Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
Project description:The intent of the experiment was to infer, from re-sequencing of genomic DNA, the coordinates of neo-insertions from activated ONSEN/COPIA78 LTR retrotrasnposon in Arabidopsis thaliana. For this, we performed Illumina 75 bp pair-end PCR-free DNA genome re-sequencing in several independent lines of RdDM mutant nrpd1-3.
Project description:The intent of the experiment was to infer from DNA sequencing the occurrence of extra-chromosomal DNA from Arabidopsis thaliana's heat-activated LTR retrotransposon Onsen/COPIA78. For this, we performed Illumina 150 bp pair-end PCR-free DNA genome re-sequencing, in both wild-type Col-0 and RdDM mutant nrpd1-3 under control and heat stress.
Project description:Purpose: The study aimed to characterize the molecular phenotype of bone marrow macrophages in NHL with RNA sequencing analysis. Methods:RNA of sorted femur macrophages (CD11b+F4/80+) were extracted with an RNA extraction kit (Qiagen). The samples were submitted to Novogene Inc. for library preparation and subsequent RNA sequencing. RNA was used for cDNA library construction using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s protocol. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina) using a paired-end 150 run (2×150 bases). Reads containing adapter or poly-N and those of low quality were trimmed, after which gene counts were obtained though mapping the clean reads to reference genome mm10 using STAR 2.5.3a.
Project description:Purpose: Examination of different forms of tocopherol treatment in mammary tumorigenesis by comparing NGS-derived transcriptome profiling (RNA-seq) Methods: Use of cDNA library construction and Illumina sequencing (NextGen 75 bp pair-end) and quality control using FastQC. Results: Differential transcriptome profiling of mammary tumors between different forms of tocopherol treatment was observed. Conclusions: Our study represents the first detailed analysis of mammary tumor transcriptomes with different tocopherol treatment generated by RNA-seq technology. The optimized data analysis reported here should provide a framework for comparative investigations of expression profiles with tocopherols.
Project description:The DNA methylome of 45 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 45 primary tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000
Project description:8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) their methylome is determined by sequencing after MBD2-capture using MethylCollector (ActiveMotif) 8 NB cell lines were included (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) in this study. After shearing (fragments of about 200 bp), DNA was captured using MBD2-capture (MethylCollector - ActiveMotif) followed by library preparation and multiplexing. Captured sequence tags were sequenced paired-end (2 x 45 bp) on Illumina GAIIx.
Project description:RNA Sequencing analysis was performed on RNA isolated from tissues(forebrain,midbrain and hindbrain) from P-25 wild type and Fmr1CRE knockin mutant mice from same litter.Random primed cDNA from poly(A) selected RNA was converted into an Illumina sequencing library using RNA Library Prep Kit from Illumina (E7420, NEB, USA) in conjunction with NEBNext® Multiplex Oligos for Illumina (E7335/E7500, NEB, USA). and single-end 50-base pair (bp) reads were generated using a NextSeq 500 (Illumina Inc, SY-415-1002). Eighteen libraries were combined in two equimolar pools of 9 based on the library quantification results and each pool was run across a single High-Output Flow Cell. Sequencing was performed at the Wellcome Trust Clinical Research Facility (WTCRF; Edinburgh). Fastq files were processed to transcript-level counts and quality control performed using the bcbio_nextgen pipeline and the illumina-RNAseq workflow template. Differential Expression (DE) analysis was performed in R. The R package bcbio-RNAseq was used to import salmon transcript level counts into DESeq2.
Project description:The DNA methylome of 15 primary stage 4S neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 15 primary stage 4S tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000
Project description:Whole genome sequencing was performed in order to uncover genomic mutations present in spontaneous neoplasias present in aged male midguts. DNA was extracted from neoplasias (marked by ProsGal4 UAS-GFP), adjacent tissue and head of the same fly. The DNA library was prepared using the DNA Nano protocol from Illumina and 2X125 bp paired-end Illumina Hi-Seq was performed by Fasteris, SA (Geneva, CHE).
