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9 protocols using hifiscript gdna removal rt mastermix kit

1

Gene Expression Profiling of Gonad Maturation

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After the gonadal status of all fish had been determined via histology, six different stages of gonads were used to ascertain gene expression patterns. Extraction of total RNA followed the TransZol Up Kit (Transgene, ET111) manufacturer’s protocol. The quantity of total RNA was determined using a NanoDrop™ 1000 spectrometer (Thermo Fisher Scientific, Waltham, MA, USA). The first-strand cDNA was synthesized from 1 μg total RNA with HiFiScript gDNA Removal RT MasterMix Kit (CWBIO, Beijing, China). cDNA synthesis was performed using the manufacturer’s protocol.
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2

Quantifying Transcriptomic Expression Profiles

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The qRT-PCR assays were performed using a CFX Touch 96-Well System (Bio-Rad, California, CA, USA) to verify the expression levels of the selected genes in the transcriptomics analysis. Six DEGs were selected, and RNA was extracted using an EASYspin Plus Kit (Aidlab, China). The RNA was then reverse transcribed into cDNA using a HifiScript gDNA Removal RT MasterMix Kit (Cwbio, China). In total, 1 μL of cDNA template, 10 μL of 2× SYBR Green Master Mix (Useverbright, China), 1.2 μL of upstream and 1.2 μL of downstream primers, and 6.6 μL of RNase-Free H2O were added in a 20-μl reaction system. Three-step PCR reactions were performed with 95°C pre-denaturation for 120 s, 95°C deformation for 5 s, 55°C annealing for 15 s, and 72°C extension for 30 s. The total reaction circle was set to 40. The 16S rRNA gene was selected as an internal control. The primers used are presented in Supplementary Table S1. The relative expression levels of the tested genes were calculated using the 2-ΔΔCt method. Three wells of each sample were used as three technical replicates, and three independent biological replicates were performed for all qPCR reactions.
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3

Quantifying Gene and miRNA Expression

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Total RNA was extracted from ipsilateral brain tissue using TriQuick Reagent (Solarbio, China). Reverse transcription was performed by HiFiScript gDNA Removal RT MasterMix kit (CWBIO, China) following the manufacturer’s instructions. qRT-PCR was implemented in CFX (Bio-rad) using MagicSYBR Mixture (CWBIO, China). The threshold cycle (CT) was evaluated to quantify transcripts. The relative expression level of a specific gene was calculated as the expression 2−ΔΔCT. The primers used in this study are listed in Table 2. To examine the expression of miRNAs, total miRNA was extracted from cells by miRcute miRNA Isolation Kit (TIANGEN, China), and reverse transcription was performed by miRcute Plus miRNA First-Strand cDNA Kit (TIANGEN, China). qRT-PCR was implemented by miRcute Plus miRNA qPCR Kit (SYBR Green, TIANGEN, China). The CT value was used to quantify transcripts. The relative expression level of a specific miRNA was calculated as the expression 2−ΔΔCT. The forward primers used in this study are shown in Table 3.
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4

Spinal Cord Injury Gene Expression

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T10 spinal cords were harvested 1 day after SCI or after laminectomy and immediately frozen and stored at –80°C (six samples in each group). Total RNA was extracted from frozen spinal cord tissues using Trizol reagent (Cat# R0016; Beyotime Biotechnology). The HiFiScript gDNA Removal RT MasterMix kit (Cat# CW2020M; CWBio, Beijing, China) was used to synthesize complementary DNA from purified RNA. To examine the expression level of STAT3, TLR4, HMOX1, JUN, ATF3, RELA, PTGS2, MAPK1, MAPK9, VEGFA in the SCI group and the sham group, real-time polymerase chain reactions were performed in a total volume of 20 μL containing 2 μL complementary DNA, 10 μL 2× UltraSYBR One Step Buffer (Cat# CW0659S; CWBio), and 8 μL of each specific primer (1 μM). Reactions were performed in the LightCycler® 96 instrument (Roche, Basel, Switzerland) in accordance with the manufacturer’s instruction. Primers for each gene are listed in Table 1. The reaction conditions were 95°C for 10 minutes for pre-denaturation; remaining cycles of 95°C for 15 seconds and 60°C for 1 minute; and the last cycle was 95°C for 15 seconds, 60°C for 1 minute, 95°C for 15 seconds and 60°C for 15 seconds. GAPDH mRNA was used for normalization. Data were calculated relative to the expression of GAPDH mRNA using the 2–ΔΔCt method (Livak and Schmittgen, 2001).
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5

Quantitative Analysis of EMT and Angiogenesis Markers

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The qRT-PCR assays were performed to measure the expression levels of Snail, Cox-2, and Vegf-c. For 4T1, HuROE 4T1, and ΔHuR 4T1, the cells were treated with 1‰ DMSO or eltrombopag (5 μmol/L) for 12 h before RNA extraction. For the RAW264.7 cells, the model group was stimulated with LPS (100 ng/mL), and the eltrombopag groups were incubated with LPS (100 ng/mL) and eltrombopag (10 μmol/L or 20 μmol/L) for 12 h. The total cellular RNA was extracted using TRIzon Reagent (CWBIO, Nanjing, China) following the manufacturer’s instructions, and the RNA concentration was quantified with Nanodrop (DeNovix, USA). cDNAs were conducted using the HiFiScript gDNA Removal RT MasterMix kit (CWBIO, Nanjing, China), and quantitative PCR was performed with the ABI QuantStudio 6 Flex system (Thermo Fisher Scientific, USA) using MagicSYBR green master mix kit (CWBIO, Nanjing, China). The mRNA levels of selected genes were normalized to β-actin and analyzed with 2−ΔΔCt method. The primers synthesized by Sangon Biotech (Shanghai, China) were as follows: Snail (F: 5′-CACAC GCTGC CTTGT GTCT3′ and R: 5′-GGTCA GCAAA AGCAC GGTT-3′), Cox-2 (F: 5′-GGTGC CTGGT CTGAT GATGT ATGC-3′ and R: 5′-GGATG CTCCT GCTTG AGTAT GTCG-3′), Vegf-c (F: 5′-CTACA GATGT GGGGG TTGCT-3′ and R: 5′-GATTG GCAAA ACTGA TTGTG AC-3′), and β-actin (F: 5′-GTGGG CCGCT CTAGG CACCA A-3′ and R: 5′-TGGCT TTAGG GTTCA GGGGG-3′).
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6

Quantifying Gene Expression in Myoblast Differentiation

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RNA was isolated from three independent biological replicates of differentiating C2C12 myoblasts expressing shScr, shPkm1 (shRNA#2), or shPkm2 (shRNA#2) with TRIzol (Invitrogen) following the manufacturer's instructions. cDNA synthesis was performed with 1 μg of RNA as template for reverse transcription and the HiFiScript gDNA Removal RT MasterMix Kit (Cwbio), following the manufacturer's protocol. Quantitative PCR was performed with Fast SYBR green master mix on the ABI StepOne Plus Sequence Detection System using the primers listed in Supp. Table 2, and the delta threshold cycle value (2ΔΔCT; (55 (link))) was calculated for each gene and represented the difference between the CT value of the gene of interest and that of the control gene, Eef1a1α.
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7

qRT-PCR Analysis of Myoblast Differentiation

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Aliquots of samples obtained for RNA-seq of proliferating and differentiating primary myoblasts were used as templates for cDNA synthesis (1 μg) and quantitative reverse transcription (qRT-PCR). Briefly, the RNA was treated with HiFiScript gDNA Removal RT MasterMix Kit (CW2020M, Cwbio, Jiangsu, China), following the manufacturer's protocol. Quantitative PCR was performed with FastSYBR Mixture (CW0955L, Cwbio) on the AriaMx Real-Time PCR System (Agilent) using the primers listed in Supp. Table 2. The delta threshold cycle value (2ΔΔCT; (121 (link))) was calculated for each gene and represented the difference between the CT value of the gene of interest and that of the control gene, Eef1a1α.
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8

Quantitative RNA Expression Analysis

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Total RNAs were extracted from tissues with Trizol reagent (Thermo Fisher Scientific, USA), and then reverse transcribed cDNA was generated by the HiFiScript gDNA Removal RT MasterMix kit (CWBIO, China). The qRT-PCR was performed using the CFX Connect real-time PCR system (Bio-Rad, USA) and MagicSYBR Mixture kits (CWBIO, China). The GAPDH was used as a control in PCR runs. And the date was analyzed by the 2−ΔΔCt method.63 (link) All experiments were performed in triplicate independent. The gene-specific primer sequences are listed as follows in Table S3.
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9

Investigating HuR-Mediated Regulation

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RIP assays were carried out as described with minor modifications [49 (link)]. The 4T1 cells and RAW264.7 cells were treated with eltrombopag as described in Section 4.7. Cell lysates were collected with RIPA Lysis Buffer (Sangong Biotech, Shanghai, China), and protein quantification was measured using a BCA protein assay kit (Beyotime Biotechnology, Shanghai, China). The experimental flow is shown in Figure 4D. Equal amounts of cell lysates (300 μg) were pre-bound with protein A/G beads (SC-2003, Santa Cruz Biotechnology, Dallas, TX, USA), and then HuR antibody (1:50, 12,582 s, Cell Signaling Technology, USA) was added to immunoprecipitation HuR-mRNAs complexes for 12 h at 4 °C. The mRNAs were isolated using TRIzon Reagent (CWBIO, Nanjing, China), and the cDNA was synthesized with the HiFiScript gDNA Removal RT MasterMix kit (CWBIO, Nanjing, China). The HuR-binding mRNAs (Snail, Cox-2, and Vegf-c) and non-HuR-binding mRNA (Gapdh) were detected with qRT-PCR and analyzed by the 2−ΔΔCt method. Mouse IgG (Sepharose® Bead Conjugate, 3420 S, Cell Signaling Technology) was used as a negative control. The primers used in the RIP analysis are listed in Section 4.7. The primers of Gapdh were 5′-AGGTC GGTGT GAACG GATTT G-3′ (F) and 5′-GGGGT CGTTG ATGGC AACA-3′ (R).
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