TY - JOUR
T1 - The transcriptional diversity of 25 Drosophila cell lines
AU - Cherbas, Lucy
AU - Willingham, Aarron
AU - Zhang, Dayu
AU - Yang, Li
AU - Zou, Yi
AU - Eads, Brian D.
AU - Carlson, Joseph W.
AU - Landolin, Jane M.
AU - Kapranov, Philipp
AU - Dumais, Jacqueline
AU - Samsonova, Anastasia
AU - Choi, Jeong-Hyeon
AU - Roberts, Johnny
AU - Davis, Carrie A.
AU - Tang, Haixu
AU - Van Baren, Marijke J.
AU - Ghosh, Srinka
AU - Dobin, Alexander
AU - Bell, Kim
AU - Lin, Wei
AU - Langton, Laura
AU - Duff, Michael O.
AU - Tenney, Aaron E.
AU - Zaleski, Chris
AU - Brent, Michael R.
AU - Hoskins, Roger A.
AU - Kaufman, Thomas C.
AU - Andrews, Justen
AU - Graveley, Brenton R.
AU - Perrimon, Norbert
AU - Celniker, Susan E.
AU - Gingeras, Thomas R.
AU - Cherbas, Peter
PY - 2011/2
Y1 - 2011/2
N2 - 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.
AB - 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.
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U2 - 10.1101/gr.112961.110
DO - 10.1101/gr.112961.110
M3 - Article
C2 - 21177962
AN - SCOPUS:79551596885
SN - 1088-9051
VL - 21
SP - 301
EP - 314
JO - Genome Research
JF - Genome Research
IS - 2
ER -