Ontology highlight
ABSTRACT:
PROVIDER: PRJNA780774 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17276384_1.fastq.gz | Fastqsanger.gz | |||
| SRR17276384_2.fastq.gz | Fastqsanger.gz | |||
| SRR17276385_1.fastq.gz | Fastqsanger.gz | |||
| SRR17276385_2.fastq.gz | Fastqsanger.gz | |||
| SRR17276386_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Tag-based approach for global gene expression analysis has been revolutionised with the advent of next generation sequencing (NGS) technology. The aim of the present study is to present comprehensive view of differentially expressed genes under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.) Methods: DeepSAGE, a tag based approach, was used to identify differentially expressed genes under cold and freeze treatments in seabuckthorn (Hippophae rhamnoides L.). The 30 days old plantlets, at six leaves stage, were subjected to cold stress (CS) at 4°C and freeze stress (FS) at -10°C treatment for 6 hr. The seedlings grown at 28°C were taken as control (CON). Total RNA from all the three samples was isolated. Illumina Gene Expression Sample Prep Kit and Solexa Sequencing Chip (Flowcell) were used for tag preparation and the main instruments used for sequencing included Illumina Cluster Station and Illumina HiSeqTM 2000 System. Bioinformatics analysis resulted in to high number of differentially expressed genes under cold and freeze stress. Results: 36.2 million raw tags including 13.9 million distinct tags were generated from three leaf tissue libraries (control, cold stress and freeze stress). After removing low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In total, 11922 differentially expressed genes (DEGs) were identified including 6539 up regulated and 5383 down regulated genes. Conclusions: DeepSAGE data of seabuckthorn provided useful resource and reference dataset for further functional genomics analysis in seabuckthorn and other important crops. The present study implicated a large number of genes with different biological functions expressing differentially in response to cold and freeze stress treatment. Isolation and further characterization of these genes will help researchers in understanding their role in cold and freeze tolerance in seabuckthorn and may provide important gene resources to be exploited for the development of stress tolerant crop plants in future.
2017-02-09 | GSE62489 | GEO
Project description:Hippophae rhamnoides strain:Seabuckthorn Transcriptome or Gene expression
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Project description:Plant-parasitic cyst nematodes induce syncytial cells in the roots of their host plants. Cyst nematodes are sexually dimorphic, with their differentiation into male or femaleis strongly influenced by host environmental conditions. Under favorable conditions with plenty of nutrients, more females develop, whereas mainly male nematodes develop under adverse conditions, such as in resistant plants. We collected root segments containing male-associated syncytia (MAS) or female-associated syncytia (FAS), isolated syncytial cells by laser microdissection, and performed a comparative transcriptome analysis using Microarrays.
2020-01-12 | E-MTAB-8648 | biostudies-arrayexpress
Project description:Simple Markov model.
There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal.
The yearly transition probabilities are:
Healthy to Dead: 0.01; Healthy to Sick: 0.2 for Male and 0.1 for Female; Sick to Healthy: 0.1; Sick to Dead: 0.3.
The transition probability now depends on the cohort (Male or Female) and can be expressed as a function of a Boolean covariate Male.
Initial conditions: Healthy = (50 Male, 50 Female), Sick = (0,0) and Dead = (0,0).
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Project description:The unraveling of heterogenous cell populations, — previously masked in bulk transcriptome measurements — are made possible through analysis of single-cell transcriptomics. The goals of this study are to examine single-cell NGS-derived gonadal cell transcriptome profiling and to evaluate heterogeneity of gonadal germ cells in avian species. We performed single-cell RNA sequencing using embryonic gonadal cells of HH stage 28 from male and female zebra finches. We identified 12,489 male transcripts and 10,046 female transcripts. We annotated 9 different cell types from a total of 20 clustered single cells and identified that primordial germ cells, which have been considered as single population, can be distinguishable into three subtypes. The three PGC subtypes were specifically enriched for genes with expression patterns related to germness or pluripotency, suggesting functional differences in PGCs according to the three subtypes. Our study represents the first single-cell RNA seq analysis of gonadal transcriptomes in zebra finch. Our results revealed the first heterogeneity and intrinsic changes of gonadal primordial germ cells, which have hitherto been considered as a single population in avian species. We conclude that single-cell RNA seq based transcriptome analysis would offers new perspectives on avian primordial germ cells.
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Project description:Tag-based identification of differentially expressed genes under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.)
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Project description:The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant. Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2017-11-16 | GSE106954 | GEO
Project description:The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome.
2015-01-21 | E-GEOD-53793 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived TOX associated transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: mRNA profiles of human CD8+ T cell overexpressed by TOX lentivirus or NC lentiviruswere generated by deep sequencing, in triplicate, using Illumina. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: Our study represents the first detailed analysis of TOX associated transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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