Transcriptome sequencing of Cleome hassleriana for different tissues
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ABSTRACT:
ORGANISM(S): Tarenaya hassleriana
PROVIDER: GSE41092 | GEO | 2013/05/01
SECONDARY ACCESSION(S): PRJNA175769
REPOSITORIES: GEO
Similar Datasets
Project description:We have sequenced the whole genome of Cleome hassleriana by NGS [SRA accession number SRA058749] and build a reference sequence for this genome. In order to improve quality of gene models, a mix transcriptome sample extracted from the bud, leaf, petiole, stems and flowers of Cleome. A mixed RNA pool extracted from the tissues of bud, leaf, petiole, stems and flower is sequenced for Cleome hassleriana.
2013-05-01 | E-GEOD-41092 | biostudies-arrayexpress
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
Project description:Arabidopsis plants transfer information from the leaf tip to the petiole base to induce adaptive upward leaf movement upon neighbour detection through Far-Red light enrichment in the leaf tip. To determine how a distally derived signal can specifically regulate growth in the abaxial petiole we analysed the transcriptome in the leaf tip and abaxial-adaxially split petiole sections during the first hours of far-red enrichment.
2022-12-20 | GSE218944 | GEO
Project description:Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development. Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana. Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.
2022-12-29 | GSE218959 | GEO
Project description:Gene expression of all tomato genes was determined by replicated (two biological replicates of each tissue) strand-specific Illumina RNA-Seq of root, leaf, flower (2 stages) and fruit (6 stages). Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2012-02-15 | E-MTAB-4812 | biostudies-arrayexpress
Project description:The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained.
2015-01-26 | GSE60105 | GEO
Project description:To reveal the molecular mechanism during de novo root regeneration from Arabidopsis leaf explants cultured on B5 medium without exogenous hormones, we carried out an RNA-seq experiment using detached leaf explants with partial petiole before culture (i.e. time 0) and 2 d after culturing (DAC) from12-d-old Col-0 seedlings. Gene expression of the wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was analyzed.
2019-10-22 | GSE139165 | GEO
Project description:Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested. Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts. Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated. Fibroblasts mRNA profiles of mouse with different treatments and adult DP and embryonic dermal fibroblasts were generated by next generation sequencing. SRA study accession: SRP081009; BioProject accession: PRJNA337890
2016-08-10 | E-GEOD-85303 | biostudies-arrayexpress
Project description:Potocki-Shaffer syndrome (PSS) is a rare contiguous gene deletion syndrome marked by haploinsufficiency of genes in chromosomal region 11p11.2p12. Approximately 50 cases of PSS have been reported; however, a syndrome with a PSS-like clinical phenotype caused by 11p11.12p12 duplication has not yet been reported. We first report the 11p11.12p12 duplication in a family with intellectual disability and craniofacial anomalies. 11p11.12p12 duplication syndrome was identified by karyotype analysis. Next-generation sequencing (NGS) analysis clarified the location of the chromosomal variations, which was confirmed by chromosome microarray analysis (CMA). Whole-exome sequencing (WES) was performed to exclude single nucleotide variations (SNVs). The raw data of NGS analysis and WES have been submitted to SRA, the accession number is PRJNA713823.
2021-03-24 | GSE169469 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. These data are associated with single-cell RNA-seq data available at SRA at accession: SRP217361
2019-08-07 | GSE135461 | GEO