Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of male strobili in fertile and sterile male strobili of Cryptomeria japonica

ABSTRACT: Investigation of comprehensive gene expression level changes in male strobili of sterile mutant, compared to the fertile plant. We designed a new custum array derived from ESTs of Cryptomeria japonica for this study. Male strobili of C. japonica were collected from Toyama 1 half-sib F2 pedigree. Toyama 1 male-sterile mutant was first reported in Saito, M. , H. Taira, and Y. Furuta (Journal of Forest Research 3(3):167-173). Microarray studies using both individual samples and pooled samples were performed. Total RNA was extracted from male strobili at four developmental stages derived from each seven fertile and male-sterile trees as individual samples. Pooled RNA samples were prepared from four to eight different fertile and sterile plants at three developmental stages.

ORGANISM(S): Cryptomeria japonica

SUBMITTER: Norihiro Futamura

PROVIDER: E-GEOD-33499 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comprehensive analysis of genic male sterility-related genes in Brassica rapa using Brassica rapa 300k microarray v2.0

Project description:To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility. A total of 14 chips were used for the microarray experiment. Experiments were performed with two biological replicates.

2013-10-22 | E-GEOD-47665 | biostudies-arrayexpress

Genome-wide expression profiling in a Fusarium graminearum lacking FgVelB, a velvet complex gene

Project description:Using a 3'-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of both a wild type and a FgVelB deletion strainn of F. graminearum at a sexual stage (3 days after perithecial induction on carrot agar) Our study is the first report elucidating regulatory pathways controlled by FgVelB in Fusarium graminearum. A total of 4 chips were used for microarray. Total RNAs were extracted from perithecia and/or ground mycelia formed on carrot agar cultures of a self-fertile wild-type and a self-sterile FgVelB-deleted strain of F. graminearum with two biological replicates.

2012-08-02 | E-GEOD-36638 | 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

label-free analysis of male-sterile line 1355A of cotton

Project description:Cotton (Gossypium spp.) is one of the most important economic crops and exhibits yield-improving heterosis in specific hybrid combinations. The genic male-sterility system is the main strategy used for producing heterosis in cotton. To better understand the mechanisms of male sterility in cotton, we carried out label-free quantitative proteomics analysis in the anthers of two near-isogenic lines, the male-sterile line 1355A and the male-fertile line 1355B, the two isogenic lines. These experiments, along with bioinformatics analyses, identified 124 proteins from the anthers at uninucleate pollen stage (stage 8) that were significantly differentially expressed between these two lines.

2019-03-19 | PXD012398 | Pride

Expression data from rice meiosis-stage young inflorescences

Project description:Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). UGPase protein accumulates in TGMS-Co27 florets at low temperatures and temperature-sensitive splicing is involved in its sterility transitions.However, details of the molecular mechanisms involved are unknown. we use microarrays to compare transcriptomic profiles during the meiosis-stage of flower development in TGMS-Co27 and wild-type (H1493) plants grown at high and low temperatures. The detected differences in expression profiles provide further understanding of the regulatory networks underlying flower development generally, identify genes involved in the TGMS process in TGMS-Co27 and may provide reference data for analyses of molecular mechanisms underlying sterility transitions in other PGMS/TGMS rice lines. Meiosis-stage inflorescences were used for this study because pollen mother cells (PMCs) of TGMS-Co27 plants begin to degenerate at this stage. Samples from H1493 grown at high temperature, TGMS-Co27 grown at high temperature, H1493 grown at low temperature and TGMS-Co27 grown at low temperature were harvested to compare the difference between fertile and sterile rice lines.

2015-04-28 | E-GEOD-56779 | biostudies-arrayexpress

5-aza-2'-cytidine and trichostatin A effect to gene expression of Epstein-Barr virus-transformed human lymphoblastoid cell lines (LCLs).

Project description:Investigation of 5-aza-2'-cytidine and trichostatin A effect to gene expression of human LCLs. LCLs estabulished from patients with genetic dissease are commonly used for mRNA or protein analysis of disease related genes. However, ofen times the gene of interset is not expressed in LCL. Epigenetic modification could be overcome this problem. Expression array study with total RNA extracted from normal male derived LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts variants.

2012-01-27 | E-GEOD-35359 | biostudies-arrayexpress

Transcriptome analysis of male flowers corresponding to anther developmental stages in Cryptomeria japonica

Project description:Investigation of gene expression changes among anther development in wild type and male sterile mutant. Male strobili of wild-type were collected at 10 stages with three biological repeats (total 30 samples) and male strobili of mutant were collected at stages 3 to 6 with three biological repeats (total 12 samples).

2016-03-01 | E-GEOD-64663 | biostudies-arrayexpress

Geographical and host plant influences on transcriptional variation in Drosophila mojavensis: mapping gene expression differences in both sexes

Project description:Geographical and host plant influences on transcriptional variation in Drosophila mojavensis: mapping gene expression differences in both sexes. (1. Punta Onah:PO07; 2. Organ Pipe National Monument:OPNM08; 3. Punta Prieta:PP08; & 4. San Quintin:SQ08). The experiment was designed to investigate effects of host plant (diet), mating status (mated:M or nonmated:V) and sex (male:male or Female:F) on transcriptome. A total of 128 hybridizations were performed in this entire experiment (127 in the final analysis). We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (1. Punta Onah:PO; 2. Organ Pipe National Monument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ), two mating status (mated:M or nonmated:V), both the sexes (male:male or Female:F) fed on two different diet regimes (Agria and Organ pipe). Each chip measures the expression level of 15528 transcripts. Four to 5 replicates were used for each type (R-1, R-2, R-3 etc.)

2016-04-01 | E-GEOD-78852 | biostudies-arrayexpress

Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types

Project description:Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Keywords: anther development, maize, male sterility 3 biological replicates of 3 different male-sterile mutants and their fertile siblings at 4 stages of anther development (36 arrays). Comparisons were done between male-sterile and fertile sibs at the same development stage.

2008-09-16 | E-GEOD-12756 | biostudies-arrayexpress

Comparative transcriptome of the fertile and sterile buds of genic multiple-allele inherited male sterile AB line in Chinese cabbage

Project description:we performed transcript profiling of male sterile and fertile buds from a multiple-allele inherited male sterile AB line using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.

2016-02-10 | GSE77427 | 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