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Title: The transcriptional diversity of 25 Drosophila cell lines

Abstract

Drosophila melanogaster cell lines are important resources for cell biologists. In this article, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are ‘‘off’’ and survival/growth pathways ‘‘on.’’ Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination.more » No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common ‘‘cell line‘‘ gene expression pattern. We report the transcriptional profiles of 25 Drosophila melanogaster cell lines, principally by whole-genome tiling microarray analysis of total RNA, carried out as part of the modENCODE project. The data produced in this study add to our knowledge of the cell lines and of the Drosophila transcriptome in several ways. We summarize the expression of previously annotated genes in each of the 25 lines with emphasis on what those patterns reveal about the origins of the lines and the stability of spatial expression patterns. In addition, we offer an initial analysis of previously unannotated transcripts in the cell lines.« less

Authors:
 [1];  [2];  [1];  [3];  [1];  [1];  [4];  [4];  [2];  [2];  [5];  [1];  [1];  [6];  [1];  [7];  [2];  [6];  [6];  [6] more »;  [7];  [3];  [7];  [6];  [7];  [4];  [8];  [8];  [3];  [9];  [4];  [10];  [1] « less
  1. Indiana Univ., Bloomington, IN (United States)
  2. Affymetrix Inc., Santa Clara, CA (United States)
  3. University of Connecticut Health Center, Farmington, Connecticut (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Harvard Medical School, Boston, MA (United States)
  6. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York (United States)
  7. Washington Univ., St. Louis, MO (United States)
  8. Indiana University, Bloomington, Indiana (United States)
  9. Harvard Medical School, Boston, MA (United States); Howard Hughes Medical Institute, Boston, MA (United States)
  10. Affymetrix Inc., Santa Clara, CA (United States); Cold Spring Harbor Laboratory, Cold Spring Harbor, New York (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1056556
Report Number(s):
LBNL-5308E
Journal ID: ISSN 1088-9051
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Genome Research; Journal Volume: 21; Journal Issue: 2
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Cherbas, Lucy, Willingham, Aarron, Zhang, Dayu, Yang, Li, Zou, Yi, Eads, Brian D., Carlson, Joseph W., Landolin, Jane M., Kapranov, Philipp, Dumais, Jacqueline, Samsonova, Anastasia, Choi, Jeong-Hyeon, Roberts, Johnny, Davis, Carrie A., Tang, Haixu, van Baren, Marijke J., Ghosh, Srinka, Dobin, Alexander, Bell, Kim, Lin, Wei, Langton, Laura, Duff, Michael O., Tenney, Aaron E., Zaleski, Chris, Brent, Michael R., Hoskins, Roger A., Kaufman, Thomas C., Andrews, Justen, Graveley, Brenton R., Perrimon, Norbert, Celniker, Susan E., Gingeras, Thomas R., and Cherbas, Peter. The transcriptional diversity of 25 Drosophila cell lines. United States: N. p., 2010. Web. doi:10.1101/gr.112961.110.
Cherbas, Lucy, Willingham, Aarron, Zhang, Dayu, Yang, Li, Zou, Yi, Eads, Brian D., Carlson, Joseph W., Landolin, Jane M., Kapranov, Philipp, Dumais, Jacqueline, Samsonova, Anastasia, Choi, Jeong-Hyeon, Roberts, Johnny, Davis, Carrie A., Tang, Haixu, van Baren, Marijke J., Ghosh, Srinka, Dobin, Alexander, Bell, Kim, Lin, Wei, Langton, Laura, Duff, Michael O., Tenney, Aaron E., Zaleski, Chris, Brent, Michael R., Hoskins, Roger A., Kaufman, Thomas C., Andrews, Justen, Graveley, Brenton R., Perrimon, Norbert, Celniker, Susan E., Gingeras, Thomas R., & Cherbas, Peter. The transcriptional diversity of 25 Drosophila cell lines. United States. doi:10.1101/gr.112961.110.
Cherbas, Lucy, Willingham, Aarron, Zhang, Dayu, Yang, Li, Zou, Yi, Eads, Brian D., Carlson, Joseph W., Landolin, Jane M., Kapranov, Philipp, Dumais, Jacqueline, Samsonova, Anastasia, Choi, Jeong-Hyeon, Roberts, Johnny, Davis, Carrie A., Tang, Haixu, van Baren, Marijke J., Ghosh, Srinka, Dobin, Alexander, Bell, Kim, Lin, Wei, Langton, Laura, Duff, Michael O., Tenney, Aaron E., Zaleski, Chris, Brent, Michael R., Hoskins, Roger A., Kaufman, Thomas C., Andrews, Justen, Graveley, Brenton R., Perrimon, Norbert, Celniker, Susan E., Gingeras, Thomas R., and Cherbas, Peter. Wed . "The transcriptional diversity of 25 Drosophila cell lines". United States. doi:10.1101/gr.112961.110. https://www.osti.gov/servlets/purl/1056556.
@article{osti_1056556,
title = {The transcriptional diversity of 25 Drosophila cell lines},
author = {Cherbas, Lucy and Willingham, Aarron and Zhang, Dayu and Yang, Li and Zou, Yi and Eads, Brian D. and Carlson, Joseph W. and Landolin, Jane M. and Kapranov, Philipp and Dumais, Jacqueline and Samsonova, Anastasia and Choi, Jeong-Hyeon and Roberts, Johnny and Davis, Carrie A. and Tang, Haixu and van Baren, Marijke J. and Ghosh, Srinka and Dobin, Alexander and Bell, Kim and Lin, Wei and Langton, Laura and Duff, Michael O. and Tenney, Aaron E. and Zaleski, Chris and Brent, Michael R. and Hoskins, Roger A. and Kaufman, Thomas C. and Andrews, Justen and Graveley, Brenton R. and Perrimon, Norbert and Celniker, Susan E. and Gingeras, Thomas R. and Cherbas, Peter},
abstractNote = {Drosophila melanogaster cell lines are important resources for cell biologists. In this article, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are ‘‘off’’ and survival/growth pathways ‘‘on.’’ Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common ‘‘cell line‘‘ gene expression pattern. We report the transcriptional profiles of 25 Drosophila melanogaster cell lines, principally by whole-genome tiling microarray analysis of total RNA, carried out as part of the modENCODE project. The data produced in this study add to our knowledge of the cell lines and of the Drosophila transcriptome in several ways. We summarize the expression of previously annotated genes in each of the 25 lines with emphasis on what those patterns reveal about the origins of the lines and the stability of spatial expression patterns. In addition, we offer an initial analysis of previously unannotated transcripts in the cell lines.},
doi = {10.1101/gr.112961.110},
journal = {Genome Research},
number = 2,
volume = 21,
place = {United States},
year = {Wed Dec 22 00:00:00 EST 2010},
month = {Wed Dec 22 00:00:00 EST 2010}
}