Ontology highlight
ABSTRACT:
PROVIDER: PRJNA991430 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Illumina technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines. RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System. Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 using CLC Genomics Workbench v9.5.2 and the primary transcripts only.
2019-01-15 | GSE112673 | GEO
Project description:Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were filtered and trimmed using erne-filter command. Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1) using TopHat2 v2.12.
2023-09-12 | GSE175506 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]
2021-10-28 | GSE186743 | GEO
Project description:We overexpressed the brassinolide synthase DET2 in 84K poplar and obtained an overexpression material.It was found that the brassinolide content of the overexpression material increased significantly.And it was found that the plant height, diameter, and number of internodes of the overexpression material increased significantly.However,the mechanism of this phenotype is unknown.We collected two-month-old DET2 overexpression material and 84K wild-type material in three parts, apex,cambium,and xylem,and conducted high-throughput sequencing.The sequencing results were mined, and the difference genes that were significantly changed in the DET2 overexpression material and the 84K wild-type material were found.Find out how the increase in brassinolide content promotes the development of wood.
2022-09-20 | GSE176470 | GEO
Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) in human lung cancer cells. The mRNA profiles of wild-type and C19orf12 knockdown A549 cells were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Burrows–Wheeler Aligner (BWA) and Bowtie2. we sequenced 6 samples of human species using RNA-Seq technology, averagely generating 24,382,600 raw sequencing reads and 24,299,184 clean reads after filtering low quality. We identified 20826 transcripts in the of WT and C19orf12 knockdown A549 samples with BWA workflow. Approximately 2% of the transcripts showed differential expression between the WT and C19orf12 knockdown A549 cells, p value <0.05. Altered expression of 21 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. We conclude that RNA-seq based transcriptome characterization would providing clues for better understanding of gene function.
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