Journal: Cell chemical biology

Article Title: A systems chemoproteomic analysis of acyl-CoA/protein interaction networks

doi: 10.1016/j.chembiol.2019.11.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal MultiMab Malonyl-Lysine antibody Cell Signaling Technologies Cat# 14942 Anti-FLAG (DYKDDDDK) Tag Antibody (HRP-linked) Cell Signaling Technologies Cat# 2044 Anti-rabbit IgG antibody (HRP-linked) Cell Signaling Technologies Cat # 7074 Bacterial and Virus Strains n/a Biological Samples Cell pellets from HeLa S3 epithelial suspension cell line Cell Culture Company Cat # HA48 Chemicals, Peptides, and Recombinant Proteins NHS-Activated Sepharose 4 Fast Flow resin GE Healthcare Cat# 71-5000-14 AD Amine-functionalized Lys-CoA-Ahx Montgomery et al,, 2016 n/a U- 13 C6-glucose Cambridge Isotope Laboratories Cat# CLM-1396 U- 13 C2-acetate Cambridge Isotope Laboratories Cat# CLM-440 acetyl-CoA Sigma-Aldrich Cat# A2056 coenzyme A Sigma-Aldrich Cat# butyryl-CoA Sigma-Aldrich Cat# B1508 crotonyl-CoA Sigma-Aldrich Cat# 28007 palmitoyl-CoA Sigma-Aldrich Cat# P9716 acetic-CoA This study n/a Critical Commercial Assays Anti-FLAG IP kit Sigma-Aldrich Cat# FLAGIPT1-1KT TRIzol reagent ThermoFisher Scientific Cat#15596026 oligo-(dT) 25 Dynabeads ThermoFisher Scientific Cat# 61005 Qubit Broad Sensitivity Protein Assay Kit ThermoFisher Scientific Cat# {"type":"entrez-protein","attrs":{"text":"Q33211","term_id":"75281052","term_text":"Q33211"}} Q33211 Deposited Data Proteomic datasets for CATNIP (Lys-CoA) pulldowns and competitions ProteomeXchange Consortium; PRIDE PXD013157 Experimental Models: Cell Lines HeLa S3 cells ATCC CCL-2.2 HEK-293T cells ATCC CRL-3216 LN229 ACLY knockout cells Zhao et al. 2016 n/a LN229 ACLY wild-type cells Zhao et al. 2016 n/a Experimental Models: Organisms/Strains Oligonucleotides Recombinant DNA Software and Algorithms DTASelect v.1.9/ CONTRAST for protein detection Tabb et al.,2002 NSAF7 Zhang, et al., 2010 QSPEC/QPROT for the statistical analysis of protein differentiation Choi, et al., 2015 http://http//sourceforge.net/p/qprot/ tSNE and k-means algorithms for proteins separation and clustering Van der Maaten, et al., 2008 R source TDA software for the topological analysis Lum et al., 2013 . https://platform.ayasdi.com/workbench (AYASDI Inc., Menlo Park CA) DAVID gene ontology for functional enrichment DAVID tool http://david.abcc.ncifcrf.gov/ ConsensusPathDB http://cpdb.molgen.mpg.de/CPDB/rlFrame Other Open in a separate window KEY RESOURCES TABLE Global profiling of acetyl-CoA binding proteins with chemoproteomic probes t-SNE clustering allows enrichment of direct and indirect acetyl-CoA binders Identification of specific and promiscuous acyl-CoA interaction signatures Development of a de novo acetyltransferase annotation workflow Significance Acyl-CoAs are essential for life.

Techniques: Cell Culture, Recombinant, Knock-Out, Software, Functional Assay

Journal: Cell chemical biology

Article Title: A systems chemoproteomic analysis of acyl-CoA/protein interaction networks

doi: 10.1016/j.chembiol.2019.11.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal MultiMab Malonyl-Lysine antibody Cell Signaling Technologies Cat# 14942 Anti-FLAG (DYKDDDDK) Tag Antibody (HRP-linked) Cell Signaling Technologies Cat# 2044 Anti-rabbit IgG antibody (HRP-linked) Cell Signaling Technologies Cat # 7074 Bacterial and Virus Strains n/a Biological Samples Cell pellets from HeLa S3 epithelial suspension cell line Cell Culture Company Cat # HA48 Chemicals, Peptides, and Recombinant Proteins NHS-Activated Sepharose 4 Fast Flow resin GE Healthcare Cat# 71-5000-14 AD Amine-functionalized Lys-CoA-Ahx Montgomery et al,, 2016 n/a U- 13 C6-glucose Cambridge Isotope Laboratories Cat# CLM-1396 U- 13 C2-acetate Cambridge Isotope Laboratories Cat# CLM-440 acetyl-CoA Sigma-Aldrich Cat# A2056 coenzyme A Sigma-Aldrich Cat# butyryl-CoA Sigma-Aldrich Cat# B1508 crotonyl-CoA Sigma-Aldrich Cat# 28007 palmitoyl-CoA Sigma-Aldrich Cat# P9716 acetic-CoA This study n/a Critical Commercial Assays Anti-FLAG IP kit Sigma-Aldrich Cat# FLAGIPT1-1KT TRIzol reagent ThermoFisher Scientific Cat#15596026 oligo-(dT) 25 Dynabeads ThermoFisher Scientific Cat# 61005 Qubit Broad Sensitivity Protein Assay Kit ThermoFisher Scientific Cat# {"type":"entrez-protein","attrs":{"text":"Q33211","term_id":"75281052","term_text":"Q33211"}} Q33211 Deposited Data Proteomic datasets for CATNIP (Lys-CoA) pulldowns and competitions ProteomeXchange Consortium; PRIDE PXD013157 Experimental Models: Cell Lines HeLa S3 cells ATCC CCL-2.2 HEK-293T cells ATCC CRL-3216 LN229 ACLY knockout cells Zhao et al. 2016 n/a LN229 ACLY wild-type cells Zhao et al. 2016 n/a Experimental Models: Organisms/Strains Oligonucleotides Recombinant DNA Software and Algorithms DTASelect v.1.9/ CONTRAST for protein detection Tabb et al.,2002 NSAF7 Zhang, et al., 2010 QSPEC/QPROT for the statistical analysis of protein differentiation Choi, et al., 2015 http://http//sourceforge.net/p/qprot/ tSNE and k-means algorithms for proteins separation and clustering Van der Maaten, et al., 2008 R source TDA software for the topological analysis Lum et al., 2013 . https://platform.ayasdi.com/workbench (AYASDI Inc., Menlo Park CA) DAVID gene ontology for functional enrichment DAVID tool http://david.abcc.ncifcrf.gov/ ConsensusPathDB http://cpdb.molgen.mpg.de/CPDB/rlFrame Other Open in a separate window KEY RESOURCES TABLE Global profiling of acetyl-CoA binding proteins with chemoproteomic probes t-SNE clustering allows enrichment of direct and indirect acetyl-CoA binders Identification of specific and promiscuous acyl-CoA interaction signatures Development of a de novo acetyltransferase annotation workflow Significance Acyl-CoAs are essential for life.

Techniques: Cell Culture, Recombinant, Knock-Out, Software, Functional Assay

Journal: Cold Spring Harbor Perspectives in Medicine

Article Title: Single-Cell Applications of Next-Generation Sequencing

doi: 10.1101/cshperspect.a026898

Figure Lengend Snippet: Examples of a single-cell RNA (scRNA) sequence analysis to detect the molecular basis of drug resistance in melanoma. (A) Scheme for generating drug resistant derivatives. (B) Testing resistant cells. (C) Using signature melanoma signature genes to cluster bulk RNA-Seq data from cell lines. (D) t-SNE map was used to display the expression profiles of 400 single cells isolated using the Fluidigm C-1 instrument. (E) Heat map showing expression of highly expressed and highly variable genes. (F) t-SNE plot of scRNA-Seq of 6545 cells performed on a 10X Chromium instrument. (G) Direct comparison of Fluidigm cells and Chromium cells showing similar differences between resistant and parental but distinct patterns for the two methods. (H) Differential expression analysis identifies genes significantly altered in the resistant cell line derivative (for details, see Ho et al. 2018).

Article Snippet: Importantly, SAKE also includes quantitative statistics to evaluate the clustering results, a feature missing from most other methods ( Deng et al. 2014 ; Ting et al. 2014 ; Zeisel et al. 2015 ), and to evaluate its performance by the ability to correctly identify clusters reported in these studies. presents an heuristic example of the manner in which these techniques can be used to rationalize scRNA-Seq data and to identify genes of interest by functional genomics ( Box 1 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2. caption a7 Examples of a single-cell RNA (scRNA) sequence analysis to detect the molecular basis of drug resistance in melanoma. ( A ) Scheme for generating drug resistant derivatives. ( B ) Testing resistant cells. ( C ) Using signature melanoma signature genes to cluster bulk RNA-Seq data from cell lines. ( D ) t-SNE map was used to display the expression profiles of 400 single cells isolated using the Fluidigm C-1 instrument. ( E ) Heat map showing expression of highly expressed and highly variable genes. ( F ) t-SNE plot of scRNA-Seq of 6545 cells performed on a 10X Chromium instrument. ( G ) Direct comparison of Fluidigm cells and Chromium cells showing similar differences between resistant and parental but distinct patterns for the two methods. ( H ) Differential expression analysis identifies genes significantly altered in the resistant cell line derivative (for details, see Ho et al. 2018 ).

Techniques: Sequencing, RNA Sequencing Assay, Expressing, Isolation

Journal: Cell chemical biology

Article Title: A systems chemoproteomic analysis of acyl-CoA/protein interaction networks

doi: 10.1016/j.chembiol.2019.11.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal MultiMab Malonyl-Lysine antibody Cell Signaling Technologies Cat# 14942 Anti-FLAG (DYKDDDDK) Tag Antibody (HRP-linked) Cell Signaling Technologies Cat# 2044 Anti-rabbit IgG antibody (HRP-linked) Cell Signaling Technologies Cat # 7074 Bacterial and Virus Strains n/a Biological Samples Cell pellets from HeLa S3 epithelial suspension cell line Cell Culture Company Cat # HA48 Chemicals, Peptides, and Recombinant Proteins NHS-Activated Sepharose 4 Fast Flow resin GE Healthcare Cat# 71-5000-14 AD Amine-functionalized Lys-CoA-Ahx Montgomery et al,, 2016 n/a U- 13 C6-glucose Cambridge Isotope Laboratories Cat# CLM-1396 U- 13 C2-acetate Cambridge Isotope Laboratories Cat# CLM-440 acetyl-CoA Sigma-Aldrich Cat# A2056 coenzyme A Sigma-Aldrich Cat# butyryl-CoA Sigma-Aldrich Cat# B1508 crotonyl-CoA Sigma-Aldrich Cat# 28007 palmitoyl-CoA Sigma-Aldrich Cat# P9716 acetic-CoA This study n/a Critical Commercial Assays Anti-FLAG IP kit Sigma-Aldrich Cat# FLAGIPT1-1KT TRIzol reagent ThermoFisher Scientific Cat#15596026 oligo-(dT) 25 Dynabeads ThermoFisher Scientific Cat# 61005 Qubit Broad Sensitivity Protein Assay Kit ThermoFisher Scientific Cat# {"type":"entrez-protein","attrs":{"text":"Q33211","term_id":"75281052","term_text":"Q33211"}} Q33211 Deposited Data Proteomic datasets for CATNIP (Lys-CoA) pulldowns and competitions ProteomeXchange Consortium; PRIDE PXD013157 Experimental Models: Cell Lines HeLa S3 cells ATCC CCL-2.2 HEK-293T cells ATCC CRL-3216 LN229 ACLY knockout cells Zhao et al. 2016 n/a LN229 ACLY wild-type cells Zhao et al. 2016 n/a Experimental Models: Organisms/Strains Oligonucleotides Recombinant DNA Software and Algorithms DTASelect v.1.9/ CONTRAST for protein detection Tabb et al.,2002 NSAF7 Zhang, et al., 2010 QSPEC/QPROT for the statistical analysis of protein differentiation Choi, et al., 2015 http://http//sourceforge.net/p/qprot/ tSNE and k-means algorithms for proteins separation and clustering Van der Maaten, et al., 2008 R source TDA software for the topological analysis Lum et al., 2013 . https://platform.ayasdi.com/workbench (AYASDI Inc., Menlo Park CA) DAVID gene ontology for functional enrichment DAVID tool http://david.abcc.ncifcrf.gov/ ConsensusPathDB http://cpdb.molgen.mpg.de/CPDB/rlFrame Other Open in a separate window KEY RESOURCES TABLE Global profiling of acetyl-CoA binding proteins with chemoproteomic probes t-SNE clustering allows enrichment of direct and indirect acetyl-CoA binders Identification of specific and promiscuous acyl-CoA interaction signatures Development of a de novo acetyltransferase annotation workflow Significance Acyl-CoAs are essential for life.

Techniques: Cell Culture, Recombinant, Knock-Out, Software, Functional Assay