Project description:Insect derived cell-lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (High Five), are ones of the most widely used systems for recombinant protein expression in Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 or absent for High Five. In this study we present an approach using different sequencing data types with short-read sequencing, long synthetic and Oxford Nanopore reads to build genomes at an unprecedented resolution. The Sf21 and High Five assemblies contain 4,020 scaffolds of size, 463 Mb with N50 of 364 Kb and 2,954 scaffolds of size, 332 Mb with N50 of 326 Kb, respectively. Furthermore, we build a new gene prediction workflow, which integrates transcriptome proteome information using pre-existing tools. Using this approach, we could predict 21,506 Sf21 genes and 14,159 High Five genes, which were then functionally annotated. Finally, we also generate and integrate proteomic datasets to validate predicted genes. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and High Five cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identifications to genome engineering and editing.

2022-03-03 | PXD010282 | Pride

Analysis of the bacterial diversity in the intestine of five skippers

Project description:microbial community density and membership within five species in family Hesperiidae Raw sequence reads

| PRJNA331003 | ENA

Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

Sequencing of siRNA from soybean containing silencing vectors and empty vectors

Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed

2021-07-21 | GSE180131 | GEO

Quantitative Analysis of Cerebral Cortex Transcriptomes of BrapcKO Mice and their Wildtype-like Control Mice by Next-Generation Sequencing

Project description:Purpose: Transcriptome profiling (RNA-seq) was performed in this study in order to assess differential gene expressions resulting from Brap loss of function in murine cerebral cortex. Methods: Cerebral cortical mRNA profiles of 3-month-old Emx1-Cre-mediated Brap conditional knockout mice (BrapcKO) and their Cre-negative control littermates (Brap flox Cre-) were generated by next-generation sequencing, using Illumina HiSeq4000. Five BrapcKO and five control samples were analyzed. The quality of raw sequencing data was assessed using FastQC. Sequence reads that passed quality filters were analyzed by several methods, including DESeq2, edgeR, and Iimma, to discover differentially expressed genes. Results: We obtained more than 30 million sequence reads per sample that are uniquely mapped to the mouse reference genome (build mm10). After alignment of reads, expression levels of individual genes were quantified and estimated using subread::featureCounts. With the removal of lowly expressed genes using the threshold at least 10 raw read counts, 14,276 out of 21,969 annotated, valid mouse genes were retained for further analysis. Data were analyzed using several state-of-the-art tools, including DESeq2, edgeR, and Iimma, with a fold change ≥1.5 and FDR < 0.1. We collected overlapped differentially expressed mRNA genes detected with more than one method, and identified 811 differentially expressed genes between BrapcKO and control group. Conclusions: Our study represents detailed analysis of transcriptomes, with biologic replicates, generated by RNA-seq technology. The data provide insight into the neurological defects of BrapcKO mice.

2021-09-05 | GSE183383 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of epididymal adipose tissue transcriptomes from mice fed either a control-diet or aWestern-diet for one or five successive generations

Project description:Purpose: Successive paternal generations of unhealthy diet induce a fat mass increase. The goal of this study is to compare epididymal adipose tissue transcriptome profiling (RNA-seq) of mice fed either a control-Diet or a High-Fat-Diet for One or Five successive generations. The aim of the study is to identify differentially expressed RNA in epididymal adipose tissue of obese males which might be involved in the exacerbation of induced by the maintenance of High Fat Diet feeding for 5 successive generations. Methods: Epididymal adipose tissue mRNA profiles of 18-months-old mice fed either a control-Diet or a Western-Diet for One or Five successive generations were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were quantitavely analyzed. Reads abundance was evaluated for each gene followed by annotation versus mouse GTF by using the featureCounts function.The R package Edger was used in order to normalize the reads and to identify differentially expressed (DE) genes. Results: RNA-seq data revealed a specific enrichment in gene related to metabolic syndrome traits in male mice obtained after successive paternal generations of Western-Diet.

2021-04-15 | GSE148972 | GEO

Sediment samples from five different sites of the Salar de Huasco (Chilean - Altiplano)

Project description:Sediment samples from five different sites of the Salar de Huasco (Chilean - Altiplano) Raw sequence reads

| PRJNA573913 | ENA