Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388517 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5630766.fastq.gz | Fastqsanger.gz | |||
| SRR5630747.fastq.gz | Fastqsanger.gz |
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Project description:Investigation of whole genome gene expression level changes in a resistance susceptible and LeHT1-silenced resistance tomato plants, infected with TYLCV and compared to the non infected control. Two inbred tomato lines (named R and S) were used issued from a breeding program describe by Vidavsky and Czosnek, 1998, and Silencing of the hexose transporter gene LeHT1 and the properties of these plants have been described by Eybishtz et al., 2010. The array was designed to include all the known tomato genes retrieved from TIGR and Sol Genomics public databases. Following filtration for redundancies, 25,591 known genes and 7,335 uncertain or unknown genes were retrieved The data were transferred to Roche NimblGen company (http://www.nimblegen.com/) who has generated a 60-mer oligonucleotide array where each of the ~30,000 tomato genes is represented by at least two specific probes, and unrelated controls. Each slide contains four arrays of ~70,000 oligos. TYLCV resistant and susceptible lines infection with TYLCV and LeHT1 silenced TYLCV resistant line infected with TYLCV
2012-09-26 | E-GEOD-41135 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a resistance susceptible and LeHT1-silenced resistance tomato plants, infected with TYLCV and compared to the non infected control. Two inbred tomato lines (named R and S) were used issued from a breeding program describe by Vidavsky and Czosnek, 1998, and Silencing of the hexose transporter gene LeHT1 and the properties of these plants have been described by Eybishtz et al., 2010.
2012-09-26 | GSE41135 | GEO
Project description:High-throughput sequence analysis of small RNAs of TYLCV-tolerant (containing tolerance gene Ty-1) and susceptible varieties indicated that miRNA-like vsRNAs and secondary vsiRNAs are mainly contributed to hotpots. Interestingly, various characteristics of vsRNAs among each sample are consistent, but in different number of expression; Deep sequencing of degradome provided evidence for the function of vsRNAs-mediated viral transcripts slicing; And bisulfite sequencing PCR suggested the geminivirus DNA methylation induced by vsRNAs. Comparison of the expression quantity and trend of viral DNA, mRNA and vsRNA inferred that the quantity of vsRNAs is significantly corresponding to the expression level of viral mRNA. Nevertheless, vsRNAs had finite effect on inhibition of virus replication and expression. Here, we also speculated that by RDR catalysis of vsRNAs amplification, the tolerance gene Ty-1 may take an effective inhibition of viral transcription at the beginning of TYLCV infection.
2016-08-22 | GSE50085 | GEO
Project description:High-throughput sequence analysis of small RNAs of TYLCV-tolerant (containing tolerance gene Ty-1) and susceptible varieties indicated that miRNA-like vsRNAs and secondary vsiRNAs are mainly contributed to hotpots. Interestingly, various characteristics of vsRNAs among each sample are consistent, but in different number of expression; Deep sequencing of degradome provided evidence for the function of vsRNAs-mediated viral transcripts slicing; And bisulfite sequencing PCR suggested the geminivirus DNA methylation induced by vsRNAs. Comparison of the expression quantity and trend of viral DNA, mRNA and vsRNA inferred that the quantity of vsRNAs is significantly corresponding to the expression level of viral mRNA. Nevertheless, vsRNAs had finite effect on inhibition of virus replication and expression. Here, we also speculated that by RDR catalysis of vsRNAs amplification, the tolerance gene Ty-1 may take an effective inhibition of viral transcription at the beginning of TYLCV infection. Examination of 6 different sRNA and 4 degradome library in 2 tomato material. The main result of our paper is distinguish the host plant sRNA and viral-derived sRNA from the .fa files (MMS_21dpi, 30dpi and TY1S_21dpi, 30dpi).
2016-08-22 | E-GEOD-50085 | biostudies-arrayexpress
Project description:Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice leaf tissue infected with M.oryzae of resistant and suceptible line. The results were validated using real time PCR. Methods: Rice leaves were collected 24 hours after M. Oryza (Mo-nwi-53) infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). RNA libraries were prepared for sequencing using standard Illumina protocols. Results: Around 30 million pairs of filtered 101 base paired reads were obtained for each biological replicate. These reads were mapped against RGAP7 using Tophat and approximately 90% aligned to the RGAP 7 while 10% reads were unaligned. Approximately 1-2 million reads returned multiple hits to the RGAP7. After alignment mapped reads were assembled using Cufflink and differentially expressed locus (DEL) were called using Cuffdiff. Statistical test was applied to find significant differentially expressed locus id after multiple corrections (FDR adjusted p value ≤0.05). We obtained 8,418 and 3336 significant (FDR adjusted p value ≤0.05) differentially expressed locus id in the resistant and susceptible rice line, respectively . The number of significant DEL with fold change value greater and les than 2.0 were 1254 (850 upregulated 404 downregulated) and 781 (466 upregulated & 313 downregulated)in in resistance and susceptible lines, respectively. The final data represents the transcriptome of both resistant and susceptible line after mock and M.oryzae infection. The pathway and gene set enrichment analysis was performed to find changes in biological process and molecular function in resistant (PB1+ Pi9) and susceptible (PB1) rice line upon M.oryzae infection. The qRT PCR was performed to validate selected candidate genes playing important role in rice defense upon M.oryzae infection. Conclusions: Our study represents the first detailed transcriptome analysis of resistant near isogenic line (PB1+ Pi9) and its susceptible control (PB1) with biological replicates upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis helps to expedite protein network analyses and dissection of complex biological functions. In summary we found that a single functional blast resistant gene Pi9 present in resistant NIL in the background of susceptible line (PB1) activates a cascade of defense response genes, leading to incompatible interaction.
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Project description:To identify blast pathogen elicited miRNAs, four sRNA libraries were constructed: 8749036, A library, susceptible rice cultivar Zhonger-Ruanzhan; 12157795, B library, mock-treated blast resistant line H4; 9937360, C library, blast-treated susceptible rice cultivar Zhonger-Ruanzhan; and 11138187 clean reads, D library, blast-treated blast resistant line H4. The Short Oligonucleotide Analysis Package (SOAP; Beijing Genomics Institute) matched 85.46% (A, 7476714), 79.35% (B, 9647324), 77.70% (C, 7721715) and 76.10% (D, 8476386) sRNA reads to the genome. After removing other RNA categories matched to NCBI Genbank, Rfam database, known rice miRNA precursor, repeat associated RNA and siRNA, the remaining reads: 1681359(A); 3829741(B); 3182403(C); and 3970132(D), were used for further novel miRNA prediction. Since some miRNAs were tissue-specific, time-specific or stress-induced, only 291, 210, 164 and 220 registered miRNAs were identified in libraries A, B, C and D respectively. Thirty-one (A, 9385 reads), 399(B, 41024 read), 351(C, 36622 reads) and 333(D, 38064 reads) unique sRNAs were projected to be candidate miRNAs.
2016-01-01 | GSE36205 | GEO
Project description:In this study, the resistant and susceptible monoclonal CIK cell lines were first established which would be the ponderable research models for the nosogenesis mechanism of the hemorrhagic disease. C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) samples were carried out RNA-Seq, MeDIP-Seq and small RNA-Seq by the next-generation sequencing strategy, bioinformatics analysis as well as experimental verification. It was discovered that the aboriginality of CIK cells were gravitated to the susceptible trait. And the discrepancies between resistance and susceptibility against GCRV could primarily attribute to antioxidant activity, cell killing activity and cell proliferation regulation. Here we comprehensively present the profiling and characteristics of DNA methylation and microRNA in the resistant and susceptible CIK cells and proposed that high mCHH methylation distribution might be a characteristic modulator in C. idella. What’s more, a series of genes modulated by DNA methylation or microRNA were designated as potential biomarkers for the resistance breeding. This study laid the foundation and opened novel avenues for nosogenesis research on hemorragic disease of C. idella.
2016-09-28 | GSE87413 | GEO
Project description:Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiations, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory gene-based marker assisted selection depends on accurate identification of stress induced miRNAs.
2017-01-17 | GSE83738 | GEO
Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
2014-04-15 | E-MTAB-1630 | biostudies-arrayexpress