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27 protocols using pgl4.23 luc2 minp

1

Enhancer Reporter Construct Synthesis

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14 oligonucleotide gBlocks (IDT), ranging in 500–1000 nt in length, and corresponding to 10 enhancer regions were synthesized. Each gBlock contained a constant 5′ GCTAGCCTCGAGGAT and 3′ ATCAAGATCTGGCCT region, for direct cloning into an EcoRV (NEB) linearized minimal promoter firefly luciferase vector pGL4.23[luc2/minP] (Promega). The resulting reporter constructs were verified by DNA sequencing. BV-2 cells were kindly provided by Dr. Bruce Yankner. N2a cells were purchased from the American Type Culture Collection and maintained following their protocols. Briefly, cells were grown in RPMI-1640 and DMEM respectively, supplemented with 10% fetal bovine serum (FBS) and 1% pen/strep, and split 1:10 every 3 days. Cells were seeded into 24-well plates 1 day before transfection. Transfections into BV-2 and N2a cells were performed with 1 μg of a pGL4.23 plasmid and 200 ng of Renilla luciferase construct pGL4.74[Rluc/TK] (Promega). Luciferase activities were measured 24 h post-transfection using the Dual-Glo Luciferase Assay (Promega) and an EnVision 2103 Multilabel Plate Reader (PerkinElmer) and normalized to Renilla luciferase activity. All assays were performed in triplicate.
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2

Cloning and Characterizing Putative Enhancers

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Putative enhancers were amplified from genomic DNA with Phusion High-Fidelity DNA Polymerase (New England Biolabs, # M0530). Betaine (1 M final concentration, Sigma Aldrich, # B0300) was added to the PCR reactions. Primers contained overhangs for cloning (primer sequences and overhangs are listed in Suppl. Table 1). PCR products were cloned into pCR4Blunt-TOPO vector (Invitrogen, # 450031) and the sequence of the cloned DNA was confirmed by Sanger sequencing. Inserts were cut out with appropriate restriction enzymes (Suppl. Table 1) and ligated with pre-digested pGL4.23[luc2/minP] (Promega, # E8411) plasmid upstream of a minimal promoter and a firefly luciferase gene. HUVEC were co-transfected using Lipofectamin 2000 (Invitrogen, # 11668027) and PLUS reagent (Invitrogen, # 11514015) with a firefly plasmid and the pRL-CMV plasmid (Promega, # E2261) containing the Renilla luciferase gene for normalization. HUVEC were exposed to shear stress (18 dyn/cm2 for 24 h) 2 h after transfection. Afterwards, cells were lysed and activity of firefly and renilla luciferase was measured with a Dual-Luciferase Reporter Assay System (Promega, # E1910).
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3

Characterizing ERRFI1 Enhancer Activity

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ERRFI1 enhancer element was PCR amplified and cloned upstream of the minimal promoter of the luciferase reporter plasmid pGL4.23luc2/minP (Promega) as described (46 (link), 47 (link)). Point mutations were introduced using the Q5 Site Directed Mutagenesis (NEB) according to the manufacturer’s instructions (48 (link)). The RD or RH4 tumor cells were transfected with a Renilla control plasmid and the respective pGL4.23 enhancer construct using Viafect transfection reagent (Promega). 48 hours after transfection, reporter activity was quantified using the Dual-Luciferase Reporter Assay System (Promega) as described (49 (link)). Enhancer activity is reported as Firefly luciferase activity normalized to Renilla luciferase.
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4

Luciferase reporter assay for SDHD promoter mutations

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Five luciferase constructs (wild-type, C523T, C524T, C541T and C544T) were generated to containing 163bp of the genomic sequence surrounding SDHD promoter mutations (Chr11: 111,957,437–111,957,599). The fragment was PCR-amplified (primers, F: CTGAACTctcgagCTCCGCCATTGTTCGCCTC, R: GTCACTGTagatctACCCGGAACCACTTAGGCGAC) from genomic DNA purified from cells harboring wild-type and mutant SDHD promoter, sub-cloned into pGL4.23[luc2/minP] (Promega) luciferase vector, and constructs sequence-verified. Constructs were co-transfected with pGL4.74 (renilla luciferase) into human melanoma cell lines using Lipofectamine 2000 (Life Technologies). Cells were collected 24 hrs after transfection and luciferase activity was measured using the Dual-Luciferase reporter system (Promega) on GLOMAX Multi Detection System (Promega).
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5

Luciferase Assay for rs933717

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Sequences of 101bp flanking rs933717 were synthesized and subcloned into pGL4.23 (luc2/minP, Promega, USA) using the KpnI and BglII restriction sites (sequences are given in supplementary Table 1). HEK 293T (1.5 × 105 cells/well) and Jurkat (2 × 105 cells/well) were transfected with 0.8 μg pGL4.23 DNA containing rs933717 and 0.08 μg pRL-TK vector (as transfection control) using lipofectamine 2000 (Thermo, USA). After 48 h, cells were lysed and analyzed for luciferase activity using the Dual-Luciferase Assay System (Promega, USA). Each experiment was repeated three times.
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6

Cloning Luciferase Reporter Constructs

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The pNL1.1.CMV [Nluc/CMV] (Cat# N1091) and pGL4.23 [luc2/minP] (Cat# E8411) vectors were obtained from Promega. Luciferase elements were generated by selecting 467 bp of the nominated region using hg38 coordinates. Both the forward and reverse complement sequences were ordered as gBlocks from Integrated DNA Technologies (IDT). Gibson assembly was performed by cloning elements into the pGL4.23 [luc2/minP] vector digested with EcoRV. Element insertion was confirmed by Sanger sequencing (MCLAB). Each element was individually prepped 3 times for a total of 6 individual plasmid preparations per nominated region.
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7

Alu, L2, and MIR Luciferase Assay

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The sequences of Alu, L2, MIR, and scrambled MIR were synthesized as a single or L2 and MIR combined element, and cloned into the firefly luciferase reporter vector pGL4.23[luc2/minP] (Promega) between the KpnI and HindIII sites by Shanghai Majorbio. All clones were validated by sequencing. HeLa cells were cotransfected with the firefly luciferase reporter construct and the internal control pRL-TK Renilla luciferase vector (Promega) at a ratio of 40:1 (reporter vector:control vector) using Lipofectamine 3000 (Life Technologies) in triplicate. Forty-eight hours after transfection, the cells were lysed and firefly and Renilla luciferase activities were measured using the Dual-Luciferase Reporter Assay System (Promega) and Synergy H1 Microplate Reader (BioTek) according to the manufacturer's protocols.
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8

Plasmid Construction and CRISPR Toolkit

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The pNL1.1.CMV [Nluc/CMV] and pGL4.23 [luc2/minP] vectors were obtained from Promega. Luciferase elements were generated by selecting 467 bp of the nominated region and both the forward and reverse complement sequences were ordered as gBlocks from Integrated DNA Technologies (IDT). Elements were cloned into the pGL4.23 [luc2/minP] vector digested with EcoRV by Gibson Assembly. Element insertion was confirmed by Sanger sequencing (MCLAB). Each element was individually prepped 3 times for a total of 6 individual plasmid preparations per nominated region. The pMD2.G, psPAX2, FUGW-H1-GFP-neomycin, and pLV hU6-sgRNA hUbC-dCas9-KRAB-T2A-Puro plasmids were obtained from Addgene (#12259, #12260, #37632, and #71236 respectively). sgRNA sequences were designed using https://benchling.com and ordered as premixed primer pools from IDT (Supplementary Table 4). The sgRNA sequences were then inserted into the pLV hU6-sgRNA hUbC-dCas9-KRAB-T2A-Puro plasmid by digesting with Esp3I and subsequent ligation.59 (link),60 (link)
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9

Cloning and Characterization of Transcription Factors

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The entire coding regions of mouse Pax1, mouse Pax9, human Sox5, human Sox6, and mouse Sox9 were obtained from RCAS(A)-Pax1, RCAS(A)-Pax910 (link), pMXs-gw/hSOX5, pMXs-gw/hSOX632 (link), and pCMV-SPORT6-Sox9 (OriGene Technologies, Rockville, USA), respectively. To construct expression plasmids, each DNA fragment was inserted into pcDNA3 or CAG-IRES-EGFP vectors. To generate N-terminal FLAG-tagged PAX1 and PAX9, each DNA fragment was amplified by PCR to add NotI sites and inserted into the pcDNA3-FLAG vector. A 359-bp UE was amplified by PCR from mouse genomic DNA with forward and reverse primers designed with BamHI and BglII sites, respectively, and then PCR products were cloned into the pCR4-TOPO vector (Thermo Fisher Scientific). Four tandem copies of UE were obtained by ligation of monomers digested with BamHI and BglII. To construct pGL4.23[luc2/minP]-1xUE-Luc or pGL4.23[luc2/minP]-4xUE-Luc, one copy or four tandem copies of UE were inserted into the pGL4.23[luc2/minP] vector (Promega, Madison, WI, USA) containing a minimal promoter and the firefly luciferase reporter gene. The 508-bp I12E or 1109-bp Nkx3.2-P were amplified by PCR from mouse genomic DNA and inserted into the pGL4.23[luc2/minP] or pGL3-Basic vector (Promega) containing the firefly luciferase reporter gene, respectively. The PCR primers for constructs are listed in Supplementary Table 2.
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10

Synthetic ICP0 Promoter Constructs

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The full-length ICP0 promoter (−800 to +150) was previously described, and provided by the late Dr. Priscilla Schafer [35 (link)]. The respective CRM constructs were synthesized by Genscript and inserted into pGL4.23[luc2/minP] (Promega; Madison, WI, USA) at SacI and XhoI unique restriction enzyme sites. The GR-α expression construct was obtained from Dr. John Cidlowski (NIEHS, Research Triangle Park, NC, USA). The KLF15 expression plasmid was obtained from Deborah Otteson (University of Houston; Houston, TX, USA).
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