Journal: Journal of Virology

Article Title: Adeno-Associated Virus Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles of Human Diploid Fibroblasts Analyzed by Third-Generation PacBio DNA Sequencing

doi: 10.1128/JVI.01356-14

Figure Lengend Snippet: Third-generation PacBio-based DNA sequencing results. (A) Number of reads per given lengths of the chromosomal parts of sequenced junctions, displayed for AAVwt or rAAV, as indicated. (B) Percentage of junctions with breakpoints at indicated distances

Article Snippet: We present here integration profiles in diploid human fibroblasts infected side by side with AAV2wt and rAAV2 vectors, analyzed by third-generation, PacBio-based genomic DNA sequencing.

Techniques: DNA Sequencing

Journal: Journal of Virology

Article Title: Adeno-Associated Virus Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles of Human Diploid Fibroblasts Analyzed by Third-Generation PacBio DNA Sequencing

doi: 10.1128/JVI.01356-14

Figure Lengend Snippet: Library preparation for third-generation PacBio sequencing of AAV integration sites. (A) Genomic DNA of AAVwt- or rAAV-infected human fibroblast (MRC-5) was digested by endonucleases, as indicated by vertical arrows. Integrated AAV genomes are represented

Article Snippet: We present here integration profiles in diploid human fibroblasts infected side by side with AAV2wt and rAAV2 vectors, analyzed by third-generation, PacBio-based genomic DNA sequencing.

Techniques: Sequencing, Infection

Journal: Nature Communications

Article Title: Scaffolding and completing genome assemblies in real-time with nanopore sequencing

doi: 10.1038/ncomms14515

Figure Lengend Snippet: Structure of a pathogenic island from K. pneumoniae ATCC BAA-2146. The island harbors three antibiotic resistance genes strep , sul1 and ebr , flanked by mobility genes integrase ( int ), inverstase ( hin ), DNA replication ( dnaC ) and IS (IS26 and IS6100). The island was fragmented into 10 contigs in the Illumina assembly, and was completely resolved with 65 Mb out of the total of 185 Mb of nanopore sequence data.

Article Snippet: MinION sequencing Library preparation was performed using the Genomic DNA Sequencing kit (Oxford Nanopore), according to the manufacturer's instructions.

Techniques: Sequencing

Journal: bioRxiv

Article Title: Towards Spider Glue: Long-read scaffolding for extreme length and repetitious silk family genes AgSp1 and AgSp2 with insights into functional adaptation

doi: 10.1101/492025

Figure Lengend Snippet: A. trifasciata Aggregate Spidroin 2 (AgSp2) schematic, aligned Oxford Nanopore gDNA reads, longest alignable mRNA read, and mapped read coverage. (A) AgSp2 consists of 20,526 bp of coding sequence and ~31,455 bp of intronic sequence, totalling ~51,981bp of genomic sequence (intronic sequence could not be corrected with short readt derived from mRNA). Abbreviations correcpond to regions of the predicted protein: NTD = N-terminal domain; QRR = glutamine -rich region (all regions in green); CTD = C-terminal domain. (B) Individual alignment of four Oxford Nanopore reads to the con-ensus AgSp2 together cover the entirety of the gene. (C) Alignment of a 16.5 kb RNA transcript to the consensus AgSp2. (D) Log read coverage of Illumina RNASeq data generated from aggregate gland tissue mapped to AgSp2.

Article Snippet: Oxford Nanopore gDNA Sequencing Two juvenile A. trifasciata were collected from Schooley Mill park on July 23, 2018 and kept overnight in containers.

Techniques: Sequencing, Derivative Assay, Generated

Journal: bioRxiv

Article Title: Towards Spider Glue: Long-read scaffolding for extreme length and repetitious silk family genes AgSp1 and AgSp2 with insights into functional adaptation

doi: 10.1101/492025

Figure Lengend Snippet: A. trifasciata Aggregate Spidroin 1 (AgSp1) schematic, aligned Oxford Nanopore gDNA reads, longest alignable mRNA read, and mapped read coverage. (A) AgSp1 consists of 42,270 bp of coding sequence and ~6,690 bp of intronic sequence, totalling ~48,960 bp of genomic sequence (intronic sequence could not be corrected with short reads derived from mRNA). Abbreviations correspond to regions of the predicted protein: NTD = N-terminal domain; NTR = N-terminal repeats; NTT = N-terminal transition; MRT = mid-rep eat transition; CTT = C-terminal transition, CTD = C-terminal domain. (B) Individual alignment of four Oxford Nanopore reads to the consensus AgSp1 together cover the entirety of the gene. (C) Alignment of a 16.4 kb mRNA transcript to the consensus AgSp1. (D) Log read coverage of Illumina RNAseq data generated from aggregate gland tissue mapped to AgSp1.

Article Snippet: Oxford Nanopore gDNA Sequencing Two juvenile A. trifasciata were collected from Schooley Mill park on July 23, 2018 and kept overnight in containers.

Techniques: Sequencing, Derivative Assay, Generated

Journal: International Journal of Medical Sciences

Article Title: MEF2C loss-of-function mutation contributes to congenital heart defects

doi: 10.7150/ijms.21353

Figure Lengend Snippet: A novel MEF2C mutation associated with congenital heart disease. (A) DNA sequence chromatograms displaying the heterozygous MEF2C mutation and its corresponding wild-type control. The arrow points to the heterozygous nucleotides of T/C in the proband (mutant type) or the homozygous nucleotides of T/T in a control individual (wild type). The rectangle marks the nucleotides comprising codon 38 of MEF2C . (B) Schematic diagram delineating the structural domains of the MEF2C protein and the location of the mutation involved in congenital heart disease. The mutation identified in patients with congenital heart disease is shown above the structural domains. NH2, amino terminus; MADS, MCM1, agamous, deficiens, serum response factor; MEF2, myocyte enhancer factor 2; TAD1, transcriptional activation domain 1; TAD2, transcriptional activation domain 2; NLS, nuclear localization signal; COOH, carboxyl terminus. (C) Pedigree structure of the family with congenital heart disease. The family was designated as family A. Family members are recognized by generations and numbers. Square indicates male family member; circle, female member; closed symbol, affected member; open symbol, unaffected member; arrow, proband; “+”, carrier of the heterozygous missense mutation; “-”, non-carrier.

Article Snippet: The referential genomic DNA sequence of the human MEF2C gene (accession no. NC_000005.10) was derived from the Nucleotide database at the National Center for Biotechnology Information ( https://www.ncbi.nlm.nih.gov/nuccore/NC_000005.10?from=88718241 & to=88904105 & report=genbank & strand=true ).

Techniques: Mutagenesis, Sequencing, Activation Assay