Meghimatium bilineatum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1012835 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25919043_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR25919044_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Meghimatium bilineatum Raw sequence reads
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Project description:Meghimatium bilineatum is a notorious pest land slug used as a medicinal resource to treat ailments in China. Although this no-model species is unique in terms of their ecological security and medicinal value, the genome resource of this slug is lacking to date. Here, we used the Illumina, PacBio, and Hi-C sequencing techniques to construct a chromosomal-level genome of M. bilineatum. With the Hi-C correction, the sequencing data from PacBio system generated a 1.61 Gb assembly with a scaffold N50 of 68.08 Mb, and anchored to 25 chromosomes. The estimated assembly completeness at 91.70% was obtained using BUSCO methods. The repeat sequence content in the assembled genome was 72.51%, which mainly comprises 34.08% long interspersed elements. We further identified 18631 protein-coding genes in the assembled genome. A total of 15569 protein-coding genes were successfully annotated. This genome assembly becomes an important resource for studying the ecological adaptation and potential medicinal molecular basis of M. bilineatum.
| S-EPMC10770140 | biostudies-literature
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
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
Project description:Purpose: The goal of this study was to identify differentially expressed genes and pathways between the cumulus of compact/unstimulated cumulus-oocyte-complex (COC) and the cumulus of expanded/stimulated COC. Methods: mRNA profiles of Compact/unstimulated cumulus cells (CCs) from germinal vesicle (GV) COC obtained from two patients undergoing unstimulated IVM procedure and expanded/stimulated CCs from metaphase 2 (MII) COC obtained from three patients undergoing IVF/ICSI were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were mapped to the human genome (hg19) using Tophat software. Differential expression analysis was done using DESeq bioconductor package. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 40-80 million sequence reads per sample were mapped to the human genome (hg19). A total of 1746 differentially expressed genes between compact and expanded CCs with fold change > 2, and adjusted p value < 0.05 were identified. Gene ontology analysis of differentially expressed genes revealed a number of cellular processes regulated during the periovulatory interval including cellular movement, inflammatory response, immune cell trafficking, tissue development, lipid metabolism, tissue morphology, DNA replication and cell cycle. A total of 116 of the differentially expressed genes were annotated as long non-coding RNAs, 10 of them coded from introns of genes known to be involved in granulosa cell processes suggesting that unique non coding RNA transcripts may contribute to the regulation of cumulus expansion and oocyte maturation. Results were validated using qRT-PCR. Conclusions: Using global transcriptome sequencing we identified new important genes and non coding RNAs involved in COC maturation and cumulus expansion, which may contribute to improve the process of in vitro maturation of immature oocytes utilized in IVM cycles mRNA profiles of Compact/unstimulated cumulus cells (CCs) from germinal vesicle (GV) COC obtained from two patients undergoing unstimulated IVM procedure and expanded/stimulated CCs from metaphase 2 (MII) COC obtained from three patients undergoing IVF/ICSI were generated by deep sequencing using Illumina HiSeq 2000.
2014-06-04 | E-GEOD-50174 | biostudies-arrayexpress