scholarly journals A robust method for RNA extraction and purification from a single adult mouse tendon

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4664 ◽  
Author(s):  
Mor Grinstein ◽  
Heather L. Dingwall ◽  
Rishita R. Shah ◽  
Terence D. Capellini ◽  
Jenna L. Galloway
Keyword(s):  
Gene Expression ◽  
Adult Mouse ◽  
Rna Extraction ◽  
Cost Effective ◽  
Mouse Genetics ◽  
Rna Integrity ◽  
Rna Quality ◽  
Rna Analysis ◽  
Rna Integrity Number ◽  
Extraction And Purification

BackgroundMechanistic understanding of tendon molecular and cellular biology is crucial toward furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts.MethodsSingle Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between three and five months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed.ResultsAfter testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis ofScxgene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyzeSox9andCol1a2gene expression changes in injured compared with uninjured control tendons.DiscussionOur work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RT-qPCR as well as RNA-seq. We show this can reduce variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues, as well as precious human samples.

scholarly journals A robust method for RNA extraction and purification from a single adult mouse tendon

2018 ◽  
Author(s):  
M Grinstein ◽  
HL Dingwall ◽  
RR Shah ◽  
TD Capellini ◽  
JL Galloway
Keyword(s):  
Gene Expression ◽  
Adult Mouse ◽  
Rna Extraction ◽  
Cost Effective ◽  
Biological Variation ◽  
Mouse Genetics ◽  
Rna Integrity ◽  
Rna Quality ◽  
Rna Analysis ◽  
Rna Integrity Number

AbstractBackgroundMechanistic understanding of tendon molecular and cellular biology is crucial towards furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts.MethodsSingle Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between 3-5 months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed.ResultsAfter testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis of Scx gene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyze Sox9 and Col1a2 gene expression changes in injured compared with uninjured control tendons.DiscussionOur work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RNA-seq and RT-qPCR. We show this can reduce biological variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues as well as precious human samples.

150 Effect of bovine seminal plasma and sperm on endometrial gene expression

2019 ◽  
Vol 31 (1) ◽  
pp. 200
Author(s):  
B. Fernandez-Fuertes ◽  
J. M. Sanchez ◽  
S. Bages ◽  
P. Lonergan
Keyword(s):  
Gene Expression ◽  
Seminal Plasma ◽  
Reproductive Tract ◽  
Epididymal Sperm ◽  
Rna Integrity ◽  
Rna Quality ◽  
Rna Integrity Number ◽  
Maternal Immune System ◽  
Negative Effect

In cattle, most pregnancy losses are sustained before implantation. Many factors are involved in implantation failure, but in mice, pigs and humans there is increased evidence of a role for the maternal immune system and its regulation by seminal plasma (SP). However, there is little evidence for a role of SP in bovine fertility, where dilution or removal of SP before AI is routine. Therefore, the aim of this work was to determine the effect of bull SP or sperm on endometrial gene expression. To this end, 6 heifers were oestrous synchronised and slaughtered 12h after the onset of oestrus. Five endometrial explants from the horn ipsilateral to the preovulatory follicle were obtained from each animal. Explants were incubated with (1) RPMI medium (control); (2) epididymal sperm (106 epididymal sperm mL−1); (3) complete ejaculate (106 ejaculated sperm mL−1+25% SP); (4) ejaculated sperm alone (106 ejaculated sperm mL−1); and (5) SP alone (25% SP). Epididymal sperm were collected and pooled from the cauda epididymis of 3 bulls slaughtered in a commercial abattoir. In addition, complete ejaculates were obtained from 3 other bulls using an artificial vagina. After pooling the samples, a small volume was washed through a density gradient to obtain the ejaculated sperm, and the rest of the ejaculate was filtered to obtain sperm-free SP. The RPMI media was used to dilute sperm and SP to the working concentrations. After 6h of incubation, explants were snap frozen. The RNA quality was assessed with an Agilent 2100 bioanalyzer (Agilent, Santa Clara, CA, USA) before RT-qPCR analysis. Interestingly, SP had a dramatic effect on endometrium RNA integrity, as evidenced by a lower RNA integrity number in explants exposed to a complete ejaculate (2.4±0.14) or SP (2.4±0.06), in comparison with the control, epididymal sperm, or ejaculated sperm treatments (6.7±0.43, 6.9±0.32, 6.7±0.30, respectively; P<0.05). Due to the low RNA quality, those treatments were excluded from further analysis. However, this finding is currently being explored, along with the possibility of this effect being inherent to species that ejaculate intravaginally. We then compared the ability of ejaculated sperm (which have been exposed to SP) and epididymal sperm (which have never had contact with SP) to regulate the endometrial expression of IL1A, IL1B, IL8, IL6, PTGES2, TNFA, and LIF. Although IL6, IL1A and LIF increased in all animals when exposed to either ejaculated or epididymal sperm, there was no effect of treatment. In conclusion, these data did not support the notion that exposure of sperm to SP is important for the immune regulation of the bovine uterus. In addition, the negative effect of SP on the endometrium, together with the fact that bulls are intravaginal ejaculators, suggests that any putative immunoregulatory role of this fluid in the cattle uterus is indirect. Further analysis of the effect of SP on the vagina and cervix will help elucidate whether this response is present in this species and whether it can propagate to more distal regions of the reproductive tract. This work was supported by Science Foundation Ireland (13/IA/1983, 16/IA/4474).

scholarly journals The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Linda Kvastad ◽  
Konstantin Carlberg ◽  
Ludvig Larsson ◽  
Eva Gracia Villacampa ◽  
Alexander Stuckey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spatial Variation ◽  
Tissue Quality ◽  
Rna Integrity ◽  
Quality Metric ◽  
Rna Quality ◽  
Rna Integrity Number ◽  
Cellular Resolution

AbstractThe RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.

scholarly journals PERBANDINGAN TIGA KIT EKSTRAKSI RNA UNTUK ANALISIS TRANSKRIPTOMIKA PADA KELAPA SAWIT (Elaeis guineensis Jacq.)

2019 ◽  
Vol 6 (1) ◽  
pp. 118
Author(s):  
Siti Zulaeha ◽  
Devit Purwoko ◽  
Imam Cartealy ◽  
Teuku Tajuddin ◽  
. Karyanti ◽  
...  
Keyword(s):  
Somatic Embryo ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Early Stage ◽  
Rna Extraction ◽  
Transcriptomic Analysis ◽  
Total Rna ◽  
Rna Integrity ◽  
Rna Quality ◽  
Rna Integrity Number

Comparison of Three RNA Extraction Kits for Transcriptome Analysis of Oil Palm (Elaeis guineensis Jacq.) ABSTRACTObtaining high-quality RNA is very important at an early stage of molecular biology research. To isolate RNA, high skill and caution are required in following laboratory procedures because RNA is easily degraded, especially samples from plant tissue culture. One of the parameters used to check the total RNA quality is RIN (RNA Integrity Number). The aim of this study was to obtain RNA extraction methods on oil palm leaves, callus and somatic embryos that were of good quality and high concentrations for transcriptomic analysis. RNA extraction was carried out using Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) and RibospinTM Plant (Geneall) kit methods. The results showed that oil palm leaf, callus and somatic embryo RNA were successfully extracted using the RibospinTM (Geneall) kit. Based on the total RNA number of more than 4 μg and the RIN value of more than 7, the extracted RNA could be used in RNA sequencing for transcriptomic analysis. Keywords: callus, oil palm, RNA analysis, RNA quality, somatic embryo ABSTRAKMenghasilkan RNA berkualitas tinggi sangatlah penting pada tahap awal penelitian biologi molekuler. Untuk mengisolasi RNA diperlukan keterampilan dan kehati-hatian tinggi dalam mengikuti prosedur di laboratorium karena RNA lebih mudah terdegradasi, khususnya sampel hasil kultur jaringan tanaman. Salah satu parameter yang digunakan pada pengecekan kualitas RNA total adalah RIN (RNA Integrity Number). Penelitian bertujuan mendapatkan metode ekstraksi RNA pada daun, kalus dan embrio somatik kelapa sawit yang berkualitas baik dan memiliki konsentrasi tinggi untuk analisa transkriptomika.  Ekstraksi RNA dilakukan menggunakan metode kit Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) dan RibospinTM Plant (Geneall). Hasil menunjukkan bahwa RNA daun, kalus dan embrio somatik kelapa sawit telah berhasil diekstraksi dengan menggunakan kit RibospinTM (Geneall). RNA hasil ekstraksi tersebut dapat digunakan untuk sekuensing RNA dengan tujuan analisis transkriptomika, dilihat dari jumlah total RNA yang lebih dari 4 μg dan nilai RIN lebih dari 7. Kata Kunci: analisis RNA, embrio somatic, kalus, kelapa sawit, kualitas RNA 

scholarly journals Effects of Storage, RNA Extraction, Genechip Type, and Donor Sex on Gene Expression Profiling of Human Whole Blood

2007 ◽  
Vol 53 (6) ◽  
pp. 1038-1045 ◽  
Author(s):  
Sung Jae Kim ◽  
David J Dix ◽  
Kary E Thompson ◽  
Rachel N Murrell ◽  
Judith E Schmid ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Extraction Technique ◽  
Interindividual Differences ◽  
Human Whole Blood ◽  
Rna Quality

Abstract Background: Gene expression profiling of whole blood may be useful for monitoring toxicological exposure and for diagnosis and monitoring of various diseases. Several methods are available that can be used to transport, store, and extract RNA from whole blood, but it is not clear which procedures alter results. In addition, characterization of interindividual and sex-based variation in gene expression is needed to understand sources and extent of variability. Methods: Whole blood was obtained from adult male and female volunteers (n = 42) and stored at various temperatures for various lengths of time. RNA was isolated and RNA quality analyzed. Affymetrix GeneChips (n = 23) were used to characterize gene expression profiles (GEPs) and to determine the effects on GEP of storage conditions, extraction techniques, types of GeneChip, or donor sex. Hierarchical clustering and principal component analysis were used to assess interindividual differences. Regression analysis was used to assess the relative impact of the studied variables. Results: Storage of blood samples for >1 week at 4 °C diminished subsequent RNA quality. Interindividual GEP differences were seen, but larger effects were observed related to RNA extraction technique, GeneChip, and donor sex. The relative importance of the variables was as follows: storage < genechip < extraction technique < donor sex. Conclusion: Sample storage and extraction methods and interindividual differences, particularly donor sex, affect GEP of human whole blood.

scholarly journals An optimised direct lysis method for gene expression studies on low cell numbers

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Anh Viet-Phuong Le ◽  
Dexing Huang ◽  
Tony Blick ◽  
Erik W. Thompson ◽  
Alexander Dobrovic
Keyword(s):  
Gene Expression ◽  
Reverse Transcription ◽  
Single Cells ◽  
Quantitative Polymerase Chain Reaction ◽  
Rna Extraction ◽  
Cost Effective ◽  
Breast Cancer Cell Lines ◽  
Cell Numbers ◽  
Ionic Detergent ◽  
Gene Expression Studies

Abstract There is increasing interest in gene expression analysis of either single cells or limited numbers of cells. One such application is the analysis of harvested circulating tumour cells (CTCs), which are often present in very low numbers. A highly efficient protocol for RNA extraction, which involves a minimal number of steps to avoid RNA loss, is essential for low input cell numbers. We compared several lysis solutions that enable reverse transcription (RT) to be performed directly on the cell lysate, offering a simple rapid approach to minimise RNA loss for RT. The lysis solutions were assessed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) in low cell numbers isolated from four breast cancer cell lines. We found that a lysis solution containing both the non-ionic detergent (IGEPAL CA-630, chemically equivalent to Nonidet P-40 or NP-40) and bovine serum albumin (BSA) gave the best RT-qPCR yield. This direct lysis to reverse transcription protocol outperformed a column-based extraction method using a commercial kit. This study demonstrates a simple, reliable, time- and cost-effective method that can be widely used in any situation where RNA needs to be prepared from low to very low cell numbers.

High quality RNA from hydroponically grown grapevine roots suitable for gene expression studies

2017 ◽  
Vol 42 (4) ◽  
Author(s):  
Synda Chenenaoui ◽  
Samia Daldoul ◽  
Ahmed Mliki
Keyword(s):  
Gene Expression ◽  
Rna Extraction ◽  
Extraction Procedure ◽  
Rna Isolation ◽  
Extraction Methods ◽  
Purification Step ◽  
High Quality ◽  
Rna Quality ◽  
Expression Studies ◽  
Gene Expression Studies

AbstractObjectives:Grapevine root system plays a great role in sensing and adapting to abiotic and biotic stresses. Identification of candidate genes involved in the tolerance to abiotic stress is becoming a crucial strategy to select and breed resilient genotypes. However, obtaining high quality RNA from grapevine roots under hydroponic culture is difficult. Hence, we have developed a new extraction procedure to improve RNA quality for root gene expression studies.Methods:Conventional RNA extraction methods using CTAB are not suitable for gene expression studies and need to be improved. Here we report the application of a CTAB- based method for RNA extraction using an additional clean-up purification step.Results:The RIN value of the resulting RNA indicated that our procedure allowed the purification of high RNA quality and quantity. Hence, the clean-up purification step efficiently eliminated contaminants which inhibit downstream applications. Derived RNA was successfully used for differential gene expression analysis in salt stressed grapevine by Northern Blot hybridizations.Conclusion:In this study, we developed an efficient RNA isolation protocol from hydroponic cultivated grapevine roots which yielded RNA suitable for gene expression studies. This will open large perspectives in grapevine functional genomics with the identification of pertinent genes of agronomic interest.

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