Service includes detection of karyotypic abnormalities in embryonic (ES) and induced pluripotent (iPS) cell lines using StemCell Technologies hPSC Genetic Analysis Kit.

Stem cell genetic analysis

Alison Killilea, Director of the Cell Culture Facility and Stem Cell Facility, is a research scientist with over 25 years of experience in laboratory processes and management with an expertise in stem cell culture, imaging, and immuno-­labeling techniques. In addition to ongoing research, she is the Director of the Fly Food and Media Prep Facilities at UC Berkeley. She has a history of collaboration with cross-­functional teams resulting in invited talks, funded grants and peer-­reviewed publications. 

The Cell Culture Facility offers services to all UC affiliated laboratories and industry clients providing human cell line authentication by short tandem repeat profiling, stem cell genetic analysis, large scale cellular projects, mycoplasma testing, cryopreservation of cell lines, drug/small molecule testing in hundreds of cell lines, and consultation on projects. The Facility has a cell repository with over 600 cell lines including panels for prostate, pancreatic, colon, liver, skin and breast cancer and paired matches of tumor and normal cell lines from the same donor.

The Cell Culture Facility has worked with small and large industry clients including Thermo Scientific, Guardant Health, Caribou, Lyterian, Novel Farms, Synthex and many more.

We use a monitoring system to survey the temperature and CO2 percentage of all of our incubators and the temperatures of all of our -20C and -80C freezers that texts us alerts when eqipment is outside of acceptable ranges. We also authenticate and mycoplasma test all of our human cell lines in house and use a unique identifier to track every cell bank and resulting thaw.

1.     Messina MS, Torrente L, Pezacki AT, Humpel HI, Li EL, Miller SG, Verdejo-Torres O, Padilla-Benavides T, Brady DC, Killilea DW, 

, Ralle M, Ward NP, Ohata J, DeNicola GM, Chang CJ. A histochemical approach to activity-based copper sensing reveals cuproplasia-dependent vulnerabilities in cancer. 

2.     Ruan X, Mueller M, Liu G, Görlitz F, Fu TM, Milkie DE, Lillvis JL, Kuhn A, Gan Chong J, Hong JL, Herr CYA, Hercule W, Nienhaus M, 

, Betzig E, Upadhyayula S. Image processing tools for petabyte-scale light sheet microscopy data. 

3.     Liu G,  Ruan X, Milkie DE, Görlitz F, Muller M, Hercule W, 

Betzig, E, Upadhyayula, S. Characterization, Comparison, and Optimization of Lattice Light Sheets. 

. Mineral requirements for mitochondrial function: A connection to redox balance and cellular differentiation. 

, Anwar M, Niknejad AM. A high-throughput flow cytometry-on-a-CMOS platform for single-cell dielectric spectroscopy at microwave frequencies. 

Top 50 acknowledged papers from users of The Cell Culture Facility:

1.     Pezacki AT, Matier CD, Gu X, Kummelstedt E, Bond SE, Torrente L, Jordan-Sciutto KL, DeNicola GM, Su TA, Brady DC, Chang CJ. Oxidation state-specific fluorescent copper sensors reveal oncogene-driven redox changes that regulate labile copper(II) pools. Proc Natl Acad Sci U S A. 2022 Oct 25;119(43):e2202736119.

2.     Hill NS, Welch MD. A glycine-rich PE_PGRS protein governs mycobacterial actin-based motility. Nat Commun. 2022 Jun 24;13(1):3608.

3.     Borgo GM, Burke TP, Tran CJ, Lo NTN, Engström P, Welch MD. A patatin-like phospholipase mediates Rickettsia parkeri escape from host membranes. Nat Commun. 2022 Jun 27;13(1):3656.

4.     Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A etc. Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nat Genet. 2022 Aug;54(8):1078-1089.

5.     Ferro LS, Fang Q, Eshun-Wilson L, Fernandes J, Jack A, Farrell DP, Golcuk M, Huijben T, Costa K, Gur M, DiMaio F, Nogales E, Yildiz A. Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7. Science. 2022 Jan 21;375(6578):326-331.

6.     Khoury MJ, Bilder D. Minimal functional domains of the core polarity regulator Dlg. Biol Open. 2022 Jul 15;11(7):bio059408.

7.     He D, Feng H, Sundberg B, Yang J, Powers J, Christian AH, Wilkinson JE, Monnin C, Avizonis D, Thomas CJ, Friedman RA, Kluger MD, Hollingsworth MA, Grandgenett PM, Klute KA, Toste FD, Chang CJ, Chio IIC. Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis. Mol Cell. 2022 Aug 18;82(16):3045-3060.e11.

8.     Jack A, Kim Y, Strom AR, Lee DSW, Williams B, Schaub JM, Kellogg EH, Finkelstein IJ, Ferro LS, Yildiz A, Brangwynne CP. Compartmentalization of telomeres through DNA-scaffolded phase separation. Dev Cell. 2022 Jan 24;57(2):277-290.e9.

9.     Hoshi K, Messina MS, Ohata J, Chung CY, Chang CJ. A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues. Nat Protoc. 2022 Jul;17(7):1691-1710.

10.   Engström P, Burke TP, Tran CJ, Iavarone AT, Welch MD. Lysine methylation shields an intracellular pathogen from ubiquitylation and autophagy. Sci Adv. 2021 Jun 25;7(26):eabg2517.

11.   Ishizawa S, Tumurkhuu M, Gross EJ, Ohata J. Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids. Chem Sci. 2022 Jan 20;13(6):1780-1788.

12.   Liu XM, Ma L, Schekman R. Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates. Elife. 2021 Nov 12;10:e71982.

13.   Biering SB, Van Dis E, Wehri E, Yamashiro LH, Nguyenla X, Dugast-Darzacq C, Graham TGW, Stroumza JR, Golovkine GR, Roberts AW, Fines DM, Spradlin JN, Ward CC, Bajaj T, Dovala D, Schulze-Gamen U, Bajaj R, Fox DM, Ott M, Murthy N, Nomura DK, Schaletzky J, Stanley SA. Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2. ACS Infect Dis. 2021 Aug 13;7(8):2337-2351.

14.   Iwashita H, Castillo E, Messina MS, Swanson RA, Chang CJ. A tandem activity-based sensing and labeling strategy enables imaging of transcellular hydrogen peroxide signaling. Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):e2018513118.

15.   Duncan-Lewis C, Hartenian E, King V, Glaunsinger BA. Cytoplasmic mRNA decay represses RNA polymerase II transcription during early apoptosis. Elife. 2021 Jun 4;10:e58342.

16.   Conboy JG. A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient. Int J Mol Sci. 2021 Dec 9;22(24):13248.

17.   Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Fox D, Costa K, Stanley S, Schaletzky J, Yildiz A. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol. 2021 Oct 11;19(10):e3001425

18.   Timblin GA, Tharp KM, Ford B, Winchester JM, Wang J, Zhu S, Khan RI, Louie SK, Iavarone AT, Ten Hoeve J, Nomura DK, Stahl A, Saijo K. Mitohormesis reprogrammes macrophage metabolism to enforce tolerance. Nat Metab. 2021 May;3(5):618-635.

19.   Iwashita H, Castillo E, Messina MS, Swanson RA, Chang CJ. A tandem activity-based sensing and labeling strategy enables imaging of transcellular hydrogen peroxide signaling. Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):e2018513118.

20.   El-Shaffey HM, Gross EJ, Hall YD, Ohata J. An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method. J Am Chem Soc. 2021 Aug 25;143(33):12974-12979. doi: 10.1021/jacs.1c06092. Epub 2021 Aug 13. Erratum in: J Am Chem Soc. 2022 May 25;144(20):9178-9180.

21.   Song L, Tian X, Schekman R. Extracellular vesicles from neurons promote neural induction of stem cells through cyclin D1. J Cell Biol. 2021 Sep 6;220(9):e202101075.

22.   Toh JDW, Crossley SWM, Bruemmer KJ, Ge EJ, He D, Iovan DA, Chang CJ. Distinct RNA N-demethylation pathways catalyzed by nonheme iron ALKBH5 and FTO enzymes enable regulation of formaldehyde release rates. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25284-25292.

23.   Lee S, Chung CY, Liu P, Craciun L, Nishikawa Y, Bruemmer KJ, Hamachi I, Saijo K, Miller EW, Chang CJ. Activity-Based Sensing with a Metal-Directed Acyl Imidazole Strategy Reveals Cell Type-Dependent Pools of Labile Brain Copper. J Am Chem Soc. 2020 Sep 2;142(35):14993-15003.

24.   Ohata J, Krishnamoorthy L, Gonzalez MA, Xiao T, Iovan DA, Toste FD, Miller EW, Chang CJ. An Activity-Based Methionine Bioconjugation Approach To Developing Proximity-Activated Imaging Reporters. ACS Cent Sci. 2020 Jan 22;6(1):32-40.

25.   Gómez-Varela AI, Stamov DR, Miranda A, Alves R, Barata-Antunes C, Dambournet D, Drubin DG, Paiva S, De Beule PAA. Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences. Sci Rep. 2020 Jan 24;10(1):1122.

26.   Greber BJ, Perez-Bertoldi JM, Lim K, Iavarone AT, Toso DB, Nogales E. The cryoelectron microscopy structure of the human CDK-activating kinase. Proc Natl Acad Sci U S A. 2020 Sep 15;117(37):22849-22857.

27.   Melville DB, Studer S, Schekman R. Small sequence variations between two mammalian paralogs of the small GTPase SAR1 underlie functional differences in coat protein complex II assembly. J Biol Chem. 2020 Jun 19;295(25):8401-8412.

28.   Lazzari-Dean JR, Gest AM, Miller EW. Optical estimation of absolute membrane potential using fluorescence lifetime imaging. Elife. 2019 Sep 23;8:e44522.

29.   Chung CY, Posimo JM, Lee S, Tsang T, Davis JM, Brady DC, Chang CJ. Activity-based ratiometric FRET probe reveals oncogene-driven changes in labile copper pools induced by altered glutathione metabolism. Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18285-18294.

30.   Brier LW, Ge L, Stjepanovic G, Thelen AM, Hurley JH, Schekman R. Regulation of LC3 lipidation by the autophagy-specific class III phosphatidylinositol-3 kinase complex. Mol Biol Cell. 2019 Apr 15;30(9):1098-1107.

31.   Temoche-Diaz MM, Shurtleff MJ, Nottingham RM, Yao J, Fadadu RP, Lambowitz AM, Schekman R. Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes. Elife. 2019 Aug 22;8:e47544.

32.   Su TA, Shihadih DS, Cao W, Detomasi TC, Heffern MC, Jia S, Stahl A, Chang CJ. A Modular Ionophore Platform for Liver-Directed Copper Supplementation in Cells and Animals. J Am Chem Soc. 2018 Oct 24;140(42):13764-13774.

33.   Yik-Sham Chung C, Timblin GA, Saijo K, Chang CJ. Versatile Histochemical Approach to Detection of Hydrogen Peroxide in Cells and Tissues Based on Puromycin Staining. J Am Chem Soc. 2018 May 16;140(19):6109-6121.

34.   Melville D, Gorur A, Schekman R. Fatty-acid binding protein 5 modulates the SAR1 GTPase cycle and enhances budding of large COPII cargoes. Mol Biol Cell. 2019 Feb 1;30(3):387-399.

35.   Parker MW, Bell M, Mir M, Kao JA, Darzacq X, Botchan MR, Berger JM. A new class of disordered elements controls DNA replication through initiator self-assembly. Elife. 2019 Sep 27;8:e48562.

36.   Yuan L, Kenny SJ, Hemmati J, Xu K, Schekman R. TANGO1 and SEC12 are copackaged with procollagen I to facilitate the generation of large COPII carriers. Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12255-E12264.

37.   Villeneuve J, Bassaganyas L, Lepreux S, Chiritoiu M, Costet P, Ripoche J, Malhotra V, Schekman R. Unconventional secretion of FABP4 by endosomes and secretory lysosomes. J Cell Biol. 2018 Feb 5;217(2):649-665.

38.   Ge L, Zhang M, Kenny SJ, Liu D, Maeda M, Saito K, Mathur A, Xu K, Schekman R. Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis. EMBO Rep. 2017 Sep;18(9):1586-1603.

39.   Sirkis DW, Aparicio RE, Schekman R. Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER-Golgi intermediate compartment. Mol Biol Cell. 2017 Oct 1;28(20):2723-2733.

40.   Brewer TF, Burgos-Barragan G, Wit N, Patel KJ, Chang CJ. A 2-aza-Cope reactivity-based platform for ratiometric fluorescence imaging of formaldehyde in living cells. Chem Sci. 2017 May 1;8(5):4073-4081.

41.   Bruemmer KJ, Walvoord RR, Brewer TF, Burgos-Barragan G, Wit N, Pontel LB, Patel KJ, Chang CJ. Development of a General Aza-Cope Reaction Trigger Applied to Fluorescence Imaging of Formaldehyde in Living Cells. J Am Chem Soc. 2017 Apr 19;139(15):5338-5350.

42.   Sirkis DW, Aparicio RE, Schekman R. Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER-Golgi intermediate compartment. Mol Biol Cell. 2017 Oct 1;28(20):2723-2733.

43.   Ge L, Zhang M, Kenny SJ, Liu D, Maeda M, Saito K, Mathur A, Xu K, Schekman R. Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis. EMBO Rep. 2017 Sep;18(9):1586-1603.

44.   Bruemmer KJ, Walvoord RR, Brewer TF, Burgos-Barragan G, Wit N, Pontel LB, Patel KJ, Chang CJ. Development of a General Aza-Cope Reaction Trigger Applied to Fluorescence Imaging of Formaldehyde in Living Cells. J Am Chem Soc. 2017 Apr 19;139(15):5338-5350.

45.   Gorur A, Yuan L, Kenny SJ, Baba S, Xu K, Schekman R. COPII-coated membranes function as transport carriers of intracellular procollagen I. J Cell Biol. 2017 Jun 5;216(6):1745-1759.

46.   Krishnamoorthy L, Cotruvo JA Jr, Chan J, Kaluarachchi H, Muchenditsi A, Pendyala VS, Jia S, Aron AT, Ackerman CM, Wal MN, Guan T, Smaga LP, Farhi SL, New EJ, Lutsenko S, Chang CJ. Copper regulates cyclic-AMP-dependent lipolysis. Nat Chem Biol. 2016 Aug;12(8):586-92.

47.   Aron AT, Loehr MO, Bogena J, Chang CJ. An Endoperoxide Reactivity-Based FRET Probe for Ratiometric Fluorescence Imaging of Labile Iron Pools in Living Cells. J Am Chem Soc. 2016 Nov 2;138(43):14338-14346.

48.   Krishnamoorthy L, Cotruvo JA Jr, Chan J, Kaluarachchi H, Muchenditsi A, Pendyala VS, Jia S, Aron AT, Ackerman CM, Wal MN, Guan T, Smaga LP, Farhi SL, New EJ, Lutsenko S, Chang CJ. Copper regulates cyclic-AMP-dependent lipolysis. Nat Chem Biol. 2016 Aug;12(8):586-92.

49.   Richardson CD, Ray GJ, Bray NL, Corn JE. Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes. Nat Commun. 2016 Aug 17;7:12463.

50.   Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, Ri S, Schekman R. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. Elife. 2016 Aug 25;5:e19276.

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Biosciences Divisional Services - Cell Culture Facility

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Stem cell genetic analysis

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