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RKI SARS-CoV-2 integrated genomic surveillance sequencing reads

ABSTRACT: SARS-CoV-2 raw sequencing reads produced at the Robert Koch Institute, primarily from samples provided by the IMSSC2 Laboratory Network.

PROVIDER: PRJEB76939 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13319800.fastq.gz	Fastqsanger.gz
	ERR13319900.fastq.gz	Fastqsanger.gz
	ERR13320000.fastq.gz	Fastqsanger.gz
	ERR13320100.fastq.gz	Fastqsanger.gz
	ERR13320200.fastq.gz	Fastqsanger.gz

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Cyprinus carpio 'koi' Raw sequence reads

Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.

2019-01-15 | GSE125039 | GEO

Urinary miRNA biomarkers of the rat kidney nephron

Project description:The Health and Environmental Sciences Institute initiated a cross-laboratory program to identify and characterize microRNA (miRNA) patterns reflecting nephron-specific localization in naïve adult male Sprague-Dawley rats.

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InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

Project description:BackgroundNext-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads generated by sequencers such as Illumina. To date, how to generate a high-quality draft assembly for metagenomic sequencing projects has not been fully addressed.ResultsWe conducted a comprehensive assessment on state-of-the-art de novo assemblers and revealed that the performance of each assembler depends critically on the sequencing depth. To address this problem, we developed a pipeline named InteMAP to integrate three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision of which assembling approaches to use according to the sequencing coverage estimation algorithm for each short read, the pipeline presents an automatic platform suitable to assemble real metagenomic NGS data with uneven coverage distribution of sequencing depth. By comparing the performance of InteMAP with current assemblers on both synthetic and real NGS metagenomic data, we demonstrated that InteMAP achieves better performance with a longer total contig length and higher contiguity, and contains more genes than others.ConclusionsWe developed a de novo pipeline, named InteMAP, that integrates existing tools for metagenomics assembly. The pipeline outperforms previous assembly methods on metagenomic assembly by providing a longer total contig length, a higher contiguity and covering more genes. InteMAP, therefore, could potentially be a useful tool for the research community of metagenomics.

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