hg19 refseq gene models  (Santa Cruz Biotechnology)

Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

Article Title: Crohn’s disease IRGM risk alleles are associated with altered gene expression in human tissues

doi: 10.1152/ajpgi.00196.2018

Figure Lengend Snippet: Relationship of immunity-related GTPase family M (IRGM) single nucleotide polymorphism to IRGM expression in human terminal ileum and whole blood. RNA-Seq data in the Genotype-Tissue Expression Project portal (https://gtexportal.org/home/) was analyzed to define the relationship of genotypes at rs13361189 (A), rs10065172 (B), and rs9637876 (C) to IRGM mRNA levels in human terminal ileum and whole blood. Box plots depict median and interquartile ranges of transcripts per million (TPM) for mRNA expression of IRGM defined by RefSeq gene models. Numbers below IRGM genotypes indicate the number of independent human specimens sampled. Tables at right depict P values for intergenotype comparisons.

Article Snippet: The annotations for this analysis are hg19 RefSeq gene models downloaded from the University of Californa, Santa Cruz Table Browser ( http://genome.ucsc.edu/ ) on September 22, 2017.

Techniques: Expressing, RNA Sequencing

Journal: Genes & Development

Article Title: Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals

doi: 10.1101/gad.314377.118

Figure Lengend Snippet: PIN1 facilitates MYC DNA binding at E-box sites, and PIN1-mediated MYC–GCN5 localization to the NPC activates resident target genes. ( A ) Heat map of MYC binding at TSSs (midline of the heat map) of all expressed genes ranked by their expression in wild-type cells. The color scale is indicated at the bottom , where the 90 percentile is marked at the black bar. ( B ) Motifs enriched at the center of MYC-binding peaks in wild-type and PIN1 knockout MEFs. ( C ) Averaged MYC-binding density profiles in a 5-kb window centered on E-box motif (CACGTG) sets near (<2 kb) the TSS or distal to (>10 kb) the TSS in wild-type (blue) or PIN1 knockout (red) MEFs. MYC binding is scaled based on total sequencing depth and the number of E-box regions per set to make the scales comparable between near and distal plots. ( D ) Heat map of genes showing more MYC binding at the TSS in wild-type than PIN1 knockout MEFs (>1.5 fold) ( Supplemental Table 2 ). Genes were ranked by average fold change of wild-type/knockout in two biological replicates. MYC-binding levels are scaled for each row (gene) independently, with red indicating high binding and blue representing low binding. University of California at Santa Cruz (UCSC) genome browser tracks for the indicated representative genes are shown in Supplemental Figure S5C . ( E ) Representative DNA FISH images of the indicated gene loci (green) in wild-type and PIN1 knockout primary MEFs at the 4-h time point in response to serum stimulation. The 0 time point is shown in Supplemental Figure S6A . ( F ) qChIP of TPR binding to the indicated PIN1-dependent ( Tubb2b , Cdc45 , Rpl36 , Twist1 , and Snai1 ) and PIN1-independent ( Mybbp1a , Gpatch4 , Atad3a , and Prdx6 ) MYC-bound target genes in wild-type (blue) and PIN1 knockout (red) MEFs at 4 h of serum stimulation. ( G ) qChIP of MYC binding to the indicated target genes in wild-type (blue) and PIN1 knockout (red) MEFs. Fold change between 0 and 4 h of serum stimulation is graphed. Primary data are shown in Supplemental Figure S7A . ( H ) qChIP of GCN5 binding to the indicated target genes in wild-type (blue) and PIN1 knockout (red) MEFs. Fold change between 0 and 4 h of serum stimulation is graphed. Primary data are shown in Supplemental Figure S7B . ( I ) qChIP of H3ac levels of the indicated target genes in wild-type (blue) and PIN1 knockout (red) MEFs. Fold change between 0 and 4 h of serum stimulation is graphed. Primary data are shown in Supplemental Figure S7C . ( J ) RT–PCR of the mRNA of the indicated genes in wild-type (blue) and PIN1 knockout (red) MEFs. Fold change at 4 h of serum stimulation is graphed. For F – J , P -values are shown for relevant significant comparisons. (*) P < 0.05; (**) P < 0.01; (***) P < 0.001. The error bars indicate standard errors from three independent experiments.

Article Snippet: Custom R scripts were used to count tags that aligned to the exons of University of California at Santa Cruz (UCSC) RefSeq gene models.

Techniques: Binding Assay, Expressing, Knock-Out, Sequencing, Reverse Transcription Polymerase Chain Reaction