Ontology highlight
ABSTRACT:
PROVIDER: PRJNA714261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13959503_1.fastq.gz | Fastqsanger.gz | |||
| SRR13959503_2.fastq.gz | Fastqsanger.gz | |||
| SRR13959504_1.fastq.gz | Fastqsanger.gz | |||
| SRR13959504_2.fastq.gz | Fastqsanger.gz | |||
| SRR13959505_1.fastq.gz | Fastqsanger.gz |
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Project description:We performed four small RNA sequencing for identification and characterization of microRNAs in Phalaenopsis aphrodite subsp. formosana. By comparing the low temperature-treated group with treated group, we concluded four miRNAs - miR156, miR162, miR528 and miR535 - as low temperature-induced miRNAs. In addition, tissue-specific expression of these miRNAs was investigated. The files contain the miRNAs analysis results in each group. Examination of low temperature-treated leaves and two other organs of Phalaenopsis orchid
2011-12-12 | E-GEOD-27585 | biostudies-arrayexpress
Project description:We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 μg of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. The degradome library was constructed by the Genomics BioSci & Tech. Company following the manufactoring protocol. In brief, 200 μg of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing. The files contain the raw data of degradome sequencing. Examination of one degradome of mixed tissues of Phalaenopsis orchid
2012-11-06 | E-GEOD-35739 | biostudies-arrayexpress
Project description:Phalaenopsis aprodite subsp. formosana is one of the most important species for Phalaenopsis breeding. A mutant line with variegated leaf is found in this species. The green leaves bear unstable yellow sectors. In order to investigate the molecular mechanism of the variegated mutant line, we sequenced the transcriptome of variegated mutant by Illumina's Solexa sequencing technology. The sequence analysis results showed 22,598 unigenes by de novo assembly method, and the average unigene length was 1,286 bp. The bioinformatics tools were used to screen the differential expression between green and yellow sectors of leaves. There were 389 differentially expressed unigenes were identified. In addition, Gene ontology (GO) and KEGG pathway analyses revealed diverse biological functions and processes from differentially expressed genes. In transcriptome analysis, seven differential expression gene between the green and yellow sectors of leaves can be identified as CHLM, CRD1, POR, CLH, SGR, psbA and Lhcb6 by RNA deep sequencing. The expression of candidate genes was confirmed using semi-quantitative reverse transcription (RT) PCR and real-time RT PCR. The result showed that the significantly differential expression of CLH and SGR between green and yellow sectors was confirmed. It is suggested that the overexpressed SGR gene promotes the function of chlorophyllase, leading to the rapid degradation of chlorophyll in yellow sector. It causes the chlorophyll to not accumulate in the yellow sector, as a result, the variegated leaves are shown.
2018-07-01 | GSE73123 | GEO
Project description:Viral siRNA generated from antiviral RNA silencing machinery was profiled using small RNA sequencing from Phalaenopsis orchid mixed infected with CymMV and ORSV
2020-01-01 | GSE94083 | GEO
Project description:Female honeybees are specified as workers or queens based on diet during early development. Workers are essentially sterile with a reduced number of ovarioles and no spermatheca. In the presence of the queen (queen mandibular pheromone) and her brood, worker ovaries are kept in an inactive quiescent state. If the queen is removed, or lost, worker bees are able to sense this change in their environment and their ovaries undergo complete remodelling producing unfertilised haploid eggs that will produce male (drone bees). In this study we analyse gene expression in queen, worker, and laying worker ovaries using RNA-seq and explore differences in the chromatin landscape (focussing on H3K27me3).
2019-09-17 | GSE120560 | GEO
Project description:Honeybees are very important eusocial insects and are involved in the pollination of many plants. Queen bees and worker bees develop from the same fertilized eggs, and are thus genetically identical despite their substantial behavioural and physiological differences. The mechanism governing developmental differences between worker and queen bees has always attracted much interest. While there are several reports on mRNA expression related to caste differentiation, no systematic investigation of small RNAs has thus far been carried out. Results: Using deep sequencing we systematically profiled small RNA expression in 4th-6th day worker larvae and queen larvae (the critical stages at which the fates of workers and queens are determined), and found that 38 miRNAs were differentially expressed between worker and queen larvae. In addition, 639 mature miRNA candidates were identified in our work for the first time, of which, 526 were expressed only in workers (318) or queens (208). Conclusion: We present the first profile of honeybee small RNAs and explore the mechanism of caste differentiation between worker and queen bees. Caste-specific expression patterns and large discrepancies in small RNA profiles between worker and queen bees indicate that small RNAs may be related to the differential development of worker and queen bee larvae. Results presented here will make a valuable contribution to understanding the caste switch between worker and queen bees.
2014-07-28 | GSE52630 | GEO
Project description:Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.
2018-06-30 | GSE70411 | GEO
Project description:Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. Importantly, we find that these regulatory regions are enriched in transcription factor binding motifs and using ATAC-seq footprinting we identify queen, worker and drone - specific occupancy and uncover novel transcription factor networks.
2022-11-09 | GSE206992 | GEO