Journal: Molecular cell

Article Title: Intragenic enhancers attenuate host gene expression

doi: 10.1016/j.molcel.2017.09.010

Figure Lengend Snippet: (A) ChIP-Seq profiles of RNAPII occupancy at select genes in mouse ESCs(Brookes et al., 2012).

Article Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS Mouse ES Cell Culture Mouse ESCs (E14Tg2a, ATCC) were maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), as previously described ( Cinghu et al., 2014 ; Oldfield et al., 2014 ).

Techniques: ChIP-sequencing

Journal: Molecular cell

Article Title: Intragenic enhancers attenuate host gene expression

doi: 10.1016/j.molcel.2017.09.010

Figure Lengend Snippet: (A) RT-qPCR analysis of mRNA levels of intragenic enhancer-containing genes Meis1 and Mapk4 in corresponding wild-type, enhancer heterozygous (+/−) and enhancer knockout (−/−) mouse ESCs. As a control, an intronic region (showing no signs of an enhancer) from Cdk6 gene was deleted and Cdk6 expression was measured. Data are normalized to Actin. Error bars represent SEM of three biological replicates. *P < 0.01 (Student’s t-test; two-sided).

Article Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS Mouse ES Cell Culture Mouse ESCs (E14Tg2a, ATCC) were maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), as previously described ( Cinghu et al., 2014 ; Oldfield et al., 2014 ).

Techniques: Quantitative RT-PCR, Knock-Out, Control, Expressing

Journal: Molecular cell

Article Title: Intragenic enhancers attenuate host gene expression

doi: 10.1016/j.molcel.2017.09.010

Figure Lengend Snippet: (A) Read density plot showing average expression (RPKM) profile in wildtype (WT) and Exosc3 knockout (KO) mouse ESCs, as measured using RNA-Seq (Pefanis et al., 2015), near transcription start site (TSS), intragenic enhancer (IE), and transcription end site (TES).

Article Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS Mouse ES Cell Culture Mouse ESCs (E14Tg2a, ATCC) were maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), as previously described ( Cinghu et al., 2014 ; Oldfield et al., 2014 ).

Techniques: Expressing, Knock-Out, RNA Sequencing

Journal: Molecular cell

Article Title: Intragenic enhancers attenuate host gene expression

doi: 10.1016/j.molcel.2017.09.010

Figure Lengend Snippet: (A) Correlation between attenuation coefficient, calculated based on mRNA data shown in Fig. S3A (summarized as Fig. 3D), and levels of nascent antisense ieRNA expression, assessed from GRO-Seq data in mouse ESCs(Jonkers et al., 2014).

Article Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS Mouse ES Cell Culture Mouse ESCs (E14Tg2a, ATCC) were maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), as previously described ( Cinghu et al., 2014 ; Oldfield et al., 2014 ).

Techniques: Expressing

Journal: Molecular cell

Article Title: Intragenic enhancers attenuate host gene expression

doi: 10.1016/j.molcel.2017.09.010

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS Mouse ES Cell Culture Mouse ESCs (E14Tg2a, ATCC) were maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore), as previously described ( Cinghu et al., 2014 ; Oldfield et al., 2014 ).

Techniques: Recombinant, Negative Control, Lysis, Luciferase, Reporter Gene Assay, cDNA Synthesis, Gel Extraction, TA Cloning, Knock-Out, Control, Amplification, Plasmid Preparation, CRISPR, ChIP-sequencing, RNA Sequencing, Hi-C, ChIA Pet Assay