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ARTICLE: Quantitative analysis of gene expression in different tissues by template-calibrated RT-PCR and laser-induced fluorescence.
- W J Karges,
- R Gaedigk,
- and H M Dosch
Genome Res. December 1994 4: 154-159
...Quantitative analysis of gene expression in different tissues by template-calibrated RT-PCR and laser-induced fluorescence. W J Karges , R Gaedigk , and H M Dosch Department of Pediatrics and Immunology, Hospital for Sick Children, Toronto, Canada...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...in megakaryocyte state. We used another gene KLF1, erythroid marker as 592 a negative control whose expression decreases in megakaryocyte state. The expression of the 593 genes was confirmed using qRT-PCR at 24, 48 and 72 hrs. 594 595 RNA Isolation and real time PCR 596 Total RNA was isolated using TRIzol reagent...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...DNA); this cDNA template is used for the quantitative PCR or real-time PCR reaction (qRT-PCR). Specific target fluorescent DNA-binding probes or fluorescent dsDNA-binding dyes (nonspecific used with target-specific primers) are incorporated during the PCR reaction, so that the increase in emitted fluorescence...
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ARTICLES: Real time quantitative PCR.
- C A Heid,
- J Stevens,
- K J Livak,
- and P M Williams
Genome Res. October 1996 6: 986-994; doi:10.1101/gr.6.10.986
...– 2100 . Gibson, U.E.M., C.A. Heid, and P.M. Williams. 1996. A novel method for real time quantitative competitive RT-PCR. Genome Res. (this issue). Gorman, C.M., Gies, D.R. and McCray. G. 1990 . Transient production of proteins using an adenovirus transformed cell line. DNA Prot. Engin. Tech. 2 : 3 – 10...
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Resource: A quantitative atlas of polyadenylation in five mammals
- Adnan Derti,
- Philip Garrett-Engele,
- Kenzie D. MacIsaac,
- Richard C. Stevens,
- Shreedharan Sriram,
- Ronghua Chen,
- Carol A. Rohl,
- Jason M. Johnson,
- and Tomas Babak
Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
...to a false-discovery rate (FDR) of 2.5% (Supplemental Fig. 2; see Methods) that was also consistent with additional RT–PCR based validation (Supplemental Figs. 3–5). Given the similar genomic and transcriptional complexities of all samples sequenced (Chan et al. 2009), we expect this number to be generally...
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Resource: Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators
- Marion Scheibe,
- Nausica Arnoult,
- Dennis Kappei,
- Frank Buchholz,
- Anabelle Decottignies,
- Falk Butter,
- and Matthias Mann
Genome Res. December 2013 23: 2149-2157; Published in Advance August 6, 2013, doi:10.1101/gr.151878.112
...selected 19 proteins (Supplemental Fig. 1) and measured the impact on TERRA molecule abundance by quantitative RT-PCR. The cellular TERRA molecules were reverse transcribed with a primer located in the UUAGGG tract. Then, for qPCR experiments, primers were designed in the subtelomeric region, between...
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Method: Quantitative evaluation of all hexamers as exonic splicing elements
- Shengdong Ke,
- Shulian Shang,
- Sergey M. Kalachikov,
- Irina Morozova,
- Lin Yu,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
...transfections of HEK293 cells, after which RT–PCR and gel purification were used to isolate the minority (;16%) of molecules that had included, rather than skipped, the central exon of theminigene.We found it necessary to transfect a relatively large number of cells (4 3 106) and to use a strong promoter (CMV...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...; Agilent 600559).The endogenous MYC, DNAJC9, RPL30, and POL2RA mRNA expression levels were measured by quantitative RT-PCR using EvaGreen dye (Biotium) on a Bio-Rad CFX real-time system. A standard curve was generated for each primer set with thermal cycle conditions for 40 PCR cycles (12 min at 95°C, 15...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...in the seven samples. (C) Plasmid constructs containing the MYOCD promoter (top) and the relative luciferase activity of the constructed plasmids in the HuH-7 and Hep G2 cell lines (bottom). (D,E) MYOCD expression levels were determined by qRT–PCR and western blotting in the HCC lines HuH-7 and Hep G2 infected...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...was observed in 475 BEAS-2B cells compared to the reference . We then selected the SNU899 cell 476 line, which has a homozygous SRE with longer insertion, and the BEAS-2B cell line 477 for quantitative real-time PCR (QPCR) to assess whether the SRE affects the 478 expression levels of TP53BP2 and FBXO28...
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