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).
Project description:Determining the role of DDX17 in the formation of DNA:RNA-hybrids around active DNA double-strand breaks (DSBs) using DRIP-seq in the damaged induced via AsiSI (DIvA) cell system that induced DSBs at known genomic loci in response to hydroxytamoxifen (OHT) treatment via and AsiSI enzyme fused to an oestrogen receptor. Sequencing was done using either control or DDX17 siRNA, and mock or 4 hours 300nM OHT treatment. Paired-end 150 cycles was completed on an Illumina NextSeq 500 and library prep was completed using the NEB NEBNext Ultra II library prep kit.
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:Urine from a patient with a urinary tract infection was plated on LB agar plate. Microcolonies appeared ~8h after plating. Microcolonies were picked and subjected to Microcolony-seq and to whole-genome sequencing. Genomic DNA of each UTI microcolony was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by BGI company, China. Concentration of samples was detected by fluorometer or Microplate Reader (Qubit Fluorometer, Invitrogen). Sample integrity and purity were detected by Agarose Gel Electrophoresis. 1μg genomic DNA was randomly fragmented by Covaris. The fragmented genomic DNA were selected by Agencourt AMPure XP-Medium kit to an average size of 200-400bp. Fragments were end repaired and then 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. PCR products were purified by the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Samples were deep-sequenced with the DNBseq G400 machine using the 150-cycles paired-end with 350 bp insert size. At least 150X sequencing depth for each nucleotide in each sample was targeted.
Project description:RNA and whole-genome DNA were isolated from control and dnmt1 morphants zebrafish cells using the TRIzol (Tiangen) reagent and phenol-chloroform extraction by following the manual, respectively. The cDNA library for RNA-seq and DNA library for MeDIP-seq were sequenced using HiSeq2000 (Illumina) in single-end read and paired-read mode, reapectively.
Project description:SDL-TOPO protocol was applied for the detection of lagging-strand in replicating budding yeast strain. Genomic DNA was extracted from cdc9 mutant strain, and served for library preparation with SDL-TOPO. To see the sensitivity of SDL-TOPO for the detection of lagging strand, various amounts of genomic DNA were used for the library preparation: 75 ng, 25 ng, 7.5 ng, 2.5 ng, 750 pg, 250 pg, 75 pg, and 25 pg. The prepared libraries were sequenced on Illumina iSeq100 with paired-end mode of 150x2. Only read 1 was served for mapping with bowtie2 against reference sequence sacSer3. The mapped reads were separated strand specifically, and read depths were visualized. The strand-biased mapping patterens were observed for libraries prepared from each amount of input DNA.
Project description:The paired-end Illumina sequencing of total genomic DNA from Arabidopsis were performed to detect unique breakpoints consistent with rearrangements of chloroplast DNA.
Project description:<p>Exome sequencing of matched pairs of tumor / normal genomic DNA was performed from high risk localized prostate cancer or lethal, metastatic, castrate resistant prostate cancer (CRPC). Exome libraries were prepared using Illumina Paired_End Genome DNA Sample Prep Kit and captured using Agilent SureSelect Capture Library or Roche EZ Exome capture library. Sequencing was performed on Illumina GAII and HiSeq 2000 platforms in paired end mde, with 80 base pair reads from the final library fragments. Copy number alterations and somatic mutations were identified.</p>