NDLI: The transcriptional diversity of 25 Drosophila cell lines.

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The transcriptional diversity of 25 Drosophila cell lines.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	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
Description	Country affiliation: United States Author Affiliation: Cherbas L ( Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA. cherbas@indiana.edu)
Abstract	Drosophila melanogaster cell lines are important resources for cell biologists. Here, 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.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.112961.110
Journal	Genome Research
Issue Number	2
Volume Number	21
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2011-02-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Drosophila Melanogaster Genetics Genetic Variation Transcription, Genetic Animals Cell Line Cluster Analysis Exons Gene Expression Profiling Molecular Sequence Data Signal Transduction Transcription Factors Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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