Ontology highlight
ABSTRACT:
PROVIDER: PRJNA679726 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:species in tribe Dorstenieae (Moraceae) Raw sequence reads
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Project description:Morus alba L. Raw protein sequence reads and sequence
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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.
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Project description:Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)
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Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
2019-12-16 | PXD016522 | Pride
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
Project description:Physcomitrium patens raw sequence reads: TRIBE and RIP
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Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.
2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to compare exosomal small RNA transcriptome of HCT116 cells to identify the target of PRDX3 under basal or knock down conditions by utilizing miRNA-seq. Methods: miRNA profilies of siCTL or siPRDX3 transfected HCT 116 exosoems were generated by illumina sequencing method, in triplicate. After sequencing, the raw sequence reads are filtered based on quality.Sequence reads were mapped with the bowtie2 software tool, which yielded bam files. Mature miRNA sequences were used as references for mapping. Read counts mapped to a mature miRNA sequence were extracted from the alignment file using bedtools v2.25.0 and Bioconductor, which use the R statistical programming language. Read counts were used to determine the expression level of miRNAs. The CPM+TMM normalization method was used for between-sample comparison. Results: We identified known miRNA in species (miRDeep2) in the HCT116 exosome transfected with siCTL or siPRDX3. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of HCT116 exosomal miRNA profiles affected by PRDX3 knockdown with biologic replicates.
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Project description:Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. We developed a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. We tested our method using bone samples from 30 vertebrate species ranging from mammals to fish.
2023-12-14 | PXD045402 | Pride