Expressed Sequence Tags: Normalization and subtraction of cDNA libraries

Marcelo Bento Soares, Maria De Fatima Bonaldo, Jeremiah D. Hackett, Debashi Bhattacharya

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Abstract

Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. ESTs have also become particularly important with recent expanded efforts in complete genome sequencing of understudied, nonmodel eukaryotes such as protists and algae. For these projects, ESTs provide an invaluable source of data for gene identification and prediction of exon-intron boundaries. The generation of EST data, although straightforward in concept, requires nonetheless great care to ensure the highest efficiency and return for the investment in time and funds. To this end, key steps in the process include generation of a normalized cDNA library to facilitate a high gene discovery rate followed by serial subtraction of normalized libraries to maintain the discovery rate. Here we describe in detail, protocols for normalization and subtraction of cDNA libraries followed by an example using the toxic dinoflagellate Alexandrium tamarense.

Original languageEnglish (US)
Title of host publicationExpressed Sequence Tags (ESTs)
Subtitle of host publicationGeneration and Analysis
PublisherHumana Press Inc.
Pages109-123
Number of pages15
ISBN (Print)9781588297594
DOIs
StatePublished - Jan 1 2009
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume533
ISSN (Print)1064-3745

Fingerprint

Expressed Sequence Tags
Gene Library
Genetic Association Studies
Eukaryota
Dinoflagellida
Poisons
Information Storage and Retrieval
Financial Management
Introns
Exons
Genome
Gene Expression
Genes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Soares, M. B., De Fatima Bonaldo, M., Hackett, J. D., & Bhattacharya, D. (2009). Expressed Sequence Tags: Normalization and subtraction of cDNA libraries. In Expressed Sequence Tags (ESTs): Generation and Analysis (pp. 109-123). (Methods in Molecular Biology; Vol. 533). Humana Press Inc.. https://doi.org/10.1007/978-1-60327-136-3_6
Soares, Marcelo Bento ; De Fatima Bonaldo, Maria ; Hackett, Jeremiah D. ; Bhattacharya, Debashi. / Expressed Sequence Tags : Normalization and subtraction of cDNA libraries. Expressed Sequence Tags (ESTs): Generation and Analysis. Humana Press Inc., 2009. pp. 109-123 (Methods in Molecular Biology).
@inbook{9088f0f6aea14d8db6b11a2469860d69,
title = "Expressed Sequence Tags: Normalization and subtraction of cDNA libraries",
abstract = "Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. ESTs have also become particularly important with recent expanded efforts in complete genome sequencing of understudied, nonmodel eukaryotes such as protists and algae. For these projects, ESTs provide an invaluable source of data for gene identification and prediction of exon-intron boundaries. The generation of EST data, although straightforward in concept, requires nonetheless great care to ensure the highest efficiency and return for the investment in time and funds. To this end, key steps in the process include generation of a normalized cDNA library to facilitate a high gene discovery rate followed by serial subtraction of normalized libraries to maintain the discovery rate. Here we describe in detail, protocols for normalization and subtraction of cDNA libraries followed by an example using the toxic dinoflagellate Alexandrium tamarense.",
author = "Soares, {Marcelo Bento} and {De Fatima Bonaldo}, Maria and Hackett, {Jeremiah D.} and Debashi Bhattacharya",
year = "2009",
month = "1",
day = "1",
doi = "10.1007/978-1-60327-136-3_6",
language = "English (US)",
isbn = "9781588297594",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "109--123",
booktitle = "Expressed Sequence Tags (ESTs)",

}

Soares, MB, De Fatima Bonaldo, M, Hackett, JD & Bhattacharya, D 2009, Expressed Sequence Tags: Normalization and subtraction of cDNA libraries. in Expressed Sequence Tags (ESTs): Generation and Analysis. Methods in Molecular Biology, vol. 533, Humana Press Inc., pp. 109-123. https://doi.org/10.1007/978-1-60327-136-3_6

Expressed Sequence Tags : Normalization and subtraction of cDNA libraries. / Soares, Marcelo Bento; De Fatima Bonaldo, Maria; Hackett, Jeremiah D.; Bhattacharya, Debashi.

Expressed Sequence Tags (ESTs): Generation and Analysis. Humana Press Inc., 2009. p. 109-123 (Methods in Molecular Biology; Vol. 533).

Research output: Chapter in Book/Report/Conference proceedingChapter

TY - CHAP

T1 - Expressed Sequence Tags

T2 - Normalization and subtraction of cDNA libraries

AU - Soares, Marcelo Bento

AU - De Fatima Bonaldo, Maria

AU - Hackett, Jeremiah D.

AU - Bhattacharya, Debashi

PY - 2009/1/1

Y1 - 2009/1/1

N2 - Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. ESTs have also become particularly important with recent expanded efforts in complete genome sequencing of understudied, nonmodel eukaryotes such as protists and algae. For these projects, ESTs provide an invaluable source of data for gene identification and prediction of exon-intron boundaries. The generation of EST data, although straightforward in concept, requires nonetheless great care to ensure the highest efficiency and return for the investment in time and funds. To this end, key steps in the process include generation of a normalized cDNA library to facilitate a high gene discovery rate followed by serial subtraction of normalized libraries to maintain the discovery rate. Here we describe in detail, protocols for normalization and subtraction of cDNA libraries followed by an example using the toxic dinoflagellate Alexandrium tamarense.

AB - Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. ESTs have also become particularly important with recent expanded efforts in complete genome sequencing of understudied, nonmodel eukaryotes such as protists and algae. For these projects, ESTs provide an invaluable source of data for gene identification and prediction of exon-intron boundaries. The generation of EST data, although straightforward in concept, requires nonetheless great care to ensure the highest efficiency and return for the investment in time and funds. To this end, key steps in the process include generation of a normalized cDNA library to facilitate a high gene discovery rate followed by serial subtraction of normalized libraries to maintain the discovery rate. Here we describe in detail, protocols for normalization and subtraction of cDNA libraries followed by an example using the toxic dinoflagellate Alexandrium tamarense.

UR - http://www.scopus.com/inward/record.url?scp=67650641732&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67650641732&partnerID=8YFLogxK

U2 - 10.1007/978-1-60327-136-3_6

DO - 10.1007/978-1-60327-136-3_6

M3 - Chapter

C2 - 19277560

AN - SCOPUS:67650641732

SN - 9781588297594

T3 - Methods in Molecular Biology

SP - 109

EP - 123

BT - Expressed Sequence Tags (ESTs)

PB - Humana Press Inc.

ER -

Soares MB, De Fatima Bonaldo M, Hackett JD, Bhattacharya D. Expressed Sequence Tags: Normalization and subtraction of cDNA libraries. In Expressed Sequence Tags (ESTs): Generation and Analysis. Humana Press Inc. 2009. p. 109-123. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60327-136-3_6