Journal: Nucleic Acids Research

Article Title: Selective single cell isolation for genomics using microraft arrays

doi: 10.1093/nar/gkw700

Figure Lengend Snippet: Comparing RNA-seq from cells isolated with microrafts and the Fluidigm C1. ( A ) Fraction of reads aligning to the human genome. ( B ) Gene body coverage plots measuring 3′ bias in read coverage. ( C ) Distribution of read coverage by genomic region. ( D ) Number of genes detected. ( E ) Read coverage for empty samples. ( F ) Heatmap of Pearson correlations among C1 and microraft cells. ( G ) Heatmap of chromosome condensation gene set, which shows strong upregulation in raft cells. ( H ) Heatmap of cell junction gene set, which shows slight upregulation in C1 cells.

Article Snippet: Libraries were created using the C1 recommended Nextera XT kit with the C1 modifications for low concentration reactions.

Techniques: RNA Sequencing, Isolation

Journal: PLoS ONE

Article Title: Integrative Omics Analysis of Rheumatoid Arthritis Identifies Non-Obvious Therapeutic Targets

doi: 10.1371/journal.pone.0124254

Figure Lengend Snippet: ( A ) Western blots showing RAC1 and Rac1-GTP levels in RA FLS following PDGF stimulation with ELMO1 and control siRNA. RAC1 activation was determined as described in Material and Methods. Cells were assayed from 0 to 15 min after they were stimulated with PDGF. ( B ) Quantification of the RAC1 assay. Mean and SEM was calculated from 3 experiments. The ratio of Rac1 and Rac1-GTP in RA FLS following PDGF stimulation with ELMO1 and control siRNA is shown and demonstrates decreased RAC1 activation when FLS are ELMO1 -deficient.

Article Snippet: Activated RAC1 was detected were using RAC1 assay reagent (GST-PAK1-PBD on glutathione-Sepharose Beads) according to the manufacturer’s instructions (Cytoskeleton, Denver CO).

Techniques: Western Blot, Control, Activation Assay

Journal: PLoS Pathogens

Article Title: EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF

doi: 10.1371/journal.ppat.1007247

Figure Lengend Snippet: A. Immunoblots of pulldown assays using Strep-tactin agarose. EspE-Strep was purified from soluble lysates of the eccCb 1 mutant expressing only EspE-Strep/EspF or EspE-Strep/EspF together with EspH-His. A strain containing empty plasmids was included as negative control. Total input material (I), unbound proteins (FT), the final washing step (W), three fractions of eluted proteins (E1, E2, E3) and boiled beads fractions were separated by SDS-PAGE and further immunoblotted using antisera directed against the Strep- or His-tag. The elution fractions were loaded 10 times more compared to the other fractions. Endogenous EspE, PPE68 and EsxA substrates were detected using anti-EspE, anti-PPE68 and anti-EsxA, respectively. B. Immunoblots of pulldown assays using Ni-NTA beads. EspH-His proteins were purified from soluble lysates of the eccCb 1 strain carrying a plasmid expressing EspH-His or the corresponding empty plasmid. Total input material (I), unbound proteins (FT), the last washing step (W), proteins eluted with 50 mM ( E1 ), 100 mM ( E2 ), and 200 mM ( E3 ) imidazole and boiled bead fraction were separated by SDS-PAGE and probed with His-specific antiserum. The elution fractions were loaded 10 times more compared to the other fractions. Endogenous EspE, PPE68 and EsxA proteins were detected using anti-EspE, anti-PPE68 and anti-EsxA, respectively.

Article Snippet: Immunoprecipitation of strep-tagged proteins was performed using the Strep-Tactin Sepharose kit (IBA), following the manufacturers protocol.

Techniques: Western Blot, Purification, Mutagenesis, Expressing, Negative Control, SDS Page, Plasmid Preparation