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7 protocols using first strand cdna kit

1

Gene Expression Analysis of HMGB1 via qRT-PCR

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After RNA isolation, cDNA was synthesized using a First-strand cDNA Kit (Roche) following the manufacturer’s instructions [30 (link)]. The cDNA products were amplified using the Fast Start Universal SYBR Green Master Mix (Roche). Amplifications were carried out using the Applied Bio-systems 7500. To quantify gene expression changes, the 2-△△Ct method was used to calculate relative fold-changes after normalizing to the value of β-actin [16 ]. The PCR primers of HMGB1 were as follows:

Forward:5′-GCTCCATAGAGACAGCGCCGGG-3′;

Reverse:5′-CCTCAGCGAGGCACAGAGTCGC-3′

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2

Quantitative Analysis of YAP and TAZ Expression

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A375 cells were pretreated with siControl or siTAZ as described before. RNA was extracted from A375 melanoma cells using TRIzol reagent (Invitrogen, Carlsbad, CA) based on the protocol provided by the manufacturer. The cDNA library was generated by using a First-strand cDNA Kit (Roche Diagnostics). FastStart Universal SYBR Green Master was procured from Roche Diagnostics. After preparing the qPCR reaction solution, a real-time quantitative PCR machine (Applied Biosystems, USA) was used for amplification. The primers for human samples were: YAP-forward (F) 5′-cacagctcagcatcttcgac-3′, YAP-reverse (R) 5′-tattctgctgcactggtgga-3′; TAZ-forward (F) 5′-ggctgggagatgaccttcac-3′, TAZ-reverse (R) 5′-ctgagtggggtggttctgct-3′; GAPDH-forward (F): 5′-tgggtgtgaaccatgagaagtatg-3′, GAPDH-reverse (R), 5′-ggtgcaggaggcattgct-3′. The data were processed by the 2−△△Ct method and normalized based on the expression of GAPDH.
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3

Transcriptome Analysis of Chondrocytes

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RNA was isolated from four biological replicates for each patient and condition (control and TNFRSF11B-overexpressing chondrocytes) while pooling two pellets together to generate two independent samples for downstream analyses. Isolations were performed as described previously [12 (link)]. Total mRNA (150 ng) was processed with the first strand cDNA kit according to the manufacturer’s protocol (Roche Applied Science, Almere, The Netherlands). CDNA was further diluted five times, and preamplification with TaqMan preamp master mix (Thermo Fisher, Landsmeer, The Netherlands) was performed. Gene expression was measured (Supplementary Table S1, available at Rheumatology online) with RT-qPCR, and average of the two biological replicates was determined as relative levels (−ΔCt values) using expression levels of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and Acidic ribosomal phosphoprotein P0 (ARP) as housekeeping genes. Quality control of the results was performed as described before [12 (link)].
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4

Quantitative PCR analysis of CRY2 expression

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Liver tissue was homogenized using TissueLyser (Qiagen), and total RNA was extracted with the RNeasy Tissue Kit from Qiagen according to the manufacturer's instructions. Total RNA treated with RNase-free DNase I was transcribed into cDNA using Avian myoblastosis virus reverse transcriptase and the first-strand cDNA kit from Roche Diagnostics (Mannheim, Germany). PCR (in technical duplicates) was performed on a LightCycler 480 (Roche Diagnostics) using Probes Master and fluorescent probes from the Universal Probe Library (Roche Diagnostics). Primers were designed using the Roche Probe Design 2 software (Roche Diagnosics) and purchased from TIB MOLBIOL (Berlin, Germany). Primer sequences and PCR conditions can be provided upon request. CRY2 mRNA data were normalised for the housekeeping gene RPS13 using the ΔΔCt method.
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5

SFRP2 Expression Analysis by RT-PCR

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A reverse transcription reaction was performed using 2 mg total RNA using a first strand cDNA kit (Roche Diagnostics, Mannheim, Germany). The mRNA expression of SFRP2 was detected by RT-PCR and GAPDH was used as an internal control of RNA integrity. The primer sequences used were as follows: SFRP2, forward 5′-TGGAGACCAAGAGCAAGAC-3′ and reverse 5′-GTGGGACAAAGACAGGGTA-3′; GADPH, forward 5′-GAAGGTGAAGGTCGGAGTC-3′ and reverse 5′-GAAGATGGTG ATGGGATTTC-3′.
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6

Chondrogenic Differentiation of hiPSCs

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Differentiations with hiPSC lines were performed in triplicate. For RNA isolations, two pellets were pooled, and isolation was performed as described previously (Bomer et al. 2015 (link)). Total mRNA (150 ng) was processed with a first strand cDNA kit according to the manufacturer’s protocol (Roche Applied Science). cDNA was further diluted five times, and preamplification with TaqMan preamp master mix (Thermo Fisher Scientific Inc.) was performed for a panel of 20 designated genes related to chondrogenesis, hypertrophy, deposition and degradation of cartilage ECM, and neo-cartilage quality (primer sequences in Supplementary Table S1). Gene expression was measured with a Fluidigm Biomark HD machine using a 96.96 IFC chip. Quality control of the data was performed, and non-detected values were imputed according to the minimum detected value. Unsuccessful differentiations, defined by the minimum detected expression of COL2A1 for hPACs and hBMSCs neo-cartilage, were disregarded.
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7

Quantitative analysis of mitochondrial genes

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RNA was isolated using the RNAeasy kit (Qiagen), and cDNA synthesis was done using the first strand cDNA kit (ROCHE). qRT–PCR was performed on a LC480 Light Cycler (Roche) using SYBR Green (Roche) and the following primers: TSC1 5′‐CAA ACT CCA GGC AAG AGG AC‐3′ (forward) and 5′‐CCA ATT CAA ACA CCT GGG TTA‐3′ (reverse), TSC2 5′‐TGC AAG CCG TCT TCC ACA T‐3′ (forward) and 5′‐ATG GAC ACA AAG TCG TTG C‐3′, β‐actin 5′‐AGA GGG AAA TCG TGC GTG AC‐3′ (forward) and 5′‐CAA TAG TGA TGA CCT GGC CGT‐3′ (reverse), ATP5G1 5′‐AGG GCT AAA GCT GGG AGA CTG AA‐3′ (forward) and 5′‐GTC TGG CCA CCT GGA GTG GGA‐3′ (reverse), CYCS 5′‐AGG GAC AGA ATT TAA ATA TGG GTG A‐3′ (forward) and 5′‐AGA TTT GGC CCA GTC TTG TG‐3′ (reverse), HPRT (for normalization) 5′‐TGA CAC TGG CAA AAC AAT GCA‐3′ (forward) and 5′‐GGT CCT TTT CAC CAG CAA GCT‐3′ (reverse). For microRNA qRT–PCR, RNA was isolated using the miRNeasy kit (Qiagen), and primers obtained from the miScript System (Qiagen) were used for expression analysis with a primer for U6 RNA used for normalization. Primers for the analysis of mitochondrial DNA to genomic DNA ratio: genomic glucagon‐intron 5′‐TGA CAA AGA CGG ACT TGA CG‐3′ (forward) and 5′‐CCC TGT GTC ACA AGC AGA TG‐3′ (reverse); mitochondrial COX2 5′‐TTC ATG ATC ACG CCC TCA TA‐3′ (forward) and 5′‐TAA AGG ATG CGT AGG GAT GG‐3′ (reverse).
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