Journal: Current HIV/AIDS Reports

Article Title: Bioinformatics and HIV Latency

doi: 10.1007/s11904-014-0240-x

Figure Lengend Snippet: Genome-wide analyses on HIV latency models

Article Snippet: Patient-derived ex vivo model , Integration , DNA shearing (Covaris Adaptive Focused Acoustics) into 300–500-bp fragments End repair (Epicentre End-it DNA End Repair) dA addition (NEB dA-tailing kit) Linker ligation First PCR (LTR-linker) Nested PCR with N6-barcoded primers containing sequencing adapters Illumina sequencing: 2 × 150-bp paired-end (MiSeq) or 2 × 105-bp paired-end (HiSeq) , Trimming: custom Perl scripts Genome alignment: BLAT, hg19 Integration site inclusion criteria for read 1: LTR primer sequence, 5 last bp of the LTR sequence followed with >20-bp DNA sequence with an average quality score >20, mapping to the human genome reference sequence within the first 3 bp and with >95 % identity Integration site inclusion criteria for read 2: alignment to the human genome reference sequence on the opposite strand compared to read 1 and within 1 kb Integration sites are considered different if the breaking point differs from >3 bp Gene ontology analysis: GREAT Statistical analysis: Fisher’s exact test , Maldarelli et al. [ •] .

Techniques: Genome Wide, Ligation, Nested PCR, Clone Assay, Transformation Assay, Sequencing, Two-Dimensional Gel Electrophoresis, Software, Chromatography, Mass Spectrometry, Quantitation Assay, Inverse PCR, Amplification, RNA Extraction, Expressing, Infection, Hybridization, Microarray, Ex Vivo

Journal:

Article Title: Nonpolar Inactivation of the Hypervariable Streptococcal Inhibitor of Complement Gene ( sic ) in Serotype M1 Streptococcus pyogenes Significantly Decreases Mouse Mucosal Colonization

doi:

Figure Lengend Snippet: Primers used to amplify DNA probes for Northern hybridization

Article Snippet: DNA probes (500 to 600 bp) corresponding to gene regions encoding the amino-terminal parts of the mature proteins were biotinylated with BrightStar labeling reagents (Ambion).

Techniques: Northern Blot, Sequencing

Journal:

Article Title: Nonpolar Inactivation of the Hypervariable Streptococcal Inhibitor of Complement Gene ( sic ) in Serotype M1 Streptococcus pyogenes Significantly Decreases Mouse Mucosal Colonization

doi:

Figure Lengend Snippet: Northern blot analysis of emm, sic, and scpA gene expression by wild-type strain MGAS 5005 (5005 wt) and by the isogenic 5005 sic mutant. No sic transcript could be detected in the mutant strain. In addition, transcription of the emm and scpA genes was unaffected. Biotinylated DNA probes were used for hybridization. The biotinylated molecular weight RNA marker was used to evaluate transcript sizes.

Article Snippet: DNA probes (500 to 600 bp) corresponding to gene regions encoding the amino-terminal parts of the mature proteins were biotinylated with BrightStar labeling reagents (Ambion).

Techniques: Northern Blot, Expressing, Mutagenesis, Hybridization, Molecular Weight, Marker