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: 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

Journal: Cell Death and Differentiation

Article Title: FOXQ1 controls the induced differentiation of melanocytic cells

doi: 10.1038/s41418-018-0066-y

Figure Lengend Snippet: FOXQ1 induces MITF-dependent differentiation. a, b NHM transduced with empty vector (VECTOR) or FOXQ1-expressing vector (FOXQ1) were probed in immunoblotting with indicated antibodies (left) or in Q-RT-PCR (right). FOXQ1/ACTB, MITF/ACTB, and TYR/ACTB signal ratios are shown. c Cells described in a were imaged as adherent cells or as cell pellets followed by quantification of total melanin content (white boxes). d, e Cells transduced with control (CL) or FOXQ1 (F1, F2) shRNAs were probed in immunoblotting with the indicated antibodies (left panel) or in Q-RT-PCR (right panel). FOXQ1/ACTB, MITF/ACTB, and TYR/ACTB signal ratios are shown. f NHM described in d, e) were imaged as adherent cells or as cell pellets followed by quantification of total melanin content (white boxes). g NHM expressing empty vector (V), FOXQ1 cDNA f, or control (CL) or FOXQ1 shRNAs (F1, F2) were counted for 72 h starting 48 h post infection. The cell numbers at 72 h were normalized by those before plating and by the ratio of these numbers in vector or control cells. h Human MITF promoter. Shown are FOXQ1-binding sites (diamonds) and PCR primers (arrows). i Q-PCR signals in reactions with DNA precipitated with FOXQ1-specific antibodies from untreated and FSK-treated NHM cells were normalized by corresponding signals in DNA precipitated with IgG antibodies and by signals obtained with MITF nonspecific control primers (NS). All data represent mean ± SEM. Statistical significance was assessed using two-tailed Student’s t-tests. A p < 0.05 (*) was considered significant

Article Snippet: Generation of Foxq1 knockout mice Two Foxq1 tm1 (KOMP)Vlcg mouse embryonic stem cell clones were obtained from the Velocigene (Regeneron) branch of the Knockout Mouse Project (KOMP).

Techniques: Transduction, Plasmid Preparation, Expressing, Western Blot, Reverse Transcription Polymerase Chain Reaction, Control, Infection, Binding Assay, Two Tailed Test

Journal: Cell Death and Differentiation

Article Title: FOXQ1 controls the induced differentiation of melanocytic cells

doi: 10.1038/s41418-018-0066-y

Figure Lengend Snippet: FOXQ1 regulates cAMP/CREB1-dependent pigmentation. a NHM were treated with the indicated doses of Forskolin (FSK) for 5 h (left panel) or with 50 μM of FSK for indicated duration (right panel) followed by immunoblotting with the indicated antibodies. b NHM were transduced with control (CL) or FOXQ1 (F1, F2) shRNAs and treated with vehicle (DMSO) or the indicated doses of Forskolin (FSK) for 5 h followed by immunoblotting with the indicated antibodies. c Melanin content in cells described in b. d Representative images of ears from Foxq1+/+ or Foxq1–/– mice (n = 3) treated with either vehicle (DMSO, left ear) or vehicle containing 100μM Forskolin (FSK, right ear). e Pigmentation was quantified using a reflectance spectrometer and represented as fold change in the coefficient of absorption “mua”. f Representative images of H&E staining of mouse ear tissues shown in d. All data represent mean ± SEM. Statistical significance was assessed using two-tailed Student’s t-tests. A p < 0.05 (*) was considered significant

Article Snippet: Generation of Foxq1 knockout mice Two Foxq1 tm1 (KOMP)Vlcg mouse embryonic stem cell clones were obtained from the Velocigene (Regeneron) branch of the Knockout Mouse Project (KOMP).

Techniques: Western Blot, Transduction, Control, Staining, Two Tailed Test

Journal: Cell Death and Differentiation

Article Title: FOXQ1 controls the induced differentiation of melanocytic cells

doi: 10.1038/s41418-018-0066-y

Figure Lengend Snippet: FOXQ1 is important for cAMP/CREB1-dependent pigmentation. a, b Cells transduced with control shRNA (CL) or CREB1 shRNA (C1) were probed in immunoblotting with the indicated antibodies or in Q-RT-PCR. CREB1/Actb, Foxq1/Actb, and Mitf/Actb signal ratios are shown. c Melanin content and representative cell pellet images of cells described in a, b. d Schematic representation of human and mouse FOXQ1 promoter. Diamonds represent potential CREB1 consensus binding sites. e NHM, Melan-a, and B16 cells treated with vehicle (DMSO) or 10 μM Forskolin were probed in ChIP assay. Shown are ratios of Q-PCR signals in reactions with DNA precipitated with CREB1 or IgG antibodies using primers corresponding to potential CREB1-binding sites in FOXQ1 promoter. NS corresponds to CREB1-nonspecific primer targeting a distal genomic region. All data represent mean ± SEM. Statistical significance was assessed using two-tailed Student’s t-tests. A p < 0.05 (*) was considered significant

Article Snippet: Generation of Foxq1 knockout mice Two Foxq1 tm1 (KOMP)Vlcg mouse embryonic stem cell clones were obtained from the Velocigene (Regeneron) branch of the Knockout Mouse Project (KOMP).

Techniques: Transduction, Control, shRNA, Western Blot, Reverse Transcription Polymerase Chain Reaction, Binding Assay, Two Tailed Test

Journal: Cell Death and Differentiation

Article Title: FOXQ1 controls the induced differentiation of melanocytic cells

doi: 10.1038/s41418-018-0066-y

Figure Lengend Snippet: BRAF-β-catenin-FOXQ1 axis controls MITF-dependent phenotypes. a NHM and Melan-a cells were transduced with indicated constructs (V = empty vector, B = BRAFV600E, F = FOXQ1) followed by immunoblotting with the indicated antibodies. b Cells were transduced with the indicated constructs and probed in Q-RT-PCR. (MITF/ACTB (Mitf/Actb) and FOXQ1/ACTB (Foxq1/Actb) signal ratios are shown. c Total melanin content in cells described in a. d NHMs transduced with the indicated constructs were probed in immunoblotting with the indicated antibodies (left panel) and in Q-RT-PCR (right panel). FOXQ1/ACTB signal ratios are shown. e Melan-a cells were transduced with the indicated constructs and assayed for the ability to form colonies in soft agar. Shown are average numbers of colonies per view field (n = 5). All data represent mean ± SEM. Statistical significance was assessed using two-tailed Student’s t-tests. A p < 0.05 (*) was considered significant

Article Snippet: Generation of Foxq1 knockout mice Two Foxq1 tm1 (KOMP)Vlcg mouse embryonic stem cell clones were obtained from the Velocigene (Regeneron) branch of the Knockout Mouse Project (KOMP).

Techniques: Transduction, Construct, Plasmid Preparation, Western Blot, Reverse Transcription Polymerase Chain Reaction, Two Tailed Test