-of-function/knock-out mutants that simultaneously target two rice genes using the CRISPR/Cas9 mutagenesis system. The selected OsRALF17 and OsRALF19 genes are strongly expressed in rice bicellular/tricellular pollen and have essential functions in the pollen tube growth. For the corresponding transcriptomic analysis, we sampled mature pollen anthers from a control group and an OsRALF17/19 knock-out mutant.

2023-09-29 | E-MTAB-12295 | biostudies-arrayexpress

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