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.
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:Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae)
Project description:Purpose: The aim was to find the differentially expressed genes between the WT1 overexpressed group and the control group Methods:Hacat cell was transfected with WT1 overexpressed plasmids and blank plasmids, then RNA from both groups of cells was sequenced. The data obtained from the sequencing is called raw reads, and then the raw reads are subject to quality control QC. After the quality control is passed, the filtered clean reads are compared to the reference genome, This was followed by gene Quantitative analysis, gene expression level based analyses, and more in depth mining analyses such as GO functional significance enrichment analysis and pathway significance enrichment analysis for the selected differentially expressed genes between samples. Conclusions:Our study was the first to analyze the transcriptome of Hacat cells overexpressing WT1 generated by RNA-seq technique and to conduct biological replication. Six samples were measured using BGISEQ-500 platform, and the average output of each sample was 21.89 m. The average ratio of sample to genome was 94.81% . A total of 17,693 genes were detected. A total of 181 differentially expressed genes between the two groups were analyzed by GO and Kegg.
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.
