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ValidationPackage

ProductType CellLineName PWSUPD1.2CellType Humaninducedpluripotentstemcell(iPSC)DonorGender FemaleSourceTissue FibroblastsReprogrammingMethod

LentivirusMethod:SommerCA,StadtfeldM,MurphyGJ,HochedlingerK,KottonDN,MostoslavskyG.Inducedpluripotentstemcellgenerationusingasinglelentiviralstemcellcassette.StemCells.2009;27(3):543-9.

Publications LangouëtM,Glatt-DeeleyHR,ChungMS,Dupont-ThibertCM,MathieuxM,BandaEC,StoddardCE,CrandallL,LalandeM;Zincfingerprotein274regulatesimprintedexpressionoftranscriptsinPrader-Willisyndromeneurons,HumanMolecularGenetics,2018;27(3):505-515

BiosafetyLevel 2ThawRecommendation

Thaw1vialinto1wellofa6wellplate

GrowthConditions

FeederDependent:irradiatedMEF(GibcoA34181),hESCmedium:DMEM/F12(Gibco11330-057)with20%KnockoutSerumReplacement(Invitrogen10828-028),1XNon-essentialaminoacids,2mML-glutamine,0.1mM2-Mercaptoethanol,8ng/mLbasicFibroblastGrowthFactor

PassageNumber 28,thesecellswereculturedfor28passagespriortofreezeDateVialed September6,2018Cryopreservation Bambanker(WakoChemicalsCat.No,302-14681)

Serum-freecellfreezingmedium,containing10%DMSOStorage Cryopreservedcellsshouldbestoredinliquidnitrogen

Cellsshouldbeculturedat37°CuponarrivalShipped FrozenvialsorambienttemperatureaslivecellsinT25flaskBankedBy StemCellCore,UConnHealth

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Contents

TestDescription TestProvider PageCultureCharacteristics:Growth,CryopreservationandRecovery

StemCellCore,UConnHealthFarmington,CTwww.health.uconn.edu/stem-cell-core

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GeneExpression(PraderWilli)StemCellCore,UConnHealth 8-9EmbryoidBodyFormationStemCellCore,UConnHealth 10-12DNAMethylationStemCellCore,UConnHealth 13-14PluripotencyTestandLineageScore(TaqManScorecard,AppliedBiosystems)

StemCellCore,UConnHealth

15-17

Cyto-SNPAnalysisUConnChromosomeCoreStorrs-Mansfield,CTwww.cgi.uconn.edu

18-19

HumanPathogenTesting

IDEXXBioAnalyticsColumbia,MOwww.idexxbioanalytics.com

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DNAProfile(MatchfibroblastsampletoiPSCline)

IDEXXBioAnalytics 20

MycoplasmaTesting IDEXXBioAnalytics 20Microbiology(BacterialandFungal)Testing

IDEXXBioAnalytics 20

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CultureCharacteristics:Cryopreservation:AspirateculturemediumfromhPSCplate,washoncewithPBS.Add1mLof0.5uMEDTA(Invitrogen,15575-038)dissociationsolution,incubate3-5minutesat37°C.AspirateEDTAsolutiongently,add1mlofculturemediumperwell.CutstemcellcoloniesusingtheStemProEZPassageDisposableStemCellPassagingTool(Invitrogen,23181-010).Useacellscrapertogentlydetachthecellsoffthesurfaceofthecultureplate.Transferthemediumcontainingcoloniestoa15mltubeandspindownat1000rpm(200g)for2min.Aspiratethesupernatantcarefullytoremovesinglecellsorcontaminatingfeedercells(MEFs)fromthepopulation.Re-suspendcoloniesinBambanker(Cat.No,302-14681)serum-freecellfreezingmedium,containing10%DMSO,andplacethecellsincryogenicvialsforfreezingandpreservation.Recovery:Rollthevialbetweenglovedhandsfor3-5secondstoremovethefrost.Immersethevialintoa37°Cwaterbath.Swirlthevialgentlyandobservetheprogressofthethaw.Whenonlyasmallicecrystalremains,wipetheoutsideofthevialwith70%ethanol.Inasterilebiologicalsafetycabinet,transferthecontentsofthecryogenicvialdirectlytothebottomofa15mLconicaltube.Slowlyadd4mLofhESCmediumtothetube.Centrifugethecellsfor5minutesat200xg.GentlyresuspendthecellsinhESCmedium.AspiratethePBSfromtheMEFfeederwellandslowlyaddthecellsuspensiontothepreparedwellofthe6-wellplate.GrowthCurve:CellsfromhPSCwerepassagedusingAccutase(EMDMillipore,SCR005)for8minutes,andthenmechanicallydissociatedintosinglecellsusingpipette1000ultips.Centrifugethecellsat200xgfor5minutes.1500cellsperwellofa6-wellplatewereplatedonMEFusinghESCmedium.MCH2-10(generatedfromanunaffecteddonor)servedasacontrol.Cellsfromthreeseparatewellswereharvestedeverypassage,accutasedandcounted.

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PWS-UPD1.2beforecryopreservationPhaseimages

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PWS-UPD1.2Day5afterrecoveryfromcryopreservationPhaseimages

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GrowthCurve:coloniesinonewellofa6wellplateintriplicatewells,1500cellsplatedtoeachforbothtestandcontrol.MCH2-10wasusedasacontrol.

CultureCharacteristics-GrowthCurve:cellnumberinonewellofa6wellplate

0

5

10

15

20

25

PWSUPD1.2 MCH2-10

ColoniesFirstPassage

0

20

40

60

80

PWSUPD1.2 MCH2-10

ColoniesSecondPassage

050001000015000200002500030000

PWSUPD1.2 MCH2-10

CellNumberFirstPassage

0

20000

40000

60000

80000

PWSUPD1.2 MCH2-10

CellNumberSecondPassage

7

GrowthCurve:Phaseimagesfromday3afterpassage;thirdpassageofassay.

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GeneExpression-PWSchromosome15q11–q13regiongenes(qRT-PCR)

RNAwasisolatedfromiPSCcellsusingQuick-DNA/RNAMiniprepKit(ZYMOResearch,D7001).cDNAwassynthesizedusingSuperScriptIIReverseTranscriptase(Invitrogen,18064-022).GeneexpressionwasanalyzedusingTaqManGeneExpressionAssays,andtheGAPDHwasusedasanendogenouscontrol.ThedatawereanalyzedusingBio-RadCFXManager3.1software,normalizedtoMCH2-10(iPSCgeneratedfromunaffecteddonor).TheTaqmanFAM-MGBqRT-PCRprimersusedtoexaminethegeneexpressionofMKRN3,MAGEL2,NDN,SNRPN,SNORD116andIPW.

TaqManGeneExpressionassaysareusedforquantitativereal-timePCRanalysisofgeneexpressionandconsistofapairofunlabeledPCRprimersandaTaqManprobewithadyelabel(FAM)onthe5’endandaminorgroovebinder(MGB)andnon-fluorescentquencher(NFQ)onthe3’end.

Mapofchromosome15q11–q13region:

GeneSymbol TaqManAssayIDMKRN3 Hs00271653_s1MAGEL2 Hs00255922_s1NDN Hs00267349_s1SNRPN Hs00243205_m1SNORD116 Hs03454084_m1IPW Hs03455409_s1GAPDH Hs99999905_m1

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Geneexpression(PraderWilli)analysisofMKRN3,MAGEL2,NDN,SNRPN,SNORD116,IPW.GADPHwasusedasanendogenouscontrolanddatawerenormalizedtoMCH2-10.

AS2.1isaniPSClinegeneratedfromadonorwithAngelmanSyndrome*PWS1.7isaniPSClinegeneratedfromadonorwithPraderWilliSyndrome(LargeDeletion)*MCH2-10isaniPSCgeneratedfromanunaffecteddonor**ChamberlainSJ,ChenPF,NgKY,etal.InducedpluripotentstemcellmodelsofthegenomicimprintingdisordersAngelmanandPrader-Willisyndromes.ProcNatlAcadSciUSA.2010;107(41):17668-73.

0.000

0.500

1.000

1.500

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

MKRN3

0.000

0.400

0.800

1.200

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

MAGEL2

0.000

0.400

0.800

1.200

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

NDN

0.000

0.400

0.800

1.200

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

SNRPN

0.000

0.400

0.800

1.200

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

SNORD116

0.000

0.400

0.800

1.200

PWSUPD1.2

PWS1.7 AS2.1 MCH2-10

IPW

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Embryoidbodies(EB)arethethree-dimensionalaggregatesformedinsuspensionbytheiPSCs.EmbryoidBodycultureisusedtoexaminethedifferentiationpotentialoftheiPSCs.Growthanddifferentiationofembryoidbodies:aspirateofftheculturemediumfromthecultureplates,andthenadd1mLpre-warmedEBmedium(hESCmediumlackingbasicfibroblastgrowthfactor)toeachwellof6-wellplate.CutstemcellcoloniesusingtheStemProEZPassagedisposablestemcellpassagingtool(Invitrogen,23181-010).Useacellscrapertogentlydetachthecellsoffthesurfaceofthecultureplate.Gentlytransferthecellclumpsintoa15-mLconicaltube.Allowthecellstogravitysedimentforapproximately5minutes.Aspiratethesupernatant,andthengentlytapthetubetoloosenthecellpellet.Transferthecellclumpstoacorningultra-Lowattachmentcellcultureflask(Sigma,CLS3815)inatotalof10mLofEBmedium.Replacedmediumandtookimageeveryotherday.RNAwascollectedatday14fortri-Lineagedifferentiationassay.

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PWSUPD1.2embryoidbodyformation(1of2)PhaseImagesDay0today14

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PWSUPD1.2embryoidbodyformation(2of2)PhaseImagesDay0today14

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DNAMethylationanalysisofPWS-ICusingamethylation-sensitiverestrictionendonucleasequantitativePCRassay.TheEpiTectIIDNAMethylationEnzymeKit(Qiagen,335452)preparesgenomicDNAsamplesforDNAmethylationanalysisusingEpiTectMethylIIPCRAssaysforindividualandpredictedmethylatedCpGislands.Usingtheenzymesandbufferprovidedinthekit,4digestsareperformedtodetectdifferentmethylatedDNAfractions.Theproductofamockdigest(Mo)containsalloftheinputgenomicDNA.Theproductofthemethylation-sensitiverestrictionenzymemixture(EnzymeA)digest(Ms)containsmethylatedDNAsequences,whiletheproductofthemethylation-dependentrestrictionenzymemixture(EnzymeB)digest(Md)containsunmethylatedDNAsequences.Theproductofadoubledigest(Msd)measuresthebackgroundandthesuccessofbothenzymaticdigestions.

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DNAMethylationanalysisofPWS-ICusingamethylation-sensitiverestrictionendonucleasequantitativePCRassay.CellLine Unmethylated MethylatedPWSUPD1.2 1.71% 98.29%PWS1.7 2.39% 97.61%AS2.1 92.61% 7.39%MCH2-10 40.96% 59.04%H9 52.11% 47.89%

AS2.1isaniPSClinegeneratedfromadonorwithAngelmanSyndrome*PWS1.7isaniPSClinegeneratedfromadonorwithPraderWilliSyndrome(LargeDeletion)*MCH2-10isaniPSCgeneratedfromanunaffecteddonor*H9hESCisfromWiCellResearchInstitute,Madison,WI*ChamberlainSJ,ChenPF,NgKY,etal.InducedpluripotentstemcellmodelsofthegenomicimprintingdisordersAngelmanandPrader-Willisyndromes.ProcNatlAcadSciUSA.2010;107(41):17668-73.

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ScorecardPluripotencyandTri-LineageDifferentiationAssayTaqManhPSCScorecardPanel384-well(AppliedBiosystems,A15870)enablesverificationofpluripotencyanddeterminationoflineagebiasforiPSCcellline.The384-wellplatecontainsfoursetsof94predefinedTaqManGeneExpressionassays(includingendogenouscontrols)dried-downinthewells.TheScorecardrunonthe7900HTReal-TimePCRSystem.ThedatawereanalyzedusingAppliedBiosystemshPSCScorecardanalysissoftware.Scorecard:Asimple-to-interpretsummaryofgeneexpressionleveldatathatconfirmspluripotencyorindicategermlayerbiasofyoursample.HeatMap:Colorsindicatethefoldchangeinexpressionrelativetotheundifferentiatedreferencesetforeachgene.ScoresBox&WhiskerPlot:Viewsamplesscores(color)inrelationtotherangeofscoresfortheundifferentiatedreferenceset(gray).CorrelationPlot:Seehowgeneexpressionlevelscorrelatebetweensamples.AssayQC:Performaquickqualitycontrolchecktomakesurethesampleamplifiedasexpected.

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Cyto-SNP

TheAffymetrixCytoScanHDArrayincludes750,000SNPsand2.6millioncopynumbermarkerstoenabledetectionofaccuratebreakpointassignmentandhigh-resolution(~25kbresolution)detectionofcopynumbervariation(CNV),lossofheterozygosity(LOH),uniparentaldisomy(importantforimprintingsyndromestudies)andlow-levelmosaicismincelllines.

• Toidentifychromosomeabnormalitiesatlessthan5MBresolution• ToconfirmG-bandandFISHfindings• Todefinespecificbreakpointsand/orgeneinsertions• WhenLOHand/orCNVanalysesareneeded• Toidentifyamplificationsordeletionsforgenesofinterest• Whenwholegenomegenotypingisneeded• Toderivegenomicinformationonsubtelomericandpericentromericregions

GenomicmicroarrayanalysisandG-bandedkaryotypingarecomplementaryandprovideacomprehensivepanelofgenomeintegrityassessment.

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Sample ID: CC18-30Sample Name: PWS_UPD 1.2

Experiment date:Report date:

Microarray type:Microarray Barcode:

SNP manifest file:Annotation DB:SNP cluster file:

Genome build name: GRCh37GTC file:

Algorithm:Smoothing:

CGH Reporting:

Significant Clones:QC Measures:

Median Log R Deviation: Ratio Intensity Signal (<0.2)Median Call Rate: genotype calling performance estimate (>0.98 )

Sample sex:

ISCN Type Chromosome End15q21.1-15q21.1 LOH 15 48,957,597

15q26.2-15q26.3 LOH 15 102,376,655

17q21.31-17q25.3 LOH 17 81,060,040

Array processing: Lisa LaBelle, MS, MB (ASCP)Data analysis and sign out: Judy Brown, PhD, CG, MB (ASCP)

Backbone = 9Minimum Del and Dup Size = 600 KbMinimum LOH Region Size (Mb) = 3.0CGH Region = 10 LOH Region = 500

BG_Annotation_Ens74_20180801.dbCytoSNP-850Kv1-Ensembl version: 74202917700009_R01C01.gtcBeadArray v2 - Standard

Case Report

December 6, 2018 Illumina CytoSNP-850K v1.2202917700009CytoSNP-850Kv1-2_NS550_B3.bpm

November 5, 2018

Warning: The results reported herein are for research use only and not to be used for patient diagnosis or treatment.

The significance of the Illumina molecular karyotyping findings should be interpreted by the principle investigator for research purposes only and include consideration of cell origin, culture conditions and experimental questions. LogR changes and B-allele frequencies were manually scanned across all chromosomes. Gains and losses at 400 Kb or larger and LOH at 5 Mb are reported . Chromosome 15 was evaluated separately. Please note: loss of heterozygosity was NOT identified for the entire length of the long arm of chromosome 15. The PWS critical region (15q11.2-q13) is reported as heterozygous. No deletions or duplications were detected.

Pass0.181

Female

Loss of heterozygosity on long arm chromosome 15 of 0.58 Mb (<1 Mb) ; overlaps 6 HGNC and 4 OMIM gene(s).

Loss of heterozygosity on long arm chromosome 17 of 39.614896 Mb ; overlaps 698 HGNC and 383 OMIM gene(s).

Loss of heterozygosity on long arm chromosome 15 of 6.99 Mb ; overlaps 54 HGNC and 16 OMIM gene(s).

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UConnStemCellCoreEmail:ucscicore@uchc.eduWebsite:www.health.uconn.edu/stem-cell-core