title: The transcriptional diversity of 25 Drosophila cell lines.
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.
authors.affiliation: Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA. cherbas@indiana.edu
authors.forename: Lucy
authors.initials: L
authors.lastname: Cherbas
authors.forename: Aarron
authors.initials: A
authors.lastname: Willingham
authors.forename: Dayu
authors.initials: D
authors.lastname: Zhang
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.forename: Yi
authors.initials: Y
authors.lastname: Zou
authors.forename: Brian D
authors.initials: BD
authors.lastname: Eads
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.forename: Jane M
authors.initials: JM
authors.lastname: Landolin
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Dumais
authors.forename: Anastasia
authors.initials: A
authors.lastname: Samsonova
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
authors.forename: Johnny
authors.initials: J
authors.lastname: Roberts
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.forename: Marijke J
authors.initials: MJ
authors.lastname: van Baren
authors.forename: Srinka
authors.initials: S
authors.lastname: Ghosh
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobin
authors.forename: Kim
authors.initials: K
authors.lastname: Bell
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: Laura
authors.initials: L
authors.lastname: Langton
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.forename: Aaron E
authors.initials: AE
authors.lastname: Tenney
authors.forename: Chris
authors.initials: C
authors.lastname: Zaleski
authors.forename: Michael R
authors.initials: MR
authors.lastname: Brent
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Kaufman
authors.forename: Justen
authors.initials: J
authors.lastname: Andrews
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.forename: Norbert
authors.initials: N
authors.lastname: Perrimon
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.forename: Peter
authors.initials: P
authors.lastname: Cherbas
mesh_terms: D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D004331:Drosophila melanogaster / Q000235:genetics*; D005091:Exons; D005260:Female; D020869:Gene Expression Profiling; D014644:Genetic Variation; D008297:Male; D008969:Molecular Sequence Data; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors