Journal: STAR Protocols

Article Title: An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions

doi: 10.1016/j.xpro.2022.101918

Figure Lengend Snippet:

Article Snippet: V6.5 mouse embryonic stem cells , Novus Biologicals , Cat#NBP1-41162.

Techniques: Recombinant, SYBR Green Assay, Next-Generation Sequencing, Agarose Gel Electrophoresis, Purification, Software, Real-time Polymerase Chain Reaction

Journal: PLoS Genetics

Article Title: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

doi: 10.1371/journal.pgen.1003791

Figure Lengend Snippet: A. Western analysis of XRN2 and L1_ORF1 accumulation in WT and Xrn2 _KD mESCs; CM: Coomassie staining of total protein. B. qRT-PCR analysis of L1_ORF2 mRNA levels in WT and Xrn2 _KD mESCs. C. qPCR analysis of L1_Tf copy-number in WT and Xrn2 _KD mESCs. D–E. qRT-PCR analysis of miR-295 (D) and L1_ORF2 mRNA (E) levels in WT and Dgcr8 _KO mESCs. F. qPCR analysis of L1_Tf copy-number in WT and Dgcr8 _KO mESCs. G–H. qRT-PCR analysis of miR-295 (G) and L1_ORF2 mRNA (H) levels upon hAgo2 deletion in Tamoxifen-treated Ago1,2,3,4_KO mESCs. I. qPCR analysis of L1_Tf copy-number in Ago1,2,3,4_KO_hAgo2 mESCs before and after hAgo2 deletion. *: p-value<0.1.

Article Snippet: TKO mESCs were described in ref. . Dgcr8 _KO mESCs were purchased from Novus Biologicals (NBA1-19349).

Techniques: Western Blot, Staining, Quantitative RT-PCR

Journal: PLoS Genetics

Article Title: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

doi: 10.1371/journal.pgen.1003791

Figure Lengend Snippet: A. Western analysis of endogenous AGO1, AGO2 and L1_ORF1 protein levels in Dcr Flx/Flx , Dcr −/− and Dgcr8 _KO ESCs; CM: Coomassie staining of total protein. B. Western analysis of endogenous AGO2 and L1_ORF1 protein levels in Dcr Flx/Flx , Dc r −/− mESCs and one representative stable line of h Dcr -complemented Dcr −/− mESC; CM: Coomassie staining of total protein. C–E. qRT-PCR analysis of L1_ORF2 mRNA levels (C), miR-295 and miR-16 levels (D), and Hmga2 and Btg2 mRNA levels (established targets of mmu-miR-196a and mmu-let-7a and mmu-miR-132, respectively) in the various cell lines depicted in (E).

Article Snippet: TKO mESCs were described in ref. . Dgcr8 _KO mESCs were purchased from Novus Biologicals (NBA1-19349).

Techniques: Western Blot, Staining, Quantitative RT-PCR

Journal: PLoS Genetics

Article Title: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

doi: 10.1371/journal.pgen.1003791

Figure Lengend Snippet: A. Visualization of Embryoid bodies from Dcr Flx/Flx , Dcr −/− and h Dcr -complemented Dcr −/− mESCs after 1, 6 and 10 days of differentiation. B. Western analysis of OCT4 and endogenous AGO2 protein levels in the cells depicted in (A) before (d0) and after 10 days of differentiation (d10); CM: Coomassie staining of total protein. C. Same as (B) but in WT, Xrn2 _KD and Dgcr8 _KO mESCs.

Article Snippet: TKO mESCs were described in ref. . Dgcr8 _KO mESCs were purchased from Novus Biologicals (NBA1-19349).

Techniques: Western Blot, Staining

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: Mouse ESCs, Dicer knock-out (KO) , Novus Biologicals , NBP1-96751.

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