Transcriptome analysis is the study of the set of all RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNAs produced in a population of cells. The transcriptome can vary between different cell types, body parts, and environmental conditions. Transcriptomics aims to catalogue all transcript species and quantify changing expression levels during development and in different conditions. The two main techniques are DNA microarrays and RNA sequencing. Microarrays involve fluorescent labeling and hybridization of samples to probe arrays, while RNA sequencing replaces hybridization with sequencing of individual cDNAs produced from target RNA.

1. Transcriptome analysis
Submitted by:-Rama Jumwal
M.sc.(biotechnology)
MAU20PBT010

2. Transcriptome
 A transcriptome is the set of all RNA molecules including mRNA,rRNA,tRNA
and other non coding RNAs(ncRNAs) produced in a population of cells
 The term can be applied to the total set of transcripts in a given organism,or
to the specific subset of transcripts present in a particular cell type under
specific conditions
 The transcriptome can vary in different parts of the body and may also differ
with external environment conditions

3. Positional information integration on
transcriptome

4. Transcriptomics
 Transcriptomics Is the study of rna in any of its forms
 A study of transcriptome elucidates the complex interactions which generally
take place among the transcripts before these are translated
 Also an independent analysis of transcriptome in thousand of cell types
,organs and tissues elucidates regulation of gene expression in time and space
through the study of relative abundance of different individual transcripts

5. Transcriptomics aims
 To catalogue all species of transcripts,including mRNAs,non codingRNAs and
small RNAs
 To determine the transcriptional structure of genes in terms of their start
sites,5’and 3’ ends, and other post transcriptional modifications
 To quantify the changing expression levels of each transcript during
development and under different conditions

6. Methods
There are two main transcriptomics techniques include
 DNA microarrays
 RNA sequencing

7. Microarrays
 “two colour” or cDNA or two channel microarrays
 “One colour or oligonucleotides or one channel microarrays

8. One channel microarray
 One channel microarrays are based on RNA of one sample which has been
labeled with a fluorescent dye and hybridized to a single array where millions
of copies of short oligonucleotide probes representing all known genes have
been synthesized
 After exposition to laser light and scanner the intensity of each location is
measured yielding a value which represents an absolute measure of
expression

9. Two colour microarrays
 Two colour microarrays are based on competitive hybridisation of two samples
each of which has been labelled with a different fluorescent dye e.g.red or
green
 After hybridisation the array is exposed to red and green laser light the array
emits fluorescent proportional to quantity of RNA
 The image produced is scanned yielding after some corrections a value which
represents the expression of one sample relative to other

11. RNA -sequencing
 RNA-sequencing transcriptomics replaces the hybridisation of nucleotides
probes with sequencing individual cDNAs produced from target RNA
 Emerging methods for these fully quantitative transcriptomic analysis have
the potential to overcome the limitations of microarray technology and there
are ongoing discussions about sequencing approaches ma replace microarrays
in the middle or even short term
 As a massively parallel process next generation sequencing (NGS) generates
hundreds of megabites to gigabites of nucleotide sequence output in a single
instrument run,depending on the platform

13. NGS technologies
 Roche 454
 Illumina genome analyzer sequencing
 Applied biosystems solid sequencing

15. References
 www.slideshre.net/mohamadoseinromena/transcriptomics
 www.slideshare.net/divyasrivastava17/transcriptomeanalysis
 https://d2cax41o7ahm5l.cloudfront.net
 Cell and molecular biology by P.K.gupta fourth revised edison /part 6 chapter-
69(genomics,transcriptomics,proteomics and metabolomics )