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14 protocols using usinglipofectamine 3000

1

NF-kB Luciferase Assay in BGC Cells

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BGC seeded into 24-well plates were transfected with 150 ng of NF-κB-Luc using
Lipofectamine™ 3000 (Invitrogen, CA, USA). The reporter plasmid pGL3Luc-5XNF-kappaB was
constructed with double-strand oligonucleotides that contain five repeats of NF-κB binding
consensus sequence (5′-GGGGAATTTCC-3′) (Wong et al., 2011 (link)), cloned in the pGL3Luc-promoter
vector (Promega, Madison, USA). Briefly, the plasmids were mixed with Optimem, p300
reagent, and Lipofectamine 3000. The mix was incubated for 10 min at room temperature, and
the cells were incubated with this mixture for 24 h. Then, the cells were treated with
caffeic acid with or without D-Asp for a further 24 h. Cells were subsequently harvested
and lysed with 150 μl of 1X reporter lysis buffer (Promega), and protein lysates were
obtained by two freeze-thawing cycles. Luciferase assays were performed with the
Luciferase Assay System (Promega) with equal amounts of the protein lysates. Detection was
performed with an Infinite M200 PRO plate reader (TECAN, Männedorf, Switzerland).
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2

Lentiviral Transduction of MIA PaCa-2 Cells

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HEK293T cells (ATCC, Manassas, VA) and MIA PaCa-2 cells (human
pancreatic cancer; ATCC, Manassas, VA) were maintained in Dulbecco’s
modified Eagle’s medium (Corning, Lowell, MA) supplemented
with 10% fetal bovine serum (Corning, Lowell, MA) and penicillin–streptomycin
(Corning, Lowell, MA). All cells were grown at 37 °C and 5% CO2 in a humidified incubator and tested negative for mycoplasma
using the MycoAlert Mycoplasma Detection Kit (LT07-318, Lonza, Morristown,
NJ).
Lentivirus was produced by transfection of HEK293T packaging
cells with three packaging plasmids30 (link) (pMDL,
pRSV-REV, and pCMV-VSVG) and the lentiviral reporter plasmid using
Lipofectamine 3000 (Invitrogen, Waltham, MA) according to the manufacturer’s
recommended protocol. The supernatant containing lentivirus was then
collected 72 h later, aliquoted and stored at −80 °C.
MIA PaCa-2 cells were seeded on a 6-well plate (Corning, Glendale,
AZ) at a density of 3 × 105 cells/well and transduced
with 500 μL lentiviral supernatant plus polybrene (MilliporeSigma,
Burlington, MA) to a final concentration of 8 μg/mL. Transduced
cells were then expanded further in culture and FACS sorted for mStrawberry
expression (BD-FACS Aria, BD Bioscience, Franklin Lakes, NJ).
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3

Transfection and Validation of miR-127 Inhibitor

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MiR-127 inhibitor and negative control (NC) were designed and synthesized by
GenePharma (Shanghai, China). Cell transfection was performed using
Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.
After transfection for 48 h, the efficiency of transfection was monitored by
quantitative real-time polymerase chain reaction (qRT-PCR).
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4

Lentiviral-Mediated HMGB3 Silencing

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HMGB3-targeting shRNAs (sh1, sh2, sh3) and negtive control shRNA plasmids were purchased from GeneCopoeia. The lentivirus mediated vectors were transfected using Lenti-Pac HIV expression packaging kit according to the manufacturer’s instructions (GeneCopoeia). Briefly, 1.3–1.5 × 10 6 293 T cells were plated into one 10 cm culture dish and were transfected with 2.5 μg shRNA expression plasmids and 5.0μllenti-Pac HIV mix usingLipofectamine 3000 (Invitrogen). After 7-8 h, the mix was replaced with fresh complete medium. The viral supernatants were collected after 48 h and used for lentiviral infection obtaining stably transduced cells.
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5

B7-H3 3'UTR Luciferase Assay

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Cells were cotransfected with B7-H3 wt/mut 3′-UTR plasmids (Invitrogen) and
either the miR-199a-mimics or miR-negative control (miR-NC; RiboBio) using
Lipofectamine 3000 (Invitrogen). After 48 hours, Luciferase activity was
assessed in the indicated cells using the Luciferase Reporter Assay System
(Promega), according to the manufacturer’s instructions. The experiments were
replicated in triplicate.
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6

Silencing FOXO3a in Pancreatic Cancer Cells

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PANC-1 and SW1990 cells at the logarithmic growth stage were trypsinized,
sub-cultured, and grown in 6-well plates (5 × 106/well). After the
cell growth was stabilized, the small interfering RNA targeting FOXO3a
(si-FOXO3a#1; si-FOXO3a#2; si-FOXO3a#3) and the corresponding negative control
fragments (si-NC) were transfected into PANC-1 and SW1990 cells using
Lipofectamine® 3000 (Invitrogen, Carlsbad, California, USA). Cells were
incubated at 37°C with 5% CO2 for 24 hours. Next, the cells were
cultured with fresh culture medium for 24 hours.
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7

Quantifying Transfection-Induced Cell Death in U2OS Cells

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U2OS cells were plated in 24-well plates at a concentration of 3 ×
104 cells/well in MEM medium (Gibco, Waltham, MA, USA) with 0.5
% antibiotic antimycotic solution (SIGMA, St. Louis, MO, USA) at
37 °C and allowed to attach overnight. Cells were transfected using
Lipofectamine 3000 (Invitrogen, Waltham, MA, USA) with 1 μg of
pIRES2-EGFP containing the HtrA2 gene. After 6 h the medium was exchanged
and cells were allowed to continue growing at 37 °C. Two days after
transfection cells were stained with DRAQ7 and imaged with an IN Cell analyzer
2000 (GE Healthcare). The fraction of dead (as indicated by DRAQ7 staining)
GFP-positive cells was calculated for each well. At least 150 GFP-positive cells
were counted in each well. Results from each of three separate biological
replicate experiments are plotted individually on Figure
3
.
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8

miR-21 Overexpression and Inhibition Protocol

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miR-21 mimic, miR-21 inhibitor, scramble, and negative control (NC) were all
designed and synthesized by GenePharma (Shanghai, China). Sequences for miR-21
mimic were as follows: 5′-UAGCUUAUCAGACUGAUGUUGA-3′ (sense) and
5′-AACAUCAGUCUGAUAAGCUAUU-3′ (antisense). Sequence for miR-21 inhibitor was as
follows: 5′-UCAACAUCAGUCUGAUAAGCUA-3′. Cell transfection was conducted using
Lipofectamine 3000 (Invitrogen) in line with the manufacturer’s protocol. The
stably transfected cells were selected using culture medium supplemented with
0.5 mg/mL G418 (Sigma–Aldrich). qRT-PCR was performed to assess the transfection
efficiency.
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9

Luciferase Assay for miR-582-3p Binding

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Synthesized sequences of circ_0001073, RGMB 3′-UTR and wild-type or
mutant miR-582-3p binding sites were cloned into the psi-CHECK2 vector
(Promega, Madison, WI, USA). Subsequently, luciferase vector and miR-582-
3p
mimics (or miR-con) were co-transfected into A549 and H460 cells using
Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA). After 48 hours of transfection,
luciferase activity was measured by using dual-luciferase assay system (Promega, Madison,
WI, USA).
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10

Modulation of Circular RNA in HCC

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Cell lines used in this study include human HCC cell lines (MHCC97 H, HCCLM3,
SK-HEP-1, Hep3B, and Huh7), normal human liver cell line (LO2), as well as
HEK293 cell line, and they were all obtained from American Type Culture
Collection (ATCC, Manassas, VA, USA). RPMI-1640 medium (Invitrogen, Carlsbad,
CA, USA) supplemented with 1/10 of fetal bovine serum (FBS) and 1%
penicillin/streptomycin was used as culture medium. The culture environment
maintained at 37′°C contains 5% CO2.
For cell transfection, short hairpin RNA (shRNA) targeting circ_101141
(sh1-circRNA and sh2-circRNA) or linear ANAPC7 (sh-ANAPC7) and negative control
(sh-NC); miR-1297 mimic, inhibitor, and their control plasmids (NC mimic, NC
inhibitor); plasmid pcDNA3.1 Rho-associated, coiled-coil-containing protein
kinase 1 (ROCK1); and control vector were purchased from Thermo Fisher
Scientific (Carlsbad, CA, USA). Transfection of cells was performed using
Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.
All cells were harvested 48 h after transfection for further tests.
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