Gene expression and transcript profiling involves determining the pattern of genes expressed at the transcriptional level under specific circumstances by measuring the expression of thousands of genes simultaneously. This allows one to understand cellular function. Common techniques for profiling include DNA microarrays, RNA sequencing, and EST tags. DNA microarrays involve hybridizing cDNA or cRNA samples to probes on a chip to determine relative abundance of sequences. RNA sequencing uses next-generation sequencing to reveal presence and quantity of RNA in a sample.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
complete Single Nucleotide Polymorphiitsm Detection methods with Advance techniques with its applications
Single nucleotide polymorphisms are single base variations between genomes within a species.
There are at least 10 million polymorphic sites in the human genome.
SNPs can distinguish individuals from one another
Denaturing Gradient Gel Electrophoresis
Chemical Cleavage Of Mismatch
Single-stranded Conformation Polymorphism (SSCP)
MutS Protein-binding Assays
Mismatch Repair Detection (MRD)
Heteroduplex Analysis (HA)
Denaturing High Performance Liquid Chromatography (DHPLC)
UNG-Mediated T-Sequencing
RNA-Mediated Finger printing with MALDI MS Detection
Sequencing by Hybridization
Direct DNA Sequencing
Single-feature polymorphism (SFP)
Invader probe
Allele-specific oligonucleotide probes
PCR-based methods
Allele specific primers
Sequence Polymorphism-Derived (SPD) markers
Targeting induced local lesions in genomes (TILLinG)
Minisequencing primers
Allele-specific ligation probes
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
complete Single Nucleotide Polymorphiitsm Detection methods with Advance techniques with its applications
Single nucleotide polymorphisms are single base variations between genomes within a species.
There are at least 10 million polymorphic sites in the human genome.
SNPs can distinguish individuals from one another
Denaturing Gradient Gel Electrophoresis
Chemical Cleavage Of Mismatch
Single-stranded Conformation Polymorphism (SSCP)
MutS Protein-binding Assays
Mismatch Repair Detection (MRD)
Heteroduplex Analysis (HA)
Denaturing High Performance Liquid Chromatography (DHPLC)
UNG-Mediated T-Sequencing
RNA-Mediated Finger printing with MALDI MS Detection
Sequencing by Hybridization
Direct DNA Sequencing
Single-feature polymorphism (SFP)
Invader probe
Allele-specific oligonucleotide probes
PCR-based methods
Allele specific primers
Sequence Polymorphism-Derived (SPD) markers
Targeting induced local lesions in genomes (TILLinG)
Minisequencing primers
Allele-specific ligation probes
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.
The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.
The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.
Usually NGS (Next generation sequencing) is extensively used in unde.pdfangeldresses
Usually NGS (Next generation sequencing) is extensively used in understanding the viral
genome by generating many billions of sequences. But of late NGS is also finding its place in
other areas of science like Transcriptomics where the measurement of mRNA is done to
understand the genomic expression better and it’s possible modifications in health and
disease.Till now microarray had been used to quantify the gene expression but this is being
replaced by NGS of transcribed RNA termed as RNA seq.
The key steps include the isolation of RNA and removal of host genomic DNA. Following
which, rRNA is also removed by selection of polyadenylated RNA or with antisense oligos.
Complementary DNA synthesis is primed either by oligo(dT) or randomly on long transcripts.
Analysis of RNA-seq data is usually achieved by mapping sequence reads to a reference
genome, in this case the comparison between the infected genome and the normal genome can be
done, using software that can map reads over gene splice junctions. Statistical analysis of the
number of reads per genome region (gene) can be used to quantify relative levels of expression.
Also, Existing ORF and the newly generated ORF can be identified.
EV71 infection induces the expressions of genes which are associated with the secretions of
inflammatory cytokines, chemokines, complementary proteins and host cell apoptosis. The major
signaling pathway affected is the MAPK signaling pathway.
Solution
Usually NGS (Next generation sequencing) is extensively used in understanding the viral
genome by generating many billions of sequences. But of late NGS is also finding its place in
other areas of science like Transcriptomics where the measurement of mRNA is done to
understand the genomic expression better and it’s possible modifications in health and
disease.Till now microarray had been used to quantify the gene expression but this is being
replaced by NGS of transcribed RNA termed as RNA seq.
The key steps include the isolation of RNA and removal of host genomic DNA. Following
which, rRNA is also removed by selection of polyadenylated RNA or with antisense oligos.
Complementary DNA synthesis is primed either by oligo(dT) or randomly on long transcripts.
Analysis of RNA-seq data is usually achieved by mapping sequence reads to a reference
genome, in this case the comparison between the infected genome and the normal genome can be
done, using software that can map reads over gene splice junctions. Statistical analysis of the
number of reads per genome region (gene) can be used to quantify relative levels of expression.
Also, Existing ORF and the newly generated ORF can be identified.
EV71 infection induces the expressions of genes which are associated with the secretions of
inflammatory cytokines, chemokines, complementary proteins and host cell apoptosis. The major
signaling pathway affected is the MAPK signaling pathway..
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
The study of the complete set of RNAs (transcriptome) encoded by the genome of a specific cell or organism at a specific time or under a specific set of conditions is called Transcriptomics.
Transcriptomics aims:
I. To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.
II. To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications.
III. To quantify the changing expression levels of each transcript during development and under different conditions.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
1. Gene expression and Transcript
profiling
priyanka Mudad
M.Sc. Biochemistry
central university of Haryana
2. next step after sequencing a genome
determination of the pattern of genes expressed, at the level
of transcription, under specific circumstances
measurement of the activity (the expression) of thousands of
genes at once, to create a global picture of cellular function.
Sequence based techniques, like RNA-Seq, provide
information on the sequences of genes in addition to their
expression level.
expression profile allows one to deduce a cell's type, state,
environment, and so forth.
4. DNA chip or biochip
collection of microscopic DNA spots attached to a solid surface.
measure the expression levels of large numbers of genes simultaneously or
to genotype multiple regions of a genome.
Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known
as probes (or reporters or oligos).
These can be a short section of a gene or other DNA element that are used
to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under
high-stringency conditions.
Probe-target hybridization is usually detected and quantified by detection
of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative
abundance of nucleic acid sequences in the target.
DNA Microarray
5. Basic
mechanism of
DNA
Microarray
Hybridization between the
cDNA reverse transcribed
from a biological sample
to a pre-designed
complementary DNA
probe arranged on a
slide, or array, is the
basis of DNA
microarrays.
6.
7. Applications of Microarrays
Gene Discovery
Disease Diagnosis
Drug Discovery
Toxicological Research
For easing the accessibility to this data, the National Center
for Biotechnology Information (NCBI) has formulated
the Gene Expression Omnibus or GEO. It is a data
repository facility which includes data on gene expression
from varied sources.
8. Limitations of DNA Microarray
cross-hybridization artifacts,
poor quantification of lowly and highly expressed
genes
needing to know the sequence a priori
10. RNA-Seq
It uses next-generation sequencing to reveal the presence and quantity of RNA in a biological
sample at a given moment.
RNA-Seq is used to analyze the continuously changing cellular transcriptome. alternative
gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and
changes in gene expression over time, or differences in gene expression in different groups or
treatments.
Fragmented cDNA is sequenced, the resulting sequences (“reads”) are mapped and
compared to known genomes or transcriptomes.
In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include
total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling.
Three most widely used NGS platforms for RNA-seq are SOLiD and Ion Torrent, both
marketed by ThermoFisher, and Illumina’s HiSeq.
11. • Get your sample
• Lyse the cells and extract
RNA
• Convert the RNA to cDNA
• The cDNA pool get
sequenced
RNA Seq Protocol
12. Steps in RNA Seq
Library
preparation
Deep
Sequencing
Data
Analysis
13. description smallmiRNA Degradome-
seq
Digital gene
expression
Poly[A]-RNA
Seq
Total RNA seq
Library
preparation-
RNA selection
Size selection-
small RNA
Poly[A] tail
selection-
miRNA
Poly[A] tail
selection-
mRNA
Poly[A] tail
selection-
mRNA
rRNA depletion
-
mRNA+IncRNA
Sequencing
cycles
50 50 50 2×100 2×100
Single vs.
paired end
Single end Single end Single end Paired end Paired end
Data analysis discovery
expression
annotation
miRNA target
ID degradation
plots
Expression
annotation
discovery
expression
annotation
discovery
expression
annotation