Journal: Stem Cells International

Article Title: Comparison of the MicroRNA Expression Profiles of Male and Female Avian Primordial Germ Cell Lines

doi: 10.1155/2018/1780679

Figure Lengend Snippet: An overview of the results of LC chicken miRNA microarray analysis. (a) The microarray analysis was performed on 4 PGC lines (2 female and 2 male) (Supplementary Tables – ). On the microarray, 991 chicken-specific miRNAs, 42 plate controls, and 6 gga-5Sb rRNA probes were placed (Supplementary ). From the 991 miRNAs, 27 miRNAs were expressed in all samples and altogether 153 miRNAs were expressed in PGC lines. (b) The Venn diagram introduces the similarities and differences between the cell lines. (c) Paired t -test analysis was conducted between the male (4ZP, FS101) and female (5ZP, FS111) PGC lines by LC Sciences Company. Paired t -test was conducted between the male and female PGC samples at the 0.05 significance level, to analyse the differences in the expression level of all expressing miRNAs in the samples. The heat map represents the result of the analysis. Only 6 differentially expressing miRNAs were found: gga-miR-1354, gga-miR-1767, gga-mir-30c-5p, gga-miR-1584, gga-miR-1599, and gga-miR-2127 (Supplementary , Supplementary Fig. ).

Article Snippet: As microRNAs (miRNAs) have been proved to play a key role in the maintenance of pluripotency and the cell cycle regulation of stem cells, a complex miRNA analysis (microarray-based, μ Paraflo® Microfluidic Biochip Technology, LC Sciences, Houston, Texas, USA) was performed to determine the difference in miRNA expression profile between 2 female and 2 male PGC lines (Supplementary Tables – ).

Techniques: Microarray, Expressing

Journal: Stem Cells International

Article Title: Comparison of the MicroRNA Expression Profiles of Male and Female Avian Primordial Germ Cell Lines

doi: 10.1155/2018/1780679

Figure Lengend Snippet: Expression pattern of miRNAs, identified in all examined samples by LC chicken miRNA microarray analysis. The microarray analysis was performed on 4 PGC lines (2 female (FS111 and 5ZP) and 2 male (FS101 and 4ZP)). (a) The expression values of miRNAs, expressing in all PGC samples, were visualized in a heat map (using GenEx software, complete linkage and Spearman correlation analysis were performed). Simultaneously, cluster analysis was performed. According to the analysis, the male cells were more related to each other. The 5ZP PGC line was the most different from the others. (b), (c) Using GenEx software, we performed a scatterplot analysis to identify the upregulated miRNAs. (b) represents the group of upregulated miRNAs in the 5ZP PGC line. These miRNAs compose cluster 1, while (c) shows the upregulated miRNAs in the highly proliferating PGC lines. These miRNAs formed cluster 2. The results of the clustering analysis highlighted a portion of miRNAs in cluster 2 which belong to the miRNA-302 cluster.

Article Snippet: As microRNAs (miRNAs) have been proved to play a key role in the maintenance of pluripotency and the cell cycle regulation of stem cells, a complex miRNA analysis (microarray-based, μ Paraflo® Microfluidic Biochip Technology, LC Sciences, Houston, Texas, USA) was performed to determine the difference in miRNA expression profile between 2 female and 2 male PGC lines (Supplementary Tables – ).

Techniques: Expressing, Microarray, Software

Journal: Stem Cells International

Article Title: Comparison of the MicroRNA Expression Profiles of Male and Female Avian Primordial Germ Cell Lines

doi: 10.1155/2018/1780679

Figure Lengend Snippet: Expression pattern of stem cell- and germ cell-specific markers in RNA samples examined at LC miRNA microarray analysis. We performed qPCR analysis to check the RNA expression profile in samples sent to LC microarray analysis. We compared one female (5ZP) and one male (4ZP) GFP PGC sample, and one female (FS111) and one male (FS101) PC PGC sample using 3 parallel samples at qPCR analysis. (a), (b) Expression of CVH, cDAZL, cPOUV, and cNANOG (relative to cGAPDH as the reference gene) and gga-miR-302a, gga-miR-302b-3p, and gga-miR-302b-5p (relative to U6 as the reference gene) was analysed. Relative gene expression values were calculated relative to the FS101 sample in each case. (c) The proliferation rate of PGCs was measured on 3 different days using CCK-8 proliferation assay. The doubling time was calculated according to the measured optical densities (OD). (d) The miR-302b-5p/miR-302b-3p ratio was calculated from the average delta Ct values of samples.

Article Snippet: As microRNAs (miRNAs) have been proved to play a key role in the maintenance of pluripotency and the cell cycle regulation of stem cells, a complex miRNA analysis (microarray-based, μ Paraflo® Microfluidic Biochip Technology, LC Sciences, Houston, Texas, USA) was performed to determine the difference in miRNA expression profile between 2 female and 2 male PGC lines (Supplementary Tables – ).

Techniques: Expressing, Microarray, RNA Expression, Gene Expression, CCK-8 Assay, Proliferation Assay

Journal: Stem Cells International

Article Title: Comparison of the MicroRNA Expression Profiles of Male and Female Avian Primordial Germ Cell Lines

doi: 10.1155/2018/1780679

Figure Lengend Snippet: Most important targets of gga-miR-302b-5p and gga-miR-302-3p miRNAs. The main molecular targets for the studied miRNAs have been presented. The molecular pathways and targets for gga-miR-302b-5p are on the left side and for gga-miR-302b-3p on the right side. MAKP signalling is responsible for maintaining pluripotency and proliferation in mammals. It can be activated by a series of intrinsic and extrinsic stimulatory signals. In chickens, gga-miR-302b-5p controls the proliferation rate via MAPK signalling. In the case of low-proliferating PGC cell lines, gga-miR-302b-3p expression was high. It can be assumed that the high gga-miR-302b-3p expression somehow causes downregulation of pathways promoting proliferation, thereby causing cell cycle arrest at the G1 stage. gga-miR-302b-5p was found to be highly expressed in high-proliferating PGC lines. Hence, it can be hypothesized that probably the high expression of gga-miR-302b-5p is contributed in controlling throughout its molecular targets in the MAPK signalling pathway. miR-302b-5p probably by inhibiting the MAPK pathway components can cause high proliferation rate in PGC lines, and miR-302a is responsible for the fast transition from the G1 to S phase in the cell cycle .

Article Snippet: As microRNAs (miRNAs) have been proved to play a key role in the maintenance of pluripotency and the cell cycle regulation of stem cells, a complex miRNA analysis (microarray-based, μ Paraflo® Microfluidic Biochip Technology, LC Sciences, Houston, Texas, USA) was performed to determine the difference in miRNA expression profile between 2 female and 2 male PGC lines (Supplementary Tables – ).

Techniques: Expressing

Journal: Biology Open

Article Title: Effects of β4 integrin expression on microRNA patterns in breast cancer

doi: 10.1242/bio.20121628

Figure Lengend Snippet: ( A ) qNPA microarray was performed in triplicate on MCF10CA1a siCtrl cells and MCF10CA1a siβ4 cells at 72 hours post-transfection. The heat map depicts the 44 miRNAs undergoing a statistically significant change in expression following transient depletion of β4 subunit in this system. ( B ) qNPA microarray was performed in triplicate on two subclones of the MDA-MB-435/β4 transfectants (3A7 and 5B3), and two subclones of the MDA-MB-435/mock transfectants (6D2 and 6D7). The heat map depicts the 50 miRNAs undergoing a statistically significant change in expression following introduction of the β4 subunit into this system. ( C ) qNPA microarray was performed in triplicate on ten β4 positive and ten β4 negative invasive breast carcinomas. The heat map depicts the 74 miRNAs differentially expressed between tumor subsets. For all array analyses, a p-value < 0.05 and a ±1.2-fold change cut-off was applied. Color was assigned to each miRNA based on relative expression across samples.

Article Snippet: A novel qNPA based miRNA Microarray high throughput platform from High Throughput Genomics (HTG Molecular Diagnostics, Inc.; Tuscon, AZ, USA) was used to study 1050 mature miRNAs in human, rat, and mouse based upon the Sanger miRBase release 9.1.

Techniques: Microarray, Transfection, Expressing

Journal: Biology Open

Article Title: Effects of β4 integrin expression on microRNA patterns in breast cancer

doi: 10.1242/bio.20121628

Figure Lengend Snippet: ( A ) Venn diagram of overlapping miRNAs that undergo differential expression in response to β4 across all three arrays. ( B ) Venn diagram of overlapping miRNA families that undergo differential expression in response to β4 across all three arrays.

Article Snippet: A novel qNPA based miRNA Microarray high throughput platform from High Throughput Genomics (HTG Molecular Diagnostics, Inc.; Tuscon, AZ, USA) was used to study 1050 mature miRNAs in human, rat, and mouse based upon the Sanger miRBase release 9.1.

Techniques: Quantitative Proteomics

Journal: Biology Open

Article Title: Effects of β4 integrin expression on microRNA patterns in breast cancer

doi: 10.1242/bio.20121628

Figure Lengend Snippet: GeneChip derived mRNA levels were ranked from the most upregulated in β4 transfected cells to the most downregulated (x-axis, 1 to 12,300, respectively). Red shading indicates mRNA is upregulated in β4 transfectants, while blue shading indicates mRNA is downregulated. Each vertical black line represents a miRNA target. The left-to-right position of each black line indicates the relative position of the predicted target within the rank ordered mRNA list. ( A ) miR-92ab predicted target gene are enriched among mRNAs up-regulated in the β4 transfectants, as illustrated by the increasing number of black lines on the left side of each graphic and the positive running enrichment scores (ES) marked by the red lines (p = 0.028). No enrichment was detected for and miR-99ab/100. ( B ) miR-15abc/16/16abc/195/322/424/497/1907 (p = 0.039), miR-23abc/23b-3p (p = 0/034), miR-27abc/27a-3p (p = 0.003), and miR-30abcdef/30abe-5p/384-5p (p = 0.0) predicted target genes are enriched among mRNAs up-regulated in the β4 transfectants.

Article Snippet: A novel qNPA based miRNA Microarray high throughput platform from High Throughput Genomics (HTG Molecular Diagnostics, Inc.; Tuscon, AZ, USA) was used to study 1050 mature miRNAs in human, rat, and mouse based upon the Sanger miRBase release 9.1.

Techniques: Derivative Assay, Transfection

Journal: Oncology Reports

Article Title: Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data

doi: 10.3892/or.2018.6205

Figure Lengend Snippet: Differentially expressed miRNAs (DE-miRNAs) in five cases of drug-resistant (DR) breast cancer tissues and five cases of drug-sensitive (DS) tissues. (A) Data are presented as a heat map. FC, fold change. (B) The chemotherapy drugs used for treating the breast cancer patients.

Article Snippet: The dataset GSE71142, based on the platform of GPL20717 μParafloTM miRNA microarray (LC Sciences, Houston, TX, USA), included five cases of chemoresistant breast cancer tissues and five cases of chemosensitive tissues.

Techniques:

Journal: Oncology Reports

Article Title: Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data

doi: 10.3892/or.2018.6205

Figure Lengend Snippet: KEGG pathway analysis of DE-miRNA target genes. (A) For upregulated miRNAs; and (B) for downregulated miRNAs. The top 10 enriched pathways are presented.

Article Snippet: The dataset GSE71142, based on the platform of GPL20717 μParafloTM miRNA microarray (LC Sciences, Houston, TX, USA), included five cases of chemoresistant breast cancer tissues and five cases of chemosensitive tissues.

Techniques:

Journal: Oncology Reports

Article Title: Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data

doi: 10.3892/or.2018.6205

Figure Lengend Snippet: miRNA-gene regulatory network based on the hub target genes. (A) For upregulated miRNAs; and (B) for downregulated miRNAs.

Article Snippet: The dataset GSE71142, based on the platform of GPL20717 μParafloTM miRNA microarray (LC Sciences, Houston, TX, USA), included five cases of chemoresistant breast cancer tissues and five cases of chemosensitive tissues.

Techniques:

Journal: Oncology Reports

Article Title: Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data

doi: 10.3892/or.2018.6205

Figure Lengend Snippet: Enriched transcription factors by DE-miRNA target genes. (A) For upregulated miRNAs; and (B) for downregulated miRNAs. The top 10 most significant transcription factors are presented.

Article Snippet: The dataset GSE71142, based on the platform of GPL20717 μParafloTM miRNA microarray (LC Sciences, Houston, TX, USA), included five cases of chemoresistant breast cancer tissues and five cases of chemosensitive tissues.

Techniques:

Journal: Oncology Reports

Article Title: Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data

doi: 10.3892/or.2018.6205

Figure Lengend Snippet: Validated miRNA-gene interactions in breast carcinoma. (A) The validated miRNA-gene-human phenotype ontology (HPO) interactions in breast carcinoma were searched from miRWalk2.0. (B) The validated miRNA-gene network was constructed.

Article Snippet: The dataset GSE71142, based on the platform of GPL20717 μParafloTM miRNA microarray (LC Sciences, Houston, TX, USA), included five cases of chemoresistant breast cancer tissues and five cases of chemosensitive tissues.

Techniques: Construct