Rna Seq Experimental Design Analysis And Interpretation Essays


Found 125949 essays.

Report on RNA-seq Transcriptomics

In order to do the analysis, the Tuxedo Suit software was used.More specifically, the whole RNA transcripts or parts of them are purified and then reverse transcribed into c DNAs.In this report, analysis of the differential expression between two groups of samples corresponding to two Drosophila melanogaster tissues was implemented.The prototype method, MPSS, applies four rounds of restriction enzyme digestion and ligation reactions to determine the nucleotide sequence of c DNA ends, generating a 17-20 bp sequence as the fingerprint of a corresponding RNA (Brenner et al., 2000)... .. Transcriptomics is the field of biology that studies the RNA transcripts in a large scale manner.


2172 words (5.4 pages)
Transcript Expression Level of White Kelampayan

RNA was extracted from the collected tissues and further prepared for cDNA library construction (Ho , 2014).On proportions analysis, especially Z test (Kal , 1999), four columns (“Proportions difference”, “Fold Change”, “Test statistics” and “P-value”) will be created and added to the experiment table for each analyzed groups pairs: Xylem and leaves tissue groups.Results of statistical analysis on transcript expression level will be visualized in volcano plots with CLC Genomics Workbench 7.5 (Qiagen, Denmark).Furthermore, there are several applications used in NGS technology such as transcriptome sequencing or RNA-Sequencing (RNA-Seq), genomic sequencing and epigenetic applications which use CHIP-Seq and methylation profiling to work o...


1912 words (4.8 pages)
Prioritising Drug Targets for Antimalarial Drugs

This assignment will first provide the result after sifting through the genome and promising targets are PF3D7_0623200 , then presenting the bioinformatic analysis and data on the characteristics of this selection of preferred desirable drug targets.As figure 7 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.As figure 10 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.As figure 4 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.As figure 14 shows, nine different stages during the development of P. falciparum 3D7...


1902 words (4.8 pages)
CRM Prediction and CRM Validation Approaches

Another commonly used database website is the University of California Santa Cruz (UCSC) Genome Browser Database, which provide all aspects of information for CRM prediction including experimental (DNase hypersensitivity clusters, epigenetic marks of histone proteins, and binding of transcription factors from ChIP seq) as well as computational (conservation level among vertebrates from DNA sequence alignment) study[181].By using the reference genome database containing epigenetic as well as DNase hypersensitivity regions, where the information is obtained from ChIP seq [176], and DNase seq experiments, the substantial rate of validation of selected CRMs from 43 to 100% in many study models[169-171, 176, 177] indicates the robustness of t...


2745 words (6.9 pages)
Understanding an Unknown Protein Sequence

This does show that the query protein is the predicted protein with Seq ID: gi|168001481|ref|XP_001753443.1 as we have found out previously.Figure 2: (A) PSI-BLAST shows similarity index to query sequence (B) ClustalW2 results showing alignment between predicted protein (Seq ID: gi|168001481|ref|XP_001753443.1) and predicted protein (Seq ID: gi|168035394|ref|XP_001770195.1).The full identification name given in the results page is the predicted protein [Physcomitrella patens] >gi|162695322|gb|EDQ81666.1| Seq ID: gi|168001481|ref|XP_001753443.1 .When a report was generated for the predicted protein of Physcomitrella patens Seq ID: gi|168001481|ref|XP_001753443.1, it is clearly seen that Physcomitrella patens has 4 hits, followed by Sel...


2749 words (6.9 pages)
Analysis of GATA3 ChIP-seq in the Four Cells

In this study, pathway enrichment analysis and GO enrichment analysis revealed that AKR1C1 was enriched in process related with xenobiotics metabolism.Motif analysis revealed that significant enrichment of “GAT” motif was identified in GATA3 binding site among the four tumor cells.Motif analysis revealed that the motifs achieved among the four cells were in good agreement with known GATA3 motif.Pathway enrichment analysis revealed that the common GATA3 target genes were enriched in pathways related with cancer, cell cycle and cell migration, which indicated that these common GATA3 target genes might be the core node of tumor progression related with GATA3.MACS (Model-based Analysis of ChIP-Seq) [19] and CisGenome [20] are two different ...


2788 words (7.0 pages)
Controlling Pol II Pausing

Checkpoint of early elongation: Pol II carrying Ser5P serves as a platform to interact with the 5’ capping enzyme, which adds 5’-methyl cap when nascent RNA is ~20-30 nt in length (reviewed in Adelman and Lis, 2012).Combining different assays, which all point to a similar conclusion, these experiments suggest that poised Pol II near the TSS primarily exists in paused form, with very little in the PIC (not imitating RNA synthesis), arrested (stably engaged in elongation but backtracked), or terminating (unstably elongating and in the process of dissociating from DNA) states (reviewed in Adelman and Lis, 2012; Gaertner and Zeitlinger, 2014).Therefore, pausing may function as a checkpoint for RNA processing before proceeding into productive...


2262 words (5.7 pages)
Genes and Mechanisms in Colorectal Cancer (CRC)

The functional enrichment analysis results showed that down-regulated genes were significantly enriched in cytokine-cytokine receptor interaction and TNF signaling pathways, while up-regulated genes were related to bile secretion function.However, further studies are still needed to confirm our results.The clustering analysis result was shown in Figure 1.Total 23 pathways were obtained in KEGG enrichment analysis.The functional enrichment analysis was performed.


2192 words (5.5 pages)
The Polymerase Chain Reaction Pcr

RNA was isolated from cell pellets using Trizol procedure.This error could be introduced at one or more stages throughout the experimental protocol; (input sample, RNA extraction, etc.)The quantity of the isolated RNA was determined by nanodrop spectrophotometry (absorbance at 260 nm of a 40µg/ml solution of RNA is 1.0) using nuclease-free water as a blank.The principle of RT-qPCR is straight forward: following the reverse transcription of RNA in to cDNA, it needs an appropriate detection chemistry to detect the presence of PCR products, an instrument to monitor the amplification in real-time and compatible software for quantitative analysis.Wearing gloves while handling reagents and RNA samples, changing gloves frequently, keeping tube...


1090 words (2.7 pages)
Real Time Pcr Essay

The amplicon being studied can be cloned, or a synthetic oligonucleotide (RNA or DNA) can be used.Figure: Ampliflour primer PROBE-BASED DETECTION SYSTEMS Probe-based systems provide highly sensitive and specifi c detection of DNA and RNA.STANDARD CURVE TO ASSESS EFFICIENCY, SENSITIVITY, AND REPRODUCIBILITY The final stage before assay employment is validating that all the experimental design parameters result in a highly efficient, sensitive, and reproducible experiment.Two-step qRT-PCR Two-step qRT-PCR starts with the reverse transcription of either total RNA or poly(A)+ RNA into cDNA using a reverse transcriptase (RT).RNA was reverse transcribed into cDNA.


4694 words (11.7 pages)
Genes of Calcium Transporters

Therefore, in the parallel studies on rice, sorghum, and finger millet (high & low calcium variety), have been studied to identify possible candidate genes of calcium transporters and calcium binding proteins across different stages of seed that may be responsible for the accumulation of calcium in the developing grain.Such a combined approach of analyses and experimental follow-up will lead to comprehensive understanding of the crucial events of seed development in cereal grains.Furthermore the genes identified to be up-regulated in the high grain calcium content genotype can be used as a candidate gene for improving the calcium content of genotypes which are agronomically better performers but contain low calcium.Hence RNA-seq ha...


2307 words (5.8 pages)
Biology: Determining the Lengths of Telomeres Using Flow FISH Method Essay

The major limitation of flow-FISH is the requirement of the equipment to do the analysis which is expensive, the configuration of the equipment (flow cytometer) and the nature of the probe used for hybridization is also expensive and requires a well trained personnel.A variety of sources can be used as standard template such as plasmid which has a cloned gene of interest, genomic DNA, copy DNA, synthetic oligos, in vitro transcripts and total RNA besides others.Fluorescence readings at early amplification cycles will gauge the amplified template quantity where the reaction is much more reproducible from sample to sample than at the endpoint.Most often, fluoresceine isothiocyanate (FITC) is used as a label.If flow cytometer is equipped wi...


428 words (1.1 pages)
RNA structure Essay

The availability of experimental data to calculate the free enthalpy associated with a given folding of RNA has paved the way for the ab initio prediction of its secondary structure.The classic core of the transfer RNA structure contains several triple interactions which stabilize the interaction of the four helices and give these RNAs their overall "L" shaped topology from their secondary structure in clover leaf shape.The RNA of interest is processed by either of these enzymes under very partial digestion conditions, where only zero or one cleavage occurs per RNA molecule.We then have a structure locally associating three RNA strands.The structure of RNA describes the arrangement of base pairs and the conformation of RNA in three dimen...


3066 words (7.7 pages)
Effect of Stimulus Uncertainty Essay

A within-subject counterbalanced experimental design was used for this study (ABBA).Figure SEQ Figure \* ARABIC 1 The Y-Axis represents the averages of the groups.In this design, each participant received each condition and served as his or her own control.The independent variable in this experiment was the method of sorting; condition A was a 2-sort alternative and condition B was a 4 sort alternative.Before the experiment could begin, the students counted the cards, to make sure that there were 52 cards.


767 words (1.9 pages)
Ebola virus Essay

It is a single-stranded RNA virus of negative polarity (order Mononegavirales) and an unsegmented genome (group V of the Baltimore classification).The Ebola virus genome, about 19 kilobases long, contains seven genes which encode seven structural proteins and two additional proteins secreted by a stuttering polymerase phenomenon: capsid nucleoprotein NP, the cofactor of viral polymerase VP35, major matrix protein VP40, GP, sGP and ssGP glycoproteins from the GP gene, minor nucleoprotein VP30, template protein VP24 and RNA-dependent RNA polymerase L. .Following WHO approval for the use of experimental treatments in the 2014 outbreak, Nigeria's Minister of Health Onyebuchi Chukwu on August 15 announced the arrival in the country of a treat...


4378 words (10.9 pages)
Categories of Multimeters for Electronics

It is much simpler to complete this test as thought about from the past investigations since the experimenters considered having great working materials, for example, the multitester, resistors, wires, breadboard, and so forth.Leads of a  Digital Multimeter are its result is shown on the screen which displays the practical or analysis value,  high precision, aptitude to read both +ve and –ve values .Figure SEQ Figure \* ARABIC 3 .We can point VΩ and the COM jack on the right of the figure used for detecting voltages, resistance and for analysis a diode.Also, digital multimeters aren’t good in the analysis of semiconductor.


2884 words (7.2 pages)
Artifact Essay

In fantasy universes, role-playing games and their derivatives, the word artifact is sometimes used to designate a relic, a magical object, unique and very powerful.According to Rabardel, an artefact is "therefore any technical or symbolic object that has undergone a transformation of human origin, no matter how small.Bioengineering engineers like George McDonald Church are announcing tomorrow the possibility of recreating extinct species or entirely new organisms, possibly designed with an equivalent of artificial DNA or RNA (which would therefore be also artefacts).Artefact - eclectic culture is a bilingual (French-English) online journal published since September 2012 (ISSN 2262-2780 ) and an information portal of the Artéfact associa...


488 words (1.2 pages)
Artifact Essay

From this point of view, the name artefact is directly related to any human action or activity ".In several scientific fields, an artefact is a phenomenon or an artificial signal whose appearance, linked to the method used during an experiment, causes an analysis error.According to Rabardel, an artefact is "therefore any technical or symbolic object that has undergone a transformation of human origin, no matter how small.Artefact - eclectic culture is a bilingual (French-English) online journal published since September 2012 (ISSN 2262-2780 ) and an information portal of the Artéfact association.Bioengineering engineers like George McDonald Church are announcing tomorrow the possibility of recreating extinct species or entirely new organ...


489 words (1.2 pages)
White Spot Syndrome Virus (WSSV) Experiment

This works may help to design a novel non-toxic drug to treat WSSV infection.Cumulative mortality graph for the experimental groups.The viral suspensions for all groups were incubated at room temperature for 3 h. Later it was injected into respective experimental groups intramuscularly.The experimental animals were examined twice per day for gross signs of disease, and the number of deaths was recorded until end of the experiment.For RT-PCR analysis; Gill, head-soft tissue, heart and muscle tissue were excised from each crabs of the experimental group and pooled together for extraction of total RNA using Trizol (Invitrogen, USA) according to the manufacturer’s instructions.


1802 words (4.5 pages)
Oligopoly pricing: Old ideas and new tools

Interpretation.Figure SEQ Figure * ARABIC 1: when people expect civil unrest the demand is high but and the prices go up.Figure SEQ Figure * ARABIC 4: the graph show decrease in demand for high fuel efficient cars when the price of petrol goes up .Figure SEQ Figure * ARABIC 6: (Tax increase the price for tobacco leading to low demand and eventually low consumption) .Figure SEQ Figure * ARABIC 2: price of petrol increases when tax is imposed .


1549 words (3.9 pages)
Economics question and answer Essay

Figure SEQ Figure * ARABIC 5 : Excess supplies of chicken in the market results to low demand and eventually falls in price.Figure SEQ Figure * ARABIC 6: (Tax increase the price for tobacco leading to low demand and eventually low consumption) .Cambridge, Mass.In addition oligopolistic firms constantly differentiate their products in terms of quality and always struggle to come up with new products design that outshine those of competitors.Figure SEQ Figure * ARABIC 4: the graph show decrease in demand for high fuel efficient cars when the price of petrol goes up .


1598 words (4.0 pages)
Friedrich Miescher’s Experiments on the Nuclei

He finally came out with four properties that the genetic material must meet to fulfill its role .. After his experiment other scientists did other experiments that helped understand as the role of DNA.To verify their points that DNA was actually what caused the transformation, they treated samples of the DNA extract with enzymes that digest DNA, RNA and protein... Now the question was what was going on in the fourth experiment?Now from here he carried out an experiment that involved the injection of live and/or heat-killed bacteria into mice to observe whether or not the bacteria caused any lethal infection.Now it was argued that the DNA extract may have been contaminated by some portion of RNA or proteins.


979 words (2.4 pages)
Effects Of Implementing Animation In Teaching Chemistry

Students in were divided into two groups as experimental group and comparison group and involved in a quasi experimental design by pre-test post-test.Also conceptual change texts accompanied with animations, decrease alternative conceptions or misunderstanding in experimental group.Also he showed that the attitudes of the experimental group toward science as a school subject became more positive than those of the control group after treatment.Demonstrations in chemistry are visualizations at a macroscopic level that enable the student to observe phenomena, as they would be experienced in an experimental laboratory setting (Vel ´azquez-Marcano et al.Their achievements are evaluated in experimental design by post-test scores.


2543 words (6.4 pages)
The Inhibitory Effects of Low Power Radiofrequency

Nucleic acid total level decreased exponentially with exposure time t, experimental fitting curves following 20.72 + 42.37e-t/1.44 equation with R2=0.94227.The level of DNA and RNA for the plantlets provided by electromagnetic field exposed seeds .. .Statistic analysis of the experimental data, resulted from the three repetitions of the whole experiment, was accomplished by means of ANOVA test – applied using MsExcell soft package – to evaluate reliability of modifications induced by electromagnetic field exposure in comparison to the control ones as well as among the samples corresponding to different exposure time, considering the significance criterion of 0.05 (p value).The contents of photosynthesis pigments ( and chlorophylls and ...


2530 words (6.3 pages)
Polymerase chain reaction Essay

It should be noted that it is very difficult to know if a variation in an observed PCR efficiency comes from the very nature of this method, from a variation in the experimental protocol (lack of reproducibility of reagents or handling) a variation in data acquisition (variations in fluorescence, different reading channels, bias in mathematical analysis).Reverse transcription remains delicate (low reproducibility; fragility of the RNA, frequent contamination by DNA.It is now widely used by virologists working on RNA viruses which can have high mutability.Utility: it is used for clinical diagnosis, via quantitative measurements by real-time PCR (study of viral loads in RNA viruses) and via qualitative measurements (analysis of the product...


3785 words (9.5 pages)
Pulmonary Hypertension Syndrome in Fast-growing Broilers

The reverse transcription mix was heated to 75°C for 15 min to denature the RNA and then stored at -20°C.The amount and quality of RNA were determined by spectrophotometry.Total RNA was treated with RNase-free DNase (Sinaclon Bioscience, Karaj, Iran) to avoid amplification of contaminating genomic DNA.Only RNA of sufficient purity, having an absorbance ratio (A260/280) greater than 1.9, was considered for synthesis of cDNA.The right and left ventricles of the heart were immediately frozen in liquid nitrogen and stored at -70°C for subsequent RNA analysis.


3101 words (7.8 pages)
Encoding RIP from Elaeis Guaneensis Jacq

For each experiment, the relative band quantity obtained by densitometrric analysis was normalized to the value of the internal control (house-keeping gene) bands which were run in parallel.Figure : Total RNA from various treated and untreated oil palm tissues.The RNA was dissolved in 5ml diethypyrocarbonate (DEPC) – treated water.Identification of differentially expressed genes was based on consistent ford-change across experimental replicates relative to untreated negative control.Equal amounts of RNA (1ug) extracted from control and treated oil palm root samples were converted into cDNA by using the Omniscript two step Reverse Transcription Kit for cDNA Synthesis (Qiagen, USA) following the manufacturer’s instructions.


2168 words (5.4 pages)
Personal Statement for Microbiology and Biotechnology Msc

As a consequence, there is now an urgent need for well-qualified graduates who can interpret these new advances and apply their knowledge in careers within the food industry, DEFRA and the Food Standards Agency, as well as in Local Government and hospital laboratories.Because of their ease of manipulation and rapid growth, such organisms are frequently used as experimental systems for research in biochemistry and molecular biology.The objective of the Master of Science in this course is to provide future biotechnologists with the skills and competencies needed today to design biotechnological research, implement biotechnological projects, and planning decision, create and apply research modalities to larger schemes set in large research ...


812 words (2.0 pages)
Horizontal Gene Transfer In Prokaryotes Biology Essay

It is see-through that to a large extent of the disparity was attributable to differential genetic material loss, outstandingly in parasites, but horizontal RNA relocate is the new foremost evolutionary thing with the intention of may possibly avoid give explanation the emerging complex photo of prokaryotic genomes.Although fitness peaks may not at all be explored if they ought to be reached one genetic material at a time, many genes may be secured as bacterial operons and RNA clusters (Lawrence et al.Acknowledgment of RNA reassignment surrounded by and in the middle of lineages restructures microbial evolution in further conduct than submission new interpretations of the imitate of microbial phylogeny.It is fine with the intention of a ...


4713 words (11.8 pages)
Expression of KITLG and KIT-Receptor Analysis

Half of each testis were immediately frozen in liquid nitrogen and stored at -70°C for subsequent RNA analysis.However, in the present study, it appears that reduction of KITLG/KIT-receptor transcript was not mainly influenced by variation in expression of mentioned cytokines (i.e., TNF and IL-4) in the experimental varicocele of dogs.To induce experimental varicocele by surgery, inguinal canal region of dogs was prepared aseptically for operation.Total RNA from left (non-varicocele) and right (varicocele) testes was extracted using Rimazol reagent (Sinaclon Bioscience, Tehran, Iran).Gel agarose (2%) electrophoresis (stained with ethidium bromide) was applied to analyze RNA.


2818 words (7.0 pages)

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