Journal: iScience

Article Title: Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response

doi: 10.1016/j.isci.2024.111529

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Article Snippet: The primary antiserum and antibodies used were an anti-BACH2 anti-serum (BACH2-N2), and anti-TBK1/NAK (3504, Cell Signaling Technology), anti-DNMT1 (ab13537, Abcam), anti-GST (GE27–4577-01, Sigma Aldrich), anti-phospho-p70S6K (9205, Cell Signaling Technology), anti-p70S6K (9202, Cell Signaling Technology), anti-Lamin B (C-20) (sc-6216, Santa Cruz Biotechnology) and anti-GAPDH antibodies (ab8245, Abcam).

Techniques: Virus, Recombinant, Protease Inhibitor, Transfection, Multiplex sample analysis, Protein Purification, Reporter Assay, Luciferase, Cell Isolation, Plasmid Preparation, Reverse Transcription, SYBR Green Assay, ChIP-qPCR, Sequencing, Negative Control, Software

Journal: Cell chemical biology

Article Title: Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein

doi: 10.1016/j.chembiol.2019.04.001

Figure Lengend Snippet: A. Plot comparing mRNA level for high confidence ALLC interacting proteins (measured by RNAseq in (Plate et al., 2016); n=3 biological replicates) vs. their increased interactions with FTALLC in HEK293DAX cells following stress-independent ATF6 activation (n=7 biological replicates). The dashed line shows least-squares linear regression. The solid lines show 95% confidence intervals. B. Plot comparing cellular protein level for high confidence ALLC interacting proteins (measured by whole cell quantitative proteomics in (Plate et al., 2016); n=3 biological replicates) vs. their increased interactions with FTALLC in HEK293DAX cells following stress-independent ATF6 activation (n=7 biological replicates). The dashed line shows least-squares linear regression. The solid lines show 95% confidence intervals. C. Plot comparing cellular protein level for high confidence ALLC interacting proteins (measured by whole cell quantitative proteomics in (Plate et al., 2016); n=3 biological replicates) vs. their increased interactions with FTALLC in HEK293DAX cells following stress-independent XBP1s activation (n=7 biological replicates). The dashed line shows least-squares linear regression. The solid lines show 95% confidence intervals. D. Plot comparing cellular protein level for high confidence ALLC interacting proteins (measured by whole cell quantitative proteomics in (Plate et al., 2016); n=3 biological replicates) vs. their increased interactions with FTALLC in HEK293DAX cells following stress-independent ATF6 and XBP1s co-activation (n=4 biological replicates). The dashed line shows least-squares linear regression. The solid lines show 95% confidence intervals. E. Graph showing changes in protein levels (open symbols; n=3) or FTALLC interactions (solid bars; n=4-7) for PDIA4 in HEK293DAX cells following stress-independent XBP1s (red), ATF6 (blue), or XBP1s and ATF6 (green) activation. Error bars show SEM for the individual replicates. F. Graph showing changes in protein levels (open symbols; n=3) or FTALLC interactions (solid bars; n=4-7) for HYOU1 in HEK293DAX cells following stress-independent XBP1s (red), ATF6 (blue), or XBP1s and ATF6 (green) activation. Error bars show SEM for the individual replicates.

Article Snippet: PDIA4 (ERp72) (rabbit polyclonal) , ProteinTech , Cat#14712-1-AP.

Techniques: Activation Assay, Quantitative Proteomics

Journal: Cell chemical biology

Article Title: Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein

doi: 10.1016/j.chembiol.2019.04.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: PDIA4 (ERp72) (rabbit polyclonal) , ProteinTech , Cat#14712-1-AP.

Techniques: Virus, Recombinant, Sequencing, Modification, Purification, Labeling, Multiplex sample analysis, Expressing, Plasmid Preparation, Cloning, Software

Journal: Developmental Cell

Article Title: Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells

doi: 10.1016/j.devcel.2020.10.006

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Article Snippet: p70 S6 Kinase , Cell signalling , Cat#2708; RRID: AB_390722.

Techniques: Virus, Cloning, Recombinant, Western Blot, Staining, Plasmid Preparation, RNAscope, Multiplex Assay, Control, CRISPR, Modification, Transfection, Fractionation, Peptide Fractionation, Sequencing, Cell Viability Assay, Viability Assay, RNA HS Assay, Bicinchoninic Acid Protein Assay, SYBR Green Assay, Quantitative Proteomics, Multiplex sample analysis, Generated, Stable Transfection, Expressing, Negative Control, Software, Membrane, Cell Culture

Journal: Cell reports

Article Title: Phenotypic Screen with TSC-Deficient Neurons Reveals Heat-Shock Machinery as a Druggable Pathway for mTORC1 and Reduced Cilia

doi: 10.1016/j.celrep.2020.107780

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Article Snippet: Rabbit monoclonal anti-Hsp70 , Santa Cruz Biotechnology , Cat# sc-24; RRID:AB_627760.

Techniques: Virus, Recombinant, Plasmid Preparation, cDNA Synthesis, SYBR Green Assay, RNA Sequencing, Expressing, Luciferase, Software, Cell Analysis