A simple laboratory practical to illustrate RNA mediated gene interference using drosophila cell culture

2010 ◽  
Vol 38 (6) ◽  
pp. 393-399 ◽  
Author(s):  
Laki Buluwela ◽  
Tahereh Kamalati ◽  
Andy Photiou ◽  
Dean A. Heathcote ◽  
Michael D. Jones ◽  
...  
Keyword(s):  
Cell Culture ◽  
Drosophila Cell ◽  
Drosophila Cell Culture

scholarly journals Disruption of Topoisomerase II Perturbs Pairing in Drosophila Cell Culture

Genetics ◽  
2007 ◽  
Vol 177 (1) ◽  
pp. 31-46 ◽  
Author(s):  
Benjamin R. Williams ◽  
Jack R. Bateman ◽  
Natasha D. Novikov ◽  
C.-Ting Wu
Keyword(s):  
Cell Culture ◽  
Topoisomerase Ii ◽  
Drosophila Cell ◽  
Drosophila Cell Culture

Drosophila Cell Culture and Transformation

2007 ◽  
Vol 2007 (8) ◽  
pp. pdb.top6-pdb.top6 ◽  
Author(s):  
L. Cherbas ◽  
P. Cherbas
Keyword(s):  
Cell Culture ◽  
Drosophila Cell ◽  
Drosophila Cell Culture

Isozyme and allozyme patterns in embryonic Drosophila cell culture lines

1977 ◽  
Vol 15 (9-10) ◽  
pp. 877-883 ◽  
Author(s):  
Stamatis Alahiotis ◽  
Edward Berger
Keyword(s):  
Cell Culture ◽  
Drosophila Cell ◽  
Drosophila Cell Culture

scholarly journals Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Genetics ◽  
2021 ◽  
Author(s):  
Shunhua Han ◽  
Preston J Basting ◽  
Guilherme B Dias ◽  
Arthur Luhur ◽  
Andrew C Zelhof ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
Loss Of Heterozygosity ◽  
Cell Lines ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Drosophila Cell ◽  
Genome Wide ◽  
Cell Culture Systems ◽  
Cell Line Identity

Abstract Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabelling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of LTR retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.

scholarly journals Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sub-lines.

2021 ◽  
Author(s):  
Shunhua Han ◽  
Guilherme B. Dias ◽  
Preston J. Basting ◽  
Michael G. Nelson ◽  
Sanjai Patel ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
System Analysis ◽  
Cultured Cells ◽  
Animal Cell ◽  
Insertion Site ◽  
Site Occupancy ◽  
Drosophila Cell ◽  
Model Animal

Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element (TE) content than whole flies, but whether this increase in TE content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here we sequence the genomes of 25 sub-lines of Drosophila S2 cells and show that TE insertions provide abundant markers for the phylogenetic reconstruction of diverse sub-lines in a model animal cell culture system. Analysis of DNA copy number evolution across S2 sub-lines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using TE insertions. Analysis of TE insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for sub-line identity.

scholarly journals A novel transposable element based authentication protocol for Drosophila cell lines

2021 ◽  
Author(s):  
Daniel Mariyappa ◽  
Douglas B. Rusch ◽  
Shunhua Han ◽  
Arthur Luhur ◽  
Danielle Overton ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
Cell Lines ◽  
Wide Distribution ◽  
Small Scale ◽  
Double Blind ◽  
Cell Line Authentication ◽  
Drosophila Cell ◽  
Genomic Changes ◽  
Genome Wide

Drosophila cell lines are used by researchers to investigate various cell biological phenomena. It is crucial to exercise good cell culture practice. Poor handling can lead to both inter- and intraspecies cross-contamination. Prolonged culturing can lead to introduction of large- and small-scale genomic changes. These factors, therefore, make it imperative that methods to authenticate Drosophila cell lines are developed to ensure reproducibility. Mammalian cell line authentication is reliant on short tandem repeat (STR) profiling, however the relatively low STR mutation rate in D. melanogaster at the individual level is likely to preclude the value of this technique. In contrast, transposable elements (TE) are highly polymorphic among individual flies and abundant in Drosophila cell lines. Therefore, we investigated the utility of TE insertions as markers to discriminate Drosophila cell lines derived from the same or different donor genotypes, divergent sub-lines of the same cell line, and from other insect cell lines. We developed a PCR-based next-generation sequencing protocol to cluster cell lines based on the genome-wide distribution of a limited number of diagnostic TE families. We determined the distribution of five TE families in S2R+, S2-DRSC, S2-DGRC, Kc167, ML-DmBG3-c2, mbn2, CME W1 Cl.8+, and OSS Drosophila cell lines. Two independent downstream analyses of the NGS data yielded similar clustering of these cell lines. Double-blind testing of the protocol reliably identified various Drosophila cell lines. In addition, our data indicate minimal changes with respect to the genome-wide distribution of these five TE families when cells are passaged for at least 50 times. The protocol developed can accurately identify and distinguish the numerous Drosophila cell lines available to the research community, thereby aiding reproducible Drosophila cell culture research.

scholarly journals A novel transposable element based authentication protocol for Drosophila cell lines

2021 ◽  
Author(s):  
Daniel Mariyappa ◽  
Douglas B Rusch ◽  
Shunhua Han ◽  
Arthur Luhur ◽  
Danielle Overton ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
Cell Lines ◽  
Wide Distribution ◽  
Small Scale ◽  
Double Blind ◽  
Cell Line Authentication ◽  
Drosophila Cell ◽  
Genomic Changes ◽  
Genome Wide

Abstract Drosophila cell lines are used by researchers to investigate various cell biological phenomena. It is crucial to exercise good cell culture practice. Poor handling can lead to both inter- and intraspecies cross-contamination. Prolonged culturing can lead to introduction of large- and small-scale genomic changes. These factors, therefore, make it imperative that methods to authenticate Drosophila cell lines are developed to ensure reproducibility. Mammalian cell line authentication is reliant on short tandem repeat (STR) profiling, however the relatively low STR mutation rate in D. melanogaster at the individual level is likely to preclude the value of this technique. In contrast, transposable elements (TE) are highly polymorphic among individual flies and abundant in Drosophila cell lines. Therefore, we investigated the utility of TE insertions as markers to discriminate Drosophila cell lines derived from the same or different donor genotypes, divergent sub-lines of the same cell line, and from other insect cell lines. We developed a PCR-based next-generation sequencing protocol to cluster cell lines based on the genome-wide distribution of a limited number of diagnostic TE families. We determined the distribution of five TE families in S2R+, S2-DRSC, S2-DGRC, Kc167, ML-DmBG3-c2, mbn2, CME W1 Cl.8+, and OSS Drosophila cell lines. Two independent downstream analyses of the NGS data yielded similar clustering of these cell lines. Double-blind testing of the protocol reliably identified various Drosophila cell lines. In addition, our data indicate minimal changes with respect to the genome-wide distribution of these five TE families when cells are passaged for at least 50 times. The protocol developed can accurately identify and distinguish the numerous Drosophila cell lines available to the research community, thereby aiding reproducible Drosophila cell culture research.

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