Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet: Validation of microarray results by qRT-PCR [3] .

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Biomarker Discovery, Microarray

Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet: List of primers used in the validation of microarray results by qRT-PCR.

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Biomarker Discovery, Microarray, Sequencing, Amplification

Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet:

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Microarray, Comparison

Journal: Scientific Reports

Article Title: A Novel and Conserved Plasmodium Sporozoite Membrane Protein SPELD is Required for Maturation of Exo-erythrocytic Forms

doi: 10.1038/srep40407

Figure Lengend Snippet: ( A ) The amino acid sequence of PbSPELD was aligned with other Plasmodium orthologues P. chabaudi , PCHAS_0712200; P. yoelii , PY17X_0912300; P. cynomolgi , PCYB_094370; P. falciparum , PF3D7_1137800; P. knowlesi , PKNH_0936000 and P. vivax PVX_092505 using the Clustal Omega program. The conserved residues are shaded turquoise and physico-chemically similar residues are shaded grey. All orthologues contain a tyrosine-rich domain (underlined) and a putative transmembrane region (boxed). ( B ) The table shows amino acid identities between the indicated proteins. ( C ) The expression of pbspeld across P. berghei life cycle stages. The gene expression was analysed by quantitative real time PCR that revealed highest gene expression in the salivary gland sporozoites (SG Spz) followed by day 14 midgut sporozoites (MG Spz). The normalized data was expressed as a ratio of absolute copy numbers of pbspeld versus Pb18srRNA (internal control) for each stage of the Plasmodium life cycle. Ring: Ring stages, MBS: mixed blood stages, MG Spz: Midgut sporozoites, SG Spz: salivary gland sporozoites, LS16H: Liver stage 16 h, LS25H: Liver stage 25 h, LS42H: Liver stage 42 h, LS50H: Liver stage 50 h, LS65H: Liver stage 65 h.

Article Snippet: For microarray analysis of speld mutants, an Agilent Custom Plasmodium berghei gene expression microarray slide having 4 × 44k format designed by Genotypic Technology Private Limited was used that comprised of a total number of 43803 features including 5155 numbers of probes, and 1417 Agilent control features.

Techniques: Sequencing, Expressing, Real-time Polymerase Chain Reaction

Journal: Scientific Reports

Article Title: A Novel and Conserved Plasmodium Sporozoite Membrane Protein SPELD is Required for Maturation of Exo-erythrocytic Forms

doi: 10.1038/srep40407

Figure Lengend Snippet: ( A ) Genomic locus of pbspeld showing ORF, 3′ region and position of the primers. ( B ) Cloning of ORF (without stop codon) and 3′ region in the targeting vector pBC-mCherry-hDHFR. The pbspeld ORF was PCR amplified using primer set FP6/RP6 and cloned into ApaI/XhoI site of the targeting vector. The 3′ region of pbspeld was PCR amplified using primer set FP2/RP2 and cloned in the NotI/AscI site of the targeting vector. ( C ) Agarose gel showing products of diagnostic PCR with primer set FP7/RP7 and primer set FP8/RP8 indicating correct integration respectively in pbspeldmCherry transgenic clones C1 and C2. No product was amplified from genomic DNA of WT parasites using same set of primers. ( D ) pbspeldmCherry transgenic parasites express the reporter in oocyst and salivary gland sporozoite stages. (i) Dissected mosquito midgut showing oocyst expressing mCherry. Scale bar 200 μm. (ii) Higher magnification (100X) of oocyst showing mCherry expression in sporozoites within oocyst. Scale bar 10 μm. (iii) Dissected salivary gland lobe showing sporozoites expressing mCherry. Scale bar 10 μm. ( E ) Circles with white outline indicate sporozoites showing SPELD mCherry localization to the plasma membrane with in dissected salivary gland lobes. Scale bar 5 μm. ( F ) and ( G ) Colocalisation of mCherry with CSP in midgut sporozoites and salivary gland sporozoites respectively. The sporozoites were incubated with 3D11, a monoclonal antibody that recognizes the repeats of P. berghei CSP protein. Scale bar 10 μm. ( H ) pbspeldmCherry transgenic express reporter only at 17 h EEF development. The development of EEFs was monitored at indicated post-invasion time points by IFA using UIS4 antibody specific for the parasitophorous vacuolar membrane (PVM) and DAPI that facilitated visualizing host and parasite nuclei. Scale bar 10 μm.

Article Snippet: For microarray analysis of speld mutants, an Agilent Custom Plasmodium berghei gene expression microarray slide having 4 × 44k format designed by Genotypic Technology Private Limited was used that comprised of a total number of 43803 features including 5155 numbers of probes, and 1417 Agilent control features.

Techniques: Clone Assay, Plasmid Preparation, Amplification, Agarose Gel Electrophoresis, Diagnostic Assay, Transgenic Assay, Expressing, Incubation

Journal: Scientific Reports

Article Title: A Novel and Conserved Plasmodium Sporozoite Membrane Protein SPELD is Required for Maturation of Exo-erythrocytic Forms

doi: 10.1038/srep40407

Figure Lengend Snippet: ( A ) Heat map showing global gene expression changes in P. berghei liver stages at 36 hrs from WT and pbspeld ko. B) Pie diagram indicating the major functional pathways upregulated ( B ) and downregulated ( C ) in pbspeld ko. ( D ) Few of the well characterised liver stage specific genes downregulated in pbspeld ko. The plasmoDB ID of each of these genes with their probable functions are indicated. ( E ) Quantitative real time PCR showing downregulation of transcripts: LISP2, UIS4, FABL and EXP1 in pbspeld ko. (*p < 0.05,**p < 0.005, ***p < 0.0005 as compared to WT).

Article Snippet: For microarray analysis of speld mutants, an Agilent Custom Plasmodium berghei gene expression microarray slide having 4 × 44k format designed by Genotypic Technology Private Limited was used that comprised of a total number of 43803 features including 5155 numbers of probes, and 1417 Agilent control features.

Techniques: Expressing, Functional Assay, Real-time Polymerase Chain Reaction

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: Different microarray printing strategies: ( A ) Fabrication of PDA patterned CYTOP (perfluoropolymer) glass slides via photolithography approach (reprinted with permission from ), ( B ) a representative of various steps involved in inkjet printing process (taken from https://gesim-bioinstruments-microfluidics.com/microarray-printer/ ; Accessed on 12 December 2022), and ( C ) GLAD method used to fabricate silver nanorods on glass slides (reprinted with permission from ).

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Microarray

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: Detection methods: ( A ) FRET based approach to detect target DNA. In presence of target DNA only, the existing complex of fluorescence dye (Cy3) and quencher (BHQ2) is disrupted and generates fluorescence signal (). ( B ) CL based enzymatic approach. This approach involves multiple steps: immunoreaction, HCR amplification, enzyme conjugation, and enzyme-CL (luminol p-iodophenol) substrate reaction (). ( C ) Colorimetric detection (use of streptavidin-coated gold nanoparticles) of isothermal DNA amplification. Interaction of biotin and streptavidin was explored (). ( D ) OIRD, a label-free detection method to study protein/antibody interactions with target molecules on a protein microarray chip ().

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Fluorescence, Amplification, Conjugation Assay, Microarray

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: ( A ) A pictorial workflow presentation of hybrid tetrahedral DNA structured probe in conjugation with hybridization chain reaction (DTSP-HCR) concept used to distinguish single-base mismatches in DNA () and ( B ) an overview of acute tuberculosis (ATB) biomarker identification using a two-phase strategy (discovery phase and validation phase) (). Venn diagram and microarray chip visual analysis revealed the potential of 5 protein biomarkers to distinguish ATB and LTBI/HC. LTBI represents latent tuberculosis infection, and HC represents healthy control.

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Conjugation Assay, Hybridization, Biomarker Assay, Microarray, Infection

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: A generic workflow of the application of glycan microarray chip to efficiently profile enzyme activities and determine enzyme inhibitor IC 50 values ().

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Microarray