Journal: Genomics Data

Article Title: Transcriptional profiling of differentially expressed long non-coding RNAs in breast cancer

doi: 10.1016/j.gdata.2015.09.020

Figure Lengend Snippet:

Article Snippet: The labeled cRNAs were hybridized onto the Human lncRNA array V4.0 (4 × 180 K, Agilent), including the global profiling of 78,243 human lncRNAs and 30,215 coding transcripts.

Techniques: Microarray

Journal: Nucleic Acids Research

Article Title: LncRNA Meg3 protects endothelial function by regulating the DNA damage response

doi: 10.1093/nar/gky1190

Figure Lengend Snippet: Transcriptome analysis identifies p53 signaling as the most significantly upregulated pathway upon Meg3 knockdown. HUVECs were transfected with control or Meg3 GapmeRs. 24 h after transfection, cells were treated with 10 ng/ml TNF-α for 3 h and collected for microarray gene chip analysis. Chromatin immunoprecipitation was performed using transfected cells with or without 10 ng/ml TNF-α treatment for 1 h. ( A ) Volcano plot shows differentially expressed mRNAs in ECs upon Meg3 knockdown. ( B ) KEGG signaling pathways analysis identified significantly regulated pathways among upregulated genes upon Meg3 knockdown. ( C ) Venn diagram shows p53 target genes that are regulated by Meg3. ( D ) qPCR analysis of a group of p53 target genes that were induced upon Meg3 knockdown. (E) Enrichment of p53 at the promoters of indicated genes was identified by chromatin immunoprecipitation using anti-p53 antibodies followed by qPCR analysis. Data show mean ± S.E.M., n = 3; * P < 0.05.

Article Snippet: Arraystar Human LncRNA Microarray v4.0, performed by Arraystar Inc. (Rockville, MD, USA), is designed for the global expression profiling of 40 173 human lncRNA and 20,730 protein-coding mRNA transcripts.

Techniques: Knockdown, Transfection, Control, Microarray, Chromatin Immunoprecipitation, Protein-Protein interactions

Journal: Nucleic Acids Research

Article Title: LncRNA Meg3 protects endothelial function by regulating the DNA damage response

doi: 10.1093/nar/gky1190

Figure Lengend Snippet: LncRNA pull-down assay identifies PTBP3 as a binding partner of Meg3. ( A ) LncRNA pull-down assay was used to identify the proteins associated with Meg3 transcript variant 1 (TV1) by incubating the cell lysates with biotinylated sense or antisense Meg3 RNA. The RNA–protein complexes captured by T-1 beads were subjected to silver stain after separation on SDS-PAGE gel. ( B ) The RNA–protein complexes from lncRNA pulldown using antisense Meg3 (negative control RNA), sense Meg3 (TV1), and Meg3 deletion mutants were subjected to western blot analysis of PTBP3 and GAPDH after separation on SDS-PAGE gel. GAPDH was examined as a negative control protein. ( C ) The interaction of endogenous PTBP3 with Meg3 was detected by RNA immunoprecipitation. EC lysates were immunoprecipitated with anti-PTBP3 antibody or Isotype matched control IgG. Meg3 was examined by qPCR in the immuno-precipitates using primer set 2 as shown in (D). LncRNA Neat1 was used as a positive control RNA that interacts with PTBP3. ( D ) Different sets of Meg3 primers were used to detect Meg3 by qPCR following RNA immunoprecipitation using anti-PTBP3 antibodies. Primer sets 1, 2, 5 detect Meg3 transcript variants 1 and 6 (TV1 and TV6); primer sets 3 and 4 detect Meg3 TV1; and primer sets 6 and 7 detect Meg3 TV6. ( E ) Dual-staining of Meg3 and PTBP3 in HUVECs. Linear trajectories (yellow line) crossing the cells with the intensities of Meg3 and PTBP3 signals were presented at the right side of images. White and black arrows indicate partial colocalization of Meg3 and PTBP3 in the nucleus of HUVECs. Data show mean ± S.E.M., n = 3; * P < 0.05.

Article Snippet: Arraystar Human LncRNA Microarray v4.0, performed by Arraystar Inc. (Rockville, MD, USA), is designed for the global expression profiling of 40 173 human lncRNA and 20,730 protein-coding mRNA transcripts.

Techniques: Pull Down Assay, Binding Assay, Variant Assay, Silver Staining, SDS Page, Negative Control, Western Blot, RNA Immunoprecipitation, Immunoprecipitation, Control, Positive Control, Staining