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Abi 7900ht sequence detection machine

Manufactured by Thermo Fisher Scientific
Sourced in United States

The ABI 7900HT is a sequence detection machine designed for qPCR (quantitative Polymerase Chain Reaction) analysis. It is capable of accurately quantifying nucleic acid samples in real-time. The machine utilizes fluorescent dyes or probes to detect and measure the amplification of target sequences during the PCR process.

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8 protocols using abi 7900ht sequence detection machine

1

Quantitative Analysis of circRNA, mRNA, and miRNA

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Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Reverse transcription was performed by using a PrimeScriptTMRT Reagent Kit (TaKaRa) to obtain cDNA. The cDNA was subjected to quantitative real-time PCR on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific). The 2−ΔΔCT method was used to calculate differences in expression. GAPDH was used as the control gene for circRNA and mRNA. U6 was used as an internal control for the level of miRNA expression.
The primers were as follows:

GAPDH forward: 5′-CAAGGCTGAGAACGGGAAG-3′

GAPDH reverse: 5′-TGAAGACGCCAGTGGACTC-3′

RBPMS forward: 5′-CATTGCCAGAGAGCCATATGAG-3′

RBPMS reverse: 5′-AGGTGAAAGCAGGAGGAGGTA-3′

circRBPMS forward: 5′-TTAAGGGCTATGAGGGTT-3′

circRBPMS reverse: 5′-GTGTTGGGCAGAGGAGTA-3′

U6 forward: 5′-CTCGCTTCGGCAGCACA-3′

U6 reverse: 5′-AACGCTTCACGAATTTGCGT-3′

hsa-miR-1278 forward: 5′-ACACTCCAGCTGGGTAGTACTGTGCATATC-3′

hsa-miR-1179 forward: 5′-ACACTCCAGCTGGGAAGCATTCTTTCATT-3′

hsa-miR-330-3p forward: 5′-ACACTCCAGCTGGGGCAAAGCACACGGCCTG-3′

miRNA reverse: 5′-TGGTGTCGTGGAGTCG-3′

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2

Quantitative RT-PCR for Gene Expression

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RNA extraction was carried out using TRIzol reagent (Invitrogen) as previously reported.4 cDNA was obtained using a pTRUEscript 1st Strand cDNA Synthesis Kit (Aidlab, Beijing, China). qRT‐PCR was carried out using the 2× SYBR Green qPCR Mix (Aidlab) on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Waltham, MA, USA). Expression fold changes were determined using the 2−ΔΔCT method.
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3

Quantifying RNA Expression Levels

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Total RNAs were isolated from tumor cells using TRIzol (Invitrogen, Grand Island, NY). A complementary DNA (cDNA) synthesis kit (Aidlab, Beijing, China) was then used to initiate cDNA synthesis. Quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) was carried out on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Waltham, MA) with SYBR Green qPCR Mix (Aidlab). All experiments were done in duplicate. The 2-ΔΔCt method was utilized to compute the results. (METTL3 Forward Primer: TTGTCTCCAACCTTCCGTAGT, Reverse Primer: CCAGATCAGAGAGGTGGTGTAG; BLACAT2 Forward Primer: GCAGAATCGCTTGAACCCAGGAG, Reverse Primer: AGATGGAGTTTCGCTCTTGTTGCC; mir-193b-5p Forward Primer: CGGGCCGGGGTTTTGAGGGC, Reverse Primer: CAGCCACAAAAGAGCACAAT).
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4

RNA Extraction and RT-qPCR Analysis

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Total RNAs were extracted from tissues by using Trizol (Invitrogen, USA) following the manufacturer's instruction as previously described.21 Reverse transcription was performed by using Hifair® III 1st Strand cDNA Synthesis SuperMix for qPCR (Yeason Biotechnology, Shanghai) to obtain cDNA. RT‐qPCR was performed by using Hieff UNICON® Universal Blue qPCR SYBR Green Master Mix (Yeason Biotechnology, Shanghai) on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Massachusetts, USA). GAPDH RNA was used as an internal control. The 2−ΔΔCT method was used to calculate different expression of RNAs. The experiments were repeated three times. All primers used were listed in Table S3.
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5

Quantification of miR-135a-5p, BMI1, and DANCR

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Total RNA was isolated from tissue samples or cells using a Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA). The first-strand cDNA for miR-135a-5p, BMI1 and DANCR was synthesized from total RNA using MicroRNA Reverse Transcription Kit and TaqMan Reverse Transcription Kits (Applied Biosystems, Foster City, CA, USA), respectively. The first-strand cDNA was used to carry out qRT-PCR with 2× SYBR Green qPCR Mix (Aidlab, Beijing, China) on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific). The primers used were presented as below: for DANCR, 5′-GCCACAGGAGCTAGAGCAGT-3′ (forward) and 5′-GCAGAGTATTCAGGGTAAGGGT-3′ (reverse); for miR-135a-5p, 5′-CCGGCGTATGGCTTTTTATTCC-3′ (forward) and 5′-CAGTGCAGGGTCCGAGGT-3′ (reverse); for BMI1 5′-ACTGGAAAGTGACTCTGGGA-3′ (forward) and 5′-TACTGGGGCTAGGCAAACAA-3′ (reverse); for GAPDH, 5′-TATGATGATATCAAGAGGGTAGT-3′ (forward) and 5′-TGTATCCAAACTCATTGTCATAC-3′ (reverse); for U6 (Forward, 5′-CTCGCTTCGGCAGCACATATACT-3′ (forward) and 5′-ACGCTTCACGAATTTGCGTGTC-3′ (reverse). GAPDH was deemed as a reference gene of BMI1 and DANCR, while U6 was an internal control of miR-135a-5p. The relative expression levels of miR-135a-5p, BMI1 and DANCR were evaluated with 2−ΔΔCt method.
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6

Quantifying linc-ROR expression via qRT-PCR

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Total RNA was extracted from tissue samples and cells on ice using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and reverse-transcribed into cDNA using the TRUEscript 1st Strand cDNA Synthesis Kit (Aidlab, Beijing, China) following the manufacturer’s protocol; reactions were incubated for 30 min at 42°C, 5 min at 85°C, and then stored at −20°C. qRT-PCR reactions were performed using 2×SYBR Green qPCR Mix (Aidlab) on an ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Waltham, MA, USA); reactions were incubated at 95°C for 3 min, followed by 40 cycles of 95°C for 15 s and 60°C for 40 s. GAPDH was used as an internal control. The primer sequences were as follows: linc-ROR forward: 5'-GAAGGTTCAACATGGAAACTGG-3', and reverse: 5'-TGAGACCTGCTGATCCCATTC-3'; GAPDH forward: 5'-CTCAGACACCATGGGGAAGGTGA-3', and reverse: 5'-ATGATCTTGAGGCTGTTGTCATA-3'. Both target (linc-ROR) and reference (GAPDH) genes were amplified in separate wells and run in triplicate. Statistical analyses of the results were performed using the 2−ΔΔCT relative quantification method.
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7

RNA Extraction, cDNA Synthesis, and RT-qPCR Analysis

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We conducted RNA extraction using TRIzol reagent (Invitrogen) as previously described [33 (link)]. We obtained cDNA using a pTRUEscript 1st Strand cDNA Synthesis Kit (Aidlab, Beijing, China). We conducted RT-qPCR with the 2× SYBR Green qPCR Mix (Aidlab) on the ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Waltham, MA, USA). Expression fold differences were determined via the 2−ΔΔCT method.
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8

Profiling lncRNAs and mRNAs in Ovarian Cancer

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Expression levels of lncRNAs and mRNAs were validated by RT-qPCR analysis among 20 high-grade ovarian serous cancer samples. Total RNA was extracted from the tissue samples using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). Total RNA was reverse-transcribed to cDNA using a TRUEscript 1st strand cDNA synthesis kit (Aidlab Biotechnologies Co., Ltd., Beijing, China) following the manufacturer's protocol. Reactions were incubated for 30 min at 42°C, 5 min at 85°C, and then samples were stored at −20°C. qPCR was performed using 2X SYBR green qPCR mix (Aidlab Biotechnologies Co., Ltd.) in an ABI 7900HT sequence detection machine (Thermo Fisher Scientific, Inc.). The reactions were incubated at 95°C for 3 min, followed by 40 cycles at 95°C for 15 sec and at 60°C for 40 sec. Primer sequences for 5 lncRNAs and 5 mRNAs were designed and synthesized (Table I). GAPDH was used as an internal control. Target and reference (GAPDH) genes were amplified in separate wells and run in triplicate. Statistical analyses of the results were performed using the 2−∆∆Cq relative quantification method (24 (link)).
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