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6 protocols using pcdnatm3.1

1

Reverse Transfection of Cells with Plasmid and siRNA

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Cells were reverse transfected with either plasmid DNA or siRNA. Plasmid transfection was performed using the X-tremeGENE HP DNA transfection reagent (Merck, Germany) according to the manufacturer’s instructions. In brief, 100 µL transfection mix containing serum-free RPMI-1640 cell culture medium, 2 µg plasmid DNA, and 2 µL transfection reagent was incubated for 15 min at room temperature and directly added to 4 × 105 cells in 2 mL of medium after seeding. The TYRO3 and the control expression vectors were purchased from OriGene, USA and Thermofisher, USA (TYRO3:pCMV6-XL4, CAT#: SC108283, pcDNATM3.1(+), CAT#: V790-20). For siRNA transfection, HiPerFect (Qiagen, Germany) was used according to the manufacturer’s protocol. Briefly, a transfection mix of 100 µL serum-free RPMI-1640, 100 nM siRNA, and 12 µL transfection reagent was incubated for 5 min and added to 4 × 105 cells in 2.3 mL medium and incubated for 24 h before treatment. siRNAs were purchased from Qiagen, Germany (SI00288344, SI00288351). Cell viability was measured using the CellTiter 96® AQueous One Solution Cell Proliferation Assay (Promega, Madison, WI, USA) according to the manufacturer’s recommendations. Absorbance was measured using a Tecan Plate Reader 2000 (Tecan, Switzerland).
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2

Cloning and Validation of DmHsp22 Constructs

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Full-length cDNA of DmHsp22 was inserted into the eukaryotic expression vector pcDNATM3.1 (+) (Thermo Fisher Scientific) at Hind III and Xho I cloning sites. Polymerase chain reaction (PCR) (TransGen Biotech) and Gibson assembly (New England Biolabs) were used to construct three recombinant vectors pcDNADmHsp22, pcDNADmHsp22Flag and pcDNAFlag using oligonucleotide primers (Invitrogen) as described in Table 1. Constructs were verified by DNA profile upon restriction enzyme digestion on agarose gel and by DNA sequencing (Genomic Analysis Platform, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada).
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3

LINC00526 Cloning and Silencing Protocol

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LINC00526 full‐length sequences were PCR‐amplified by the PfuUltra II Fusion HS DNA Polymerase (Agilent Technologies, Santa Clara, CA, USA) and the primers 5′‐CGGGATCCGCGGACTCCGCGGACAAG‐3′ (sense) and 5′‐GGAATTCCAAAATGCATCTTGTTTATTTGGC‐3′ (antisense). Then, the PCR products were cloned into the BamH I and EcoR I sites of pcDNATM3.1(+) (Invitrogen) and pSPT19 (Roche, Mannheim, Germany) plasmids, named as pcDNA‐LINC00526 and pSPT19‐LINC00526, respectively. The cDNA oligonucleotides silencing LINC00526 were synthesized by GenePharma (Shanghai, China) and inserted into the GenePharma SuperSilencingTM shRNA expression plasmid pGPU6/Neo. The shRNAs target sites were 5′‐GCTCAATGTCTCATAGCTACA‐3′ (shLinc‐1) and 5′‐GGTCCTCCAAGATGAGCTTAA‐3′ (shLinc‐2). AXL ORF expression plasmid (Catalog EX‐Z7835‐M68) was purchased from GeneCopoeia (Guangzhou, China).
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4

Construction of ATP7B Mini-Gene Plasmid

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The ATP7B exon11-12-13 mini-gene plasmid has been described previously [7 (link)] (Fig. 1A). Briefly, the ATP7B (from exon11 to exon13, total 4.5 kb) mini-gene construct was polymerase chain reaction (PCR)-amplified from control genomic DNA by using the forward primer (5 - GTGAGATGGCTTGTTTCATGT-3) and the reverse primer (5 - AACCCAGTGCAGGGCTCACAC-3). The PCR-amplified fragment was cloned into a pcDNATM 3.1 (Invitrogen) vector, and this fragment was verified by DNA sequencing.
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5

Cloning and Characterization of Sperm-Specific Proteins

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The full-length cDNA of AKAP3, TSSK4, ODF2, and QRICH2 was synthesized and separately cloned into pENTER (Vigene), pCMV6-Entry (Origene), pCMV6-Entry, and pcDNATM3.1(+) (Invitrogen) vectors containing a FLAG, Myc, and HA tag sequence. CABYR and ODF2 promoter fragments were amplified and cloned into the pGL3-Basic luciferase reporter vector (Promega). The shRNAs designed to interfere with QRICH2 expression and the negative control SuperSilencing shRNA (shNC) were synthesized and cloned into the psi-LVRU6GP vector by GeneCopoeia. The target sequences of QRICH2 shRNAs were 5′-GGGTTCACTTCCTTAACATCA-3′. The primers for promoter region amplification are listed in Supplementary Table 5.
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6

Lentivirus Production and RNAi Knockdown

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Plasmids and RNA interference sequences are listed in Supplementary Table S2. Full length of molecules or its mutants were amplified by PCR using primers (GenBank). Molecules or mutants with a GFP label, HA label, or 3×Flag label were cloned into pCDH-CMV-MCS-EF1-Puro lentiviral vector (http://www.addgene.org/) or pcDNA TM 3.1(+) (InvitrogenTM, V790-20) [13 (link)]. The sequences of the inserts were 100% correct. TopoIIα and β-catenin-specific shRNAs and scrambled sequence were synthesized and cloned into pLKO.1 pure vector, respectively. Lentiviruses were produced by co-transfection of a lentiviral plasmid, packing plasmids ΔR and pVSVg into HEK-293T cells. After transfection, supernatant was collected and the virus was used to infect cells. Stable lentivirus-infected cells were selected with puromycin or G418 and verified by western blot analysis.
The control siRNA and siβ-catenin were synthesized at GenePharma Inc. (Shanghai, China). The siRNA oligonucleotides were transfected into cells using X-tremeGENE HP DNA Transfection Reagent (Roche) following the manufacturer’s recommendations. The interference efficiency of siRNA was routinely assessed by western blot at 48 h after transfection.
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