human circrna array v2.0, 8 × 15k  (Arraystar inc)

Journal: BMC Neuroscience

Article Title: Circ VRK1/microRNA-17/PTEN axis modulates the angiogenesis of human brain microvascular endothelial cells to affect injury induced by oxygen-glucose deprivation/reperfusion

doi: 10.1186/s12868-023-00774-8

Figure Lengend Snippet: OGD/R treatment decreases HBMVEC viability and upregulates Circ VRK1 expression. A the viability of HBMVECs exposed to OGD for 2 h, 4 h and 8 h detected by CCK8 assay. B The cytotoxicity of HBMVECs exposed to OGD for 2 h, 4 h and 8 h measured by LDH release assay. C circRNA microarray analysis of differentially expressed circRNAs in cells exposed to OGD/R. D circ_0000566 expression changes in HBMVECs exposed to OGD for 2 h, 4 h and 8 h by RT-qPCR. E The genome position and source genes of circ_0000566 queried in circBase. F the localization of Circ VRK1 in HBMVECs determined by subcellular fractionation. G PCR validation of Circ VRK1 siRNA transfection efficiency in HBMVEC. Error bars represented the mean ± SD from 3 independent experiments. Unpaired t test ( G ) and one-way ( A – D ) or two-way ANOVA ( F ) were used

Article Snippet: The enriched circRNA was then amplified, and the labeled cRNA was hybridized to an Arraystar circRNA array (8 × 15k, Arraystar) using a random primer method (Arraystar Super RNA Labeling Kit; Arraystar).

Techniques: Expressing, CCK-8 Assay, Lactate Dehydrogenase Assay, Microarray, Quantitative RT-PCR, Fractionation, Transfection

Journal: BioMed Research International

Article Title: Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

doi: 10.1155/2017/8421614

Figure Lengend Snippet: circRNA expression in CRR-HCT116 and parental HCT116 cells. Heat plots of circRNA in CRR-HCT116 and parental HCT116 cells. Each column represents the expression profile of a cell sample, and each row corresponds to a circRNA. “Red” indicates higher expression level, and “green” indicates lower expression level.

Article Snippet: Lastly, Arraystar Human circRNA Array (8 × 15K, Arraystar) was used to hybridize the labeled cRNAs.

Techniques: Expressing

Journal: BioMed Research International

Article Title: Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

doi: 10.1155/2017/8421614

Figure Lengend Snippet: Top modulated circRNAs in chemoradiation-resistant colorectal cancer.

Article Snippet: Lastly, Arraystar Human circRNA Array (8 × 15K, Arraystar) was used to hybridize the labeled cRNAs.

Techniques:

Journal: BioMed Research International

Article Title: Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

doi: 10.1155/2017/8421614

Figure Lengend Snippet: Chromosomal locations of variably expressed circRNA. The x -axis represents the ordinal of the chromosome, and the y -axis represents the percentage of circRNAs that were expressed differently between CRR-HCT116 and parental HCT116 cells (fold change > 2).

Article Snippet: Lastly, Arraystar Human circRNA Array (8 × 15K, Arraystar) was used to hybridize the labeled cRNAs.

Techniques:

Journal: BioMed Research International

Article Title: Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

doi: 10.1155/2017/8421614

Figure Lengend Snippet: circRNA-miRNA-target gene network of top three upregulated circRNAs in cancer signaling pathways. Interactions between circRNAs and miRNAs and those between miRNAs and target genes in cancer signaling were shown in the map.

Article Snippet: Lastly, Arraystar Human circRNA Array (8 × 15K, Arraystar) was used to hybridize the labeled cRNAs.

Techniques:

Journal: bioRxiv

Article Title: A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

doi: 10.1101/2022.07.18.500467

Figure Lengend Snippet: (A) hsa_circ_0001400 transcript levels are shown in KSHV-infected HUVECs (microarray), LECs (RNA-Seq), EBV-positive Burkitt’s lymphoma line Akata (microarray), and HCMV-infected fibroblast (RNA-Seq). n=2-3. Significances were computed with limma. *:p-value < 0.05. (B) Fold-changes of top 30 most abundant human circRNAs in KSHV-infected HUVECs. Transcript levels of circRNAs and corresponding linear mRNAs were quantitated from total RNA-Seq with circExplorer3 as FPBs (fragments per billion mapped base). Fold-changes of circRNAs and linear RNAs (infected vs mock) are calculated (n=3) and mean values are shown. Genes are sorted by circRNA FPBs (Abundance) and host genes of both circRNA and linear RNAs are shown on the left. FPBs and ratios are available in Table S1. (C) Log 2 fold-changes of all detected human circRNAs/counterpart linear mRNAs (KSHV-infected vs mock HUVECs) are shown as a scatter plot. Data is same as in and Table S1. Pearson correlation value was calculated. n=3 and mean values are shown.

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

Techniques: Infection, Microarray, RNA Sequencing

Journal: bioRxiv

Article Title: A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

doi: 10.1101/2022.07.18.500467

Figure Lengend Snippet: (A) Infographic for sequencing techniques performed. (B) Total and 4SU RNA-Seq delta transcript ratio (circular reads/linear reads) for unique human circRNA (1 or 3 d). Positive Δtranscript ratios (Induced – Uninduced) indicate a shift after lytic reactivation in transcript abundance, favoring the circular transcript. circ_001400 is highlighted in orange. n=2 and mean values are shown.

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

Techniques: Sequencing, RNA Sequencing

Journal: bioRxiv

Article Title: A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

doi: 10.1101/2022.07.18.500467

Figure Lengend Snippet: (A) circ_0001400 transcript levels after manipulation of circ_0001400. circ_0001400 was ectopically expressed with lentivirus (left) or treated with siRNA (right) in KSHV-infected HUVECs. MOIs were 0.5 (Low) or 1.0 (High) for lentivirus and 0.5 for the siRNA condition. Total RNAs were extracted followed by RT-qPCR at 3 days post infection (n=3). (B) circ_0001400 transcript levels after manipulation of circ_0001400. circ_0001400 was depleted by siRNAs in KSHV-infected LECs. Total RNAs were extracted followed by RT-qPCR at 3 days post infection (n=3). (C) Log 2 fold changes of KSHV transcript levels after manipulation of circ_0001400 in HUVECs. circ_0001400 was ectopically expressed with lentivirus or depleted by siRNAs in KSHV-infected HUVECs. At 3 days post infection, total RNAs were extracted for RNA-Seq. x-axis shows the effect of circ_0001400 depletion while y-axis describes the result of circ_0001400 ectopic expression. The list of fold changes is available in Table S2. (D) Flow cytometry analysis of HUVECs dually infected with KSHV and lentiviruses. KSHV BAC16 contains a GFP reporter gene whereas circRNA-expressing lentivirus contains mCherry reporter gene. Both markers are under constitutive promoters and useful to track infection (n=3). Infectivity of HUVECs was measured at 3 days post infection with KSHV BAC16.

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

Techniques: Infection, Quantitative RT-PCR, RNA Sequencing, Expressing, Flow Cytometry

Journal: bioRxiv

Article Title: A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

doi: 10.1101/2022.07.18.500467

Figure Lengend Snippet: (A) Diagram of the RNA-pulldown assay is shown. Total RNA was incubated with biotinylated DNA oligos that is specific to circ_0001400 and circRNA-RNA complexes are purified using streptavidin beads. Next generation sequencing (NGS) was performed to determine their identities. (B) A volcano plot of transcripts identified by the circ_0001400 RNA pulldown assay in 293T cells. Mapped reads were median-scaled and enrichments were calculated by voom (limma package). ZKSCAN1 and RELL1 are partially included in the circ_0001400 expression plasmid vectors and thus serve as positive control of pulldown. Transcripts that were confirmed in are depicted as orange rectangles. n=3. (C) RT-qPCR of enriched transcripts after RNA-pulldown. circ_0001400 was ectopically expressed in 293T cells for 24 hours and RNA-pulldowns were performed (n=3). Enrichment of circ_0001400 and candidate mRNAs (listed in Table S5) are shown. (D) TTI1 transcript levels after manipulation of circ_0001400 transcript levels. circ_0001400 was ectopically expressed (n=6) or depleted by siRNAs (n=3) in 293T cells for 48 hours. Total RNAs were extracted followed by RT-qPCR. (E) Proposed model of circ_0001400’s regulation of PI3K/AKT/mTOR pathway. Significances were calculated with paired-t tests. *:p-value < 0.05.

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

Techniques: Incubation, Purification, Next-Generation Sequencing, Expressing, Plasmid Preparation, Positive Control, Quantitative RT-PCR

Journal: bioRxiv

Article Title: A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

doi: 10.1101/2022.07.18.500467

Figure Lengend Snippet: hsa_circ_0001400 is induced by multiple herpesviruses. The circRNA allows activation of PI3K/AKT/mTOR pathway and promote cell growth of latently KSHV-infected cells. On the other hand, lytic infection is suppressed by inhibition of virus production and increase of co-stimulatory molecules by circ_0001400.

Article Snippet: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

Techniques: Activation Assay, Infection, Inhibition, Virus