Valsa pyri
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA849363 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Valsa mali var. pyri isolate:Vp297 Raw sequence reads
| PRJNA588311 | ENA
Project description:Valsa mali var. pyri strain:SXYL134 Genome sequencing and assembly
| PRJNA268128 | ENA
Project description: Not available
| S-EPMC6965324 | biostudies-literature
Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .
2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate differential genes expression with RNA-seq in primary cultured astrocytes treated with the Tgf-beta1 receptor inhibitor SB431542, the Runx1 inhibitor Ro5-3335 and the E2f1 inhibitor HLM006474. Methods: Primary cultured astrocytes were isolated from either C57BL/6 wild-type neonatal mice. Total RNA was extracted from SB431542, Ro5-3335 and HLM006474-treated astrocytes with the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays. Results: After quality control and data filtering, about 50 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts vehicle, SB431542, Ro5-3335 and HLM006474 group. Differentially expressed genes (DEGs) were analyzed with a fold change ≥1.5 and p value <0.05. A total of 748 DEGs were identified in SB431542 group with 347 upregulated genes and 401 downregulated genes. A total of 397 DEGs were identified in Ro5-3335 group with 82 upregulated genes and 315 downregulated genes. A total of 856 DEGs were identified in HLM006474 group with 216 upregulated genes and 640 downregulated genes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in the C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474-treated astrocytes.
2022-11-23 | GSE174523 | GEO
Project description:Comparative transcriptome analysis was performed to study gene expression profiles in resistant (Yanyan 97, YY97, 25) and susceptible (Huanghuadajinyuan, HD, 36) tobacco in responding to Ralstonia solanacearum infection. Illumina sequencing yielded a total of 67,619,833,668 bases data, and about 223.99 M and 223.82 M raw reads for Hd and Yy97 plants, respectively. About 209.73 M and 209.18 M clean reads of Hd and Yy97 were mapped to reference genome via Hisat2, respectively. The ratio of mapped clean reads for eight libraries ranged from 93.92% to 96.67% (average: 95.9%). By comparing gene expression levels in Rs infected and control tobacco stems, we identified 15374 DEGs in Hd plants after Rs infection, which included 7220 up-regulated and 8154 down-regulated DEGs. We identified 2120 DEGs in Yy97 plants after Rs infection, which included 1794 up-regulated and 326 down-regulated DEGs.
2019-04-20 | GSE113473 | GEO
Project description:Two ramie cultivars, Zhongzhu no 2(Z2) and Huazhu no 4 (H4), showed constructing adventitious root formation (ARF) rate. Comparative transcriptome analysis was performed to study gene expression profiles in Z2 and H4 ramie during adventitious root formation. Illumina sequencing yielded a total of 92,794,556,688 bases data, and about 301.47 M and 313.06 M raw reads for Z2 and H4 plants, respectively. After quality control, every library obtained over 43 million reads, which is enough for the quantitative analysis of gene expression. Using Trinity software, these clean reads were first assembled into 121,492 transcripts, finally into 66,881 unigenes with an average length of 1144.25 bp. About 148.74 M and 138.72 M clean reads of H4 and Z2 were mapped to reference genes via Bowtie, respectively. The ratio of mapped clean reads for eight libraries ranged from 74.47% to 75.38% (average: 74.8%). By comparing gene expression levels in Tm and CK ramie stems, we identified 772 DEGs in H4 plants during RPF, including 7220 up-regulated and 8154 down-regulated DEGs. We identified 1256 DEGs in Z2 plants during RPF, which included 779 up-regulated and 447 down-regulated DEGs. We also identified 1919 DEGs between Z2 and H4 plants. There were 1147 (731 up-regulate and 416 down-regulated) DEGs uniquely in Z2, and 603 (202 up-regulate and 461 down-regulated) DEGs uniquely in H4 plants. The two genotypes shared 109 DEGs, which indicates some common pathways during ARF.
2019-06-20 | GSE116063 | GEO