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

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

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: Basic information of four circRNAs.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques:

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: Primers for RT-qPCR.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques:

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: Differential expression between AS and HC groups. ( A) Volcano plot of differentially expressed circRNAs. (B) Hierarchical clustering of differentially expressed circRNAs. (C) Chromosome distribution of differentially expressed circRNAs. (D) Source distribution of differentially expressed circRNAs. (E) Relative expression levels of eight circRNAs in six AS patients and six HCs. (The Y-axis is the ratio of the relative expression level of circRNA in the AS group to the HC group.) AS: Ankylosing spondylitis; circRNA: Circular RNA; HC: Healthy controls.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques: Expressing

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: Bioinformatics analysis results of differentially expressed circRNAs. (A) GO analysis results of upregulated circRNAs. (B) GO analysis results of downregulated circRNAs. (C) KEGG pathway analysis results of upregulated circRNAs. (D) KEGG pathway analysis results of downregulated circRNAs. circRNA: Circle RNA; GO: Gene ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques:

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: RT-qPCR results of circRNA. (A) Differentially expressed circRNA between the AS group and HC group (hsa_circRNA_001544, hsa_circRNA_102532, hsa_circRNA_008961, and hsa_circRNA_12732). (B) Differentially expressed circRNAs among the ASA group, ASS group, and HC group (hsa_circRNA_001544, hsa_circRNA_102532, hsa_circRNA_008961, and hsa_circRNA_12732). AS: Ankylosing spondylitis; ASA: Active AS; ASS: Stable AS; circRNA: Circular RNA; HC: Healthy controls; RT-qPCR: Real-time fluorescence quantitative polymerase chain reaction. ∗ means P <0.05, † means P <0.001, ns means no significance.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques: Quantitative RT-PCR, Fluorescence, Real-time Polymerase Chain Reaction

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: Correlation analysis of circRNA and AS-related indicators. The correlation analysis among hsa_circRNA_012732 and LY, MCV, ALB, BASDAI, BASFI, hsCRP level, and GLOB. The correlation analysis between hsa_circRNA_008961and PLT. ALB: Albumin; AS: Ankylosing spondylitis; BASDAI: Bath Ankylosing Spondylitis Disease Activity Index; BASFI: Bath Ankylosing Spondylitis Functional Index; circRNA: Circle RNA; GLOB: Globulin; hsCRP: High-sensitivity C-reactive protein; LY: Lymphocyte count; MCV: Mean corpusular volume; PLT: Platelet.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques: Activity Assay, Functional Assay

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: AUC of hsa_circRNA_001544, hsa_circRNA_102532, hsa_circRNA_008961, and hsa_circRNA_012732. AUC: Area under curve; circRNA: Circle RNA.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques:

Journal: Chinese Medical Journal

Article Title: Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis

doi: 10.1097/CM9.0000000000001815

Figure Lengend Snippet: The target miRNAs of six circRNAs.

Article Snippet: The circRNAs were amplified and labeled by Arraystar Super RNA labeling kits (Arraystar, Rockville, MD, USA) and then using Arraystar Human circRNA Array v2 (8 × 15K) (Arraystar) for hybridization, and the array was scanned with an Agilent scanner G2505C (Agilent, Santa Clara, CA, USA).

Techniques: