Cell Lines

Abstract

We review the properties and uses of cell lines in Drosophila research, emphasizing the variety of lines, the large body of genomic and transcriptional data available for many of the lines, and the variety of ways the lines have been used to provide tools for and insights into the developmental, molecular, and cell biology of Drosophila and mammals.

1. Introduction

In this paper we describe the range of Drosophila cell lines that are currently available, and the ways in which they are useful for research. Most lines are distributed by the Drosophila Genomics Resource Center (DGRC), whose staff includes the authors of this paper. The DGRC website (https://dgrc.cgb.indiana.edu) publishes regularly updated descriptions of each of the lines, along with specific, individualized culture requirements and we will not reproduce that material here. Instead, we offer general guidelines and suggestions for the use of the lines. For a different, though dated, perspective, we recommend Echalier’s monograph on Drosophila cell lines [1].

2. The uses of cell lines in Drosophila developmental biology

Drosophila cell lines have been available for almost 50 years, and have progressively become more integral to the toolkit for Drosophila research. Permanent cell lines are, without question, not normal cells; one must use common sense in choosing the experiments for which they are suitable and validate the results in vivo. Substantial genomic rearrangements have occurred in all cell lines [2,3], and they do not behave identically to the cells from which they are derived. But thoughtful use of cell lines rarely gives misleading results, and often provides invaluable insights. Table 1 lists a series of examples of the successful use of Drosophila cell lines to support this claim. Several points are worth emphasizing here:

Table 1.

Examples of uses of cell lines

Type of application	Examples
Source of large quantity of homogeneous material for preparation of extract or protein purification	Isolation of non-muscle myosin from S2, S3, and Kc 1
	Isolation and characterization of basement membrane components from S2, Kc, and DM 2–4
	Preparation of cell-free transcription system from Kc 5,6
Studies of basic cellular mechanisms	Processing and function of siRNAs, miRNAs, piRNAs 4–9
	Alignment of chromosomes at the metaphase plate 10
	Somatic cell chromosome pairing 11
	Validation of computationally predicted splice enhancers 12
	Studies of cytoskeletal mechanics using fluorescent- or epitope-tagged markers 13–23
Isolation and characterization of purified transgene products following transformation	Atlantic salmon serum C-type lectin 24
	human clotting factor IX 25
In vivo test tubes for detecting interaction and properties of transgenes and their products	“promoter-bashing” studies of (1) miRNA genes 26, nkd 27, chicken GAS41 28, mammalian erythroid promoters 29 (all in S2)
	Examination of surveillance systems for splicing errors using the human β-globin gene 30
	Characterization of a Drosophila muscarinic acetylcholine receptor 31
	Description of an inhibitory factor for transcription of mammalian NGFI-A 32
	Examination of interactions between Notch and its ligands Delta and Serrate 33,34
	Identification of ecdysone response elements in hsp27 35,36 and Eip71CD 37 and functional elements in the ecdysone receptor 38
Dissection of pathways by RNAi screening in a suitable cell line	(see Mohr39 for details)
Study of pathogens, using Drosophila cells as a heterologous host	Yersinia enterocolitica40
	Plasmodium 41
	Rabies virus 42
Studies of distinct properties of individual lines	mbn2 and S2 as models for studies of the fly immune response 43–43
	The long axon-like processes of the CNS line BG2-c2 for studies of mitochondrial transport 47
	ML-DmD8 as a model for myogenesis 48
	ML-DmD17-c3 as a model for cell migration 49
Genomic analysis, using modENCODE data as baseline	Demonstration that band, interband, and band/interband boundary properties are conserved between polytene and diploid cells 50–52
	Demonstration that HSF binds preferentially in regions of open chromatin structure 53
	Demonstration that X-chromosome binding of the dosage compensation complex MSL is targeted to open chromatin structures, using the male lines S2-DRSC and ML-DmBG3-c2 and the female line Kc167 54
Secretion of labile signaling proteins for use in vitro	Wg 55
	Fog 56

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1. Cell line work complements genetic and developmental experiments in flies. The following are just three of many possible examples: Dominant-negative versions of the ecdysone receptor subunit EcR that were identified by transient expression experiments in Kc cells [4] have become standard tools for genetic studies of the ecdysone pathways in flies [5–10]. Interactions of S2 cells expressing Notch and its receptors [11] led to an extended study of the Notch pathway with complementary experiments in S2 cells and flies [12–15]. The recent identification in S2 cells of a receptor for the secreted morphogen Fog led to the verification of that receptor as a critical component of Fog function in gastrulation [16].

2. Because cell lines provide large amounts of homogeneous tissue which can easily be manipulated, they make possible molecular and biochemical work that is otherwise extremely difficult in an organism as small and complex as Drosophila. A recent modENCODE meta-analysis [17] illustrates this point forcefully. Predictive models could be built only for cell lines because it was only in the cell lines that histone marks, polymerase localization, origins of replication, and transcription could be aligned in a single cell type. Until we can perform single-cell analyses of transcription and chromatin immunoprecipitation, we must rely on cell lines as an alternative. Table 1 cites several additional studies making use of the same approach.

3. Cell lines are frequently used in studies of human genes or pathogens, offering an alternate environment which complements observations in the normal host. Several examples of such studies are listed in the Table 1.

The utility of cell lines has increased enormously in the past decade for two reasons: The Drosophila Genomics Resource Center (DGRC), established in 2003, has made over 150 diverse cell lines available to the community; and the NIH-sponsored project Model Organism Encyclopedia of DNA elements (modENCODE, 2007–2012) produced an enormous amount of high quality, publicly available genomic data on Drosophila cell lines, including chromatin marks [18–20], insulators [21], replication origins and timing [22,23], and histone variants [24] for 4 “core” cell lines (the embryonic lines Kc167 and S2-DRSC, the wing disc line CME Cl.8+, and the CNS line ML-DmBG3-c2), plus transcription data for these 4 and 23 additional cell lines [25–28].

3. Available cell lines

Drosophila cell lines were originally made from embryos at various stages of development [29–32]; this continues to be the most common starting material for generating new lines [33,34]. Several of these lines were observed to have properties characteristic of hemocytes [35,36], but global transcriptome analysis shows a remarkable diversity among the embryonic lines (see below). Cell lines have also been made from embryos of about a dozen non-melanogaster species of Drosophila [37,38]. During the 1980s, cell lines were established from two tissues of late third-instar larvae: imaginal discs [39,40] and the central nervous system [41]. A cell line was also established from tumorous blood cells of larvae mutant for l(2)mbn [42]. The cell line fGS/OSS was made from a mixture of germ cells and somatic sheath cells of adult ovaries mutant for bam [43]; two lines containing only the sheath cells were then derived from fGS/OSS [43,44]. While Drosophila cell lines have traditionally been made without benefit of the malignant transformation that underlies the establishment of most mammalian cell lines, the Simcox lab has recently shown that the over-expression of specific oncogenes or null mutations in specific tumor-suppressor genes in fly embryos greatly enhances the efficiency of the establishment of new cell lines [33,45].

We will not attempt here to describe techniques for the production of new cell lines from flies. For help on this subject, we refer the reader to a Miyake lab protocol available on the DGRC website [46], and to the laboratories of Amanda Simcox and Alain Debec, where new cell lines continue to be established.

Some lines, particularly the embryonic line S2, have been stably transformed to produce large numbers of variants suitable for a variety of specialized purposes. Some of these transformants are listed in Table 1, and a few examples of transformed lines expressing fluorescent markers are illustrated in Fig. 1. In addition, embryonic lines have been made from mutant flies to serve a variety of purposes; a recent example is a series of lines made from embryos homozygous for both a gene-trap transposon that tags the tubulin-binding protein Jupiter with GFP and a null mutation in the centrosome-organizing gene Sas- 4; these lines permit the study of the centrosome’s role using real-time imaging of the tubulin cytoskeleton [47].

Figure 1.

Three stable transformants expressing GFP-labeled tracers. (A) ML-DmBG3-c2-Mt-GFP-Act5C, in which a GFP-tagged actin is expressed in a CNS cell line. (B) S2-act-GFP-alphaTub84B, in which a GFPtagged tubulin is expressed in S2 cells. (C) S2-GFP-SKL, in which GFP is targeted to peroxisomes in S2 cells. All 3 lines are unpublished, but are available from the DGRC. Line A was made by L. Cherbas, using a reporter plasmid provided by S. L. Rogers, B was made by Gohta Goshima and S.L. Rogers, and C was made in the S. L. Rogers laboratory. Photographs of living cells were taken by Jared Bass.

Transcriptome data from 25 cell lines are summarized in Figure 2, which shows a principal component analysis of gene expression levels for the subset of genes which show most variation among the lines [25]. In this graphical representation, the distance between 2 cell lines represents the extent of difference in the expression of those genes that are most responsible for the variation among cell lines. Several striking conclusions can be drawn from this analysis: (1) Multiple cell lines made from the same tissue show striking variation. This is true even for multiple lines made in the same laboratory from the same genetic stock, e.g. S1, S2R+, and S3 [30]. Indeed, 3 different isolates from the original Schneider’s line 2 (S2R+, S2-DRSC, and Sg4) show widely different patterns of transcription, indicating substantial divergence during long periods of proliferation in separate laboratories. By contrast, sibling clones that have undergone very limited growth since cloning (D20-c2 and D20-c5) are quite similar. All of the independent lines are distinct in their transcriptional properties, although imaginal disc-derived lines are more similar to each other than to embryo-derived lines. The distinct character of the individual lines is supported by the observation that each wing disc-derived line shows expression of spatial markers characteristic of a particular region of the wing disc, and those regions are different for each of the wing disc-derived lines that were examined [25].

Figure 2.

Principal component analysis of transcriptomes from 25 diverse cell lines. (Figure reproduced from reference [25]).

Only about 3000 genes are expressed at detectable levels in all the lines included in the modENCODE study [25]. A few are universally expressed in all cell lines at levels higher than are seen in the intact organism and are therefore presumably associated with proliferation and immortality; this list includes the anti-apoptotic miRNA gene bantam, whose functions suggest a role in the establishment of permanent cell lines, and others, like Karl, of unknown function [25,26]. Overall, the cell lines behave as if they retain the transcriptional properties of the founder cells from which they are derived, with a superimposed set of transcriptional properties characteristic of cell lines.

At the level of DNA variations, all of the cell lines have substantial levels of aneuploidy. The establishment of cell lines is associated with an explosive proliferation of transposable elements [48]. Individual cell lines show distinct patterns of copy number variation throughout the genome, though here the variation between isolates of the same line are much less pronounced than the variations among lines [2]. Remarkably, regions of abnormally high or low copy number in cell line genomes often correspond to the locations of oncogenes or tumor suppressor genes, respectively. This observation nicely complements the discovery that changes in oncogene and tumor-suppressor gene expression can be used to promote the establishment of cell lines (see above). Note that all the lines are subject to occasional, usually temporary, doubling of their chromosome content in response to variations in culture conditions [49]; this is superimposed on the more fine-grained genomic alterations described above.

Taken together, the DNA and transcriptome analyses suggest that DNA rearrangements take place predominantly during the establishment of cell lines and play an essential role in the transition to immortality, while changes in patterns of gene expression may occur well after the establishment of a line. The transcriptional pattern usually resembles the pattern seen in some subset of cells in normal Drosophila; it is unclear whether this reflects the actual origin of a cell line, or is merely a consequence of the fact that the expression of only certain combinations of spatially limited genes is compatible with survival of the cell.

4. General techniques for Drosophila cell culture

4.1 General considerations

The major features of Drosophila cell culture that differ from mammalian cell culture are the temperature and the pH of the culture medium. Most Drosophila lines are grown at 25° and at a pH around 6.5, consistent with the temperature requirements of Drosophila and the pH of its hemolymph. Because the desired temperature is near ambient temperature, a refrigerated incubator is standard, though the cell lines, like the flies from which they are derived, can be maintained at room temperature in buildings where temperature fluctuations are not excessive. Because of the relatively low pH of the medium, the bicarbonate/CO₂ buffering system that is standard for mammalian cell culture is not used, and Drosophila cell culture does not require a CO₂ incubator. In addition, because Drosophila cells do not harbor human pathogens, it is acceptable to use a simple pharmaceutical laminar flow hood, rather than the biosafety cabinet that is required for mammalian cell culture. People who have experience with mammalian cell culture will find Drosophila cells – at least the commonly used lines -- relatively easy to maintain. Cells can be grown in tissue culture grade plastic petri dishes or flasks; we have also had success growing large volumes of the standard lines in spinner flasks, but we do not know whether the more delicate lines can be grown this way. For routine work, we grow our cultures in petri dishes, which are kept in airtight food storage boxes inside the incubator to maintain humidity.

People who are new to cell culture altogether should be reminded that the standards of sterility and cleanliness are much more stringent for cell culture than for the routine microbiology as practiced in a molecular biology laboratory. For sterility procedures, glassware cleanliness, water quality and general procedure of maintaining Drosophila cell culture, refer to the DGRC website and to previously published reviews [50]. In the following sections, we highlight some of the most common problems that arise in laboratories to which the DGRC sends cell lines. For specific information about individual lines, refer to the DGRC website.

4.2 Media

Most Drosophila cell lines can be grown in a few basic medium formulations, but the individual lines have specific requirements. Insulin is required by some lines, and is toxic to others. Some lines require a crude extract from flies, and occasional lines require other additions to the medium. As a rule, all the cell lines require that the medium be supplemented with heat-treated fetal calf serum, though the concentration of serum varies somewhat, and an occasional line is able to grow in one of the serum-free media have been developed for baculovirus culture in lepidopteran cell lines. The more delicate lines are very particular about the source of the serum. Many laboratories routinely supplement their media with antibiotics (usually penicillin and streptomycin), but we have found this to be unnecessary if good sterile technique is used. Requirements for the individual lines, recipes for media, and suggestions for buying fetal calf serum can be found on the DGRC website.

4.3 Contamination

Drosophila cell lines are subject to the same contamination problems (bacteria, fungi, yeasts) as any other cell cultures. Some (perhaps most) of the lines contain virus-like particles of mysterious origin [51–53] which do not appear to replicate or harm the cells. We have heard sporadic reports of possible viral or mycoplasma infections, but do not know of any verified cases. Unhealthy cell cultures, including cells that are recovering from thawing or from being shipped, often contain small black particles of debris (perhaps mitochondria from broken cells) which may move by Brownian motion and look a lot like bacteria. If the particles do not proliferate and the cells continue to grow, the particles are debris, not bacteria, and they can be ignored.

4.4 Culture conditions

Cell lines vary in their rates of proliferation, and in the range in which they maintain exponential growth. S2 and Kc, the most commonly used and most robust of the Drosophila lines both grow with a doubling time of about 1 day, and grow exponentially in the range 5×10⁵ – 1×10⁷ cells/ml [50]. Note that Drosophila cells are approximately an order of magnitude smaller than mammalian cells, as befits their smaller genome size, and their exponential range measured as mass of cells per ml is similar to that of mammalian cells. Many of the lines have a narrower range of exponential growth, and doubling times may be as long as a week or more. To keep the culture healthy, keep the cell density within the exponential range. In general, we recommend resuspending the cells in the medium in which they have been growing, and then simply diluting the cell suspension in an appropriate volume of fresh medium.

Many Drosophila lines adhere weakly, if at all, to the substrate, and can easily be resuspended by pipetting up and down using a serological pipet. For more strongly adhering lines, we recommend the following techniques, in order of increasing force of resuspension: blowing medium at the cells from a Pasteur pipet, scraping with a cell scraper, and, if all else fails, trypsinization.

4.5 Frozen stocks

The freezing, storage, and thawing of cells require care; specific protocols may be downloaded from the DGRC website. The important points are the following: Cells are frozen by putting cells from a healthy culture into a protective freezing medium and gradually lowering the temperature to −80°C. They should then be transferred to liquid nitrogen for permanent storage. The cells may be stored for short periods at −80°C, but at this temperature they degrade relatively quickly (half-life of weeks or months). In liquid nitrogen (−196°C) they are stable indefinitely. Repeated or prolonged warming (e.g. frequent removal of a box of frozen ampoules from liquid nitrogen to retrieve samples, or shipment of frozen ampoules on dry ice) reduces the viability of the frozen cells; the extent of the damage depends on the cell line, with the most robust lines (Kc and S2) being most impervious to the effects of these temperature changes. For this reason the DGRC no longer ships imaginal disc and CNS lines as frozen ampoules on dry ice. We also strongly recommend that when a laboratory receives a dry ice shipment of frozen cells, the cells be immediately thawed, rather than being stored at −80°C or on liquid nitrogen; the already damaged cells would only be further damaged by either continued storage at −80°C or by another cycle through liquid nitrogen.

5. Some specific techniques

5.1. Transfection and transformation

Specific protocols for many of the procedures described in this section can be found in published reviews [50,54–57].

5.1.1. Approaches

5.1.1.1. Transient expression

This approach consists of transfecting a population of cells and analyzing them within hours or days. It is fast and easy, widely used, and satisfactory for many purposes. The disadvantages are that the population is not uniform, in most cases the majority of cells do not express the transfected DNA, and there is no way to know the number of copies or the chromatin structure of the transfected DNA.

5.1.1.2. Stable transformation leading to extended tandem arrays

Almost all stably transformed Drosophila cell lines were made by transfecting a transgene and a drug resistance marker, either on a single plasmid or on two co-transfected plasmids, and then using the corresponding drug to select stably transfected cells. Most of these transformed lines are simply selected populations, and the individual cells vary somewhat in their properties (see Fig. 1C). One can, with a little more effort, clone the selected cells; the resulting clonal lines are generally more nearly homogeneous, and individual clones may differ sufficiently in their properties that the experimenter can choose a clone most suitable for his purposes. The molecular properties of such transformants have been described carefully only for S2 cells [54,58]; in these cells the transfected plasmids form long tandem arrays by homologous recombination. These arrays, often containing 1000 or more plasmid copies, are subsequently inserted into the genome. Although transformed clones can be analyzed, they are not entirely stable (probably because of recombination events within the arrays), and it is very likely that the chromatin structure of these long repeated sequences adopts heterochromatic properties. Despite these deficiencies, such stably transformed lines have proved very useful. Most of the experimental systems described in Table 1 involve either transient expression or stable transformation of this type.

5.1.1.3. Transposons

Single copies of a DNA fragment can be inserted into more-or-less random genomic sites using the same transposable elements that are used for this purpose in flies. This approach has been used successfully in Kc cells with P elements [59] and in S2 cells with Minos [60]. It is not frequently used because it is laborious; the transformed cells must be cloned, and the clones must analyzed to identify transformants carrying a single transposon and to map the insertion site of the transposon. The transposon must carry a selectable or visible marker for which a single copy is sufficient to provide rescue or visibility; act-DHFR (methotrexate resistance) [59], a mutant copy of RpII215 (α-amanitin resistance) [59,61], act-eGFP [62], and mCherry in combination with a suitable genomic promoter [60] meet this requirement. We use electroporation for generating single transposon insertions in Kc cells, because it permits the use of very low concentrations of the transposon and transposase plasmid in the transfection, maximizing the frequency of single insertions [62].

5.1.1.4. Targeted insertion

φC31 integrase-mediated insertion and replacement are widely used in Drosophila [63–65]. φC31 integrase is used to target attB-containing plasmids to endogenous pseudo-attP sites in mammalian cells [66] and to inserted attP sites in a variety of cell types [67,68]. The basic steps have been shown to occur in cell lines from Drosophila and other insects [60,69]. An effort is now underway at the DGRC to make tools for φC31 integrase-mediated targeting in cell lines generally available.

5.1.1.5. Baculoviruses

These viruses are commonly used for expression of transgenes in lepidopteran cell lines [70]. Although they do not replicate in Drosophila cells, baculoviruses that have been replicated in lepidopteran cells can infect Drosophila cells [71,72], and do so in virtually all Drosophila cell lines at very high efficiency [73]. The construction of baculovirus vectors and the preparation of a stock of the packaged virus are time-consuming, but if one plans to do repeated transient expression experiments with a single transgene construct, or requires high transfection efficiency in one of the difficult-to-transform imaginal disc or CNS lines, the baculovirus system may be very helpful. Note that with baculovirus, the DNA is introduced by infection; none of the transfection techniques described below is required.

5.1.2. Transfection techniques

5.1.2.1

Calcium phosphate-DNA co-precipitation is the oldest commonly used technique for transfection into cultured cells, both mammalian [74] and Drosophila [75]. This technique has been almost totally replaced by more modern techniques which generally provide transfection of a wider range of cell lines, higher transfection efficiency, lower toxicity, and higher reproducibility.

5.1.2.2

Electroporation works well on many cell lines; in those lines for which both calcium phosphate and electroporation work, the efficiency of the transfection is similar (measured either as per cent of cells that express a transfected reporter or as the amount of a reporter that is assayed in an extract of a transfected population). Electroporation is easy to do, but requires specialized equipment. It can be of particular value for generating single transposon insertions because, unlike other transfection techniques, electroporation produces uptake in approximate proportion to the amount of input DNA over a very large range of DNA concentrations [76].

5.1.2.3

Lipofection and other lipid-based systems have become the dominant method for transfecting cultured animal cells in the past 25 years [77]. There are now many commercially available products for this purpose; those that we have tested give very similar results. Both electroporation and lipofection generally give much higher transfection efficiency with embryonic lines than with imaginal disc or CNS lines [78].

5.1.3. Promoters

In stably transformed cells, it is often desirable to use an inducible promoter to avoid toxic effects of high-level expression of a transgene while the cells are growing. A Cu⁺⁺-inducible metallothionein promoter derived from MtnA [79] is commonly used for this purpose, though Cu⁺⁺ treatment has subtle toxic effects on the cells [49]. The hsp70 promoter that is commonly used in fly transformants is also an option, though translational repression by heat shock interferes with heat-shock induction of the transgene product [58]. It is to be hoped that new and better inducible promoters for use in Drosophila cell lines will soon be developed, with fewer pleiotropic effects than those in current use; an obvious candidate is the Tet-ON system, which has already proved useful in flies [80,81] and in Bombyx cell lines [82]. For transient expression experiments, a constitutive promoter is desirable, since the cells are not required to grow for an extended period. For high-level constitutive expression, the commonly used promoters are from Act5C and from Ubi-p63E.

5.1.4. Selection systems

A number of markers can be used to isolate stable transformants. These include drugs (e.g. methotrexate, α-amanitin, hygromycin, blasticidin), for which resistance plasmids are available, and fluorescent markers, which enable the selection of expressing cells. The choice of marker will depend on such issues as rapidity of selection (e.g. α-amanitin gives very rapid selection, methotrexate takes weeks, during which the drug-sensitive cells can act as a feeder layer to support the growth of sparse drug-resistant cells) and strength of expression (a single copy of the plasmid pPC4 is sufficient to confer resistance to α-amanitin, and a single copy of act-DHFR confers resistance to methotrexate, but copia-DHFR has to be present in multiple copies to work, and most other resistance markers have not been tested at 1 copy per cell) [59]. When cells are transfected with a plasmid expressing a fluorescent-tagged transgene, the transformed cells may be isolated by FACS, without need of drug selection.

5.2. RNAi

RNAi knockouts are widely used in many cell lines. Refer to Mohr’s review in this issue [83] for more detailed information.

5.3. Cloning

We know of no Drosophila cell lines that can be grown from single cells without the use of a feeder layer. Feeder layers consist of cells which have been treated so that they are incapable of proliferation but remain metabolically functional; the procedure was described originally in 1955 for HeLa cells [84]. They have traditionally been made by subjecting cells to heavy doses of ionizing radiation; in recent years, mitomycin C has come into use as an alternative to radiation for mammalian feeder cells [85], but mitomycin-treated cells have been reported to be much less effective at feeding than irradiated cells [86]. Protocols for cloning Drosophila cells using an irradiated feeder layer can be found in several reviews [50,54–57]. An alternate approach is to begin with cells carrying a selective drug resistance, and use as feeder cells a population that is sensitive to the drug; once the cells to be cloned have grown sufficiently, the feeder cells can be killed by adding the selective drug. This approach has been used successfully with S2R+ cells and blasticidin [87]. The cells to be cloned may be diluted into a suspension of feeder cells, and then dispensed into a 96-well plate, or alternatively, the feeder cells can be dispensed into a 96-well plate, and then a single viable cell can be added to each well by a cell sorter. Detailed protocols for cloning can be found in reference [50].

5.4 Resources

Cell lines

Most of the extant Drosophila cell lines can be purchased from the DGRC (https://dgrc.cgb.indiana.edu). Additional isolates of S2 cells may be purchased from the American Type Culture Collection (http://www.atcc.org) and from Life Technologies Corp. (http://www.lifetechnologies.com). Since there are in general no legal restrictions on the distribution of Drosophila cell lines, many of the lines can also be obtained from individual research laboratories. It is important to keep track of the provenance of a cell line when using it and when publishing the results, since experiments may not be reproducible from one isolate to another. This is especially true of the widely dispersed and widely mistreated populations of S2 (also known as Schneider’s line 2 or SL2); see Figure 1. Most of the analyses by modENCODE were performed on samples from the DGRC; the FlyAtlas transcriptome data on S2 cells came from cells obtained from Life Technologies [88].

Major sources of data from cell lines

All modENCODE data are deposited in the public databases; see Celniker’s review in this issue [89] for details on accessing them. Many modENCODE data can be viewed as browser presentations at FlyBase (flybase.org). Tabular presentations of modENCODE transcriptome data are available on the DGRC website (https://dgrc.cgb.indiana.edu). Additional transcriptome data from cell lines are available from FLIGHT (http://flight.icr.ac.uk) and from FlyAtlas (flyatlas.org). Results of global RNAi screens can be found at the DRSC website (www.flyrnai.org) and at FLIGHT.

Plasmid vectors

A variety of plasmids for use in transfecting cell lines are available from the DGRC; many are not published. These include vectors with promoters, epitope and fluorescent tags, and selectable markers.

Highlights.

• About 150 Drosophila cell lines from a variety of tissues sources exist in a community resource.

• Extensive genomic and transcriptional data are available for many of these lines.

• We review basic techniques for culture, transformation, and storage of cell lines.

• We survey the wide range of applications for which Drosophila lines have been successfully used.

Abbreviations footnote

DGRC

Drosophila Genomics Resource Center

modENCODE

Model Organism Encyclopedia of DNA Elements