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5 protocols using absolute blue sybr green rox

1

Comprehensive myeloma cell analysis

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RPMI 8226, U266-B1, and NCI-H929 were purchased and cultured as described (ATCC). RPMI 8226 cells were plated at a cell density of 250,000 cells/mL; U266-B1, 600,000 cells/mL; and NCI-H929, 450,000 cells/mL. Cells were split every 48 hours. Cytokine Array Panel A, MIF Neutralizing antibody (NAB), recombinant MIF (rMIF), MIF Immunoassay all from (R&D); PD 0332991, CFSE (carboxyfluorescein succinimidyl ester) all from SelleckChem; 4-IPP (4-iodo-6-phenylpyrimidine) (Santa Cruz Biotech); MIF RNeasy mini kit (Qiagen); Verso cDNA kit (Thermo Scientific) and Quanititative PCR using gene-specific primers with Absolute Blue SyBr Green ROX (Thermo Scientific) were used per manufacturer’s instructions.
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2

RT-qPCR Analysis of Neural Markers

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RNA was extracted from cells using the NucleoSpin RNA Kit (Macherey-Nagel) from which cDNA was made from each sample using the iScript cDNA Synthesis Kit (Bio-Rad). RT-qPCR was performed using TaqMan Gene Expression Assays (Applied Biosystems; for human H3F3A, H3F3B, MYC, MYCN, normalized to GAPDH) or Absolute Blue SYBR Green ROX (ThermoFisher; for human ASCL1, NOTCH1, HES5, DNER, DCX, GRIA4, RAP1GAP, ATCAY, normalized to PPIA) on a LightCycler 480 (Roche). Primers are listed (5’-to-3’) as follows:
ASCL1 forwardCAAGCAAGTCAAGCGACAGC
ASCL1 reverseGCCCAGGTTGACCAACTTGAC
NOTCH1 forwardCACGCTGACGGAGTACAAGTG
NOTCH1 reverseCAGTGGCAGATGTAGGAGGC
HES5 forwardCAGCCCCAAAGAGAAAAACC
HES5 reverseCAGCCATCTCCAGGATGTCG
DNER forwardCGAAAACAGGGCAGAAAGTTG
DNER reverseGACTGAGGTGTTCTGTGGCAC
DCX forwardCCTTGCTGGCTGACCTGACGC
DCX reverseCAGTTGGGATTGACATTCTTGG
GRIA4 forwardCTCAAGGAGAGGAAATGCTGG
GRIA4 reverseGAACATTCCCTGTCAGCC
RAP1GAP forwardCATTCCATACCCGAGCGTG
RAP1GAP reverseGTGATTTCGTGGTTGGTGCC
ATCAY forwardGGAATGGCAACGAACTGGAG
ATCAY reverseGGTGCTCTTGCTCCCCGATG
PPIA forwardCTCGAATAAGTTTGACTTGTGT
PPIA reverseCTAGGCATGGGAGGGAACA
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3

Quantifying Bone Marker Expression in hMSCs

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RNA was extracted from both control hMSC cultures, grown on a polystyrene coated tissue culture surface and Gelfoam®-embedded hMSCs at days 7 and 21 of differentiation. Total RNA was isolated using TRIzol extraction agent (Thermo Fisher) as per the manufacturer's protocol and as reported earlier [18 (link)]. Briefly, total RNA was prepared and further purified using a RNeasy mini kit (Qiagen); cDNA was prepared using a high-capacity cDNA reverse transcription kit (Applied Biosystems); and qPCR analysis of the expression of the bone-specific markers osteopontin (OPN) and osteocalcin (OCN) was carried out using SYBR green master mix (Thermo Fisher) with GAPDH serving as the housekeeping gene using MX3005P real-time PCR cycler (Agilent).
Several preliminary experiments were run to determine ideal qPCR protocol, PCR mix, and annealing temperatures. qPCR was run using ABsolute Blue qPCR Mix (Thermo Fisher Scientific), with each reaction comprising of 5.0 μL cDNA solution, 12.5 μL ABsolute Blue SYBR Green ROX, 5.0 μL RNase Free Water, and 2.5 μL of the appropriate primers. All primer sequences and PCR conditions were derived from a previously published report [5 (link)].
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4

cDNA Synthesis and RT-qPCR Normalization

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cDNA was prepared by first strand synthesis using the TURBO DNA-free Kit (REF AM1907; Invitrogen) and Superscript III (REF 5675; Invitrogen). First, 2.5 µg of total RNA was treated with DNase I and incubated at 37°C for 30 min. After inactivation with DNase Inactivation Reagent, 2 μl of DNase-treated RNA was combined with 4.5 μl of a master mix containing random hexamers Roche and dNTPs. Samples were incubated at 65°C for 5 min, then placed on ice. While on ice, 3.5 μl of RT master mix (1X first-strand buffer, DTT, RNaseOUT, SSIII [REF 56575; Invitrogen]) was added to each tube, then samples were incubated at 25°C for 5 min, 50°C for 1 h, and 70°C for 15 min. For RT-qPCR, 5.2 μl Absolute Blue SYBR Green ROX (REF AB-4162; Thermo Fisher Scientific) and 4.8 μl cDNA (diluted 1:20 prior to use) was added to each well of qPCR plates (REF 4346906; Life Technologies). Samples were run on a StepOnePlus RT-qPCR machine (Applied Biosystems). Average CT values of triplicate reactions were used to calculate expression changes. RT-qPCR data was normalized to ACT1 for mitotic experiments and PFY1 for meiotic experiments (primers listed in Table S3).
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5

Pancreatic RNA Extraction and Analysis

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Total RNA was isolated from whole pancreas using TRIzol reagent (Invitrogen) and an RNeasy Mini Kit (Qiagen, Valencia, CA). Total RNA was isolated from isolated pancreatic acini using an RNeasy Mini Kit. First-strand cDNA was synthesized using a TaqMan RT-PCR kit (Applied Biosystems, Branchburg, NJ). Intactness of RNA was assessed based on OD 260/280 and agarose gel electrophoresis. One microgram of cDNA was used in each PCR reaction. Amplification with Taq DNA polymerase from an Expand High Fidelity Enzyme Mix kit (Roche Diagnostics, Indianapolis, IN) was conducted using specific primers. These PCR primers are listed in Table 1. Relative expression was evaluated by qRT-PCR analysis using Absolute Blue SYBR Green ROX (Thermo Fisher Scientific, Waltham, MA). Quantum RNA 18S internal standard (Ambion) was used as a reference.
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