Molecular Biology Techniques and Applications

Manufacturing DNA in E. coli yields higher fidelity DNA than in vitro enzymatic synthesis

This study compares DNA fidelity between in vitro enzymatic synthesis and E. coli-produced DNA, finding that E. coli yields significantly fewer mutations.

Flexible Methods for Standard Error Calculation in digital PCR Experiments

This paper introduces three new statistical methods for variance estimation in digital PCR experiments, showing they provide more accurate results than classical binomial methods.

CryoGrid-PIXUL-RNA: High throughput RNA isolation platform for tissue transcript analysis

The paper introduces a low-cost system for high-throughput RNA isolation from tissues, combining CryoGrid for storage/sampling with PIXUL-based methods using a PK buffer to enable efficient transcript analysis.

Hydrogel Capsule-Based Digital Quantitative Polymerase Chain Reaction

This paper introduces a novel hydrogel capsule-based digital PCR method that improves stability, sensitivity, and cost-effectiveness compared to traditional ddPCR.

Robust higher-order multiplexing in digital PCR by color-combination

This paper introduces a method to increase digital PCR multiplexing to 15-plex using color combination and validates its statistical framework and sensitivity.

Transcriptomic-based selection of reference genes for quantitative real-time PCR in an insect endosymbiotic model

The paper identifies stable reference genes for qRT-PCR in insect endosymbiotic models using transcriptomic data from Sitophilus oryzae.

A quick and cost-effective method for DNA-free total RNA isolation using magnetic silica beads

The paper introduces an in-house RNA isolation method using magnetic silica beads that produces high-quality RNA comparable to commercial kits, without DNA digestion or separate small RNA kits.

pHAPE: a plasmid for production of DNA size marker ladders for gel electrophoresis

The paper describes a plasmid, pHAPE, that allows the generation of DNA size markers through restriction enzyme digestions, reducing costs associated with commercial DNA ladders.

An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model.

This paper develops an optimized RNA extraction method for rat intrinsic laryngeal muscles, achieving high-quality RNA suitable for RNA-seq.

Accurate Direct PCR with Arabidopsis and rice

The paper introduces and compares two Direct PCR methods for Arabidopsis and rice, finding Line-PCR to be faster, cheaper, and more accurate than existing methods.

OverFlap PCR - a reliable approach for generation of plasmid DNA libraries containing random sequences without template bias.

Next generation digital PCR: high dynamic range single molecule DNA counting via ultra-partitioning

This paper introduces Ultra-dPCR, a next generation digital PCR system that enables single-molecule DNA counting with a 6-log dynamic range, demonstrating its potential for non-invasive prenatal testing.

Degraded RNA from human anterior cruciate ligaments yields valid gene expression profiles

The paper shows that gene expression profiles from partially degraded RNA can still be valid, using PCR-based analysis and normalization to housekeeping genes.

Laser Capture Microdissection optimization for high-quality RNA in mouse brain tissue

The paper describes an optimized LCM protocol for extracting high-quality RNA from specific mouse brain regions.

Using total RNA quality metrics for time since deposition estimates in degrading bloodstains

This paper develops a method to estimate time since deposition of bloodstains using RNA quality metrics from degrading blood samples without amplification.

Delayed processing of blood samples impairs the accuracy of mRNA-based biomarkers

This study shows that delayed processing of blood samples affects mRNA-based biomarkers by altering transcript abundance in peripheral white blood cells.

An adaptive filtering framework for non-specific and inefficient reactions in multiplex digital PCR based on sigmoidal trends

This paper introduces an adaptive filtering framework to improve classification accuracy in multiplex digital PCR by removing non-specific and low-efficient reactions using sigmoidal trends and outlier detection.

RNA-Seq is not required to determine stable reference genes for qPCR normalization

This study shows that using a robust statistical method to select reference genes from randomly chosen candidates is as effective as selecting stable genes from RNA-Seq data for qPCR normalization.

Virtual partition digital PCR for high precision chromosomal counting applications

This paper introduces VPdPCR, a method that enhances digital PCR's ability to detect multiple targets per sample, improving accuracy and reducing variance in chromosomal counting.

freqpcr: estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples

The paper develops a statistical model to estimate population allele frequency from qPCR ΔΔCq measures of bulk samples, showing improved precision over simple averaging.

Assessment of Sex Bias in Housekeeping Gene Expression in Adipose Tissue Through the Massive Analysis of Transcriptomics Data

This paper evaluates sex bias in housekeeping gene expression in adipose tissue using transcriptomics data and identifies sex-unbiased housekeeping genes suitable for use as internal controls.

A cost-effective and efficient approach for generating and assembling reagents for conducting real-time PCR

The paper describes a cost-effective method for preparing cDNA synthesis and real-time PCR mastermixes that match commercial kits' efficiency, addressing financial barriers in low-resource settings.

Evaluation of endogenous miRNA reference genes across different zebrafish strains, developmental stages and kidney disease models

This study evaluates miRNA reference genes in zebrafish across strains, developmental stages, and kidney disease models, identifying dre-miR-92b-3p as the most stable reference gene.

A method to quantitate maternal transcripts localized in sea urchin egg cortex by RT-qPCR with accurate normalization

The paper evaluates the reliability of RT-qPCR for quantifying maternal transcripts in sea urchin egg cortices using normalization with reference genes.

Auto-qPCR: A Python based web app for automated and reproducible analysis of qPCR data

Auto-qPCR automates qPCR data analysis, reducing errors and time by providing a web-based tool for DNA quantification and gene expression analysis.

Double-check the zebrafish 18s rRNA qPCR primers: they may be wrong

The paper identifies an incorrect qPCR primer for zebrafish 18s rRNA and recommends corrected primer sets to avoid erroneous results in future studies.

Declining RNA integrity in control autopsy brain tissue is robustly and asymmetrically associated with selective neuronal mRNA signal loss

The paper investigates how RNA integrity numbers (RINs) affect mRNA expression in control autopsy brain tissue, finding pathway-specific and non-linear degradation patterns.

Selection of reference genes for quantitative analysis of microRNA expression in three cancers.

This study identifies stable miRNA expression markers in three tissues for use as reference genes in qPCR analysis of miRNA expression in cancer.

Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions

This paper identifies optimal reference genes for qPCR normalization in mesangial cells and podocytes under high-glucose and losartan treatment conditions.

A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis

The paper identifies stable reference genes for normalizing gene expression in human pancreatic beta cells under stress conditions using RNA-seq and qPCR validation.