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: Frontiers in Immunology

Article Title: Resolvin D1 Reduces Lung Infection and Inflammation Activating Resolution in Cystic Fibrosis

doi: 10.3389/fimmu.2020.00581

Figure Lengend Snippet: RvD1 regulates select genes related to microbial clearance and inflammatory signaling in CF MΦ and epithelial cells. (A) Homozygous ΔF508 peripheral blood monocyte-derived MΦ (0.5–1 × 10 6 cells/plate) and CFBEC (2.5 × 10 6 cells/plate) were treated with RvD1 (10 nM) or vehicle (0.01% EtOH) for 15 min at 37°C and infected with RP73 P. aeruginosa (∼7.5 × 10 6 CFU/plate). Medium was removed after 3 h, and total RNA was used for microarray analysis. Shown here are heat map view (Cluster 3.0, TreeView, Stanford University Labs) and scatter plots of gene expression patterns (mean from five different donors). (B) IPA findings of biological functions associated with RvD1-regulated genes in MΦ and CFBEC. (C) Top RvD1-regulated genes and associated functions identified by IPA. Blue symbols, upregulated genes; yellow symbols, downregulated genes; blue dotted lines, expression leading to activation; yellow dotted lines, expression leading to inhibition; gray dotted lines, expression leading to unpredictable effect of function; blue boxes, activated functions; yellow boxes, inhibited functions.

Article Snippet: Total RNA extracted from CFBEC and MΦ cells was linearly amplified, labeled with Cy3/5, and hybridized on HOA_007 Human Whole Genome OneArray Microarray V7 (29,264 probes; Phalanx Biotech, San Diego, CA, United States) analyzed as in ref. ( ).

Techniques: Derivative Assay, Infection, Microarray, Gene Expression, Expressing, Activation Assay, Inhibition

Journal: BMC Cancer

Article Title: Receptor and secreted targets of Wnt-1/β-catenin signalling in mouse mammary epithelial cells

doi: 10.1186/1471-2407-5-3

Figure Lengend Snippet: (a) Analysis of HIG2 mRNA expression on a human cDNA array containing matched tumour and normal samples from 68 patients. For each pair, the tumour sample is on top. The bottom row of the array contains cDNA from cell lines (left to right: HeLa, Daudi, K562, HL-60, G361, A549, MOLT-4, SW480 and Raji). (b) Quantitative analysis by phosphorimager. Vertical dashed lines indicate ± 2-fold difference. HIG2 expression is broadly similar in most pairs, but is strongly and consistently downregulated in most of the kidney and stomach tumours analysed.

Article Snippet: Total RNA was isolated, from which mRNA was purified. cDNAs were labelled and hybridized to an 8962 element Incyte mouse GEM1 cDNA microarray (Incyte Genomics, Palo Alto, CA).

Techniques: Expressing