Screening of cDNA libraries on glass slide microarrays

Dave K Berger, Bridget G Crampton, Ingo Hein, Wiesner Vos

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

4 Citations (Scopus)

Abstract

A quantitative screening method was developed to evaluate the quality of cDNA libraries constructed by suppression subtraction hybridization (SSH) or other enrichment techniques. The SSH technique was adapted to facilitate screening of the resultant library on a small number of glass slide microarrays. A simple data analysis pipeline named SSHscreen using "linear models for microarray data" (limma) functions in the R computing environment was developed to identify clones in the cDNA libraries that are significantly differentially expressed, and to determine if they were rare or abundant in the original treated sample. This approach facilitates the choice of clones from the cDNA library for further analysis, such as DNA sequencing, Northern blotting, RT-PCR, or detailed expression profiling using a custom cDNA microarray. Furthermore, this strategy is particularly useful for studies of nonmodel organisms for which there is little genome sequence information.

Original languageEnglish
Title of host publicationMicroarrays
Subtitle of host publicationApplications and Data Analysis
EditorsJang B. Rampal
PublisherHumana Press
Pages177-203
Number of pages27
Volume2
Edition2nd
ISBN (Electronic)9781597453042
DOIs
Publication statusPublished - 2007

Publication series

NameMethods in Molecular Biology (Clifton, N.J.)
PublisherSpringer Verlag
Volume382
ISSN (Print)1064-3745

Fingerprint

Gene Library
Glass
Clone Cells
Subtraction Technique
Oligonucleotide Array Sequence Analysis
DNA Sequence Analysis
Northern Blotting
Libraries
Linear Models
Genome
Polymerase Chain Reaction

Keywords

  • Cloning, Molecular
  • Gene Expression Profiling/methods
  • Gene Library
  • Glass/chemistry
  • Nucleic Acid Hybridization/methods
  • Oligonucleotide Array Sequence Analysis/methods
  • Pennisetum/genetics
  • Plant Leaves/metabolism
  • Plant Proteins/genetics
  • RNA, Plant/genetics
  • Suppression, Genetic/genetics

Cite this

Berger, D. K., Crampton, B. G., Hein, I., & Vos, W. (2007). Screening of cDNA libraries on glass slide microarrays. In J. B. Rampal (Ed.), Microarrays: Applications and Data Analysis (2nd ed., Vol. 2, pp. 177-203). (Methods in Molecular Biology (Clifton, N.J.); Vol. 382). Humana Press. https://doi.org/10.1007/978-1-59745-304-2_12
Berger, Dave K ; Crampton, Bridget G ; Hein, Ingo ; Vos, Wiesner. / Screening of cDNA libraries on glass slide microarrays. Microarrays: Applications and Data Analysis. editor / Jang B. Rampal. Vol. 2 2nd. ed. Humana Press, 2007. pp. 177-203 (Methods in Molecular Biology (Clifton, N.J.)).
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Berger, DK, Crampton, BG, Hein, I & Vos, W 2007, Screening of cDNA libraries on glass slide microarrays. in JB Rampal (ed.), Microarrays: Applications and Data Analysis. 2nd edn, vol. 2, Methods in Molecular Biology (Clifton, N.J.), vol. 382, Humana Press, pp. 177-203. https://doi.org/10.1007/978-1-59745-304-2_12

Screening of cDNA libraries on glass slide microarrays. / Berger, Dave K; Crampton, Bridget G; Hein, Ingo; Vos, Wiesner.

Microarrays: Applications and Data Analysis. ed. / Jang B. Rampal. Vol. 2 2nd. ed. Humana Press, 2007. p. 177-203 (Methods in Molecular Biology (Clifton, N.J.); Vol. 382).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

TY - CHAP

T1 - Screening of cDNA libraries on glass slide microarrays

AU - Berger, Dave K

AU - Crampton, Bridget G

AU - Hein, Ingo

AU - Vos, Wiesner

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N2 - A quantitative screening method was developed to evaluate the quality of cDNA libraries constructed by suppression subtraction hybridization (SSH) or other enrichment techniques. The SSH technique was adapted to facilitate screening of the resultant library on a small number of glass slide microarrays. A simple data analysis pipeline named SSHscreen using "linear models for microarray data" (limma) functions in the R computing environment was developed to identify clones in the cDNA libraries that are significantly differentially expressed, and to determine if they were rare or abundant in the original treated sample. This approach facilitates the choice of clones from the cDNA library for further analysis, such as DNA sequencing, Northern blotting, RT-PCR, or detailed expression profiling using a custom cDNA microarray. Furthermore, this strategy is particularly useful for studies of nonmodel organisms for which there is little genome sequence information.

AB - A quantitative screening method was developed to evaluate the quality of cDNA libraries constructed by suppression subtraction hybridization (SSH) or other enrichment techniques. The SSH technique was adapted to facilitate screening of the resultant library on a small number of glass slide microarrays. A simple data analysis pipeline named SSHscreen using "linear models for microarray data" (limma) functions in the R computing environment was developed to identify clones in the cDNA libraries that are significantly differentially expressed, and to determine if they were rare or abundant in the original treated sample. This approach facilitates the choice of clones from the cDNA library for further analysis, such as DNA sequencing, Northern blotting, RT-PCR, or detailed expression profiling using a custom cDNA microarray. Furthermore, this strategy is particularly useful for studies of nonmodel organisms for which there is little genome sequence information.

KW - Cloning, Molecular

KW - Gene Expression Profiling/methods

KW - Gene Library

KW - Glass/chemistry

KW - Nucleic Acid Hybridization/methods

KW - Oligonucleotide Array Sequence Analysis/methods

KW - Pennisetum/genetics

KW - Plant Leaves/metabolism

KW - Plant Proteins/genetics

KW - RNA, Plant/genetics

KW - Suppression, Genetic/genetics

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DO - 10.1007/978-1-59745-304-2_12

M3 - Chapter (peer-reviewed)

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T3 - Methods in Molecular Biology (Clifton, N.J.)

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Berger DK, Crampton BG, Hein I, Vos W. Screening of cDNA libraries on glass slide microarrays. In Rampal JB, editor, Microarrays: Applications and Data Analysis. 2nd ed. Vol. 2. Humana Press. 2007. p. 177-203. (Methods in Molecular Biology (Clifton, N.J.)). https://doi.org/10.1007/978-1-59745-304-2_12