title: Patient481

description: Gene expression data


title: SJINF003

status: Public on Mar 24 2015

type: RNA

city: Memphis

first: Steven

middle: William

last: Paugh

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences Department

country: USA

institute: St. Jude Children's Research Hospital

description: Gene expression data

hyb_protocol: Affymetrix U133A

scan_protocol: Affymetrix U133A

data_processing: R/Bioconductor MAS5

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Leukemia cells

label_protocol: Affymetrix U133A

extract_protocol: Trisol

value: #N/A

tag: lin


title: Patient478

description: Gene expression data


title: Patient477

description: Gene expression data


title: Patient486

description: Gene expression data


title: SJPHALL022425

description: Gene expression data


title: Patient473

description: Gene expression data


title: SJTALL058

description: Gene expression data


title: Patient474

description: Gene expression data


title: Patient484

description: Gene expression data


title: Patient472

description: Gene expression data


title: Patient471

description: Gene expression data


title: Patient470

description: Gene expression data


title: SJBALL032

description: Gene expression data


title: SJERG023

description: Gene expression data


title: Patient464

description: Gene expression data


title: Patient465

description: Gene expression data


title: Patient475

description: Gene expression data


title: Patient469

description: Gene expression data


title: Patient468

description: Gene expression data


title: Patient463

description: Gene expression data


title: SJETV033

description: Gene expression data


title: SJTALL161

description: Gene expression data


title: Patient458

description: Gene expression data


title: Patient462

description: Gene expression data


title: Patient461

description: Gene expression data


title: Patient452

description: Gene expression data


title: Patient446

description: Gene expression data


title: Patient459

description: Gene expression data


title: Patient451

description: Gene expression data


title: Patient454

description: Gene expression data


title: Patient455

description: Gene expression data


title: Patient444

description: Gene expression data


title: Patient449

description: Gene expression data


title: Patient453

description: Gene expression data


title: Patient447

description: Gene expression data


title: Patient456

description: Gene expression data


title: Patient448

description: Gene expression data


title: Patient450

description: Gene expression data


title: Patient445

description: Gene expression data


title: SJTALL055

description: Gene expression data


title: Patient442

description: Gene expression data


title: SJHYPER027

description: Gene expression data


title: SJETV031

description: Gene expression data


title: SJPHALL002

description: Gene expression data


title: Patient439

description: Gene expression data


title: Patient434

description: Gene expression data


title: SJBALL092

description: Gene expression data

value: RES

value: B


title: SJETV030

description: Gene expression data


title: Patient431

description: Gene expression data


title: Patient433

description: Gene expression data


title: Patient440

description: Gene expression data


title: SJHYPER137

description: Gene expression data

value: INT


title: Patient438

description: Gene expression data


title: SJBALL160

description: Gene expression data


title: SJHYPER150

description: Gene expression data

value: SEN


title: Patient436

description: Gene expression data


title: Patient437

description: Gene expression data


title: Patient516

description: Gene expression data


title: SJHYPER153

description: Gene expression data


title: SJHYPER103

description: Gene expression data


title: SJETV114

description: Gene expression data


title: SJBALL099

description: Gene expression data


title: SJBALL095

description: Gene expression data


title: SJBALL205

description: Gene expression data


title: SJTALL034

description: Gene expression data

value: T


title: SJETV022

description: Gene expression data


title: SJTALL033

description: Gene expression data


title: SJHYPER119

description: Gene expression data


title: SJETV094

description: Gene expression data


title: SJBALL097

description: Gene expression data


title: SJHYPO140

description: Gene expression data


title: SJTALL008

description: Gene expression data


title: SJHYPER114

description: Gene expression data


title: SJBALL162

description: Gene expression data


title: SJERG022

description: Gene expression data


title: SJETV093

description: Gene expression data


title: SJHYPER118

description: Gene expression data


title: SJBALL119

description: Gene expression data


title: Patient409

description: Gene expression data


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title: SJBALL096

description: Gene expression data


title: SJETV092

description: Gene expression data


title: SJETV095

description: Gene expression data


title: SJHYPER112

description: Gene expression data


title: SJHYPER131

description: Gene expression data


title: SJBALL094

description: Gene expression data


title: SJHYPER117

description: Gene expression data


title: SJHYPER116

description: Gene expression data


title: Patient476

description: Gene expression data


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description: Gene expression data


title: Patient432

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJBALL118

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJHYPER109

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJHYPER113

description: Gene expression data


title: SJBALL104

description: Gene expression data


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description: Gene expression data


title: SJTALL010

description: Gene expression data


title: SJHYPER128

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJBALL103

description: Gene expression data


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description: Gene expression data


title: SJHYPER127

description: Gene expression data


title: SJHYPER108

description: Gene expression data


title: SJHYPER124

description: Gene expression data


title: SJHYPO126

description: Gene expression data


title: SJBALL105

description: Gene expression data


title: SJE2A030

description: Gene expression data


title: SJHYPER126

description: Gene expression data


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description: Gene expression data


title: SJERG018

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJDOWN013

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJBALL100

description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


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description: Gene expression data


title: SJTALL028

description: Gene expression data


title: SJETV082

description: Gene expression data


title: SJHYPER088

description: Gene expression data


title: SJTALL029

description: Gene expression data


title: SJBALL159

description: Gene expression data


title: SJBALL117

description: Gene expression data


title: SJE2A031

description: Gene expression data


title: SJETV084

description: Gene expression data


title: SJETV111

description: Gene expression data


title: SJTALL085

description: Gene expression data


title: SJDOWN012

description: Gene expression data


title: SJETV085

description: Gene expression data


title: SJDOWN010

description: Gene expression data


title: SJTALL083

description: Gene expression data


title: SJERG014

description: Gene expression data


title: SJETV083

description: Gene expression data


title: SJHYPER136

description: Gene expression data


title: SJTALL009

description: Gene expression data


title: SJETV113

description: Gene expression data


title: SJTALL014

description: Gene expression data


title: SJHYPER149

description: Gene expression data


title: SJTALL007

description: Gene expression data


title: SJDOWN011

description: Gene expression data


title: SJHYPER201

description: Gene expression data


title: SJHYPER101

description: Gene expression data


title: SJHYPER148

description: Gene expression data


title: SJBALL086

description: Gene expression data


title: SJBALL087

description: Gene expression data


title: SJTALL006

description: Gene expression data


title: SJBALL090

description: Gene expression data


title: SJETV078

description: Gene expression data


title: SJHYPER100

description: Gene expression data


title: SJERG019

description: Gene expression data


title: SJTALL218

description: Gene expression data


title: SJETV075

description: Gene expression data


title: SJHYPER200

description: Gene expression data


title: SJBALL085

description: Gene expression data


title: SJETV081

description: Gene expression data


title: SJE2A032

description: Gene expression data


title: SJETV077

description: Gene expression data


title: SJMLL029

description: Gene expression data


title: SJETV076

description: Gene expression data


title: SJHYPO143

description: Gene expression data


title: SJHYPER102

description: Gene expression data


title: SJETV074

description: Gene expression data


title: SJBALL084

description: Gene expression data


title: SJETV079

description: Gene expression data


title: SJETV103

description: Gene expression data


title: SJTALL002

description: Gene expression data


title: SJE2A024

description: Gene expression data


title: SJTALL027

description: Gene expression data


title: SJBALL088

description: Gene expression data


title: SJHYPER098

description: Gene expression data


title: SJHYPO124

description: Gene expression data


title: SJTALL026

description: Gene expression data


title: SJETV073

description: Gene expression data


title: SJHYPER097

description: Gene expression data


title: SJHYPER096

description: Gene expression data


title: SJHYPER145

description: Gene expression data


title: SJHYPER146

description: Gene expression data


title: SJETV072

description: Gene expression data


title: SJTALL025

description: Gene expression data


title: SJTALL217

description: Gene expression data


title: SJE2A023

description: Gene expression data


title: SJHYPER094

description: Gene expression data


title: SJETV086

description: Gene expression data


title: SJBALL116

description: Gene expression data


title: SJBALL211

description: Gene expression data


title: SJE2A034

description: Gene expression data


title: SJBALL082

description: Gene expression data


title: SJERG013

description: Gene expression data


title: SJHYPER143

description: Gene expression data


title: SJBALL081

description: Gene expression data


title: SJTALL024

description: Gene expression data


title: SJE2A022

description: Gene expression data


title: SJHYPER093

description: Gene expression data


title: SJTALL216

description: Gene expression data


title: SJHYPER135

description: Gene expression data


title: SJETV071

description: Gene expression data


title: SJHYPER091

description: Gene expression data


title: SJBALL155

description: Gene expression data


title: SJBALL115

description: Gene expression data


title: SJHYPER095

description: Gene expression data


title: SJHYPER092

description: Gene expression data


title: SJBALL080

description: Gene expression data


title: SJBALL079

description: Gene expression data


title: SJETV070

description: Gene expression data


title: SJETV069

description: Gene expression data


title: SJETV100

description: Gene expression data


title: SJHYPO123

description: Gene expression data


title: SJHYPER089

description: Gene expression data


title: SJBALL210

description: Gene expression data


title: SJTALL087

description: Gene expression data


title: SJHYPER022

description: Gene expression data


title: SJETV027

description: Gene expression data


title: SJETV068

description: Gene expression data


title: SJDOWN009

description: Gene expression data


title: SJHYPER141

description: Gene expression data


title: SJHYPER198

description: Gene expression data


title: Patient224

description: Gene expression data


title: SJTALL086

description: Gene expression data


title: Patient231

description: Gene expression data


title: SJETV028

description: Gene expression data


title: SJHYPER023

description: Gene expression data


title: SJETV067

description: Gene expression data


title: SJTALL040

description: Gene expression data


title: Patient222

description: Gene expression data


title: SJBALL014

description: Gene expression data


title: SJTALL081

description: Gene expression data


title: SJETV025

description: Gene expression data


title: SJTALL215

description: Gene expression data


title: SJETV065

description: Gene expression data


title: SJBALL083

description: Gene expression data


title: SJTALL023

description: Gene expression data


title: SJETV066

description: Gene expression data


title: SJHYPO142

description: Gene expression data


title: SJTALL022

description: Gene expression data


title: SJINF016

description: Gene expression data


title: SJETV024

description: Gene expression data


title: SJETV101

description: Gene expression data


title: SJBALL089

description: Gene expression data


title: SJBALL209

description: Gene expression data


title: Patient195

description: Gene expression data


title: SJTALL042

description: Gene expression data


title: SJHYPO141

description: Gene expression data


title: SJHYPO122

description: Gene expression data


title: SJBALL208

description: Gene expression data


title: SJBALL206

description: Gene expression data


title: SJHYPER021

description: Gene expression data


title: SJETV023

description: Gene expression data


title: SJHYPER020

description: Gene expression data


title: SJBALL207

description: Gene expression data


title: Patient197

description: Gene expression data


title: SJPHALL008

description: Gene expression data


title: SJPHALL021

description: Gene expression data


title: SJHYPER019

description: Gene expression data


title: SJTALL221

description: Gene expression data


title: SJTALL084

description: Gene expression data


title: SJETV021

description: Gene expression data


title: SJHYPER086

description: Gene expression data


title: SJERG030

description: Gene expression data


title: SJTALL082

description: Gene expression data


title: SJTALL080

description: Gene expression data


title: Patient189

description: Gene expression data


title: SJHYPER084

description: Gene expression data


title: SJETV109

description: Gene expression data


title: SJHYPER134

description: Gene expression data


title: SJBALL076

description: Gene expression data


title: SJTALL214

description: Gene expression data


title: SJE2A009

description: Gene expression data


title: SJBALL161

description: Gene expression data


title: SJBALL110

description: Gene expression data


title: SJPHALL007

description: Gene expression data


title: SJETV064

description: Gene expression data


title: SJETV106

description: Gene expression data


title: Patient180

description: Gene expression data


title: SJTALL038

description: Gene expression data


title: SJBALL204

description: Gene expression data


title: SJHYPER017

description: Gene expression data


title: SJTALL037

description: Gene expression data


title: SJBALL203

description: Gene expression data


title: SJERG021

description: Gene expression data


title: SJHYPER018

description: Gene expression data


title: SJETV104

description: Gene expression data


title: SJHYPO115

description: Gene expression data


title: SJTALL021

description: Gene expression data


title: SJETV020

description: Gene expression data


title: SJHYPO128

description: Gene expression data


title: SJE2A021

description: Gene expression data


title: SJETV105

description: Gene expression data


title: SJBALL113

description: Gene expression data


title: SJETV108

description: Gene expression data


title: SJETV107

description: Gene expression data


title: SJHYPO114

description: Gene expression data


title: SJTALL020

description: Gene expression data


title: SJHYPER016

description: Gene expression data


title: SJHYPO113

description: Gene expression data


title: SJTALL079

description: Gene expression data


title: SJHYPER078

description: Gene expression data


title: SJPHALL006

description: Gene expression data


title: SJHYPER082

description: Gene expression data


title: SJETV019

description: Gene expression data


title: SJBALL012

description: Gene expression data


title: SJETV063

description: Gene expression data


title: SJBALL013

description: Gene expression data


title: SJHYPER076

description: Gene expression data


title: SJBALL201

description: Gene expression data


title: SJBALL202

description: Gene expression data


title: SJHYPER015

description: Gene expression data


title: SJBALL200

description: Gene expression data


title: SJHYPER013

description: Gene expression data


title: SJBALL011

description: Gene expression data


title: SJETV016

description: Gene expression data


title: SJBALL074

description: Gene expression data


title: SJMLL024

description: Gene expression data


title: SJHYPER014

description: Gene expression data


title: SJHYPER080

description: Gene expression data


title: SJTALL036

description: Gene expression data


title: SJTALL076

description: Gene expression data


title: SJTALL078

description: Gene expression data


title: SJHYPO137

description: Gene expression data


title: SJBALL198

description: Gene expression data


title: SJHYPER075

description: Gene expression data


title: SJHYPER011

description: Gene expression data


title: SJTALL019

description: Gene expression data


title: SJETV018

description: Gene expression data


title: SJERG029

description: Gene expression data


title: SJETV015

description: Gene expression data


title: SJETV059

description: Gene expression data


title: SJE2A006

description: Gene expression data


title: SJBALL199

description: Gene expression data


title: SJTALL077

description: Gene expression data


title: SJPHALL010

description: Gene expression data


title: SJERG028

description: Gene expression data


title: SJE2A007

description: Gene expression data


title: SJHYPO112

description: Gene expression data


title: SJTALL075

description: Gene expression data


title: SJBALL197

description: Gene expression data


title: SJHYPER012

description: Gene expression data


title: SJETV017

description: Gene expression data


title: SJMLL003

description: Gene expression data


title: SJETV014

description: Gene expression data


title: SJHYPO129

description: Gene expression data


title: SJTALL074

description: Gene expression data


title: SJMLL031

description: Gene expression data


title: SJMLL016

description: Gene expression data


title: SJETV057

description: Gene expression data


title: SJTALL041

description: Gene expression data


title: SJE2A005

description: Gene expression data


title: SJBALL071

description: Gene expression data


title: SJHYPER070

description: Gene expression data


title: SJE2A020

description: Gene expression data


title: SJBALL192

description: Gene expression data


title: SJHYPER048

description: Gene expression data


title: SJHYPER010

description: Gene expression data


title: SJHYPO146

description: Gene expression data


title: SJHYPO107

description: Gene expression data


title: SJBALL066

description: Gene expression data


title: SJBALL193

description: Gene expression data


title: SJHYPER002

description: Gene expression data


title: SJETV005

description: Gene expression data


title: SJBALL190

description: Gene expression data


title: SJETV006

description: Gene expression data


title: SJETV003

description: Gene expression data


title: SJBALL152

description: Gene expression data


title: SJTALL015

description: Gene expression data


title: SJTALL004

description: Gene expression data


title: SJETV051

description: Gene expression data


title: SJTALL016

description: Gene expression data


title: SJTALL063

description: Gene expression data


title: SJTALL070

description: Gene expression data


title: SJHYPER069

description: Gene expression data


title: SJBALL153

description: Gene expression data


title: SJE2A004

description: Gene expression data


title: SJTALL064

description: Gene expression data


title: SJHYPER064

description: Gene expression data


title: SJHYPER060

description: Gene expression data


title: SJTALL072

description: Gene expression data


title: SJETV013

description: Gene expression data


title: SJBALL070

description: Gene expression data


title: SJHYPER009

description: Gene expression data


title: Patient65

description: Gene expression data


title: SJHYPO110

description: Gene expression data


title: SJHYPER065

description: Gene expression data


title: SJBALL195

description: Gene expression data


title: Patient60

description: Gene expression data


title: SJBALL022427

description: Gene expression data


title: Patient50

description: Gene expression data


title: Patient62

description: Gene expression data


title: SJHYPER056

description: Gene expression data


title: SJHYPO109

description: Gene expression data


title: SJE2A003

description: Gene expression data


title: SJETV055

description: Gene expression data


title: SJETV002

description: Gene expression data


title: SJETV009

description: Gene expression data


title: Patient52

description: Gene expression data


title: Patient54

description: Gene expression data


title: Patient48

description: Gene expression data


title: Patient58

description: Gene expression data


title: Patient53

description: Gene expression data


title: Patient63

description: Gene expression data


title: SJTALL003

description: Gene expression data


title: SJTALL069

description: Gene expression data


title: Patient51

description: Gene expression data


title: SJBALL061

description: Gene expression data


title: SJERG009

description: Gene expression data


title: SJHYPER006

description: Gene expression data


title: SJTALL089

description: Gene expression data


title: Patient46

description: Gene expression data


title: Patient38

description: Gene expression data


title: Patient40

description: Gene expression data


title: Patient34

description: Gene expression data


title: SJBALL036

description: Gene expression data


title: Patient32

description: Gene expression data


title: SJHYPER051

description: Gene expression data


title: Patient28

description: Gene expression data


title: Patient22

description: Gene expression data


title: Patient20

description: Gene expression data


title: SJETV011

description: Gene expression data


title: SJHYPER053

description: Gene expression data


title: Patient26

description: Gene expression data


title: SJHYPER004

description: Gene expression data


title: Patient30

description: Gene expression data


title: Patient16

description: Gene expression data


title: Patient24

description: Gene expression data


title: Patient18

description: Gene expression data


title: SJTALL068

description: Gene expression data


title: SJE2A002

description: Gene expression data


title: SJETV012

description: Gene expression data


title: SJETV008

description: Gene expression data


title: Patient36

description: Gene expression data


title: SJHYPER005

description: Gene expression data


title: SJTALL017

description: Gene expression data


title: Patient14

description: Gene expression data


title: SJTALL001

description: Gene expression data


title: Patient12

description: Gene expression data


title: SJTALL065

description: Gene expression data


title: Patient10

description: Gene expression data


title: SJETV007

description: Gene expression data


title: Patient8

description: Gene expression data


title: Patient6

description: Gene expression data


title: SJE2A001

description: Gene expression data


title: SJE2A019

description: Gene expression data


title: SJETV001

description: Gene expression data


title: Patient4

description: Gene expression data


title: SJBALL189

description: Gene expression data


title: PBD_PEX12 iPS3

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: iPSC derived from PBD-ZSD patient fibroblast with PEX12 mutation, biological rep2

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

source_name: iPSC derived from PBD-ZSD patient dermal fibroblast

label_protocol: followed affymetrix protocol

growth_protocol: Fibroblasts and iPSCs are cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C, 5% CO2 until confluence

extract_protocol: as recommended by affymetrix

treatment_protocol: Fibroblasts are dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation; iPSCs are dissociated with 1mg/ml collagenase IV at 37°C, 5% CO2 for 5minutes, manually detached and collected by centrifugation

tag: cell type

value: iPSC

tag: genotype

value: PBD-ZSD patient

tag: age

value: unknown


title: Patient2

description: Gene expression data


title: PBD_PEX1fs2 iPS3

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep5


title: PBD_PEX26 iPS2

description: iPSC derived from PBD-ZSD patient fibroblast with PEX26 mutation, biological rep2


title: PBD_PEX26 iPS1

description: iPSC derived from PBD-ZSD patient fibroblast with PEX26 mutation, biological rep1


title: PBD_PEX1fs2 iPS1

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep3


title: PBD_PEX1fs1 iPS2

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep2


title: PBD_PEX10 iPS2

description: iPSC derived from PBD-ZSD patient fibroblast with PEX10 mutation, biological rep2


title: SJTALL073

description: Gene expression data


title: PBD_PEX1fs2 iPS2

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep4


title: PBD_PEX12 iPS2

description: iPSC derived from PBD-ZSD patient fibroblast with PEX12 mutation, biological rep1


title: SJTALL071

description: Gene expression data


title: PBD_PEX10 iPS1

description: iPSC derived from PBD-ZSD patient fibroblast with PEX10 mutation, biological rep1


title: PBD_PEX1fs1 iPS1

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep1


title: PBD_PEX1ms1 iPS3

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 missense mutation, biological rep2


title: PBD_PEX1ms1 iPS1

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 missense mutation, biological rep1


title: PBD_PEX1ms1 iPS5

description: iPSC derived from PBD-ZSD patient fibroblast with PEX1 missense mutation, biological rep3


title: Control2 iPS2

description: iPSC derived from healthy control fibroblast, biological rep9

source_name: iPSC derived from healthy control dermal fibroblast

value: healthy control


title: Control3 iPS2

description: iPSC derived from healthy control fibroblast, biological rep12


title: Control2 iPS3

description: iPSC derived from healthy control fibroblast, biological rep10


title: Control2 iPS1

description: iPSC derived from healthy control fibroblast, biological rep8


title: 4 day old phyb seedling, biological rep3

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description:
Sample name: Arabidopsis_phyb_3
Gene expression data from 4 day old phyb seedlings

hyb_protocol: Samples were hybridized by the Ramaciotti Centre (Sydney,  NSW, Australia) according to Affymetrix protocols

scan_protocol: Samples were washed and scanned by the Ramaciotti Centre (Sydney,  NSW, Australia) according to Affymetrix protocols

data_processing: Raw CEL files were processed using Partek Genomic Suite (i.e., RMA background correction followed by quantile normalization) using recommended settings. In brief, raw fluorescence values were log2 transformed and subsequently analyzed to detect differentially expressed genes between each line utilizing a 1-way ANOVA based on the Method of Moments (Eisenhart, 1947) and Fisher's Least Significance Difference Contrast methods for differential regulation in all pairwise comparisons using the work-flow of Partej Genomic Suite (http://www.partek.com/pgs)

organism: Arabidopsis thaliana

source_name: 4 day old phyb seedlings

label_protocol: Samples were labelled by the Ramaciotti Centre (Sydney,  NSW, Australia) according to Affymetrix protocols

growth_protocol: Seedlings grown on sterile Murashige Skoog media with 0.8% Agar under longday growth conditions (16 hr light/8hr dark).

extract_protocol: Total RNA isolated and DNAse treated using the Spectrum Total RNA Kit (Sigma, St Louis, MO, USA) according to manufacturer's instructions.

value: 4 days old

tag: tissue

value: seedlings

tag: genotype/variation

value: phyb


title: 4 day old sco3phyb seedling, biological rep3

description:
Sample name: Arabidopsis_sco3phyb_3
Gene expression data from 4 day old sco3phyb seedlings

source_name: 4 day old sco3phyb seedlings


title: Control1 iPS5

description: iPSC derived from healthy control fibroblast, biological rep5


title: Control1 iPS4

description: iPSC derived from healthy control fibroblast, biological rep4


title: 4 day old phyb seedling, biological rep1

description:
Sample name: Arabidopsis_phyb_1
Gene expression data from 4 day old phyb seedlings


title: Control1 iPS3

description: iPSC derived from healthy control fibroblast, biological rep3


title: 4 day old sco3phyb seedling, biological rep2

description:
Sample name: Arabidopsis_sco3phyb_2
Gene expression data from 4 day old sco3phyb seedlings


title: 4 day old sco3 seedling, biological rep3

description:
Sample name: Arabidopsis_sco3_3
Gene expression data from 4 day old sco3 seedlings

source_name: 4 day old sco3 seedlings


title: Control1 iPS7

description: iPSC derived from healthy control fibroblast, biological rep7


title: 4 day old Col-0 seedling, biological rep2

description:
Sample name: Arabidopsis_Col_2
Gene expression data from 4 day old Col-0 seedlings

source_name: 4 day old Col-0 seedlings

value: control


title: Control1 iPS6

description: iPSC derived from healthy control fibroblast, biological rep6


title: 4 day old sco3 seedling, biological rep1

description:
Sample name: Arabidopsis_sco3_1
Gene expression data from 4 day old sco3 seedlings


title: pBAD-RprA-proc. 2

type: mixed

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

hyb_protocol: Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. pBAD-ctrA serves as control for pBAD-RprA, pBAD-ctrB is control for pBAD-RprA-proc.

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica SL1344

label_protocol: total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System

growth_protocol: Salmonella carrying pBAD-ctr, pBAD-RprA or pBAD-RprA-proc. were grown in LB-media to OD=1.5.

extract_protocol: SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit

treatment_protocol: At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.

tag: vector

value: pBAD-RprA-proc


title: 4 day old phyb seedling, biological rep2

description:
Sample name: Arabidopsis_phyb_2
Gene expression data from 4 day old phyb seedlings


title: Control1 iPS1

description: iPSC derived from healthy control fibroblast, biological rep1


title: 4 day old Col-0 seedling, biological rep3

description:
Sample name: Arabidopsis_Col_3
Gene expression data from 4 day old Col-0 seedlings


title: PBD_PEX26 Fibroblast

description: PBD-ZSD patient fibroblast with PEX26 mutation

source_name: dermal fibroblast from PBD-ZSD patient

value: dermal fibroblast


title: pBAD-RprA-proc. 3


title: 4 day old sco3phyb seedling, biological rep1

description:
Sample name: Arabidopsis_sco3phyb_1
Gene expression data from 4 day old sco3phyb seedlings


title: PBD_PEX12 Fibroblast

description: PBD-ZSD patient fibroblast with PEX12 mutation


title: 4 day old Col-0 seedling, biological rep1

description:
Sample name: Arabidopsis_Col_1
Gene expression data from 4 day old Col-0 seedlings


title: 4 day old sco3 seedling, biological rep2

description:
Sample name: Arabidopsis_sco3_2
Gene expression data from 4 day old sco3 seedlings


title: pBAD-RprA-proc. 1


title: PBD_PEX10 Fibroblast

description: PBD-ZSD patient fibroblast with PEX10 mutation


title: Control1 iPS2

description: iPSC derived from healthy control fibroblast, biological rep2


title: PBD_PEX1fs2 Fibroblast

description: PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep2


title: PBD_PEX1fs1 Fibroblast

description: PBD-ZSD patient fibroblast with PEX1 frameshift mutation, biological rep1


title: Control3 Fibroblast

description: healthy control fibroblast, biological rep3

source_name: dermal fibroblast from healthy control


title: PBD_PEX1ms1 Fibroblast

description: PBD-ZSD patient fibroblast with PEX1 missense mutation


title: pBAD-RprA 2

value: pBAD-RprA


title: pBAD-ctrA.1

value: pBAD-ctrA


title: pBAD-ctrA.2


title: pBAD-RprA 1


title: Control2 Fibroblast

description: healthy control fibroblast, biological rep2


title: pBAD-RprA 3


title: pBAD-ctrB.1

value: pBAD-ctrB


title: pBAD-ctrB.3


title: Control1 Fibroblast

description: healthy control fibroblast, biological rep1


title: pBAD-ctrB.2


title: SJBALL194

description: Gene expression data

value: #N/A


title: SJETV010

description: Gene expression data


title: whole blood-low feed efficience-rep1

city: nanjing

first: yumeng

last: xi

state: jingsu

address: tongwei street 6

country: China

institute: nanjing agriculture university

hyb_protocol: The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.

scan_protocol: After washing, arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol.

data_processing: Feature Extraction software (GenePix® Pro 7, Axon Instruments, Inc. ) was used to analyze array  images  to get  raw data. To  begin  with,  the  raw  data  was  normalized  with  the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were  chosen  for  further  data  analysis.  Differentially  expressed  genes  were  then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.   expression pattern among samples.

organism: Bos taurus

source_name: whole blood

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed  to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA from each sample was extracted using miRNeasy Kit（QIAGEN, Cat. 217004, Total RNA Purification Kit）according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: phenotype

value: low feed efficience

value: whole blood


title: whole blood-high feed efficience-rep1

value: high feed efficience


title: pBAD-ctrA.3


title: casp1_pred_rep4

description: Gene expression data

hyb_protocol: Affymetrix Primeview

scan_protocol: Affymetrix Primeview

data_processing: R/Bioconductor RMA

label_protocol: Affymetrix Primeview

growth_protocol: RPMI1640 + 10% HI-FBS + Glutamine

treatment_protocol: Prednisolone 24 hours

tag: cell line

tag: treatment

value: predisone

value: active, overexpressed CASP1


title: blood sample_LD862

city: San Diego

first: Tiziano

last: Pramparo

address: 3611 Valley Centre Drive

department: R&D

institute: Travere

hyb_protocol: 5uL was used in the Illumina Whole Genome Gene Expression Direct Hybridization Protocol

scan_protocol: Illumina BeadArray Reader

data_processing:
Illumina GenomeStudio® software (version 1.1.1) and Lumi package in R
Log2 transformation and quantile normalization

label: Biotin

source_name: leukocyte

label_protocol: 11 uL of each sample for RNA amplification which was performed using the Illumina TotalPrep RNA Amplification Kit. Elution in 40uL of water  and then diluted samples to 150ng/uL.

extract_protocol: Total RNA was extracted following standard procedures and manufacturer's  instructions (Ambion, Austin, TX, USA). In principle, LeukoLOCK disks were freed from RNAlater and Tri-reagent was used to flush out the captured lymphocytes and lyse the cells. RNA was subsequently precipitated with ethanol and purified though washing and cartridge-based steps.

tag: dx (diagnosis)

value: ASD

tag: gender

value: male

value: leukocyte


title: blood sample_LD861-01


title: control_untreated_rep4

description: Gene expression data


title: casp1_untreated_rep4

description: Gene expression data


title: blood sample_LD867-01


title: control_pred_rep4

description: Gene expression data


title: blood sample_LD856-01


title: blood sample_LD883-01

value: Control


title: blood sample_LD877


title: blood sample_LD852-01


title: casp1_pred_rep3

description: Gene expression data


title: blood sample_LD847


title: casp1_untreated_rep3

description: Gene expression data


title: control_untreated_rep3

description: Gene expression data


title: blood sample_LD840-01


title: control_pred_rep3

description: Gene expression data


title: control_pred_rep2

description: Gene expression data


title: blood sample_LD845-01


title: blood sample_LD828-01b


title: blood sample_LD838-01


title: casp1_pred_rep2

description: Gene expression data


title: control_untreated_rep2

description: Gene expression data


title: casp1_untreated_rep2

description: Gene expression data


title: blood sample_LD841-01


title: blood sample_LD837-01


title: blood sample_LD828-01


title: blood sample_LD819-01


title: casp1_pred_rep1

description: Gene expression data


title: casp1_untreated_rep1

description: Gene expression data


title: control_pred_rep1

description: Gene expression data


title: blood sample_LD814-02


title: blood sample_LD814-01


title: control_untreated_rep1

description: Gene expression data


title: Control2 iPS4

description: iPSC derived from healthy control fibroblast, biological rep11

value: iPSC

value: healthy control

value: unknown


title: blood sample_LD808-01


title: blood sample_LD801-02


title: blood sample_LD796-02


title: blood sample_LD791-01


title: blood sample_LD810-01


title: blood sample_LD803


title: blood sample_LD790-01


title: blood sample_LD790-01b


title: SJHYPO21982-SOM-METHYLATION

type: genomic

hyb_protocol: Illuminia HumanMethylation450

scan_protocol: Illuminia HumanMethylation450

data_processing: Illuminia HumanMethylation450

label: Cy3 and Cy5

source_name: Leukemia patient tumor DNA

label_protocol: Illuminia HumanMethylation450

extract_protocol: Qiagen

tag: sample type

value: Tumor DNA


title: blood sample_LD789-02


title: blood sample_LD789-01


title: SJINF22043-SOM-METHYLATION


title: SJETV021980-SOM-METHYLATION


title: blood sample_LD779-01


title: SJE2A067-SOM-METHYLATION


title: blood sample_LD770-01


title: SJTALL022066-SOM-METHYLATION


title: SJTALL022067-SOM-METHYLATION


title: SJHYPER22042-SOM-METHYLATION


title: SJETV021981-SOM-METHYLATION


title: SJTALL22064-SOM-METHYLATION


title: SJTALL022065-SOM-METHYLATION


title: blood sample_LD763-01


title: SJETV021977-SOM-METHYLATION


title: blood sample_LD768-02


title: SJETV022041-SOM-METHYLATION


title: blood sample_LD738-01


title: SJTALL022063-SOM-METHYLATION


title: blood sample_LD737-01


title: blood sample_LD739-01


title: SJTALL022062-SOM-METHYLATION


title: R1_5.13.12_3rdleaf

city: St. Paul

first: Steve

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the arrays according to the array manufacturer's protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the MS2000 Scanner (NimbleGen) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files that were exported from NimbleScan were imported into the Bioconductor statistical environment (Gentleman et al., 2004). Signal was first loess normalized within each array to minimize space effect and then quantile normalized across arrays to minimize batch effect. This was done through the Ringo Bioconductor package in R for the management and normalization of NimbleGen microarray data.

organism: Zea mays

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the array and washed according to the array manufacturer's protocol. Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

growth_protocol: Maize plants (A188 genotype) were grown under controlled conditions in a greenhouse at the University of Wisconsin-Madison (Madison, WI) with a light cycle of 15 hours lights on and 9 hours lights off each day. Maize plants were watered daily as needed.

extract_protocol: Callus used for DNA extraction was collected from each cell line prior to plating onto R1 media after six months of culturing. The uppermost flag leaf of R0 plants and the 3rd leaf of R1 plants were harvested for DNA extraction to conduct meDIP-Chip profiling (Zymo Research DNA methylation IP kit D5101). All tissues were immediately flash-frozen in liquid N2. DNA was isolated using a modified CTAB method.

treatment_protocol: Genomic DNAs were sonicated, amplified, and fluorophore-labeled.

tag: line

value: third seedling leaf

tag: replication

value: input

treatment_protocol: Genomic DNAs were sonicated, methylated DNAs were isolated, amplified, and fluorophore-labeled.

value: methylated DNA (IP pulldown)


title: R1_3.7.3_3rdleaf


title: A188_callus3

source_name: CLcal3_input, callus

value: callus

source_name: CLcal3_IP, callus


title: Sample B2011-SOM-METHYLATION

description: DNA methylation data

hyb_protocol: Illuminia HumanMethylation27

scan_protocol: Illuminia HumanMethylation27

data_processing: Average Beta

label_protocol: Illuminia HumanMethylation27

tag: source

value: Primary Sample


title: A188_control2_earleaf

value: first ear leaf


title: R1_3.4.1_3rdleaf


title: blood sample_LD736-01


title: R1_5.13.11_3rdleaf


title: R0_8.4_earleaf

source_name: CL8.4_input, R0


title: R1_3.7.7_3rdleaf


title: R0_5.8_earleaf

source_name: CL5.8_input, R0


title: blood sample_LD730-01


title: SJETV023-SOM-METHYLATION

description: DNA methylation data

source_name: Leukemia cells


title: R0_5.3_earleaf

source_name: CL5.3_input, R0


title: SJHYPER021974-SOM-METHYLATION


title: A188_control1_earleaf


title: R1_3.4.3_3rdleaf


title: A188_control3_earleaf


title: SJETV21975-SOM-METHYLATION


title: blood sample_LD715-01


title: blood sample_LD716-01


title: SJTALL030-SOM-METHYLATION

description: DNA methylation data


title: blood sample_LD719-01


title: SJTALL024-SOM-METHYLATION

description: DNA methylation data


title: R0_5.2_earleaf

source_name: CL5.2_input, R0


title: SJBALL021973-SOM-METHYLATION


title: blood sample_LD713-01


title: blood sample_LD708-01


title: SJHYPER094-SOM-METHYLATION

description: DNA methylation data


title: blood sample_LD705-01


title: SJETV021972-SOM-METHYLATION


title: SJTALL005-SOM-METHYLATION

description: DNA methylation data


title: SJTALL040-SOM-METHYLATION

description: DNA methylation data


title: SJETV070-SOM-METHYLATION

description: DNA methylation data


title: R0_5.9_earleaf

source_name: CL5.9_input, R0


title: SJBALL21971-SOM-METHYLATION


title: blood sample_LD699-01b


title: SJETV028-SOM-METHYLATION

description: DNA methylation data


title: SJTALL081-SOM-METHYLATION

description: DNA methylation data


title: SJTALL022061-SOM-METHYLATION


title: R0_4.10_earleaf

source_name: CL4.10_input, R0


title: R0_8.10_earleaf

source_name: CL8.10_input, R0


title: R0_3.7_earleaf

source_name: CL3.7_input, R0


title: SJE2A009-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER022039-SOM-METHYLATION


title: SJHYPER022053-SOM-METHYLATION


title: SJTALL023-SOM-METHYLATION

description: DNA methylation data


title: SJHYPO122-SOM-METHYLATION

description: DNA methylation data


title: SJTALL022060-SOM-METHYLATION


title: SJMLL003-SOM-METHYLATION

description: DNA methylation data


title: SJTALL079 -SOM-METHYLATION

description: DNA methylation data


title: blood sample_LD691-01


title: R0_3.12_earleaf

source_name: CL3.12_input, R0


title: R0_3.4_earleaf

source_name: CL3.4_input, R0


title: SJBALL255-SOM-METHYLATION


title: SJHYPER021970-SOM-METHYLATION


title: R0_3.11_earleaf

source_name: CL3.11_input, R0


title: SJHYPER21976-SOM-METHYLATION


title: SJBALL107-SOM-METHYLATION

description: DNA methylation data


title: SJTALL007-SOM-METHYLATION

description: DNA methylation data


title: SJETV021969-SOM-METHYLATION


title: blood sample_LD682-01


title: blood sample_LD682-02


title: SJTALL085-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER22036-SOM-METHYLATION


title: R0_3.5_earleaf

source_name: CL3.5_input, R0


title: SJBALL21968-SOM-METHYLATION


title: blood sample_LD668-01

source_name: leukocyte


title: R0_5.13_earleaf

source_name: CL5.13_input, R0


title: blood sample_LD665-01b


title: blood sample_LD663-01


title: blood sample_LD689-01b


title: SJHYPER21965-SOM-METHYLATION

source_name: Leukemia patient tumor DNA


title: blood sample_LD665-01


title: blood sample_LD672-01b


title: SJHYPER021966-SOM-METHYLATION


title: blood sample_LD678-01


title: SJBALL102-SOM-METHYLATION

hyb_protocol: Illuminia HumanMethylation27K

scan_protocol: Illuminia HumanMethylation27K

data_processing: Illuminia HumanMethylation27K

label_protocol: Illuminia HumanMethylation27K


title: SJHYPER126-SOM-METHYLATION


title: SJETV021967-SOM-METHYLATION


title: blood sample_LD666-01


title: blood sample_LD661-01


title: SJETV102-SOM-METHYLATION


title: R0_3.10_earleaf

source_name: CL3.10_input, R0


title: blood sample_LD699-01


title: SJBALL022035-SOM-METHYLATION


title: SJHYPER022034-SOM-METHYLATION


title: blood sample_LD656-01


title: blood sample_LD651-01


title: blood sample_LD655-01


title: SJHYPER147-SOM-METHYLATION


title: SJBALL099-SOM-METHYLATION


title: SJETV021963-SOM-METHYLATION


title: SJTALL022058-SOM-METHYLATION


title: SJTALL035-SOM-METHYLATION


title: SJHYPER120-SOM-METHYLATION


title: SJTALL010-SOM-METHYLATION


title: SJERG016-SOM-METHYLATION


title: SJBALL21962-SOM-METHYLATION


title: blood sample_LD646-01


title: SJBALL022052-SOM-METHYLATION


title: SJHYPER022033-SOM-METHYLATION


title: SJBALL119-SOM-METHYLATION


title: blood sample_LD645-01b


title: SJBALL247-SOM-METHYLATION


title: blood sample_LD697-01


title: SJHYPER112-SOM-METHYLATION


title: SJBALL21964-SOM-METHYLATION


title: SJHYPER022032-SOM-METHYLATION


title: SJINF075-SOM-METHYLATION


title: SJETV114-SOM-METHYLATION


title: SJERG020-SOM-METHYLATION


title: SJBALL094-SOM-METHYLATION


title: SJTALL033-SOM-METHYLATION


title: blood sample_LD634-01


title: SJTALL034-SOM-METHYLATION


title: blood sample_LD631-01


title: SJHYPO145-SOM-METHYLATION


title: SJMLL022031-SOM-METHYLATION


title: SJHYPER111-SOM-METHYLATION


title: SJETV096-SOM-METHYLATION


title: blood sample_LD636-01


title: SJBALL118-SOM-METHYLATION


title: SJTALL032-SOM-METHYLATION


title: SJERG022-SOM-METHYLATION


title: SJHYPER113-SOM-METHYLATION


title: SJHYPER108-SOM-METHYLATION


title: blood sample_LD630-01


title: blood sample_LD626-01


title: SJTALL22057-SOM-METHYLATION


title: SJETV083-SOM-METHYLATION


title: SJPHALL028-SOM-METHYLATION


title: blood sample_LD616-01b


title: SJBALL022051-SOM-METHYLATION


title: SJTALL022056-SOM-METHYLATION


title: SJDOWN012-SOM-METHYLATION


title: R0_5.10_earleaf

source_name: CL5.10_input, R0


title: blood sample_LD676-01b


title: blood sample_LD614-01b


title: SJMLL029-SOM-METHYLATION


title: SJDOWN010-SOM-METHYLATION


title: SJBALL022029-SOM-METHYLATION


title: blood sample_LD635-01


title: SJBALL101-SOM-METHYLATION


title: SJETV113-SOM-METHYLATION


title: SJHYPER103-SOM-METHYLATION


title: SJHYPER102-SOM-METHYLATION


title: blood sample_LD601-01


title: SJERG014-SOM-METHYLATION


title: SJHYPER022027-SOM-METHYLATION


title: SJHYPER100-SOM-METHYLATION


title: SJETV103-SOM-METHYLATION


title: SJMLL009-SOM-METHYLATION


title: SJHYPER21961-SOM-METHYLATION


title: SJBALL090-SOM-METHYLATION


title: SJBALL243-SOM-METHYLATION


title: SJMLL22028-SOM-METHYLATION


title: SJHYPO143-SOM-METHYLATION


title: blood sample_LD600-01


title: SJTALL002-SOM-METHYLATION


title: blood sample_LD602-01


title: SJBALL085-SOM-METHYLATION


title: SJHYPO124-SOM-METHYLATION


title: blood sample_LD592-01


title: blood sample_LD577-01


title: SJTALL025-SOM-METHYLATION


title: SJETV082-SOM-METHYLATION


title: SJDOWN013-SOM-METHYLATION


title: SJBALL083-SOM-METHYLATION


title: blood sample_LD576-01


title: SJETV22026-SOM-METHYLATION


title: SJHYPER146-SOM-METHYLATION


title: SJE2A034-SOM-METHYLATION


title: blood sample_LD574-01b


title: SJHYPER096-SOM-METHYLATION


title: SJBALL021960-SOM-METHYLATION


title: blood sample_LD606-01


title: SJHYPO022024-SOM-METHYLATION


title: SJERG013-SOM-METHYLATION


title: SJE2A066-SOM-METHYLATION


title: blood sample_LD572-01


title: blood sample_LD565-01


title: SJBALL211-SOM-METHYLATION


title: blood sample_LD564-01


title: SJBALL082-SOM-METHYLATION


title: SJETV076-SOM-METHYLATION


title: SJHYPER095-SOM-METHYLATION


title: SJHYPER143-SOM-METHYLATION


title: SJTALL022054-SOM-METHYLATION


title: blood sample_LD570-01


title: SJETV021959-SOM-METHYLATION


title: SJBALL115-SOM-METHYLATION


title: SJETV086-SOM-METHYLATION


title: SJTALL022055-SOM-METHYLATION


title: SJBALL241-SOM-METHYLATION


title: SJBALL081-SOM-METHYLATION


title: blood sample_LD562-01


title: blood sample_LD556-01b


title: SJBALL114-SOM-METHYLATION


title: SJHYPO123-SOM-METHYLATION


title: SJHYPER023-SOM-METHYLATION


title: blood sample_LD540-01


title: SJHYPER141-SOM-METHYLATION


title: SJBALL021958-SOM-METHYLATION


title: blood sample_LD531-01


title: blood sample_LD532-01b


title: SJBALL014-SOM-METHYLATION


title: SJETV025-SOM-METHYLATION


title: SJBALL010-SOM-METHYLATION


title: SJMLL008-SOM-METHYLATION


title: SJETV024-SOM-METHYLATION


title: SJBALL207-SOM-METHYLATION


title: SJETV068-SOM-METHYLATION


title: blood sample_LD530-01


title: SJHYPO142-SOM-METHYLATION


title: SJBALL206-SOM-METHYLATION


title: SJBALL209-SOM-METHYLATION


title: blood sample_LD523-01


title: SJBALL208-SOM-METHYLATION


title: SJBALL239-SOM-METHYLATION


title: SJETV21956-SOM-METHYLATION


title: SJBALL021955-SOM-METHYLATION


title: SJPHALL021-SOM-METHYLATION


title: SJERG030-SOM-METHYLATION


title: SJTALL084-SOM-METHYLATION


title: blood sample_LD518-01b


title: SJTALL080-SOM-METHYLATION


title: SJHYPER21954-SOM-METHYLATION


title: SJETV022-SOM-METHYLATION


title: blood sample_LD520-01


title: blood sample_LD517-02


title: SJETV021952-SOM-METHYLATION


title: blood sample_LD516-01


title: SJERG021-SOM-METHYLATION


title: SJETV021953-SOM-METHYLATION


title: SJBALL210-SOM-METHYLATION


title: SJBALL205-SOM-METHYLATION


title: SJHYPER018-SOM-METHYLATION


title: SJBALL113-SOM-METHYLATION


title: blood sample_LD510-01b


title: SJTALL036-SOM-METHYLATION


title: SJETV104-SOM-METHYLATION


title: blood sample_LD509-01b


title: SJHYPER021950-SOM-METHYLATION


title: SJETV014-SOM-METHYLATION


title: blood sample_LD505-01


title: SJTALL021920-SOM-METHYLATION


title: SJHYPER021951-SOM-METHYLATION


title: SJHYPO112-SOM-METHYLATION


title: SJTALL041-SOM-METHYLATION


title: blood sample_LD499-01


title: SJHYPER123-SOM-METHYLATION


title: SJTALL012-SOM-METHYLATION


title: SJBALL087-SOM-METHYLATION


title: SJHYPER153-SOM-METHYLATION


title: SJHYPER069-SOM-METHYLATION


title: SJETV022023-SOM-METHYLATION


title: SJTALL021919-SOM-METHYLATION


title: blood sample_LD491-01


title: blood sample_LD495-01


title: blood sample_LD503-01


title: SJHYPER021957-SOM-METHYLATION


title: SJBALL021901-SOM-METHYLATION


title: Total RNA from S4 112 PD

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description: Post-crisis cell culture sample

hyb_protocol: Standard Illumina hybridization protocol. Illumina HT-12 V.3 arrays.

scan_protocol: Standard Illumina scanning protocol. Scanned in a BeadArray reader.

data_processing: The data were extracted with the HumanHT-12_V3_0_R2_11283641_A manifest and normalised using rank invariant normalization in the GenomeStudio Gene expression module.

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit. Quality control was performed with the Agilent Bioanalyzer.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with the Agilent Bioanalyzer.

value: Post-crisis T-cell culture


title: total RNA from S4 48 PD

description: Pre-crisis cell culture sample

source_name: S4 48 PD

value: Pre-crisis T-cell culture


title: blood sample_LD490-01


title: total RNA from stimulated Tcell P7/R2

description: Stimulated T cells

source_name: Control-P7/R2 14 PD

value: Stimulated T cells


title: total RNA from S4 12 PD

description: Pre-crisis cell culture sample

source_name: S4 12 PD


title: blood sample_LD488-01

value: ASD


title: SJTALL021918-SOM-METHYLATION


title: total RNA from S3R 27 PD

description: Post-crisis cell culture sample

source_name: S3R 27 PD


title: blood sample_LD483-01

value: male


title: blood sample_LD486-01

value: leukocyte


title: SJTALL021917-SOM-METHYLATION


title: total RNA from S3R 192 PD

description: Post-crisis cell culture sample

source_name: S3R 192 PD


title: blood sample_LD480-01

value: Control


title: SJPHALL027-SOM-METHYLATION


title: total RNA from S3R 76 PD

description: Post-crisis cell culture sample

source_name: S3R 76PD


title: SJETV021949-SOM-METHYLATION


title: total RNA from S3R 17 PD

description: Pre-crisis cell culture sample

source_name: S3R 17 PD


title: total RNA from S4 223 PD

description: Post-crisis cell culture sample


title: SJBALL022035

description: Gene expression data

hyb_protocol: Affymetrix HG-U133_Plus_2

scan_protocol: Affymetrix HG-U133_Plus_2

source_name: Leukemia cells

label_protocol: Affymetrix HG-U133_Plus_2

value: SEN

value: B


title: SJBALL022052

description: Gene expression data

value: INT


title: SJHYPER021966

description: Gene expression data


title: SJMLL007-SOM-METHYLATION

value: Tumor DNA


title: SJBALL21964

description: Gene expression data

value: RES


title: blood sample_LD478-01


title: SJTALL022058

description: Gene expression data

value: T


title: blood sample_LD473-01


title: blood sample_LD474-01


title: SJBALL021947-SOM-METHYLATION


title: SJBALL022029

description: Gene expression data


title: SJETV021948-SOM-METHYLATION


title: SJETV022023

description: Gene expression data


title: SJHYPER022027

description: Gene expression data


title: SJETV022022-SOM-METHYLATION


title: SJHYPO022024

description: Gene expression data


title: SJTALL021919

description: Gene expression data


title: blood sample_LD472-01b


title: SJETV022049-SOM-METHYLATION


title: blood sample_LD464-01


title: SJETV022049

description: Gene expression data


title: SJBALL247

description: Gene expression data


title: SJBALL022020-SOM-METHYLATION


title: SJETV021948

description: Gene expression data


title: blood sample_LD471-01


title: SJETV022018

description: Gene expression data


title: SJHYPER227-SOM-METHYLATION


title: blood sample_LD462-01


title: SJTALL021916

description: Gene expression data


title: blood sample_LD461-01


title: blood sample_LD460-01


title: SJETV022019-SOM-METHYLATION


title: SJTALL021917

description: Gene expression data


title: SJHYPER022017

description: Gene expression data


title: SJETV021949

description: Gene expression data


title: blood sample_LD459-01


title: SJHYPER021935

description: Gene expression data


title: SJETV022015

description: Gene expression data


title: SJETV021945

description: Gene expression data


title: SJETV022010

description: Gene expression data


title: SJBALL022020

description: Gene expression data


title: blood sample_LD450-01


title: SJETV022018-SOM-METHYLATION


title: SJINF074-SOM-METHYLATION


title: SJHYPER021946-SOM-METHYLATION


title: SJTALL021912

description: Gene expression data


title: SJETV021937

description: Gene expression data


title: SJBALL230

description: Gene expression data


title: blood sample_LD458-01


title: SJTALL021911

description: Gene expression data


title: SJE2A065-SOM-METHYLATION


title: SJHYPER022008

description: Gene expression data


title: SJETV021936

description: Gene expression data


title: blood sample_LD448-01b


title: blood sample_LD443-01


title: blood sample_LD438-01


title: SJPHALL026

description: Gene expression data


title: SJBALL227

description: Gene expression data


title: SJHYPER022017-SOM-METHYLATION


title: SJTALL098

description: Gene expression data


title: blood sample_LD429-01


title: SJTALL021916-SOM-METHYLATION


title: SJTALL011-SOM-METHYLATION


title: SJETV021945-SOM-METHYLATION


title: SJE2A064

description: Gene expression data


title: SJHYPER022016-SOM-METHYLATION


title: SJBALL022002

description: Gene expression data


title: SJETV021927

description: Gene expression data


title: SJHYPER022001

description: Gene expression data

value: #N/A


title: blood sample_LD426-01


title: blood sample_LD419-01


title: SJE2A063

description: Gene expression data


title: blood sample_LD422-01


title: SJHYPER021928

description: Gene expression data


title: SJHYPER022003

description: Gene expression data


title: SJTALL021906

description: Gene expression data


title: SJETV21993

description: Gene expression data


title: blood sample_LD423-01


title: SJETV021997

description: Gene expression data


title: SJETV021943-SOM-METHYLATION


title: SJHYPO021991

description: Gene expression data


title: blood sample_LD416-01


title: SJETV021942-SOM-METHYLATION


title: SJTALL021903

description: Gene expression data


title: SJHYPO147

description: Gene expression data


title: blood sample_LD411-01


title: SJBALL215

description: Gene expression data


title: blood sample_LD408-01


title: SJBALL231-SOM-METHYLATION


title: SJMLL021940-SOM-METHYLATION


title: SJBALL021941-SOM-METHYLATION


title: SJETV22014-SOM-METHYLATION


title: SJETV021990

description: Gene expression data


title: SJTALL021910

description: Gene expression data


title: SJBALL021983

description: Gene expression data


title: SJBALL021944-SOM-METHYLATION


title: SJMLL005

description: Gene expression data


title: SJBALL022047

description: Gene expression data


title: SJHYPER021984

description: Gene expression data


title: SJHYPER022429

description: Gene expression data


title: SJETV021939-SOM-METHYLATION


title: SJETV022015-SOM-METHYLATION


title: blood sample_LD407-01


title: blood sample_LD406-01


title: blood sample_LD409-01


title: SJBALL022428

description: Gene expression data


title: SJTALL021914-SOM-METHYLATION


title: SJBALL022426

description: Gene expression data


title: SJTALL021913-SOM-METHYLATION


title: SJETV022424

description: Gene expression data


title: SJHYPER022425

description: Gene expression data


title: blood sample_LD404-01b


title: SJTALL021915-SOM-METHYLATION


title: SJTALL22064

description: Gene expression data


title: blood sample_LD402-01


title: SJHYPER022033

description: Gene expression data


title: SJHYPER022423

description: Gene expression data


title: blood sample_LD401-01


title: SJMLL009

description: Gene expression data


title: SJBALL241

description: Gene expression data


title: SJBALL230-SOM-METHYLATION


title: SJBALL21938-SOM-METHYLATION


title: SJTALL022054

description: Gene expression data


title: SJBALL22050

description: Gene expression data


title: blood sample_LD400-01


title: blood sample_LD405-01


title: SJHYPER022013-SOM-METHYLATION


title: SJMLL008

description: Gene expression data


title: blood sample_LD395-01


title: SJTALL012

description: Gene expression data


title: blood sample_LD394-01


title: SJETV21926

description: Gene expression data


title: SJETV22014

description: Gene expression data


title: SJHYPER227

description: Gene expression data


title: SJTALL21908

description: Gene expression data


title: SJETV022012-SOM-METHYLATION


title: SJHYPER021998

description: Gene expression data


title: SJBALL021931

description: Gene expression data


title: blood sample_LD390-01


title: SJBALL022011-SOM-METHYLATION


title: blood sample_LD393-01


title: SJETV021937-SOM-METHYLATION


title: SJETV21988

description: Gene expression data


title: blood sample_LD388-01b


title: blood sample_LD391-01


title: SJHYPER021923

description: Gene expression data


title: SJETV022010-SOM-METHYLATION


title: SJHYPO21982

description: Gene expression data


title: SJTALL022427

description: Gene expression data


title: SJTALL021911-SOM-METHYLATION


title: SJINF22043

description: Gene expression data


title: SJE2A067

description: Gene expression data


title: SJETV021981

description: Gene expression data


title: SJTALL022067

description: Gene expression data


title: SJHYPER022009-SOM-METHYLATION


title: SJTALL022066

description: Gene expression data


title: blood sample_LD387-01


title: SJBALL227-SOM-METHYLATION


title: SJHYPER022008-SOM-METHYLATION


title: SJETV021977

description: Gene expression data


title: SJETV021936-SOM-METHYLATION


title: SJETV021980

description: Gene expression data


title: SJETV022041

description: Gene expression data


title: blood sample_LD378-01


title: SJTALL022065

description: Gene expression data


title: SJTALL022062

description: Gene expression data


title: SJBALL021973

description: Gene expression data


title: SJTALL021912-SOM-METHYLATION


title: SJHYPER021974

description: Gene expression data


title: SJETV021972

description: Gene expression data


title: SJTALL022060

description: Gene expression data


title: SJBALL21971

description: Gene expression data


title: SJTALL022061

description: Gene expression data


title: SJHYPER022039

description: Gene expression data


title: SJBALL255

description: Gene expression data


title: SJPHALL026-SOM-METHYLATION


title: SJTALL021910-SOM-METHYLATION


title: SJHYPER022053

description: Gene expression data


title: SJETV021969

description: Gene expression data


title: SJHYPER021970

description: Gene expression data


title: SJETV021967

description: Gene expression data


title: SJHYPER021935-SOM-METHYLATION


title: SJE2A064-SOM-METHYLATION


title: SJBALL21968

description: Gene expression data


title: SJHYPER021934-SOM-METHYLATION


title: SJETV021963

description: Gene expression data


title: SJHYPER021933-SOM-METHYLATION


title: SJHYPER022034

description: Gene expression data


title: SJBALL021931-SOM-METHYLATION


title: SJHYPER21965

description: Gene expression data


title: SJINF075

description: Gene expression data


title: SJHYPER022032

description: Gene expression data


title: SJMLL022031

description: Gene expression data


title: blood sample_LD388-01


title: SJMLL22028

description: Gene expression data


title: SJPHALL028

description: Gene expression data


title: SJBALL224-SOM-METHYLATION


title: SJE2A066

description: Gene expression data


title: SJBALL022051

description: Gene expression data


title: SJETV022005-SOM-METHYLATION


title: SJBALL243

description: Gene expression data


title: SJTALL022056

description: Gene expression data


title: SJTALL021909-SOM-METHYLATION


title: SJBALL021960

description: Gene expression data


title: SJHYPER21961

description: Gene expression data


title: SJETV22026

description: Gene expression data


title: SJMLL006-SOM-METHYLATION


title: SJETV022004-SOM-METHYLATION


title: SJTALL022055

description: Gene expression data


title: SJHYPER021957

description: Gene expression data


title: SJBALL022047-SOM-METHYLATION


title: SJETV021959

description: Gene expression data


title: SJBALL021958

description: Gene expression data


title: SJBALL010

description: Gene expression data


title: SJBALL239

description: Gene expression data


title: SJETV21956

description: Gene expression data


title: SJTALL022063

description: Gene expression data


title: SJHYPER21954

description: Gene expression data


title: SJE2A062-SOM-METHYLATION


title: SJHYPER021928-SOM-METHYLATION


title: SJBALL021955

description: Gene expression data


title: SJETV021953

description: Gene expression data


title: SJTALL021920

description: Gene expression data


title: SJTALL21908-SOM-METHYLATION


title: SJHYPER021951

description: Gene expression data


title: SJBALL022002-SOM-METHYLATION


title: SJHYPER022003-SOM-METHYLATION


title: SJE2A063-SOM-METHYLATION


title: SJETV021952

description: Gene expression data


title: SJPHALL027

description: Gene expression data


title: SJBALL021901

description: Gene expression data


title: SJETV021927-SOM-METHYLATION


title: SJHYPER021950

description: Gene expression data


title: SJTALL021918

description: Gene expression data


title: SJBALL021947

description: Gene expression data


title: SJE2A065

description: Gene expression data


title: SJHYPER021946

description: Gene expression data


title: SJINF074

description: Gene expression data


title: SJTALL021906-SOM-METHYLATION


title: SJHYPER022001-SOM-METHYLATION


title: SJHYPER021999-SOM-METHYLATION


title: SJETV022019

description: Gene expression data


title: SJHYPER21925-SOM-METHYLATION


title: SJBALL021944

description: Gene expression data


title: SJTALL011

description: Gene expression data


title: SJMLL021940

description: Gene expression data


title: SJHYPER022016

description: Gene expression data


title: SJBALL231

description: Gene expression data


title: SJETV021939

description: Gene expression data


title: SJETV021942

description: Gene expression data


title: SJHYPER021996-SOM-METHYLATION


title: SJTALL021915

description: Gene expression data


title: SJBALL021941

description: Gene expression data


title: SJETV021997-SOM-METHYLATION


title: SJTALL21907-SOM-METHYLATION


title: SJHYPER022045-SOM-METHYLATION


title: SJTALL21904

description: Gene expression data


title: SJTALL021914

description: Gene expression data


title: SJBALL021995-SOM-METHYLATION


title: SJHYPER021934

description: Gene expression data


title: SJHYPO021991-SOM-METHYLATION


title: SJBALL224

description: Gene expression data


title: SJHYPER022013

description: Gene expression data


title: SJTALL021913

description: Gene expression data


title: SJINF022-SOM-METHYLATION


title: SJE2A062

description: Gene expression data


title: SJTALL021909

description: Gene expression data


title: SJHYPER021996

description: Gene expression data


title: SJETV022004

description: Gene expression data


title: SJTALL021903-SOM-METHYLATION


title: SJBALL021995

description: Gene expression data


title: SJMLL006

description: Gene expression data


title: SJBALL021992-SOM-METHYLATION


title: SJHYPER021999

description: Gene expression data


title: SJETV021990-SOM-METHYLATION


title: SJHYPER21925

description: Gene expression data


title: SJBALL215-SOM-METHYLATION


title: SJBALL021992

description: Gene expression data


title: SJHYPO147-SOM-METHYLATION


title: ATCC17978_HBA_15min

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

country: South Korea

institute: Korea university

description: EtOH_A vs. HBA_C

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Acinetobacter_baumannii_ATCC-1797 30K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The data quantification was performed using GenePix Pro 6.0 (Axon Instrument, CA).

organism: Acinetobacter baumannii ATCC 17978

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: Overnight culture was diluted 1:100 in 5 mL LB medium at 37°C with aeration

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: 512 μg/ml HBA, 32 μg/ml Cm, combination of 256 μg/ml Cm and 16 μg/ml HBA and 25.6 μg ethanol (same volume with all treatment) were treated for 15min

tag: strain type

value: multi drug resistant pathogen

tag: treated with

value: EtOH for 15min

value: 1/2MIC 4-hydroxybenzaldehyde (HBA)


title: SJBALL218

description: Gene expression data

tag: lin


title: SJTALL021902-SOM-METHYLATION


title: ATCC17978_Mix_15min

description: EtOH_A vs. MIX_D

value: 1/4MIC combination of  Cm and HBA


title: SJMLL007

description: Gene expression data


title: ATCC17978_Cm_15min

description: EtOH_A vs. CLM_B

value: 1/2MIC chloramphenicol (Cm)


title: SJHYPER022044-SOM-METHYLATION


title: SJINF022

description: Gene expression data


title: SJETV021986

description: Gene expression data


title: SJHYPER022044

description: Gene expression data


title: SJHYPER022045

description: Gene expression data


title: SJBALL021987

description: Gene expression data


title: SJTALL021902

description: Gene expression data


title: SJBALL021924

description: Gene expression data


title: SJETV021986-SOM-METHYLATION


title: SJBALL021924-SOM-METHYLATION


title: SJHYPER206-SOM-METHYLATION


title: SJHYPER206

description: Gene expression data


title: SJBALL218-SOM-METHYLATION


title: SJHYPER021998-SOM-METHYLATION


title: SJMLL005-SOM-METHYLATION


title: Naïve CD4 T cells

city: Seoul

first: Seonghoe

last: Park

address: 71, Ihwajang-gil

department: Department of Pathology

institute: Seoul National University, College of Medicine

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

organism: Mus musculus

source_name: wild-type spleen

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

extract_protocol: Extraction of total RNA was performed using Rneasy Micro Kit (Qiagen, Cat#74004) according to manufacturer's instructions.

treatment_protocol: CD4+CD62Lhi T cells of wild-type spleen

tag: strain background

value: wild type

value: 8 week-old

value: spleen

tag: cell type

value: Naïve (CD4+CD62Lhi) CD4 T cells


title: SJTALL021902-GERM-METHYLATION

source_name: Leukemia patient remission normal DNA

value: Normal DNA


title: SJETV21993-SOM-METHYLATION


title: SJHYPER021984-SOM-METHYLATION


title: SJBALL021987-SOM-METHYLATION


title: SK-Hep1_mock-treated, biological replicate 2

city: Cambridge

first: Dmitri

last: Wiederschain

state: MA

address: 640 Memorial Drive

department: Oncology

institute: Sanofi

description: Gene expression data from SK-Hep1 cell line treated with mock compound

hyb_protocol: Hybridized fragmented, biotin-labeled cRNA to the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array overnight at 45C for 16 to 18 hours according to the manufacturer’s recommendations.

scan_protocol: Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) performed according to the manufacturer’s recommendations.

data_processing: The data was analyzed with Array Studio (OmicSoft) software using GC-RMA as normalization method

label_protocol: Starting with 1 ug total RNA, produced amplified biotin-labeled cRNA targets using the Enzo Target Labeling method.

growth_protocol: Plate 5.5x10^6 SK-Hep1 cells/ 15 cm dish 24 hours prior to transfection in antibiotic free DMEM+10% FBS media (30-50% confluent 24 hours later)

extract_protocol: 16 hours later cells were harvested on ice using Argonaute Immunoprecipitation (AgoIP) protocol as described in Hogan et al. (PLoS One. 2014; 9(7): e100951). Subsequently, isolated RNA for profiling using protocol for the RNeasy kit (Qiagen) (however substituting 1.5 volumes of isopropanol for ethanol and elute 2x in 30uL of water)

treatment_protocol: 24 hours after plating, cells were transfected with or without 20 nM of anti-miR-21 using 50ul of Lipofectamine RNAiMAX per 15cm dish (Invitrogen/Life Technologies).


title: TT naïve CD4 T cells

source_name: CIITAtg thymus

treatment_protocol: CD4+CD62L+CXCR3- T cells of CIITAtg thymus

value: CIITAtg mice

tag: age

tag: tissue

value: thymus

value: TT Naive (CD4+CD62L+CXCR3-) thymocytes


title: SK-Hep1_mock-treated, biological replicate 1

source_name: SK-Hep1 cell line treated with mock compound


title: Natural Th1(nTh1) cells

treatment_protocol: CD4+CD62L+CXCR3+ T cells of CIITAtg thymus

tag: genotype/variation

value: nTh1 cells; CD4+CD62L+CXCR3+ thymocytes


title: SK-Hep1_anti-mir21-treated, biological replicate 1

description: Gene expression data from SK-Hep1 cell line treated with anti-mir21 compound


title: SK-Hep1_anti-mir21-treated, biological replicate 2

source_name: SK-Hep1 cell line treated with anti-mir21 compound


title: SK-Hep1_anti-mir21-treated, biological replicate 3


title: SK-Hep1_mock-treated, biological replicate 3


title: SJTALL022065-GERM-METHYLATION


title: SJHYPER021985-SOM-METHYLATION

value: Tumor DNA


title: SJTALL022063-GERM-METHYLATION


title: SJHYPER021923-SOM-METHYLATION


title: SJBALL021973-GERM-METHYLATION


title: SJE2A067-GERM-METHYLATION


title: Classic Th1(cTh1) cells

treatment_protocol: cTh1 cells differentiated from Naïve CD4 T cells of wild-type spleen in Th1-polarizing condition: CD4+CD62Lhi T cells (2.5 x 105) of wild-type spleen were incubated with Dynabeads Mouse T-Activator CD3/CD28 (1:1 ratio, Life Technologies AS, Norway) in 96-well round-bottom plates and differentiated for 5 days under the Th1 conditions: IL-12 (2 ng/ml), IL-2 (50 U/ml), and anti-IL-4 Ab (5 mg/ml).

value: classic Th1 cells; naive T cells differentiated in Th1-polarizing condition


title: SJBALL021983-SOM-METHYLATION


title: SJETV021981-GERM-METHYLATION


title: SJINF075-GERM-METHYLATION


title: SJBALL022052-GERM-METHYLATION


title: SJBALL21968-GERM-METHYLATION


title: SJMLL009-GERM-METHYLATION


title: SJBALL247-GERM-METHYLATION


title: SJPHALL026-GERM-METHYLATION


title: SJHYPER022027-GERM-METHYLATION


title: SJETV022022-GERM-METHYLATION


title: SJTALL021920-GERM-METHYLATION


title: SJHYPO21982-GERM-METHYLATION


title: SJTALL22057-GERM-METHYLATION


title: SJTALL022058-GERM-METHYLATION


title: SJETV021953-GERM-METHYLATION


title: SJTALL021918-GERM-METHYLATION


title: SJBALL022029-GERM-METHYLATION


title: SJBALL010-GERM-METHYLATION


title: SJMLL008-GERM-METHYLATION


title: SJBALL021941-GERM-METHYLATION


title: SJTALL011-GERM-METHYLATION


title: SJHYPER022017-GERM-METHYLATION


title: SJBALL022020-GERM-METHYLATION


title: SJINF074-GERM-METHYLATION


title: VIT_donor9_3_PB1

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor9_3_PB1_Pb H-258048B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor9_3_PB1_Pb H-258048B_top_Cy3_male_fused.txt
combined: VIT_donor9_3_PB1_Pb H-258048B_top_Cy3_combined_fused.txt

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in BlueFuse Multi 3.0

source_name: Fertilized Embryo

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

value: Fertilized Embryo

tag: sample

tag: assayed molecule

value: Amplified DNA

source_name: female/male reference

value: reference


title: SJETV021945-GERM-METHYLATION


title: SJETV021952-GERM-METHYLATION


title: SJTALL021916-GERM-METHYLATION


title: SJETV022018-GERM-METHYLATION


title: SJETV021937-GERM-METHYLATION


title: VIT_donor6_15_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_15_PB2_exp 5-258042B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor6_15_PB2_exp 5-258042B_top_Cy5_male_fused.txt
combined: VIT_donor6_15_PB2_exp 5-258042B_top_Cy5_combined_fused.txt


title: SJHYPER022008-GERM-METHYLATION


title: SJTALL021912-GERM-METHYLATION


title: SJETV022049-GERM-METHYLATION


title: VIT_donor6_14_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_14_PB2_exp 5-258041B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor6_14_PB2_exp 5-258041B_top_Cy5_male_fused.txt
combined: VIT_donor6_14_PB2_exp 5-258041B_top_Cy5_combined_fused.txt


title: VIT_donor6_15_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_15_PB1_exp 5-258042B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor6_15_PB1_exp 5-258042B_top_Cy3_male_fused.txt
combined: VIT_donor6_15_PB1_exp 5-258042B_top_Cy3_combined_fused.txt


title: SJTALL021917-GERM-METHYLATION


title: SJETV022015-GERM-METHYLATION


title: SJETV21993-GERM-METHYLATION


title: VIT_donor9_3_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor9_3_PB2_Pb H-258048B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor9_3_PB2_Pb H-258048B_top_Cy5_male_fused.txt
combined: VIT_donor9_3_PB2_Pb H-258048B_top_Cy5_combined_fused.txt


title: SJTALL021919-GERM-METHYLATION


title: VIT_donor6_14_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_14_PB1_exp 5-258041B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor6_14_PB1_exp 5-258041B_top_Cy3_male_fused.txt
combined: VIT_donor6_14_PB1_exp 5-258041B_top_Cy3_combined_fused.txt


title: VIT_donor6_13_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_13_PB1_exp 5-258040B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor6_13_PB1_exp 5-258040B_bottom_Cy3_male_fused.txt
combined: VIT_donor6_13_PB1_exp 5-258040B_bottom_Cy3_combined_fused.txt


title: SJBALL227-GERM-METHYLATION


title: SJTALL021911-GERM-METHYLATION


title: SJBALL022047-GERM-METHYLATION


title: SJHYPER021935-GERM-METHYLATION


title: SJTALL021910-GERM-METHYLATION


title: SJETV021936-GERM-METHYLATION


title: SJBALL230-GERM-METHYLATION


title: SJHYPER021928-GERM-METHYLATION


title: VIT_donor5_9_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor5_9_PB2_exp 4-258039B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor5_9_PB2_exp 4-258039B_top_Cy5_male_fused.txt
combined: VIT_donor5_9_PB2_exp 4-258039B_top_Cy5_combined_fused.txt


title: VIT_donor3_3_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor3_3_PB2_3rd expe-102028B_bottom_Cy5_female_fused.txt
sample vs male reference: VIT_donor3_3_PB2_3rd expe-102028B_bottom_Cy5_male_fused.txt
combined: VIT_donor3_3_PB2_3rd expe-102028B_bottom_Cy5_combined_fused.txt


title: VIT_donor6_13_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor6_13_PB2_exp 5-258040B_bottom_Cy5_female_fused.txt
sample vs male reference: VIT_donor6_13_PB2_exp 5-258040B_bottom_Cy5_male_fused.txt
combined: VIT_donor6_13_PB2_exp 5-258040B_bottom_Cy5_combined_fused.txt


title: VIT_donor5_9_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor5_9_PB1_exp 4-258039B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor5_9_PB1_exp 4-258039B_top_Cy3_male_fused.txt
combined: VIT_donor5_9_PB1_exp 4-258039B_top_Cy3_combined_fused.txt


title: VIT_donor4_9_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor4_9_PB2_2nd exp-102024B_bottom_Cy5_female_fused.txt
sample vs male reference: VIT_donor4_9_PB2_2nd exp-102024B_bottom_Cy5_male_fused.txt
combined: VIT_donor4_9_PB2_2nd exp-102024B_bottom_Cy5_combined_fused.txt


title: VIT_donor5_7_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor5_7_PB2_exp 4-258038B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor5_7_PB2_exp 4-258038B_top_Cy5_male_fused.txt
combined: VIT_donor5_7_PB2_exp 4-258038B_top_Cy5_combined_fused.txt


title: VIT_donor3_3_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor3_3_PB1_3rd expe-102028B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor3_3_PB1_3rd expe-102028B_bottom_Cy3_male_fused.txt
combined: VIT_donor3_3_PB1_3rd expe-102028B_bottom_Cy3_combined_fused.txt


title: VIT_donor4_9_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor4_9_PB1_2nd exp-102024B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor4_9_PB1_2nd exp-102024B_bottom_Cy3_male_fused.txt
combined: VIT_donor4_9_PB1_2nd exp-102024B_bottom_Cy3_combined_fused.txt


title: SJTALL021906-GERM-METHYLATION


title: SJHYPER022003-GERM-METHYLATION


title: VIT_donor10_3_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_3_PB2_Pb H 3.2-258051B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor10_3_PB2_Pb H 3.2-258051B_top_Cy5_male_fused.txt
combined: VIT_donor10_3_PB2_Pb H 3.2-258051B_top_Cy5_combined_fused.txt


title: VIT_donor2_7_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor2_7_PB1_exp 4-258037B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor2_7_PB1_exp 4-258037B_bottom_Cy3_male_fused.txt
combined: VIT_donor2_7_PB1_exp 4-258037B_bottom_Cy3_combined_fused.txt


title: SJTALL098-GERM-METHYLATION


title: SJBALL022002-GERM-METHYLATION


title: VIT_donor10_3_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_3_PB1_Pb H manual  3.1-258051B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor10_3_PB1_Pb H manual  3.1-258051B_top_Cy3_male_fused.txt
combined: VIT_donor10_3_PB1_Pb H manual  3.1-258051B_top_Cy3_combined_fused.txt


title: VIT_donor10_2_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_2_PB2_PB H bis-258050B_top_Cy5_female_fused.txt
sample vs male reference: VIT_donor10_2_PB2_PB H bis-258050B_top_Cy5_male_fused.txt
combined: VIT_donor10_2_PB2_PB H bis-258050B_top_Cy5_combined_fused.txt


title: SJTALL021903-GERM-METHYLATION


title: SJINF022-GERM-METHYLATION


title: VIT_donor10_2_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_2_PB1_PB H bis-258050B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor10_2_PB1_PB H bis-258050B_top_Cy3_male_fused.txt
combined: VIT_donor10_2_PB1_PB H bis-258050B_top_Cy3_combined_fused.txt


title: VIT_donor1_1_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor1_1_PB1_2nd exp-102022B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor1_1_PB1_2nd exp-102022B_bottom_Cy3_male_fused.txt
combined: VIT_donor1_1_PB1_2nd exp-102022B_bottom_Cy3_combined_fused.txt


title: SJBALL021983-GERM-METHYLATION


title: SJHYPER021999-GERM-METHYLATION


title: FRESH_Donor8-1_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH-Donor8-1_PB2_exp 6-258045B_top_Cy5_female_fused.txt
sample vs male reference: FRESH-Donor8-1_PB2_exp 6-258045B_top_Cy5_male_fused.txt
combined: FRESH-Donor8-1_PB2_exp 6-258045B_top_Cy5_combined_fused.txt

value: top


title: SJHYPO021991-GERM-METHYLATION


title: SJETV021990-GERM-METHYLATION


title: SJBALL021924-GERM-METHYLATION


title: VIT_donor3_4_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor3_4_PB1_exp 4-258038B_top_Cy3_female_fused.txt
sample vs male reference: VIT_donor3_4_PB1_exp 4-258038B_top_Cy3_male_fused.txt
combined: VIT_donor3_4_PB1_exp 4-258038B_top_Cy3_combined_fused.txt


title: VIT_donor10_1_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_1_PB2_PB H bis-258049B_bottom_Cy5_female_fused.txt
sample vs male reference: VIT_donor10_1_PB2_PB H bis-258049B_bottom_Cy5_male_fused.txt
combined: VIT_donor10_1_PB2_PB H bis-258049B_bottom_Cy5_combined_fused.txt


title: HuCCT1_zebularine1000μM_72h-3

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

description: Sample name: HuCCT1_Z1000-3

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing:
Genome Studio V2011.2
The methylation level of each of the > 480,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using "Normalization to Internal Controls" and "Background Subtraction" options implemented in the Methylation Module 1.9.0.
GSE60446_methylated_unmethylated_signals: Unmethylated and methylated signal intensities.

label: Cy3, Cy5

source_name: An intrahepatic cholangiocarcinoma-derived cell line, HuCCT1, with zebularine treatment (1000μM for 72h)

label_protocol: Standard Illumina labelling protocol.

growth_protocol: TFK-1 cells (extrahepatic bile duct, RCB2537) and HuCCT1 cells (intrahepatic bile duct, RCB1960) were provided by the RIKEN BRC though the National Bio-Resource Project of the MEXT, Japan, and were maintained at 37oC under an atmosphere of 95% air and 5% CO2 in RPMI1069 containing 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. Cells were immersed in a culture medium containing zebularine (1000 μM) for 72 h or in a culture medium without zebularine as a control.

extract_protocol: Genomic DNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen).

tag: cell line

value: intrahepatic cholangiocarcinoma cell line

tag: treatment

value: zebularine


title: SJHYPO147-GERM-METHYLATION


title: SJETV021986-GERM-METHYLATION


title: FRESH_Donor9_2_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor9_2_PB2_Pb H-258047B_top_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor9_2_PB2_Pb H-258047B_top_Cy5_male_fused.txt
combined: FRESH_Donor9_2_PB2_Pb H-258047B_top_Cy5_combined_fused.txt


title: FRESH_Donor9_2_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor9_2_PB1_Pb H-258047B_top_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor9_2_PB1_Pb H-258047B_top_Cy3_male_fused.txt
combined: FRESH_Donor9_2_PB1_Pb H-258047B_top_Cy3_combined_fused.txt


title: FRESH_Donor9_1_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor9_1_PB2_Pb H-258046B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor9_1_PB2_Pb H-258046B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor9_1_PB2_Pb H-258046B_bottom_Cy5_combined_fused.txt


title: VIT_donor10_1_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor10_1_PB1_PB H bis-258049B_bottom_Cy3_female_fused.txt
sample vs male reference: VIT_donor10_1_PB1_PB H bis-258049B_bottom_Cy3_male_fused.txt
combined: VIT_donor10_1_PB1_PB H bis-258049B_bottom_Cy3_combined_fused.txt


title: VIT_donor1_1_pB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: VIT_donor1_1_PB2_2nd exp-102022B_bottom_Cy5_female_fused.txt
sample vs male reference: VIT_donor1_1_PB2_2nd exp-102022B_bottom_Cy5_male_fused.txt
combined: VIT_donor1_1_PB2_2nd exp-102022B_bottom_Cy5_combined_fused.txt


title: ERCC1-proficient_3

city: Rotterdam

first: Jurgen

last: Haanstra

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: ErasmusMC

description: gene expression data from LSK cells sorted from lineage-depleted bone marrow

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with MAS 5.0 in R using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set 100.

source_name: LSKs isolated from Ercc1-proficient mice; littermate of Ercc1-/d_3

label_protocol: Standard Affymetrix protocol

growth_protocol: mice were bred and housed according to institutional guidelines

extract_protocol: RNA was extracted with the RNeasy Micro Kit (Qiagen). After two steps of linear amplification with the RNA MessageAmp II aRNA Kit (Ambion, Applied Biosystems), aRNA was labelled and hybridized on the Mouse Genome 430 Affymetrix 2.0 Array according to Affymetrix standard protocols.

treatment_protocol: Bone marrow was harvested from 20- to 22-week-old mice. After lineage depletion, cells were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells and sorted by FACS. Cells were immediately sorted into RLT buffer (Qiagen).

tag: strain

value: F1 from a crossing of  C57BL/6 x FVB/n

tag: genotype

value: ERCC1-proficient (+/d)

value: 20 weeks

value: bone marrow

value: LSK hematopoietic stem cells


title: FRESH_Donor9_1_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor9_1_PB1_Pb H-258046B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor9_1_PB1_Pb H-258046B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor9_1_PB1_Pb H-258046B_bottom_Cy3_combined_fused.txt


title: ERCC1-deficient_3

source_name: LSKs isolated from Ercc1-deficient mice; littermate of Ercc1wt_3

value: ERCC1-deficient (-/d)


title: SJTALL21908-GERM-METHYLATION

tag: sample type

value: Normal DNA


title: HuCCT1_zebularine1000μM_72h-2

description: Sample name: HuCCT1_Z1000-2


title: SJBALL215-GERM-METHYLATION


title: TFK1_zebularine1000μM_72h-1

description: Sample name: TFK1_Z1000-1

source_name: An extrahepatic cholangiocarcinoma-derived cell line, TFK1, with zebularine treatment (1000μM for 72h)

value: extrahepatic cholangiocarcinoma cell line


title: HuCCT1_control-3

description: Sample name: HuCCT1_Z0-3

source_name: An intrahepatic cholangiocarcinoma-derived cell line, HuCCT1, without zebularine treatment