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.
Project description:Methods: The cDNA libraries from 3 pooled samples of liver tissues for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 22.67 M reads with an average length of 100 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.
Project description:Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.
Project description:In this study, we sequenced small RNA content from three different rice cultivars employing Illumina technology. More than 15 million reads were generated using Illumina high-throughput sequencing platform. After pre-processing, distinct small RNA sequences were identified for each rice cultivars. We collected seedlings of different rice cultivars and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were pre-processed using modified perl script provided in the miRTools software. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the rice genome to find their location.
Project description:We constructed strand-specific cDNA libraries of 23 total RNA samples (human cell lines and patient samples) and sequenced the libraries using Hiseq 4000 platform. More than 80 millions of mappable reads for each sample have been obtained.
Project description:Whole blood samples were collected from seven elite female skaters on the peak of altitude adaptation (day 18), before and after ~ 1h long exercise. Samples were globin-depleted and polyA-selected, converted to cDNA, and sequenced using Illumina paired-end reads (12-40M reads).
Project description:In this study, we aim to present the complete transcriptome of Asian wild rice, Porteresia. We generated about 375 million high-quality reads for five different conditions (ranging from 65 to 90 million reads for each condition) using Illumina high-throughput sequencing GAII platform. We mapped the reads to Porteresia transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during conditions. We collected different tissue samples after various treatments (control, in water; salt450, in 450 mM sodium chloride solution; salt700, in 700 mM sodium chloride solution; submergence, submerged in water; salt+submergence, submerged in 450 mM sodium chloride solution) and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Porteresia transcripts and reads per kilobase per million (RPKM) was calculated for each transcript in all the samples to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes showing differential expression under various stress conditions were identified.
Project description:The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia Cryopreserved leukemic bone marrow samples were thawed, and 50,000 bulk leukemia (GFP+) cells were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared. Quantitative PCR using the Library Quantitation kit (Kapa Biosystems) was used to estimate library concentrations. Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample. Libraries were sequenced on the Illumina HiSeq 2000 platform.
