Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Microarray analysis was applied to detect the lncRNAs and mRNAs in glioma compared to normal peritumoral tissue. A – Differentially expressed lncRNAs were detected in gliomas. A, B – Differentially expressed mRNAs were detected in gliomas. C – Clustering data of lncRNAs in gliomas were analyzed. D – Clustering data of mRNAs in gliomas were analyzed

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Summary of data from microarray for three pairs of glioma and adjacent normal tissues

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray, RNA Expression

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: LncRNA-mRNA co-expression network: nodes with red cycle represent lncRNAs, nodes without cycle represent mRNAs, straight lines represent interactions between genes, purple represents increased expression, and blue represents decreased expression. The size of the node represents the degree; the higher the degree, the more genes interact with the particular node in the network

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Expressing

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Degree was used to assess interactions in the lncRNA/mRNA network. This table is a collection of a series of key lncRNA/mRNAs

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques:

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Comparison of microarray data and qPCR results. A – qPCR was used to verify expression of lncRNAs ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc003qmb.2. B – Distribution of lncRNA expression levels were provided. All six lncRNAs of ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc- 003qmb.2 were validated by qPCR analysis in the 40 paired glioma and peritumoral tissues. Each histogram represents the average fold change (T/N) with logarithmic conversion. Error bars are indicative of standard deviation. Distribution of lncRNA expression

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Comparison, Microarray, Expressing, Standard Deviation

Journal: Redox Report : Communications in Free Radical Research

Article Title: LncRNA Fendrr: involvement in the protective role of nucleolin against H 2 O 2 -induced injury in cardiomyocytes

doi: 10.1080/13510002.2023.2168626

Figure Lengend Snippet: lncRNAs regulated by nucleolin in cardiomyocytes. (A) Heatmap profile of lncRNA microarray analysis. Green to red colors indicate low to high transcriptional levels. The lncRNAs differentially expressed between the two groups were identified through paired t-test P ≤ 0.05 and a fold change (FC) ≥ 2.5; n = 3 independent biological samples for each group. (B) The expression of 15 selected lncRNAs in chip test, where 10 differentially expressed up-regulated lncRNAs (up) and 5 differentially expressed down-regulated lncRNAs (down) were selected. (C) The interactions between nucleolin and lncRNAs were confirmed by RIP and identified via qRT-PCR. *, P < 0.05, vs. IgG group, n = 3. pcDNA3.1, the empty vector served as negative control; pcDNA3.1-Nuc, overexpression nucleolin group. (D) Bioinformatics website predicted Fendrr binding elements with nucleolin.

Article Snippet: Using the Aglient Rat lncRNA microarray V2.0 (Arraystar, Rockville, MD, USA), three sample pairs were prepared for lncRNA microarray analysis in the nucleolin-overexpressing rat cardiomyocyte cell line and control group.

Techniques: Microarray, Expressing, Quantitative RT-PCR, Plasmid Preparation, Negative Control, Over Expression, Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Interleukin-1β Processing Is Dependent on a Calcium-mediated Interaction with Calmodulin *

doi: 10.1074/jbc.M115.680694

Figure Lengend Snippet: Identification of pro-IL-1β interacting proteins on a human proteome microarray. A human proteome microarray was incubated with human recombinant pro-IL-1β (+) or with reagent diluent alone as a negative control (−) and probed with a mouse anti-human IL-1β antibody. An SNR value was generated for each probe set, with an SNR of >3 considered to be a hit. A comprehensive list of all identified pro-IL-1β interacting proteins (hits) is shown, including one representative negative result (for brain protein 44-like) and a positive control (anti-biotin mouse monoclonal IgG). The identity of each protein, the corresponding images for each duplicate set of proteins on the array, and the mean SNR for the duplicate protein spots are shown.

Article Snippet: Two HuProt human protein microarray slides (v.2.0) containing 19,951 probe sets spotted in duplicate were purchased from CDI Laboratories (Mayaguez, PR).

Techniques: Microarray, Incubation, Recombinant, Negative Control, Generated, Positive Control

Journal: Frontiers in Pharmacology

Article Title: Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach

doi: 10.3389/fphar.2020.00927

Figure Lengend Snippet: Transcriptomic data information for Noonan syndrome, LEOPARD syndrome, and hypertrophic cardiomyopathy (HCM).

Article Snippet: GSE68316 , Human myocardial tissues , CapitalBio Human LncRNA Microarray v2.0 , • 7 patient samples: 7 HCM patients • 5 Control samples: 5 disease-free individuals.

Techniques: Expressing, Mutagenesis, Control, Microarray

Journal: eLife

Article Title: NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency

doi: 10.7554/eLife.54993

Figure Lengend Snippet: ( A ) Representation of NuRD complex according to and ( B ) Expression levels, as normalized counts, of the displayed NuRD subunits (CHD4 in orange, HDAC2 in pink, MTA2 in dark pink, and RBBP4 in dark orange) obtained from RNA-seq data of RH4 cells expressing a tetracycline-inducible shRNA scramble construct at 24 and 48hrs of doxycycline treatment (n=3, see Materials and methods for details). ( C ) Violin plot depicting the expression levels of NuRD subunits in FP-RMS tumor tissue. Displayed are microarray data from three independent studies ( ; ; ) available on the R2 gene expression database (r2.aml.nl). ( D ) Immunoblot depicting Cas9 expression in RH4-Cas9 cells. GAPDH was used as a loading control and wildtype RH4 cells (WT) served as negative control. ( E ) Box plot depicting the tumor dependency scores, calculated as CERES, of the indicated NuRD members in 6 FP-RMS cell lines (CRISPR Avana Public 19Q2, depmap.org ). ( F ) Results of CRISPR/Cas9 double knockoutsdisplayed as ratio between the indicated NuRD members double knockout (DKO) population and the control population (sgAAVS1) at day 12 normalized to day 2. Each point represents the average of 3 biological replicates.

Article Snippet: Recombinant DNA reagent , PX459; pSpCas9(BB)−2A-Puro (plasmid) , Addgene , #62988; RRID: Addgene_ 62988 , Cas9 and sgRNA expression construct.

Techniques: Expressing, RNA Sequencing, shRNA, Construct, Microarray, Gene Expression, Western Blot, Control, Negative Control, CRISPR, Double Knockout

Journal: eLife

Article Title: NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency

doi: 10.7554/eLife.54993

Figure Lengend Snippet: ( A ) Illustrative scheme of the NuRD centered CRISPR/Cas9-based screen. Briefly, RH4 cells stably expressing Cas9 were transduced with lentiviral expression vectors containing either a BFP-labelled control sgRNA (sgAAVS1) or a RFP-la-belled sgRNA targeting a certain NuRD subunit. Two days after transduction, the blue and red populations were mixed 1:1 and their evolution was analyzed by flow cytometry at day 2 and 12 after transduction. ( B ) CRISPR/Cas9 screen results displayed as ratio between the indicated NuRD member knockout (KO) population and the control population (RFP/BFB ratio) at day 12 normalized to day 2. Each point represents the average of 3 biological replicates. Five sgRNAs were used per NuRD member. ( C ) Representative phase-contrast images of RH4 cells 5 days after doxycycline-mediated (Dox) RBBP4, CHD4, and PAX3-FOXO1 (P3F) depletion by shRNA. A scramble shRNA was used as negative control. Scale bar - 100μm. ( D ) Percentage of dead cells, measured by 7-AAD staining, observed in the same samples described in ( C ). Data are represented as mean ± SD (n=3; *p< 0.1, **p < 0.01, ***p < 0.001, ratio paired t test). ( E, F and G ) Expression levels (relative to GAPDH) of the indicated P3F target genes quantified by qPCR in RH4 cells at 48hrs upon RBBP4, P3F and CHD4 induced knockdown by doxycycline treatment. Data were normalized to untreated cells and are represented as mean ± SD (n=3; *p<0.1, **p < 0.01, ***p < 0.001, ratio paired t test). Figure 1—source data 1. Raw data and statistics related to and its supplements.

Article Snippet: Recombinant DNA reagent , PX459; pSpCas9(BB)−2A-Puro (plasmid) , Addgene , #62988; RRID: Addgene_ 62988 , Cas9 and sgRNA expression construct.

Techniques: CRISPR, Stable Transfection, Expressing, Transduction, Control, Flow Cytometry, Knock-Out, shRNA, Negative Control, Staining, Knockdown

Journal: eLife

Article Title: NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency

doi: 10.7554/eLife.54993

Figure Lengend Snippet: ( A ) Illustrative scheme of the affinity purification-mass spectrometry (AP-MS) studies performed to identify CHD4 interactors. CRISPR/Cas9-mediated repair was used to endogenously Flag tag CHD4 on RH4 cells at the N- and C-terminus, creating two new clonal cell lines (N-CHD4 and C-CHD4) (left). Endogenous CHD4 was immunoprecipitated from the N- and C-CHD4 cell lines using an anti-Flag antibody and interactors were identified by liquid chromatography-mass spectrometry (LC-MS)(right). ( B ) Overlap of CHD4 putative interactors identified in the Flag pull-downs of CHD4. ( C ) Top 10 gene ontology terms found enriched on CHD4 interactome by Metascape online tool. ( D ) Distribution of the putative CHD4 interactors according to their protein class. ( E and F ) Western blots of Flag immunoprecipitation assays (IP). Figure 2—source data 1. List of CHD4 candidate interactors.

Article Snippet: Recombinant DNA reagent , PX459; pSpCas9(BB)−2A-Puro (plasmid) , Addgene , #62988; RRID: Addgene_ 62988 , Cas9 and sgRNA expression construct.

Techniques: Affinity Purification, Mass Spectrometry, Protein-Protein interactions, CRISPR, FLAG-tag, Immunoprecipitation, Liquid Chromatography, Liquid Chromatography with Mass Spectroscopy, Western Blot

Journal: eLife

Article Title: NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency

doi: 10.7554/eLife.54993

Figure Lengend Snippet:

Article Snippet: Recombinant DNA reagent , PX459; pSpCas9(BB)−2A-Puro (plasmid) , Addgene , #62988; RRID: Addgene_ 62988 , Cas9 and sgRNA expression construct.

Techniques: Recombinant, Plasmid Preparation, Expressing, Construct, shRNA, Sequencing, CRISPR, Enzyme-linked Immunosorbent Assay, Bicinchoninic Acid Protein Assay, Sample Prep, Software