whole human genome 44 k microarray chips  (Agilent technologies)

Journal: Arthritis Research & Therapy

Article Title: Genome-wide expression profiles of subchondral bone in osteoarthritis

doi: 10.1186/ar4380

Figure Lengend Snippet: Characteristics of the samples used for microarray analysis

Article Snippet: Cyanine 3-labeled cRNA was then purified and hybridized to Agilent whole human genome 44 k microarray chips (Agilent Technologies).

Techniques: Microarray

Journal: Arthritis Research & Therapy

Article Title: Genome-wide expression profiles of subchondral bone in osteoarthritis

doi: 10.1186/ar4380

Figure Lengend Snippet: Microarray analyses of gene expression of osteoarthritis and non-osteoarthritis of subchondral bone and qRT-PCR validation in osteoarthritis knee subchondral bone. (A) Differentially expressed genes were classified based on their expression levels with a minimum of twofold, threefold, fourfold, sixfold, and eightfold changes. (B) Unsupervised hierarchical clustering of osteoarthritis (OA) and non-OA samples was performed for genes whose differential expression exceeded twofold (972 genes). Distances between samples were detected with a Euclidean algorithm and clustered with a centroid linkage method. The OA medial tibial (MT) samples (gray) were clustered together and clearly separated from the OA lateral tibial (LT) (brown) and non-OA samples. Non-OA LT samples (N-LT, red) and non-OA MT samples (N-MT, blue) were clustered together with OA LT samples. (C) Eighty-five genes (plus GAPDH ) were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) validation on a separate group of nine OA subchondral bone specimens. The results of qRT-PCR were strongly consistent with those of microarray analysis ( R 2 = 0.5764, P <0.0001). FC, fold-change.

Article Snippet: Cyanine 3-labeled cRNA was then purified and hybridized to Agilent whole human genome 44 k microarray chips (Agilent Technologies).

Techniques: Microarray, Expressing, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction

Journal: Arthritis Research & Therapy

Article Title: Genome-wide expression profiles of subchondral bone in osteoarthritis

doi: 10.1186/ar4380

Figure Lengend Snippet: Top ten upregulated and downregulated genes comparing lateral tibial bone (below intact cartilage) with medial tibial bone (below lesioned cartilage)

Article Snippet: Cyanine 3-labeled cRNA was then purified and hybridized to Agilent whole human genome 44 k microarray chips (Agilent Technologies).

Techniques: Microarray, Expressing, Binding Assay

Journal: Arthritis Research & Therapy

Article Title: Genome-wide expression profiles of subchondral bone in osteoarthritis

doi: 10.1186/ar4380

Figure Lengend Snippet: Genes representative of gene clusters associated with osteoarthritis

Article Snippet: Cyanine 3-labeled cRNA was then purified and hybridized to Agilent whole human genome 44 k microarray chips (Agilent Technologies).

Techniques: Microarray

Journal: Scientific Reports

Article Title: Increased expression of secreted frizzled related protein 1 (SFRP1) predicts ampullary adenocarcinoma recurrence

doi: 10.1038/s41598-020-69899-8

Figure Lengend Snippet: Expression of WNT-associated genes by microarray of primary culture cells. ( A ) Primary culture cells of ampullary adenocarcinoma were analysed by microarray of oligo-chips. A heatmep was generated by comparison with normal duodenal cells (N01) with early and advanced ampullary cancer. Red represents upregulated genes, and blue represents downregulated genes. ( B ) Gene set enrichment analysis (GSEA), using the MSigDB hallmark gene set collection database in primary culture cells, associated with WNT-β-catenin signalling. Enrichment score is shown in the upper third of the graph. Each bar over the middle third represents one gene located in the ranking. Red indicates a positive correlation and blue as a negative correlation. The rank distribution along with the gene list is shown as the grey part in the lower-third of each graph. ( C ) Protein–protein interaction of WNT-associated genes was predicted by STRING software. SFRP1 was linked with multiple genes. N01, primary culture cells from normal duodenum. AC01, primary culture cells from well-differentiated ampullary adenocarcinoma, T1N0, stage IA. AC02, primary culture cells from moderately-differentiated ampullary adenocarcinoma, T2N1, stage IIB. GSEA, gene set enrichment analysis; SFRP1 , secreted frizzled related protein 1; STRING, search tool for the retrieval of interacting genes.

Article Snippet: The Agilent Human Whole Genome Oligo 4 × 44 K Microarray chip (Agilent) was hybridised with Cy-labelled complementary RNA.

Techniques: Expressing, Microarray, Generated, Software

Journal: Scientific Reports

Article Title: Increased expression of secreted frizzled related protein 1 (SFRP1) predicts ampullary adenocarcinoma recurrence

doi: 10.1038/s41598-020-69899-8

Figure Lengend Snippet: Expression of SFRP1-associated genes by microarray of primary culture cells. ( A ) Primary culture cells of ampullary adenocarcinoma was analysed by oligochip microarray. Most WNT-associated genes were downregulated in these cells. Upregulation of SFRP1 and oncogenes, CCND1 and WNT5A, were detected. ( B ) ClueGo and CluePedia were used to create the network with gene GO terms. SFRP1 was shown in the centre (red), and the other genes were located in the inner track of concentric circles (dark red). Downstream genes were placed in the middle track (blue), and the phenotypes were placed in the outer two rings. The first inner ring included PTCH1 , JAG2 , LRP5 , CCND1 , EGFR and WNT5A . Interaction between SFRP1 and the first-ring genes was deduced to genes in the middle circle (blue). The correlated phenotypes were presented in the outer two circles. The node size reflected the enrichment of genes in each of the GO terms. The connecting lines showed the correlation between genes and/or pathways. N01, primary culture cells from normal duodenum. AC01, primary culture cells from well-differentiated ampullary adenocarcinoma, T1N0, stage IA. AC02, primary culture cells from moderately-differentiated ampullary adenocarcinoma, T2N1, stage IIB. APC , adenomatosis polyposis coli; BMP, bone morphogenetic protein; BOC , BOC cell adhesion associated, oncogene regulated; CCND1 , cyclin D1; CDH1 , cadherin 1; CRYAB , crystallin alpha B; CTNNB1 , catenin beta 1; CX3CL1 , C-X3-C motif chemokine ligand 1; EGFR , epidermal growth factor receptor; ESC, embryonic stem cell; FOXC1 , forkhead box C1; FZD7 , frizzled class receptor 7; IL33 , interleukin 33; IL34 , interleukin 34; JAG2 , jagged canonical notch ligand 2; KIT , KIT proto-oncogene, receptor tyrosine kinase; LRP5 , low-density lipoprotein receptor-related protein 5; PTCH1 , protein patched 1; SERPINB5 , serpin family b member 5; SFRP1 , secreted frizzled related protein 1; SOSTDC1 , sclerostin domain containing 1; WNT1 , Wnt family member 1; WNT5A , WNT family member 5A.

Article Snippet: The Agilent Human Whole Genome Oligo 4 × 44 K Microarray chip (Agilent) was hybridised with Cy-labelled complementary RNA.

Techniques: Expressing, Microarray

Journal: Protein & Cell

Article Title: MiR-139-5p inhibits migration and invasion of colorectal cancer by downregulating AMFR and NOTCH1

doi: 10.1007/s13238-014-0093-5

Figure Lengend Snippet: AMFR and NOTCH1 are the direct target genes of miR-139-5p . (A) Initial screening of miR-139-5p target genes using a microarray assay, bioinformatics predictions and the luciferase reporter assay. Five downregulated genes (AMFR, NOTCH1, HNRNPF, TOP1, and LAPTM4B) were selected from the 31 genes in the initial screening based on the functional analysis of these genes, and their 3′UTRs were assessed using the luciferase reporter assay. (B and C) Analyses of the luciferase activity of the luciferase reporter plasmids containing either wild-type (WT) or mutant-type (MT) 3′UTRs of AMFR and NOTCH1 in HEK-293T and HCT-116 cells. A mutation was generated in the site complementary to the miR-139-5p seed region of the 3′UTR of AMFR or NOTCH1, as indicated. (D) The protein levels of AMFR and NOTCH1 were determined by Western blot assays using LoVo and HCT-116 cells transfected with miR-139-5p mimic, miR-139-5p inhibitor (anti-miR-139-5p) or their corresponding negative control (NC or anti-NC). Beta-actin protein was used as an internal control

Article Snippet: Expression profiling was performed using an Agilent human whole genome oligo microarray chip (4 × 44 K) (Agilent, USA).

Techniques: Microarray, Luciferase, Reporter Assay, Functional Assay, Activity Assay, Mutagenesis, Generated, Western Blot, Transfection, Negative Control