E-GEOD-76917
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-76917 | ExpressionAtlas | 2018-01-04
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-76917-analysis-methods.tsv | Tabular | |||
| E-GEOD-76917-analytics.tsv | Tabular | |||
| E-GEOD-76917-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-76917-configuration.xml | Xml | |||
| E-GEOD-76917-g2_g1-mvaPlot.png | Other |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line âFTâ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type âFTâ, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of âFTâ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between âFTâ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. âFTâ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage. The RNA from the developing flower buds of a female sterility mutant (fsm) and its wild typeâFTâat the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-06-02 | E-GEOD-76917 | biostudies-arrayexpress
Project description:PURPOSE:To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line ‘CX001’ and Chinese cabbage DH line ‘FT’, obtained from isolated microspore culture, were used in the experiments. Transcriptome analysis indicated that BraA09g066480.3C was expressed in ‘FT’ but not in ‘CX001’.The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage ‘CX001’
2022-12-29 | GSE221778 | GEO
Project description:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line ‘FT’ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type ‘FT’, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of ‘FT’ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between ‘FT’ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. ‘FT’ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage.
2016-06-02 | GSE76917 | GEO
Project description:Pistil development is a complicated process in plants, and female sterile mutant is an ideal material for screening and cloning the pistil development-related genes. In our previous study, a female sterile mutant fsm (namely fsm1 here) was obtained from a Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. BraA04g009730.3C was predicted as the candidate gene for mutant fsm1. BraA04g009730.3C encoded STERILE APETALA (SAP), a transcriptional regulator, which played a role in regulating floral organ development. In this study, another female sterile mutant (namely fsm2) was derived from a population combining EMS mutagenesis and germinating seeds of ‘FT’. The phenotype of mutant fsm2 was consistent with that of fsm1, exhibiting pistil abortion, and smaller floral organs. Genetic analysis indicated that the phenotype of mutant fsm2 was controlled by a single recessive nuclear gene. Allelism testing showed that the mutant genes of fsm1 and fsm2 were allelic, named as Brfsm. A single-nucleotide mutation (G-to-A) in the first exon of BraA04g009730.3C caused a missense mutation from GAA (glutamic acid) to GGA (glycine) in mutant fsm2. Comparative transcriptome analysis on the pistils of wild-type ‘FT’ and mutant fsm1 revealed that a total of 3,855 differentially expressed genes (DEGs) were obtained, among which 29 genes related to ovule development and 16 genes related to organ size were identified. Based on the validation of qRT-PCR, we proposed the possible regulatory pathways whereby SAP may mediate pistil development in the fsm mutant. The mutation of BraA04g009730.3C in fsm plants was involved in the pistil abortion and smaller floral organ in Chinese cabbage. These results lay a solid foundation for elucidating the molecular mechanism of pistil development in Chinese cabbage.
2020-03-25 | GSE147438 | GEO
Project description:The hybrid seed production was performed using the male sterility line, which is an important way of heterosis utilization in Chinese cabbage. A stably inherited male sterile mutant msm was obtained from a Chinese cabbage DH line ‘FT’ using the isolated microspore culture combined with 60Co γ-rays mutagenesis. Compared to the wild type ‘FT’, the msm exhibited completely degenerated stamens and no pollen phenotype, and other characters had no significant difference except for stamen. The genetic analysis indicated that the msm mutant phenotype was controlled by a single recessive nuclear gene. Cytological observation showed that the stamen abortion of msm began at the tetrad period, and tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Comparative transcriptome analysis on the flower buds of ‘FT’ and msm using RNA-Seq technology revealed a total of 1,653 differentially expressed genes (DEGs). Among which, a large number of genes associated with male sterility were found, including 64 pollen development and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes and 16 transcription factor-related genes, and the overwhelming majority of these genes were down-regulated in the msm vs. ‘FT’ comparison. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, a total of 24,476 single nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results facilitate to elucidate the regulatory mechanisms of male sterility in Chinese cabbage.
2019-01-23 | GSE125485 | GEO
Project description:We performed microRNA profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differentially expressed miRNAs.
2018-03-30 | GSE111610 | GEO
Project description:We performed microRNA profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differentially expressed miRNAs.
2018-03-31 | GSE112035 | GEO
Project description:We performed transcript profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.
2018-03-30 | GSE111607 | GEO
Project description:We performed transcript profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.
2018-03-31 | GSE112034 | GEO
Project description:To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences. Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).
2014-03-14 | E-GEOD-45037 | biostudies-arrayexpress