Cardamine sp. SIM-2007
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA103741 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The annual cleistogamous herb Cardamine kokaiensis is an endemic plant along the Kokai River in Japan. We examined the differences in gene expression patterns among cleistogamous (CL), intermediate (INT), and chasmogamous (CH) flower by cross-species microarray analysis using an Arabidopsis thaliana Affymetrix high-density oligonucleotide microarray (GeneChip ATH1). We then discuss the molecular basis of the evolution of cleistogamy. Our results help to clarify the molecular basis of the evolution of plant mating systems that depend on environmental conditions. CITATION: Ecogenomics of cleistogamous and chasmogamous flowering: genome-wide gene expression patterns from cross-species microarray analysis in Cardamine kokaiensis (Brassicaceae); Journal of Ecology 2008; Shin-Ichi Morinaga, Atsushi J. Nagano, Saori Miyazaki, Minoru Kubo, Taku Demura, Hiroo Fukuda, Satoki Sakai, Mitsuyasu Hasebe Experiment Overall Design: gDNA hybridyzation data was used to calibration of cross-species microarray using Affymetrix ATH1. CH, INT, and CL flowers of C. kokaiensis were induced the chilling treatment before germination for 14 days or after germination for 14 or 28 days, respectively. We performed two biological replications per flower. Data analysis was conducted according to Hammond et al. (2005) that described the methods of calibration by gDNA hybridization.
2008-06-18 | E-GEOD-9799 | biostudies-arrayexpress
Project description:The annual cleistogamous herb Cardamine kokaiensis is an endemic plant along the Kokai River in Japan. We examined the differences in gene expression patterns among cleistogamous (CL), intermediate (INT), and chasmogamous (CH) flower by cross-species microarray analysis using an Arabidopsis thaliana Affymetrix high-density oligonucleotide microarray (GeneChip ATH1). We then discuss the molecular basis of the evolution of cleistogamy. Our results help to clarify the molecular basis of the evolution of plant mating systems that depend on environmental conditions. Keywords: flower type comparison
2008-05-27 | GSE9799 | GEO
Project description:RNA from etiolated seedlings, light-treated seedlings, leaves and flowers was hybridized to ATH1 and AGRONOMICS1 arrays.
2010-01-01 | E-MEXP-2472 | biostudies-arrayexpress
Project description:Peripheral monocytes in humans are conventionally divided into classical (CL, CD14++CD16−), intermediate (INT, CD14++CD16+) and non-classical (NC, CD14dim/−CD16++) cells, based on their expression levels of CD14 and CD16. A major fraction of the NC-monocytes has been shown to express the 6-sulfo LacNAc (slan) antigen, but whether these slan+/NC-monocytes represent the prototypical non-classical monocytes or whether they are simply a sub-fraction with identical features as the remainder of NC monocytes is still unclear. Therefore, we analysed transcriptome, proteome, cell surface markers and production of discrete cytokines by peripheral slan+/NC- and slan−/NC-monocytes, in comparison to total NC-, CL- and INT- monocytes. By bulk RNA-seq and proteomic analysis, we found that slan+/NC-monocytes express higher levels of genes and proteins specific of NC-monocytes than slan−/NC-monocytes do. Unsupervised clustering of scRNA-seq data generated one cluster of NC- and one of INT-monocytes, where all slan+/NC-monocytes were allocated to the NC-monocyte cluster, while slan−/NC-monocytes were found, in part (13.38 %), within the INT-monocyte cluster. In addition, total NC- and slan−/NC-monocytes, but not slan+/NC-monocytes, were found by both bulk RNA-seq and scRNA-seq to contain a small percentage of natural killer cells. Altogether, in addition to comparatively characterize total NC-, slan−/NC- and slan+/NC-monocyte transcriptomes and proteomes, our data prove that slan+/NC-, but not slan−/NC-, monocytes are more representative of prototypical NC-monocytes.
2023-10-19 | GSE242301 | GEO
Project description:Peripheral monocytes in humans are conventionally divided into classical (CL, CD14++CD16−), intermediate (INT, CD14++CD16+) and non-classical (NC, CD14dim/−CD16++) cells, based on their expression levels of CD14 and CD16. A major fraction of the NC-monocytes has been shown to express the 6-sulfo LacNAc (slan) antigen, but whether these slan+/NC-monocytes represent the prototypic non-classical monocytes or whether they are simply a sub-fraction with identical features as the remainder of NC monocytes is still unclear. Unsupervised clustering of scRNAseq data generated one cluster of NC- and one of INT-monocytes, where all slan+/NC-monocytes were allocated to the NC-monocyte cluster, while slan−/NC-monocytes were found, in part (13.38 %), within the INT-monocyte cluster. In addition, total NC- and slan−/NC-monocytes, but not slan+/NC-monocytes, were found to contain a small percentage of natural killer cells. Altogether, this data prove that slan+/NC-, but not slan−/NC-, monocytes are more representative of prototypical NC-monocytes.
2023-10-19 | GSE241266 | GEO
Project description:Although two genes responsive to GABA were characterized previously in plants (Kathiresan et al 1997), a comprehensive study in reproductive and vegetative tissues has not been performed. Consequently, genes that mediate GABA response in plants remain unknown. We therefore used microarrays to survey the genome, identifying genes modulated in response to GABA in reproductive tissues. Flowers were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays. Gene expression in wild-type and pop2-1 mutant flowers containing high levels of endogenous GABA were compared.
2010-06-16 | E-GEOD-21945 | biostudies-arrayexpress
Project description:DNA microarray analysis (Affymetrix ATH1 GeneChip) on mutant lines of the gene At-FAX1 (At3g57280) in Arabidopsis thaliana was performed as described in Li et al. (2015). In total we analyzed the following comparisons: (A) flowers: fax1 knockout (n = 5) versus wild type (n = 5); (B) flowers: FAX1 over-expressors (n = 8, 4-times each line ox#2, ox#4) versus wild type (n = 5); (C) stems: fax1 knockout (n = 4) versus wild type (n = 4). Additional files containing processed data are provided (see http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3090).
2015-02-04 | E-MTAB-3090 | biostudies-arrayexpress
Project description:The ovary is the most important sexual organ of female mammals, and its corpus luteum plays a significant role in mammalian reproduction during the estrus cycle. Here we conducted a quantitative proteomic analysis using tandem mass tag (TMT)-labeling coupled with Nano-LC-MS/MS to explore the mechanisms of the estrus cycle in protein level. A total of 2,103 proteins were quantified in three groups, corpus hemorrhagicum (CH), corpus luteum (CL), and corpus fibrosum (CF). Thirty-two proteins were identified as differentially expressed in the CH group, and 116 proteins were identified as differentially expressed in the CF group, with the CL group serving as the control. Notably, we found that many enzymes, including kinase and phosphatase, are upregulated in the CL stage of the ovary, and three upregulated proteins in the CL stage (PLK1, PGP, and HGS) were confirmed using western blotting, quantitative RT-PCR, and immunohistochemistry analysis. The results of these validations were consistent with the TMT-label quantitative analysis, which indicated that they may play a crucial role in the normal reproductive cycle of the CL. Our study not only provides a deeper understanding of the formation and regression of the CL, but also suggests some potential proteins related to the estrus cycle.
2019-10-30 | PXD016072 |
Project description:The investigators aim to evaluate and compare the diagnostic accuracy of FIT and the novel panel of bacterial gene markers (Fn, m3, Ch and Bc) collectively named as M3, in detecting colorectal advanced neoplasia.
| 2733246 | ecrin-mdr-crc
Project description:Cardamine hupingshanensis Transcriptome or Gene expression
| PRJNA360038 | ENA