title: genomic DNA from skin peri-umbilical punch biopsy 271

source_name: skin peri-umbilical punch biopsy 271


title: genomic DNA from skin peri-umbilical punch biopsy 290

status: Public on Jan 04 2017

type: genomic

city: London

first: Tim

last: Spector

address: Westminster Bridge road

department: Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Beadchips were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The Intensity Data files (*.txt) from GenomeStudio were uploaded into R (version 3.1.1). The methylation values were calculated as: beta = methylated signal/(methylated signal + unmethylated signal + 100). Further data quality control was all performed in R. Probes were removed that: 1) failed detection (p > 0.01) in one or more samples and/or had a bead count less than 3 in more than 5% of samples (n = 3,325), 2) aligned to more than one location in the human genome with their 50 bp sequence, 3) located on the sex chromosomes. This data set includes probes with genetic variants as used for part of the analysis in manuscript.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: skin peri-umbilical punch biopsy 290

label_protocol: Cy5 and Cy3

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples

tag: tissue

value: skin

tag: beadchip and order on beadchip (sentrix id)

tag: age at biopsy

tag: gender

value: female

tag: relatedness identification id

tag: age at total body naevus count

tag: total body naevus count

tag: bisulphite conversion average

tag: bmi

tag: smoking status


title: genomic DNA from skin peri-umbilical punch biopsy 283

source_name: skin peri-umbilical punch biopsy 283


title: genomic DNA from skin peri-umbilical punch biopsy 268

source_name: skin peri-umbilical punch biopsy 268


title: genomic DNA from skin peri-umbilical punch biopsy 286

source_name: skin peri-umbilical punch biopsy 286


title: genomic DNA from skin peri-umbilical punch biopsy 264

source_name: skin peri-umbilical punch biopsy 264


title: genomic DNA from skin peri-umbilical punch biopsy 280

source_name: skin peri-umbilical punch biopsy 280


title: genomic DNA from skin peri-umbilical punch biopsy 266

source_name: skin peri-umbilical punch biopsy 266


title: genomic DNA from skin peri-umbilical punch biopsy 277

source_name: skin peri-umbilical punch biopsy 277


title: genomic DNA from skin peri-umbilical punch biopsy 267

source_name: skin peri-umbilical punch biopsy 267


title: genomic DNA from skin peri-umbilical punch biopsy 282

source_name: skin peri-umbilical punch biopsy 282


title: genomic DNA from skin peri-umbilical punch biopsy 272

source_name: skin peri-umbilical punch biopsy 272


title: genomic DNA from skin peri-umbilical punch biopsy 269

source_name: skin peri-umbilical punch biopsy 269


title: genomic DNA from skin peri-umbilical punch biopsy 265

source_name: skin peri-umbilical punch biopsy 265


title: genomic DNA from skin peri-umbilical punch biopsy 281

source_name: skin peri-umbilical punch biopsy 281


title: genomic DNA from skin peri-umbilical punch biopsy 275

source_name: skin peri-umbilical punch biopsy 275


title: genomic DNA from skin peri-umbilical punch biopsy 279

source_name: skin peri-umbilical punch biopsy 279


title: genomic DNA from skin peri-umbilical punch biopsy 270

source_name: skin peri-umbilical punch biopsy 270


title: genomic DNA from skin peri-umbilical punch biopsy 276

source_name: skin peri-umbilical punch biopsy 276


title: genomic DNA from skin peri-umbilical punch biopsy 284

source_name: skin peri-umbilical punch biopsy 284


title: genomic DNA from skin peri-umbilical punch biopsy 285

source_name: skin peri-umbilical punch biopsy 285


title: genomic DNA from skin peri-umbilical punch biopsy 278

source_name: skin peri-umbilical punch biopsy 278


title: genomic DNA from skin peri-umbilical punch biopsy 274

source_name: skin peri-umbilical punch biopsy 274


title: genomic DNA from skin peri-umbilical punch biopsy 262

source_name: skin peri-umbilical punch biopsy 262


title: genomic DNA from skin peri-umbilical punch biopsy 273

source_name: skin peri-umbilical punch biopsy 273


title: genomic DNA from skin peri-umbilical punch biopsy 263

source_name: skin peri-umbilical punch biopsy 263


title: genomic DNA from skin peri-umbilical punch biopsy 261

source_name: skin peri-umbilical punch biopsy 261


title: genomic DNA from skin peri-umbilical punch biopsy 260

source_name: skin peri-umbilical punch biopsy 260


title: genomic DNA from skin peri-umbilical punch biopsy 259

source_name: skin peri-umbilical punch biopsy 259


title: Severe_Peripheral_Patient_40

type: RNA

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

description: Epithelial brushings gene expression data from the peripheral airways of a severe asthmatic

hyb_protocol: Samples were hybridized to Affymetrix HG U133 plus 2.0 beadchips.

scan_protocol: Not provided.

data_processing:
Raw microarray gene expression data was normalized using GCRMA in R and subjected to several quality control procedures. Batch effects based on the date of microarray hybridization were removed. Differentially expressed genes were identified using a linear modelling approach in the limma package in R and only genes with FDR corrected p-values < 0.05 for multiple testing (using the Benjamini-Hochberg method) were considered significant.
For RT-qPCR, RNA was isolated and reverse transcribed into cDNA using a High Capacity cDNA Reverse Transcription Kit with random hexamers. RT-qPCR was performed for each gene target in duplicate using Taqman Universal PCR Master Mix, No AmpErase UNG on 7900HT Fast Real-Time PCR System. GAPDH was used as a normalizer to obtain fold changes and t-tests were performed to determine significance. Thermal cycling conditions were 95˚C for 10 minutes followed by 40 cycles of 95˚C for 15 seconds and 60˚C for 1 minute.

label: biotin

molecule: total RNA

source_name: Epithelial brushings from the peripheral airways of a severe asthmatic

label_protocol: Not provided.

growth_protocol: Epithelial brushings were collected at fibre optic bronchoscopy under local anaesthesia using disposable, sheathed bronchial brushes with 4 brushes from the central and 4 fromperipheral airways. Brushings were placed separately in sterile universal tubes with 5 ml PBS and 5 ml of RPMI medium (with 1% Pen/strep, 1% L-glutamine and 20% FBS) was added and the tubes spun at 1000 rpm for 5 minutes to pellet the cells. The medium was discarded and 1 ml of RNA later Reagent was added to the cell pellet in each universal tube, followed by pipetting up and down to solubilise the cells and incubation at room temperature for 5 minutes.

extract_protocol: RNA was isolated from the samples using the Qiagen miRNeasy Kit. RNA quality was assessed using a Bioanalyzer 2100.

tag: patient id

tag: diagnosis

value: Severe Asthmatic

tag: Sex

value: M

tag: age

tag: date of hybridization

tag: cell type

value: Peripheral airway epithelium


title: Severe_Peripheral_Patient_39

value: F


title: genomic DNA from skin peri-umbilical punch biopsy 256

source_name: skin peri-umbilical punch biopsy 256


title: genomic DNA from skin peri-umbilical punch biopsy 253

source_name: skin peri-umbilical punch biopsy 253


title: genomic DNA from skin peri-umbilical punch biopsy 257

source_name: skin peri-umbilical punch biopsy 257


title: Severe_Peripheral_Patient_38


title: genomic DNA from skin peri-umbilical punch biopsy 255

source_name: skin peri-umbilical punch biopsy 255


title: Severe_Peripheral_Patient_37


title: genomic DNA from skin peri-umbilical punch biopsy 249

source_name: skin peri-umbilical punch biopsy 249


title: genomic DNA from skin peri-umbilical punch biopsy 254

source_name: skin peri-umbilical punch biopsy 254


title: genomic DNA from skin peri-umbilical punch biopsy 252

source_name: skin peri-umbilical punch biopsy 252


title: genomic DNA from skin peri-umbilical punch biopsy 241

source_name: skin peri-umbilical punch biopsy 241


title: Severe_Peripheral_Patient_36


title: genomic DNA from skin peri-umbilical punch biopsy 235

source_name: skin peri-umbilical punch biopsy 235


title: genomic DNA from skin peri-umbilical punch biopsy 242

source_name: skin peri-umbilical punch biopsy 242


title: genomic DNA from skin peri-umbilical punch biopsy 248

source_name: skin peri-umbilical punch biopsy 248


title: genomic DNA from skin peri-umbilical punch biopsy 251

source_name: skin peri-umbilical punch biopsy 251


title: genomic DNA from skin peri-umbilical punch biopsy 250

source_name: skin peri-umbilical punch biopsy 250


title: genomic DNA from skin peri-umbilical punch biopsy 236

source_name: skin peri-umbilical punch biopsy 236


title: genomic DNA from skin peri-umbilical punch biopsy 245

source_name: skin peri-umbilical punch biopsy 245


title: genomic DNA from skin peri-umbilical punch biopsy 244

source_name: skin peri-umbilical punch biopsy 244


title: Severe_Peripheral_Patient_34

source_name: Epithelial brushings from the peripheral airways of a severe asthmatic


title: genomic DNA from skin peri-umbilical punch biopsy 234

source_name: skin peri-umbilical punch biopsy 234


title: genomic DNA from skin peri-umbilical punch biopsy 239

source_name: skin peri-umbilical punch biopsy 239


title: genomic DNA from skin peri-umbilical punch biopsy 238

source_name: skin peri-umbilical punch biopsy 238


title: genomic DNA from skin peri-umbilical punch biopsy 247

source_name: skin peri-umbilical punch biopsy 247


title: genomic DNA from skin peri-umbilical punch biopsy 246

source_name: skin peri-umbilical punch biopsy 246


title: Severe_Peripheral_Patient_35


title: genomic DNA from skin peri-umbilical punch biopsy 237

source_name: skin peri-umbilical punch biopsy 237


title: genomic DNA from skin peri-umbilical punch biopsy 258

source_name: skin peri-umbilical punch biopsy 258


title: genomic DNA from skin peri-umbilical punch biopsy 232

source_name: skin peri-umbilical punch biopsy 232


title: Severe_Peripheral_Patient_32


title: Severe_Peripheral_Patient_27


title: genomic DNA from skin peri-umbilical punch biopsy 230

source_name: skin peri-umbilical punch biopsy 230


title: genomic DNA from skin peri-umbilical punch biopsy 240

source_name: skin peri-umbilical punch biopsy 240


title: Severe_Peripheral_Patient_30


title: Severe_Peripheral_Patient_28


title: Severe_Peripheral_Patient_29


title: Severe_Peripheral_Patient_26


title: genomic DNA from skin peri-umbilical punch biopsy 243

source_name: skin peri-umbilical punch biopsy 243


title: genomic DNA from skin peri-umbilical punch biopsy 231

source_name: skin peri-umbilical punch biopsy 231


title: genomic DNA from skin peri-umbilical punch biopsy 229

source_name: skin peri-umbilical punch biopsy 229


title: genomic DNA from skin peri-umbilical punch biopsy 233

source_name: skin peri-umbilical punch biopsy 233


title: Severe_Central_Patient_37

description: Epithelial brushings gene expression data from the central airways of a severe asthmatic

source_name: Epithelial brushings from the central airways of a severe asthmatic

value: Central airway epithelium


title: Severe_Central_Patient_34


title: Severe_Central_Patient_40


title: Severe_Peripheral_Patient_31


title: Severe_Central_Patient_39


title: Severe_Central_Patient_38


title: Severe_Peripheral_Patient_25


title: Severe_Central_Patient_33


title: Severe_Central_Patient_35


title: Severe_Central_Patient_29


title: Severe_Central_Patient_28


title: Severe_Central_Patient_36


title: genomic DNA from skin peri-umbilical punch biopsy 224

source_name: skin peri-umbilical punch biopsy 224


title: genomic DNA from skin peri-umbilical punch biopsy 222

source_name: skin peri-umbilical punch biopsy 222


title: genomic DNA from skin peri-umbilical punch biopsy 226

source_name: skin peri-umbilical punch biopsy 226


title: genomic DNA from skin peri-umbilical punch biopsy 225

source_name: skin peri-umbilical punch biopsy 225


title: Healthy_Peripheral_Patient_23

description: Epithelial brushings gene expression data from the peripheral airways of a healthy control

source_name: Epithelial brushings from the peripheral airways of a healthy control

value: Healthy


title: genomic DNA from skin peri-umbilical punch biopsy 227

source_name: skin peri-umbilical punch biopsy 227


title: genomic DNA from skin peri-umbilical punch biopsy 223

source_name: skin peri-umbilical punch biopsy 223


title: genomic DNA from skin peri-umbilical punch biopsy 221

source_name: skin peri-umbilical punch biopsy 221


title: Severe_Central_Patient_25


title: genomic DNA from skin peri-umbilical punch biopsy 228

source_name: skin peri-umbilical punch biopsy 228


title: Healthy_Peripheral_Patient_21


title: Healthy_Peripheral_Patient_22


title: Severe_Central_Patient_26


title: genomic DNA from skin peri-umbilical punch biopsy 216

source_name: skin peri-umbilical punch biopsy 216


title: genomic DNA from skin peri-umbilical punch biopsy 217

source_name: skin peri-umbilical punch biopsy 217


title: genomic DNA from skin peri-umbilical punch biopsy 214

source_name: skin peri-umbilical punch biopsy 214


title: genomic DNA from skin peri-umbilical punch biopsy 218

source_name: skin peri-umbilical punch biopsy 218


title: genomic DNA from skin peri-umbilical punch biopsy 215

source_name: skin peri-umbilical punch biopsy 215


title: Healthy_Peripheral_Patient_20


title: genomic DNA from skin peri-umbilical punch biopsy 220

source_name: skin peri-umbilical punch biopsy 220


title: genomic DNA from skin peri-umbilical punch biopsy 212

source_name: skin peri-umbilical punch biopsy 212


title: genomic DNA from skin peri-umbilical punch biopsy 213

source_name: skin peri-umbilical punch biopsy 213


title: Healthy_Peripheral_Patient_19


title: genomic DNA from skin peri-umbilical punch biopsy 219

source_name: skin peri-umbilical punch biopsy 219


title: Healthy_Peripheral_Patient_18


title: Healthy_Peripheral_Patient_17


title: genomic DNA from skin peri-umbilical punch biopsy 211

source_name: skin peri-umbilical punch biopsy 211


title: Healthy_Peripheral_Patient_16


title: Healthy_Peripheral_Patient_15


title: genomic DNA from skin peri-umbilical punch biopsy 208

source_name: skin peri-umbilical punch biopsy 208


title: genomic DNA from skin peri-umbilical punch biopsy 207

source_name: skin peri-umbilical punch biopsy 207


title: Healthy_Peripheral_Patient_14

source_name: Epithelial brushings from the peripheral airways of a healthy control


title: genomic DNA from skin peri-umbilical punch biopsy 210

source_name: skin peri-umbilical punch biopsy 210


title: genomic DNA from skin peri-umbilical punch biopsy 209

source_name: skin peri-umbilical punch biopsy 209


title: Healthy_Peripheral_Patient_10


title: Severe_Central_Patient_24

source_name: Epithelial brushings from the central airways of a severe asthmatic


title: genomic DNA from skin peri-umbilical punch biopsy 205

source_name: skin peri-umbilical punch biopsy 205


title: Healthy_Peripheral_Patient_9


title: Healthy_Peripheral_Patient_11


title: genomic DNA from skin peri-umbilical punch biopsy 206

source_name: skin peri-umbilical punch biopsy 206


title: Healthy_Peripheral_Patient_12


title: Healthy_Peripheral_Patient_6


title: genomic DNA from skin peri-umbilical punch biopsy 202

source_name: skin peri-umbilical punch biopsy 202


title: Healthy_Peripheral_Patient_3


title: genomic DNA from skin peri-umbilical punch biopsy 204

source_name: skin peri-umbilical punch biopsy 204


title: Healthy_Peripheral_Patient_13


title: Healthy_Peripheral_Patient_1


title: Healthy_Peripheral_Patient_2


title: Healthy_Central_Patient_21

description: Epithelial brushings gene expression data from the central airways of a healthy control

source_name: Epithelial brushings from the central airways of a healthy control


title: Healthy_Central_Patient_22


title: Healthy_Central_Patient_20


title: Healthy_Central_Patient_23


title: genomic DNA from skin peri-umbilical punch biopsy 199

source_name: skin peri-umbilical punch biopsy 199


title: genomic DNA from skin peri-umbilical punch biopsy 194

source_name: skin peri-umbilical punch biopsy 194


title: Healthy_Central_Patient_18


title: genomic DNA from skin peri-umbilical punch biopsy 200

source_name: skin peri-umbilical punch biopsy 200


title: genomic DNA from skin peri-umbilical punch biopsy 191

source_name: skin peri-umbilical punch biopsy 191


title: genomic DNA from skin peri-umbilical punch biopsy 203

source_name: skin peri-umbilical punch biopsy 203


title: Healthy_Central_Patient_15


title: Healthy_Central_Patient_14


title: genomic DNA from skin peri-umbilical punch biopsy 190

source_name: skin peri-umbilical punch biopsy 190


title: genomic DNA from skin peri-umbilical punch biopsy 192

source_name: skin peri-umbilical punch biopsy 192


title: genomic DNA from skin peri-umbilical punch biopsy 195

source_name: skin peri-umbilical punch biopsy 195


title: genomic DNA from skin peri-umbilical punch biopsy 197

source_name: skin peri-umbilical punch biopsy 197


title: genomic DNA from skin peri-umbilical punch biopsy 198

source_name: skin peri-umbilical punch biopsy 198


title: genomic DNA from skin peri-umbilical punch biopsy 196

source_name: skin peri-umbilical punch biopsy 196


title: genomic DNA from skin peri-umbilical punch biopsy 188

source_name: skin peri-umbilical punch biopsy 188


title: Healthy_Central_Patient_16


title: Healthy_Central_Patient_19


title: genomic DNA from skin peri-umbilical punch biopsy 187

source_name: skin peri-umbilical punch biopsy 187


title: Healthy_Central_Patient_17


title: genomic DNA from skin peri-umbilical punch biopsy 193

source_name: skin peri-umbilical punch biopsy 193


title: genomic DNA from skin peri-umbilical punch biopsy 201

source_name: skin peri-umbilical punch biopsy 201


title: genomic DNA from skin peri-umbilical punch biopsy 186

source_name: skin peri-umbilical punch biopsy 186


title: Healthy_Central_Patient_12

source_name: Epithelial brushings from the central airways of a healthy control


title: genomic DNA from skin peri-umbilical punch biopsy 185

source_name: skin peri-umbilical punch biopsy 185


title: Healthy_Central_Patient_10


title: genomic DNA from skin peri-umbilical punch biopsy 181

source_name: skin peri-umbilical punch biopsy 181


title: Healthy_Central_Patient_11


title: genomic DNA from skin peri-umbilical punch biopsy 189

source_name: skin peri-umbilical punch biopsy 189


title: Healthy_Central_Patient_13


title: Healthy_Central_Patient_9


title: Healthy_Central_Patient_6


title: genomic DNA from skin peri-umbilical punch biopsy 184

source_name: skin peri-umbilical punch biopsy 184


title: Healthy_Central_Patient_5


title: genomic DNA from skin peri-umbilical punch biopsy 183

source_name: skin peri-umbilical punch biopsy 183


title: Healthy_Central_Patient_4


title: Healthy_Central_Patient_7


title: genomic DNA from skin peri-umbilical punch biopsy 176

source_name: skin peri-umbilical punch biopsy 176


title: Healthy_Central_Patient_1


title: Healthy_Central_Patient_2


title: genomic DNA from skin peri-umbilical punch biopsy 175

source_name: skin peri-umbilical punch biopsy 175


title: Healthy_Central_Patient_3


title: genomic DNA from skin peri-umbilical punch biopsy 172

source_name: skin peri-umbilical punch biopsy 172


title: genomic DNA from skin peri-umbilical punch biopsy 174

source_name: skin peri-umbilical punch biopsy 174


title: genomic DNA from skin peri-umbilical punch biopsy 177

source_name: skin peri-umbilical punch biopsy 177


title: genomic DNA from skin peri-umbilical punch biopsy 179

source_name: skin peri-umbilical punch biopsy 179


title: genomic DNA from skin peri-umbilical punch biopsy 182

source_name: skin peri-umbilical punch biopsy 182


title: genomic DNA from skin peri-umbilical punch biopsy 167

source_name: skin peri-umbilical punch biopsy 167


title: genomic DNA from skin peri-umbilical punch biopsy 180

source_name: skin peri-umbilical punch biopsy 180


title: genomic DNA from skin peri-umbilical punch biopsy 173

source_name: skin peri-umbilical punch biopsy 173


title: genomic DNA from skin peri-umbilical punch biopsy 170

source_name: skin peri-umbilical punch biopsy 170


title: genomic DNA from skin peri-umbilical punch biopsy 166

source_name: skin peri-umbilical punch biopsy 166


title: genomic DNA from skin peri-umbilical punch biopsy 164

source_name: skin peri-umbilical punch biopsy 164


title: genomic DNA from skin peri-umbilical punch biopsy 169

source_name: skin peri-umbilical punch biopsy 169


title: genomic DNA from skin peri-umbilical punch biopsy 178

source_name: skin peri-umbilical punch biopsy 178


title: genomic DNA from skin peri-umbilical punch biopsy 159

source_name: skin peri-umbilical punch biopsy 159


title: genomic DNA from skin peri-umbilical punch biopsy 155

source_name: skin peri-umbilical punch biopsy 155


title: genomic DNA from skin peri-umbilical punch biopsy 163

source_name: skin peri-umbilical punch biopsy 163


title: genomic DNA from skin peri-umbilical punch biopsy 162

source_name: skin peri-umbilical punch biopsy 162


title: genomic DNA from skin peri-umbilical punch biopsy 165

source_name: skin peri-umbilical punch biopsy 165


title: genomic DNA from skin peri-umbilical punch biopsy 158

source_name: skin peri-umbilical punch biopsy 158


title: Healthy_Central_Patient_8

source_name: Epithelial brushings from the central airways of a healthy control


title: genomic DNA from skin peri-umbilical punch biopsy 151

source_name: skin peri-umbilical punch biopsy 151


title: genomic DNA from skin peri-umbilical punch biopsy 153

source_name: skin peri-umbilical punch biopsy 153


title: genomic DNA from skin peri-umbilical punch biopsy 152

source_name: skin peri-umbilical punch biopsy 152


title: genomic DNA from skin peri-umbilical punch biopsy 161

source_name: skin peri-umbilical punch biopsy 161


title: genomic DNA from skin peri-umbilical punch biopsy 156

source_name: skin peri-umbilical punch biopsy 156


title: genomic DNA from skin peri-umbilical punch biopsy 157

source_name: skin peri-umbilical punch biopsy 157


title: genomic DNA from skin peri-umbilical punch biopsy 149

source_name: skin peri-umbilical punch biopsy 149


title: genomic DNA from skin peri-umbilical punch biopsy 171

source_name: skin peri-umbilical punch biopsy 171


title: genomic DNA from skin peri-umbilical punch biopsy 160

source_name: skin peri-umbilical punch biopsy 160


title: genomic DNA from skin peri-umbilical punch biopsy 150

source_name: skin peri-umbilical punch biopsy 150


title: genomic DNA from skin peri-umbilical punch biopsy 142

source_name: skin peri-umbilical punch biopsy 142


title: genomic DNA from skin peri-umbilical punch biopsy 168

source_name: skin peri-umbilical punch biopsy 168


title: genomic DNA from skin peri-umbilical punch biopsy 147

source_name: skin peri-umbilical punch biopsy 147


title: genomic DNA from skin peri-umbilical punch biopsy 144

source_name: skin peri-umbilical punch biopsy 144


title: genomic DNA from skin peri-umbilical punch biopsy 148

source_name: skin peri-umbilical punch biopsy 148


title: genomic DNA from skin peri-umbilical punch biopsy 140

source_name: skin peri-umbilical punch biopsy 140


title: genomic DNA from skin peri-umbilical punch biopsy 136

source_name: skin peri-umbilical punch biopsy 136


title: genomic DNA from skin peri-umbilical punch biopsy 154

source_name: skin peri-umbilical punch biopsy 154


title: genomic DNA from skin peri-umbilical punch biopsy 146

source_name: skin peri-umbilical punch biopsy 146


title: genomic DNA from skin peri-umbilical punch biopsy 143

source_name: skin peri-umbilical punch biopsy 143


title: genomic DNA from skin peri-umbilical punch biopsy 145

source_name: skin peri-umbilical punch biopsy 145


title: genomic DNA from skin peri-umbilical punch biopsy 139

source_name: skin peri-umbilical punch biopsy 139


title: genomic DNA from skin peri-umbilical punch biopsy 141

source_name: skin peri-umbilical punch biopsy 141


title: genomic DNA from skin peri-umbilical punch biopsy 137

source_name: skin peri-umbilical punch biopsy 137


title: genomic DNA from skin peri-umbilical punch biopsy 126

source_name: skin peri-umbilical punch biopsy 126


title: genomic DNA from skin peri-umbilical punch biopsy 135

source_name: skin peri-umbilical punch biopsy 135


title: genomic DNA from skin peri-umbilical punch biopsy 128

source_name: skin peri-umbilical punch biopsy 128


title: genomic DNA from skin peri-umbilical punch biopsy 133

source_name: skin peri-umbilical punch biopsy 133


title: genomic DNA from skin peri-umbilical punch biopsy 125

source_name: skin peri-umbilical punch biopsy 125


title: genomic DNA from skin peri-umbilical punch biopsy 130

source_name: skin peri-umbilical punch biopsy 130


title: genomic DNA from skin peri-umbilical punch biopsy 129

source_name: skin peri-umbilical punch biopsy 129


title: genomic DNA from skin peri-umbilical punch biopsy 138

source_name: skin peri-umbilical punch biopsy 138


title: genomic DNA from skin peri-umbilical punch biopsy 134

source_name: skin peri-umbilical punch biopsy 134


title: genomic DNA from skin peri-umbilical punch biopsy 132

source_name: skin peri-umbilical punch biopsy 132


title: genomic DNA from skin peri-umbilical punch biopsy 127

source_name: skin peri-umbilical punch biopsy 127


title: genomic DNA from skin peri-umbilical punch biopsy 124

source_name: skin peri-umbilical punch biopsy 124


title: genomic DNA from skin peri-umbilical punch biopsy 120

source_name: skin peri-umbilical punch biopsy 120


title: genomic DNA from skin peri-umbilical punch biopsy 114

source_name: skin peri-umbilical punch biopsy 114


title: genomic DNA from skin peri-umbilical punch biopsy 110

source_name: skin peri-umbilical punch biopsy 110


title: genomic DNA from skin peri-umbilical punch biopsy 118

source_name: skin peri-umbilical punch biopsy 118


title: genomic DNA from skin peri-umbilical punch biopsy 117

source_name: skin peri-umbilical punch biopsy 117


title: genomic DNA from skin peri-umbilical punch biopsy 131

source_name: skin peri-umbilical punch biopsy 131


title: genomic DNA from skin peri-umbilical punch biopsy 113

source_name: skin peri-umbilical punch biopsy 113


title: genomic DNA from skin peri-umbilical punch biopsy 123

source_name: skin peri-umbilical punch biopsy 123


title: genomic DNA from skin peri-umbilical punch biopsy 115

source_name: skin peri-umbilical punch biopsy 115


title: genomic DNA from skin peri-umbilical punch biopsy 111

source_name: skin peri-umbilical punch biopsy 111


title: genomic DNA from skin peri-umbilical punch biopsy 119

source_name: skin peri-umbilical punch biopsy 119


title: genomic DNA from skin peri-umbilical punch biopsy 116

source_name: skin peri-umbilical punch biopsy 116


title: genomic DNA from skin peri-umbilical punch biopsy 121

source_name: skin peri-umbilical punch biopsy 121


title: genomic DNA from skin peri-umbilical punch biopsy 107

source_name: skin peri-umbilical punch biopsy 107


title: genomic DNA from skin peri-umbilical punch biopsy 109

source_name: skin peri-umbilical punch biopsy 109


title: genomic DNA from skin peri-umbilical punch biopsy 112

source_name: skin peri-umbilical punch biopsy 112


title: genomic DNA from skin peri-umbilical punch biopsy 100

source_name: skin peri-umbilical punch biopsy 100


title: genomic DNA from skin peri-umbilical punch biopsy 108

source_name: skin peri-umbilical punch biopsy 108


title: genomic DNA from skin peri-umbilical punch biopsy 102

source_name: skin peri-umbilical punch biopsy 102


title: genomic DNA from skin peri-umbilical punch biopsy 96

source_name: skin peri-umbilical punch biopsy 96


title: genomic DNA from skin peri-umbilical punch biopsy 105

source_name: skin peri-umbilical punch biopsy 105


title: genomic DNA from skin peri-umbilical punch biopsy 97

source_name: skin peri-umbilical punch biopsy 97


title: genomic DNA from skin peri-umbilical punch biopsy 99

source_name: skin peri-umbilical punch biopsy 99


title: genomic DNA from skin peri-umbilical punch biopsy 103

source_name: skin peri-umbilical punch biopsy 103


title: genomic DNA from skin peri-umbilical punch biopsy 95

source_name: skin peri-umbilical punch biopsy 95


title: genomic DNA from skin peri-umbilical punch biopsy 93

source_name: skin peri-umbilical punch biopsy 93


title: genomic DNA from skin peri-umbilical punch biopsy 101

source_name: skin peri-umbilical punch biopsy 101


title: genomic DNA from skin peri-umbilical punch biopsy 90

source_name: skin peri-umbilical punch biopsy 90


title: genomic DNA from skin peri-umbilical punch biopsy 106

source_name: skin peri-umbilical punch biopsy 106


title: genomic DNA from skin peri-umbilical punch biopsy 84

source_name: skin peri-umbilical punch biopsy 84


title: genomic DNA from skin peri-umbilical punch biopsy 91

source_name: skin peri-umbilical punch biopsy 91


title: genomic DNA from skin peri-umbilical punch biopsy 87

source_name: skin peri-umbilical punch biopsy 87


title: genomic DNA from skin peri-umbilical punch biopsy 122

source_name: skin peri-umbilical punch biopsy 122


title: genomic DNA from skin peri-umbilical punch biopsy 88

source_name: skin peri-umbilical punch biopsy 88


title: genomic DNA from skin peri-umbilical punch biopsy 86

source_name: skin peri-umbilical punch biopsy 86


title: genomic DNA from skin peri-umbilical punch biopsy 94

source_name: skin peri-umbilical punch biopsy 94


title: genomic DNA from skin peri-umbilical punch biopsy 82

source_name: skin peri-umbilical punch biopsy 82


title: genomic DNA from skin peri-umbilical punch biopsy 89

source_name: skin peri-umbilical punch biopsy 89


title: genomic DNA from skin peri-umbilical punch biopsy 79

source_name: skin peri-umbilical punch biopsy 79


title: genomic DNA from skin peri-umbilical punch biopsy 81

source_name: skin peri-umbilical punch biopsy 81


title: genomic DNA from skin peri-umbilical punch biopsy 80

source_name: skin peri-umbilical punch biopsy 80


title: genomic DNA from skin peri-umbilical punch biopsy 85

source_name: skin peri-umbilical punch biopsy 85


title: genomic DNA from skin peri-umbilical punch biopsy 76

source_name: skin peri-umbilical punch biopsy 76


title: genomic DNA from skin peri-umbilical punch biopsy 104

source_name: skin peri-umbilical punch biopsy 104


title: genomic DNA from skin peri-umbilical punch biopsy 73

source_name: skin peri-umbilical punch biopsy 73


title: genomic DNA from skin peri-umbilical punch biopsy 92

source_name: skin peri-umbilical punch biopsy 92


title: genomic DNA from skin peri-umbilical punch biopsy 78

source_name: skin peri-umbilical punch biopsy 78


title: genomic DNA from skin peri-umbilical punch biopsy 67

source_name: skin peri-umbilical punch biopsy 67


title: genomic DNA from skin peri-umbilical punch biopsy 72

source_name: skin peri-umbilical punch biopsy 72


title: genomic DNA from skin peri-umbilical punch biopsy 69

source_name: skin peri-umbilical punch biopsy 69


title: genomic DNA from skin peri-umbilical punch biopsy 63

source_name: skin peri-umbilical punch biopsy 63


title: genomic DNA from skin peri-umbilical punch biopsy 64

source_name: skin peri-umbilical punch biopsy 64


title: genomic DNA from skin peri-umbilical punch biopsy 75

source_name: skin peri-umbilical punch biopsy 75


title: genomic DNA from skin peri-umbilical punch biopsy 65

source_name: skin peri-umbilical punch biopsy 65


title: genomic DNA from skin peri-umbilical punch biopsy 68

source_name: skin peri-umbilical punch biopsy 68


title: genomic DNA from skin peri-umbilical punch biopsy 70

source_name: skin peri-umbilical punch biopsy 70


title: genomic DNA from skin peri-umbilical punch biopsy 57

source_name: skin peri-umbilical punch biopsy 57


title: genomic DNA from skin peri-umbilical punch biopsy 77

source_name: skin peri-umbilical punch biopsy 77


title: genomic DNA from skin peri-umbilical punch biopsy 59

source_name: skin peri-umbilical punch biopsy 59


title: genomic DNA from skin peri-umbilical punch biopsy 66

source_name: skin peri-umbilical punch biopsy 66


title: genomic DNA from skin peri-umbilical punch biopsy 60

source_name: skin peri-umbilical punch biopsy 60


title: genomic DNA from skin peri-umbilical punch biopsy 56

source_name: skin peri-umbilical punch biopsy 56


title: genomic DNA from skin peri-umbilical punch biopsy 83

source_name: skin peri-umbilical punch biopsy 83


title: genomic DNA from skin peri-umbilical punch biopsy 74

source_name: skin peri-umbilical punch biopsy 74


title: genomic DNA from skin peri-umbilical punch biopsy 53

source_name: skin peri-umbilical punch biopsy 53


title: genomic DNA from skin peri-umbilical punch biopsy 62

source_name: skin peri-umbilical punch biopsy 62


title: genomic DNA from skin peri-umbilical punch biopsy 58

source_name: skin peri-umbilical punch biopsy 58


title: genomic DNA from skin peri-umbilical punch biopsy 61

source_name: skin peri-umbilical punch biopsy 61


title: genomic DNA from skin peri-umbilical punch biopsy 52

source_name: skin peri-umbilical punch biopsy 52


title: genomic DNA from skin peri-umbilical punch biopsy 54

source_name: skin peri-umbilical punch biopsy 54


title: genomic DNA from skin peri-umbilical punch biopsy 51

source_name: skin peri-umbilical punch biopsy 51


title: genomic DNA from skin peri-umbilical punch biopsy 49

source_name: skin peri-umbilical punch biopsy 49


title: genomic DNA from skin peri-umbilical punch biopsy 55

source_name: skin peri-umbilical punch biopsy 55


title: genomic DNA from skin peri-umbilical punch biopsy 50

source_name: skin peri-umbilical punch biopsy 50


title: genomic DNA from skin peri-umbilical punch biopsy 98

source_name: skin peri-umbilical punch biopsy 98


title: CGVHD_22

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

country: USA

institute: CC/DTM/NIH

description: gene expression data

hyb_protocol: 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit). Next cDNAs were fragmented, biotinylated, and hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).

scan_protocol: scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control(all from Affymetrix, Santa Clara, CA).

data_processing: Expression data were normalized, background-corrected, and summarized using the RNA algorithm

label: Biotin

source_name: CGVHD

growth_protocol: Monocytes from cryopreserved PBMC of normal and CGVHD patients were enriched by gating  on FSChi SSChi CD3– CD4dim cells using an Influx Cell Sorter (Becton Dickinson  Immunocytometry Systems)

extract_protocol: Total RNA was extracted from monocytes by using RNeasy kit (Qiagen, Germantown, , MD, USA)

value: Monocyte

tag: disease status

value: CGVHD


title: genomic DNA from skin peri-umbilical punch biopsy 45

source_name: skin peri-umbilical punch biopsy 45

tag: tissue


title: genomic DNA from skin peri-umbilical punch biopsy 44

source_name: skin peri-umbilical punch biopsy 44

tag: beadchip and order on beadchip (sentrix id)


title: CGVHD_26

description: gene expression data

label_protocol: 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit). Next cDNAs were fragmented, biotinylated, and hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).


title: CGVHD_20

description: gene expression data


title: CGVHD_25

description: gene expression data


title: CGVHD_21

description: gene expression data


title: CGVHD_24

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 43

source_name: skin peri-umbilical punch biopsy 43

tag: age at biopsy


title: genomic DNA from skin peri-umbilical punch biopsy 46

source_name: skin peri-umbilical punch biopsy 46

tag: gender


title: genomic DNA from skin peri-umbilical punch biopsy 71

source_name: skin peri-umbilical punch biopsy 71

tag: relatedness identification id


title: genomic DNA from skin peri-umbilical punch biopsy 47

source_name: skin peri-umbilical punch biopsy 47

tag: age at total body naevus count


title: CGVHD_17

description: gene expression data


title: CGVHD_18

description: gene expression data


title: CGVHD_23

description: gene expression data


title: CGVHD_19

description: gene expression data


title: CGVHD_16

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 39

source_name: skin peri-umbilical punch biopsy 39

tag: total body naevus count


title: genomic DNA from skin peri-umbilical punch biopsy 35

source_name: skin peri-umbilical punch biopsy 35

tag: bisulphite conversion average


title: genomic DNA from skin peri-umbilical punch biopsy 34

source_name: skin peri-umbilical punch biopsy 34

tag: bmi


title: genomic DNA from skin peri-umbilical punch biopsy 48

source_name: skin peri-umbilical punch biopsy 48

tag: smoking status


title: genomic DNA from skin peri-umbilical punch biopsy 36

source_name: skin peri-umbilical punch biopsy 36


title: genomic DNA from skin peri-umbilical punch biopsy 40

source_name: skin peri-umbilical punch biopsy 40


title: genomic DNA from skin peri-umbilical punch biopsy 37

source_name: skin peri-umbilical punch biopsy 37


title: genomic DNA from skin peri-umbilical punch biopsy 42

source_name: skin peri-umbilical punch biopsy 42


title: genomic DNA from skin peri-umbilical punch biopsy 38

source_name: skin peri-umbilical punch biopsy 38


title: genomic DNA from skin peri-umbilical punch biopsy 32

source_name: skin peri-umbilical punch biopsy 32


title: genomic DNA from skin peri-umbilical punch biopsy 41

source_name: skin peri-umbilical punch biopsy 41


title: genomic DNA from skin peri-umbilical punch biopsy 33

source_name: skin peri-umbilical punch biopsy 33


title: CGVHD_12

description: gene expression data

source_name: CGVHD


title: CGVHD_15

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 25

source_name: skin peri-umbilical punch biopsy 25


title: CGVHD_14

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 30

source_name: skin peri-umbilical punch biopsy 30


title: CGVHD_10

description: gene expression data


title: CGVHD_13

description: gene expression data


title: CGVHD_11

description: gene expression data


title: CGVHD_9

description: gene expression data


title: CGVHD_8

description: gene expression data


title: CGVHD_4

description: gene expression data


title: CGVHD_6

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 22

source_name: skin peri-umbilical punch biopsy 22


title: ND_10

description: gene expression data

source_name: ND

value: healthy


title: CGVHD_7

description: gene expression data


title: CGVHD_5

description: gene expression data


title: ND_9

description: gene expression data


title: CGVHD_3

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 23

source_name: skin peri-umbilical punch biopsy 23


title: genomic DNA from skin peri-umbilical punch biopsy 31

source_name: skin peri-umbilical punch biopsy 31


title: genomic DNA from skin peri-umbilical punch biopsy 26

source_name: skin peri-umbilical punch biopsy 26


title: genomic DNA from skin peri-umbilical punch biopsy 16

source_name: skin peri-umbilical punch biopsy 16


title: ND_6

description: gene expression data


title: ND_7

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 28

source_name: skin peri-umbilical punch biopsy 28


title: genomic DNA from skin peri-umbilical punch biopsy 29

source_name: skin peri-umbilical punch biopsy 29


title: genomic DNA from skin peri-umbilical punch biopsy 21

source_name: skin peri-umbilical punch biopsy 21


title: ND_1

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 27

source_name: skin peri-umbilical punch biopsy 27


title: ND_5

description: gene expression data


title: ND_3

description: gene expression data


title: ND_8

description: gene expression data


title: ND_2

description: gene expression data


title: ND_4

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 18

source_name: skin peri-umbilical punch biopsy 18


title: genomic DNA from skin peri-umbilical punch biopsy 24

source_name: skin peri-umbilical punch biopsy 24


title: genomic DNA from skin peri-umbilical punch biopsy 15

source_name: skin peri-umbilical punch biopsy 15


title: genomic DNA from skin peri-umbilical punch biopsy 12

source_name: skin peri-umbilical punch biopsy 12


title: genomic DNA from skin peri-umbilical punch biopsy 19

source_name: skin peri-umbilical punch biopsy 19


title: genomic DNA from skin peri-umbilical punch biopsy 17

source_name: skin peri-umbilical punch biopsy 17


title: CGVHD_2

description: gene expression data

source_name: CGVHD


title: Liver metastasis of colon cancer tissue 14d-2

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

description:
Test
miRNA

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:http://pcrdataanalysis.sabiosciences.com/mirna
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, and RNU6.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

organism: Mus musculus

source_name: tissue

label_protocol: PCR assays were performed using the Qiagen miScript miRNA PCR Array Mouse miRBase Profiler following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Applied Biosystems ViiA™ 7) with 40 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with miRNeasy mini kit (Qiagen).

value: colon cancer cells metastasis

tag: time

value: 14 days


title: Liver metastasis of colon cancer tissue 14d-1

description:
Test
miRNA


title: Primary colon cancer tissue-2

description:
Test
miRNA

value: Primary colon cancer cells


title: Primary colon cancer tissue-1

description:
Test
miRNA


title: Liver metastasis of colon cancer exosomes 14d-2

description:
Test
miRNA

source_name: exosomes


title: Liver metastasis of colon cancer exosomes 14d-3

description:
Test
miRNA


title: Liver metastasis of colon cancer exosomes 14d-1

description:
Test
miRNA


title: CGVHD_1

description: gene expression data


title: genomic DNA from skin peri-umbilical punch biopsy 10

source_name: skin peri-umbilical punch biopsy 10


title: Liver metastasis of colon cancer exosomes 7d-3

description:
Test
miRNA

value: 7 days


title: genomic DNA from skin peri-umbilical punch biopsy 9

source_name: skin peri-umbilical punch biopsy 9


title: Liver metastasis of colon cancer exosomes 3d-3

description:
Test
miRNA

value: 3 days


title: Liver metastasis of colon cancer exosomes 3d-2

description:
Test
miRNA


title: Liver metastasis of colon cancer exosomes 7d-2

description:
Test
miRNA


title: genomic DNA from skin peri-umbilical punch biopsy 20

source_name: skin peri-umbilical punch biopsy 20


title: genomic DNA from skin peri-umbilical punch biopsy 14

source_name: skin peri-umbilical punch biopsy 14


title: Primary colon cancer exosomes-2

description:
Test
miRNA

value: Primary colon cancer exo


title: naïve colon exosomes-2

description:
control
miRNA

value: naïve colon derived exosomes


title: Primary colon cancer exosomes-3

description:
Test
miRNA


title: Primary colon cancer exosomes-1

description:
Test
miRNA


title: genomic DNA from skin peri-umbilical punch biopsy 11

source_name: skin peri-umbilical punch biopsy 11

value: skin

value: female


title: naïve colon exosomes-3

description:
control
miRNA


title: naïve colon exosomes-1

description:
control
miRNA


title: genomic DNA from skin peri-umbilical punch biopsy 13

source_name: skin peri-umbilical punch biopsy 13


title: CB-CD34+ AD Fraction_co-culture_rep 2

status: Public on Jan 03 2017

city: Brescia

first: Simone

last: Perucca

address: Viale Europa

department: Department of Clinical and experimental sciences

country: Italy

institute: University of Brescia

hyb_protocol: Labelled RNA were fragmented and hybridized on Affymetrix HG-U133A PLUS 2.0 GeneChip arrays that were subsequently washed and stained using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: The GeneChip was scanned and data extracted using GeneChip scanner 3000 7G (Affimetrix, SantanClara, CA).

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software and normalyzed with RMA algorithm. Subsequently analyses for differentially expressed genes cathegorization were performed with Partek® Genomics Suite software version 6.6 (Partek Inc., St. Louis, MO). The analysis of molecular pathways was carried out through the DAVID Functional Annotation Bioinformatics Microarray Analysis. Broad Institute Gene Set Enrichment Analysis (GSEA) software was performed to identify significant enrichments in differentially expressed genes signatures, in case of nominal P values corrected for False Discovery Rate (FDR) for enrichment scores minor than 0.05. The network analyses were generated through the use of Ingenuity Pathway Analysis® (IPA®, Qiagen).

source_name: Umbilical cord blood

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 50 ng total RNA using the GeneChip 3’ IVT Expression kit (Affymetrix)

growth_protocol: BM-MSCs were thawed at 37°C and 5x10^5 cells were plated in T75 flasks. Cells were cultured in complete ISCOVE’s modified Dulbecco’s medium supplemented with 10% FBS for a week until 80% confluence.  CB-CD34+ cells were seeded directly onto the MSCs layer at a final concentration of 3x10^5 cells/flask. Cells were maintained in serum-free medium (StemSpan H3000, StemCell Technologies) supplemented with 100 ng/ml Stem Cell Factor (SCF) (Peprotech), Thrombopoietin (TPO) (Peprotech) and Granulocyte Colony Stimulating Factor (G-CSF) (Italfarmaco) for 10 days at 37°C and 5% CO2.

extract_protocol: Total cellular RNA was isolated using Qiagen RNeasy kit according to manufactures’ instructions (Qiagen, Hilden, Germany).

treatment_protocol: After 10 days of culture, cells were collected and sorted by a FACSAria II flow cytometer (Becton Dickinson). Flow cytometric data were analyzed using FACSDiva software (Becton Dickinson).  MSCs were identified on the basis of CD73, CD90, CD105 co-expression and lack of CD45. CB-CD34+ cells were identified on the basis of CD45 and CD34 co-expression. At least 3x10^5 gated events were acquired for each sample. Purity of FACS-isolated cells was greater than 95%, as assessed by flow cytometric analysis of post-sorting samples.

value: Umbilical cord blood


title: BM-MSCs_co-culture_rep 1

source_name: Bone Marrow

value: Bone Marrow


title: genomic DNA from skin peri-umbilical punch biopsy 5

source_name: skin peri-umbilical punch biopsy 5


title: genomic DNA from skin peri-umbilical punch biopsy 2

source_name: skin peri-umbilical punch biopsy 2


title: genomic DNA from skin peri-umbilical punch biopsy 4

source_name: skin peri-umbilical punch biopsy 4


title: BM-MSCs_co-culture_rep 3


title: genomic DNA from skin peri-umbilical punch biopsy 3

source_name: skin peri-umbilical punch biopsy 3


title: BM-MSCs_co-culture_rep 2


title: CB-CD34+ AD Fraction_co-culture_rep 3


title: genomic DNA from skin peri-umbilical punch biopsy 8

source_name: skin peri-umbilical punch biopsy 8


title: CB-CD34+ AD Fraction_co-culture_rep 1


title: CB-CD34+ SN Fraction_co-culture_rep 2


title: CB-CD34+ SN Fraction_co-culture_rep 3


title: CB-CD34+ SN Fraction_co-culture_rep 1


title: CB-CD34+_single culture_control 3


title: genomic DNA from skin peri-umbilical punch biopsy 1

source_name: skin peri-umbilical punch biopsy 1


title: Heart-ISO-72hrs-rep6

type: protein

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

country: China

institute: Peking University Third Hospital

hyb_protocol: Antibody arrays were used according to the manufacturer’s instructions. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with HRP-conjugated streptavidin.

scan_protocol: Expose to x-ray film and detect signal using film developer or detect signal directly from membrane using chemiluminescene imaging system.

data_processing:
By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared.
IPP6.0 software computed normalized signal intensity

molecule: protein

source_name: heart, ISO, 72hrs

label_protocol: Samples were labeled according to the manufacturer’s instructions

extract_protocol: Weigh out tissue and cut into cubes. Prepare protein extraction reagent containing inhibitors. Add ice-cold Protein Extraction Reagent containing protease inhibitors. Grind in a blender on low power using 30-second bursts until fully homogenized. Allow material to cool for 1 minute between bursts. Centrifuge the lysate at 14,000xg for 15 minutes and transfer the supernatant to a new tube for further analysis.

treatment_protocol: There are 4 groups: vehicle group, mice were subcutaneous injected with a single dose of saline (10 ml/kg body weight), ISO group, mice were subcutaneous injected with a single dose of isoproterenol (5 mg/kg body weight). ISO+IL-18 nAbs group, IL-18 nAbs were intraperitoneally injected (50 μg/ mouse) at 1 hr after ISO injection. ISO+IgG group, rat IgG were intraperitoneally injected (50 μg/ mouse) at 1 hr after ISO injection. The hearts from mice were harvested at 24 hrs after saline or ISO treatment and immediately frozen in liquid nitrogen.

value: 10 weeks old

value: Male

tag: strain

value: Heart


title: Heart-ISO-72hrs-rep5

tag: Sex


title: Heart-ISO-72hrs-rep4

tag: age


title: CB-CD34+_single culture_control 1


title: Heart-ISO-24hrs-rep5

source_name: heart, ISO, 24hrs


title: Heart-ISO-24hrs-rep6


title: Heart-Vehicle-rep 5

source_name: heart, vehicle


title: Heart-ISO-24hrs-rep4


title: Heart-Vehicle-rep 4


title: Primary colon cancer tissue-3

description:
Test
miRNA

source_name: tissue


title: Liver metastasis of colon cancer exosomes 3d-1

description:
Test
miRNA

source_name: exosomes


title: Heart-Vehicle-rep 6


title: BM-MSCs_single culture_control 1


title: Liver metastasis of colon cancer tissue 14d-3

description:
Test
miRNA


title: Liver metastasis of colon cancer exosomes 7d-1

description:
Test
miRNA


title: BM-MSCs_single culture_control 2


title: BM-MSCs_single culture_control 3


title: genomic DNA from skin peri-umbilical punch biopsy 7

source_name: skin peri-umbilical punch biopsy 7


title: Sp_W_D7_16680x8016_37

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Gene expression data from West Nile Virus infected Mice at Day 7 post infection

hyb_protocol: Individual sense-strand DNA targets were hybridized to Mouse Gene 2.1 ST 24-Array Plates (Affymetrix, Inc.) using the GeneTitan Multi-Channel (MC) Instrument for hybridization, array staining and washing and scanning.  Quality Control Metrics for Hybridization, Labeling and Sample quality were generated using the Affymetrix Expression Console software.  All samples passed the QC criteria.

scan_protocol: Affy arrays were scanned with an Affymetrix GeneTitan

data_processing: Data was analyzed using R(3.01) and oligo and limma packages. Matrix was generated use RMA. Samples were background corrected and quantile normalized

source_name: Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 7 post infection

label_protocol: RNA samples were prepared for whole transcriptome expression analysis using the WT PLUS Reagent Kit following the manufacturer’s recommended protocol (Affymetrix, Inc. Santa Clara, CA).  100 ng of total RNA was used to prepare the hybridization ready targets.

growth_protocol: spleen was isolated for RNA extraction.

extract_protocol: Spleen tissues were thawed, transferred to lysis buffer either TRIzol (Life Technologies) or RLT Reagent (Qiagen Inc.) and homogenized. RNA was isolated using Qiagen miRNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip.

treatment_protocol: Per the manufacturer's protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation  overnight, tissue was removed from RNAlater and stored at -80°C until RNA isolation in TRIzol or RLT buffer.

tag: batch

value: m

value: Spleen

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

tag: treatment

value: West Nile Virus infected

tag: days post-infection

tag: collaborative cross line (genetic background, unc_id)


title: Sp_W_D12_8002X8010_73

description: Gene expression data from West Nile Virus infected Mice at Day 12 post infection

source_name: Spleen Tissue from West Nile Virus infected Line 8002X8010 at Day 12 post infection

tag: tissue


title: Sp_W_D2_16680x8016_m87

description: Gene expression data from West Nile Virus infected Mice at Day 2 post infection

source_name: Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 2 post infection


title: Main Lacrimal Gland 3b

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: biologic duplicate

hyb_protocol: Labeled double stranded cDNA was hybridized.

scan_protocol: “Human Transcriptome Array (HTA) 2.0” Array from Affymetrix ® for main lacrimal gland.  “GeneChip1 Human Gene (HuGene) 1.0 ST” Array from Affymetrix ® for accessory lacrimal gland.

data_processing: We obtained transformed raw RMAs using the R oligo package for each array individually: arrays were duplicated and expression levels were obtained using the rma function for each duplicate set of arrays (the rma function requires at least 2 arrays to be provided). The probe sets in the expression table for each array were annotated with array-type-specific probe set annotation csv files obtained from Affymetrix’s website, and the duplicated expression entries were removed. The various microarray datasets in this study ranged over 4 array types: pd.hg.u133a.2, pd.hg.u133.plus.2, pd.hta.2.0, and pd.hugene.1.0. To match gene annotations across array types, we compared the “Gene Symbol” columns in pd.hg.u133a.2 and pd.hg.u133.plus.2 with the “gene_assignment” columns in pd.hta.2.0 and pd.hugene.1.0. Any probe sets pairs between platforms that shared at least one gene name in these columns was included, and only the first gene assignment to a probe set was used within a given microarray. After merging these annotations, 12,398 genes were retained that could be cross-compared between platforms, for 112 samples (104 publicly available, plus 8 from this study). We then performed quantile normalization on the merged gene expression table using internal scripts: a reference distribution of expression levels was obtained across all 112 samples, and the quantiles for each individual sample were then matched to this reference distribution.

source_name: Main Lacrimal gland

label_protocol: For FFPE samples - labelled with “SensationPlus™ FFPE Amplification and WT Labeling Kit” from Affymetrix (r).

growth_protocol: FFPE accessory lacrimal gland tissue was obtained using laser capture microdissection.  Main lacrimal gland samples were processed for RNA extraction after obtaining tissue.

extract_protocol: Total RNA was extracted from human lacrimal gland tissue using RNeasy from QIAGEN using the manufacturer’s protocol. For FFPE samples, following RNA extraction, 25ng of total RNA was amplified.  Extracted RNA was analyzed using Qubit quantification and Tape Station 2200 quantification-sizing quality control system.

value: Main Lacrimal gland


title: Sp_M_D2_8002X8010_101

description: Gene expression data from Mock infected Mice at Day 2 post infection

source_name: Spleen Tissue from Mock infected Line 8002X8010 at Day 2 post infection

value: Mock infected


title: Sp_W_D12_5489x16557_104

source_name: Spleen Tissue from West Nile Virus infected Line 5489x16557 at Day 12 post infection


title: Sp_W_D12_8002X8010_74


title: Sp_W_D2_16680x8016_m86


title: Sp_W_D4_16680x8016_m67

description: Gene expression data from West Nile Virus infected Mice at Day 4 post infection

source_name: Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 4 post infection


title: Sp_M_D2_5489x16557_100

source_name: Spleen Tissue from Mock infected Line 5489x16557 at Day 2 post infection


title: Sp_W_D7_16680x8016_m76


title: Sp_W_D12_16680x8016_m48

source_name: Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 12 post infection


title: Sp_W_D7_16680x8016_m77


title: Sp_W_D12_16680x8016_m47


title: Main Lacrimal Gland 2 left

description: left side


title: Main Lacrimal Gland 3a


title: genomic DNA from skin peri-umbilical punch biopsy 6

source_name: skin peri-umbilical punch biopsy 6

tag: beadchip and order on beadchip (sentrix id)

tag: age at biopsy

tag: gender

tag: relatedness identification id


title: Sp_M_D12_16680x8016_m44

description: Gene expression data from Mock infected Mice at Day 12 post infection

source_name: Spleen Tissue from Mock infected Line 16680x8016 at Day 12 post infection


title: Sp_W_D4_16680x8016_m69


title: Sp_W_D4_16680x8016_m68


title: Main Lacrimal Gland1 left

description: left side


title: Sp_W_D2_16680x8016_m84


title: Main Lacrimal Gland2 right

description: right side


title: Main Lacrimal Gland1 right

description: right side


title: Sp_W_D12_5489x16557_83


title: Sp_W_D12_8002X8010_75


title: Sp_M_D12_16680x8016_m43


title: Sp_W_D2_16513x16188_m94

source_name: Spleen Tissue from West Nile Virus infected Line 16513x16188 at Day 2 post infection


title: Sp_W_D7_16680x8016_m78


title: Sp_M_D12_16513x16188_m40

source_name: Spleen Tissue from Mock infected Line 16513x16188 at Day 12 post infection


title: CB-CD34+_single culture_control 2

source_name: Umbilical cord blood


title: Sp_W_D2_16513x16188_m92


title: Sp_W_D2_16513x16188_m93


title: Sp_W_D4_16513x16188_m60

source_name: Spleen Tissue from West Nile Virus infected Line 16513x16188 at Day 4 post infection


title: Sp_W_D7_16513x16188_m6

source_name: Spleen Tissue from West Nile Virus infected Line 16513x16188 at Day 7 post infection


title: Sp_W_D12_16513x16188_m39

source_name: Spleen Tissue from West Nile Virus infected Line 16513x16188 at Day 12 post infection


title: Sp_W_D4_16513x16188_m50


title: Sp_W_D7_16513x16188_m5


title: Sp_M_D12_16513x16188_m43


title: Sp_M_D12_13067x5306_m65

source_name: Spleen Tissue from Mock infected Line 13067x5306 at Day 12 post infection


title: Sp_W_D12_16513x16188_m38


title: Sp_M_D12_16513x16188_m42


title: Sp_W_D12_16513x16188_m37


title: Sp_W_D7_13067x5306_m10

source_name: Spleen Tissue from West Nile Virus infected Line 13067x5306 at Day 7 post infection


title: Sp_M_D12_16513x16188_m41


title: Sp_W_D4_16513x16188_m51


title: Sp_W_D12_13067x5306_m58

source_name: Spleen Tissue from West Nile Virus infected Line 13067x5306 at Day 12 post infection


title: Sp_W_D7_13067x5306_m57


title: Sp_W_D4_13067x5306_m56

source_name: Spleen Tissue from West Nile Virus infected Line 13067x5306 at Day 4 post infection


title: Sp_W_D12_13067x5306_m64


title: Sp_W_D7_13067x5306_m49


title: PBMC_Primary_HCMV_infected_patient_46

city: Nantes

first: Christelle

last: Retière

address: 34 boulevard jean Monnet

country: France

institute: Blood Transfusion Center

description: Symptomatic primary HCMV infected immunocompetent adults

hyb_protocol: Fragmented samples were hybridazed 16hrs at 45°C on Affymetrix Human Gene 2.1 ST array using the Affymetrix GeneTitan® kit protocols.

scan_protocol: The GeneChip® array-plates were scanned using the GeneTitan® Multichanel Instrument

data_processing: Raw data were submitted to Expression Console (Affymetrix) for quality control and RMA normalization.

source_name: Peripheral blood

label_protocol: Biotinylated cDNA fragments were prepared according to the GeneChip® WT PLUS Reagent Kit Manual (Affymetrix) recommendations from 100ng of total RNA.

extract_protocol: Total RNA from 1M PBMCs was extracted using the NucleoSpin® RNA XS kit (Macherey Nagel), according to manufacturer's instructions.

treatment_protocol: PBMCs were isolated from citrate-phosphate-dextrose blood samples from HCMV-seronegative or -seropositive healthy controls and from primary HCMV infected patients. PBMCs were frozen prior to RNA extraction.

tag: sample type

value: HCMV Primary-infected patients

tag: hcmv exposition

value: During acute primary HCMV infection


title: PBMC_Primary_HCMV_infected_patient_39


title: Sp_M_D12_13067x5306_m59


title: PBMC_HCMV_seropositive_healthy_donor_62

description: Healthy donors latently HCMV infected, with NKG2C NK cell expansion

value: Healthy control

value: HCMV-specific IgG detected


title: PBMC_Primary_HCMV_infected_patient_38


title: PBMC_Primary_HCMV_infected_patient_41


title: PBMC_Primary_HCMV_infected_patient_53


title: Sp_M_D12_13067x5306_m68


title: PBMC_Primary_HCMV_infected_patient_44


title: PBMC_Primary_HCMV_infected_patient_42


title: PBMC_Primary_HCMV_infected_patient_48


title: PBMC_Primary_HCMV_infected_patient_47


title: PBMC_Primary_HCMV_infected_patient_40


title: PBMC_HCMV_seropositive_healthy_donor_34


title: Sp_W_D4_13067x5306_m45


title: PBMC_HCMV_seropositive_healthy_donor_36


title: Sp_W_D7_13067x5306_m46


title: PBMC_Primary_HCMV_infected_patient_37


title: PBMC_HCMV_seropositive_healthy_donor_25


title: PBMC_HCMV_seropositive_healthy_donor_64


title: Sp_W_D12_13067x5306_m47


title: PBMC_HCMV_seropositive_healthy_donor_28


title: PBMC_HCMV_seropositive_healthy_donor_29


title: PBMC_HCMV_seropositive_healthy_donor_27


title: PBMC_HCMV_seropositive_healthy_donor_63


title: Sp_W_D4_13067x5306_m48


title: Sp_W_D2_13067x5306_m38

source_name: Spleen Tissue from West Nile Virus infected Line 13067x5306 at Day 2 post infection


title: PBMC_HCMV_seropositive_healthy_donor_65


title: PBMC_HCMV_seropositive_healthy_donor_35


title: Sp_W_D2_13067x5306_m37


title: Sp_W_D2_8010x16441_m36

source_name: Spleen Tissue from West Nile Virus infected Line 8010x16441 at Day 2 post infection


title: Sp_W_D4_8010x16441_99

source_name: Spleen Tissue from West Nile Virus infected Line 8010x16441 at Day 4 post infection


title: PBMC_HCMV_seropositive_healthy_donor_17

description: Healthy donors latently HCMV infected, without NKG2C NK cell expansion


title: PBMC_HCMV_seropositive_healthy_donor_13


title: PBMC_HCMV_seropositive_healthy_donor_58


title: Sp_M_D12_8010x16441_50

source_name: Spleen Tissue from Mock infected Line 8010x16441 at Day 12 post infection


title: Sp_W_D12_8010x16441_49

source_name: Spleen Tissue from West Nile Virus infected Line 8010x16441 at Day 12 post infection


title: PBMC_HCMV_seropositive_healthy_donor_21


title: PBMC_HCMV_seropositive_healthy_donor_60


title: PBMC_HCMV_seropositive_healthy_donor_57


title: PBMC_HCMV_seropositive_healthy_donor_59


title: PBMC_HCMV_seropositive_healthy_donor_26


title: PBMC_HCMV_seropositive_healthy_donor_32


title: Sp_W_D2_8010x16441_190


title: Sp_W_D12_8010x16441_48


title: PBMC_HCMV_seronegative_healthy_donor_11

description: Healthy donors without HCMV exposure

value: No HCMV-specific IgG detected


title: Sp_W_D7_8010x16441_46

source_name: Spleen Tissue from West Nile Virus infected Line 8010x16441 at Day 7 post infection


title: PBMC_HCMV_seropositive_healthy_donor_56


title: Sp_M_D12_8010x16441_43


title: Sp_W_D7_8010x16441_45


title: PBMC_HCMV_seropositive_healthy_donor_23


title: Sp_W_D7_8010x16441_44


title: PBMC_HCMV_seropositive_healthy_donor_24


title: PBMC_HCMV_seropositive_healthy_donor_22


title: PBMC_HCMV_seronegative_healthy_donor_55

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seropositive_healthy_donor_61


title: PBMC_HCMV_seronegative_healthy_donor_10

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seronegative_healthy_donor_1

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seronegative_healthy_donor_5

description: Healthy donors without HCMV exposure


title: Sp_W_D2_8010x16441_186


title: PBMC_HCMV_seronegative_healthy_donor_50

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seronegative_healthy_donor_52

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seronegative_healthy_donor_53

description: Healthy donors without HCMV exposure


title: PBMC_HCMV_seronegative_healthy_donor_49

description: Healthy donors without HCMV exposure


title: Sp_W_D2_8010x16441_185


title: PBMC_HCMV_seronegative_healthy_donor_54

description: Healthy donors without HCMV exposure


title: Sp_M_D2_8010x16441_170

source_name: Spleen Tissue from Mock infected Line 8010x16441 at Day 2 post infection


title: PBMC_HCMV_seronegative_healthy_donor_2

description: Healthy donors without HCMV exposure


title: Sp_M_D2_8010x16441_163


title: PBMC_HCMV_seronegative_healthy_donor_12

description: Healthy donors without HCMV exposure


title: Sp_M_D2_8010x16441_162


title: Sp_W_D12_8010x16441_147


title: Sp_W_D4_5489x16557_100

source_name: Spleen Tissue from West Nile Virus infected Line 5489x16557 at Day 4 post infection


title: Sp_W_D7_5489x16557_36

source_name: Spleen Tissue from West Nile Virus infected Line 5489x16557 at Day 7 post infection


title: Sp_W_D7_5489x16557_35


title: Retina, 48 hours, euglycemic clamp, replicate 3

city: Lausanne

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

hyb_protocol: 5.5 μg of each fragmented cDNA were end-labeled with biotin and hybridized to a GeneChip Mouse Gene 1.0 ST array (Affymetrix)

scan_protocol: U133 Plus 2.0 Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Background subtraction, quantile normalization and probeset summarization was performed using the Affymetrix Power Tools apt-probeset-summarize command with the -rma option

molecule: polyA RNA

source_name: Retina

label_protocol: RNA samples isolated from retina, 4 and 48 h after the end of the clamp (3 samples per condition; 12 samples total), were diluted to 100 ng/μl and used to perform the target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

extract_protocol: Not provided

value: retina

value: 2 months


title: Sp_W_D4_8010x16441_101


title: Retina, 48 hours, euglycemic clamp, replicate 2

value: female


title: [B] OTX 24 h

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)
Log2 Normalized Data

source_name: MDA-MB-468   cell lines treated with OTX015

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with OTX015 (MK-8628) BET inhibitor

tag: cell line type

value: [B] OTX 24 h


title: [B] Control 24 h

source_name: MDA-MB-468   cell lines untreated

value: [B] Control 24 h


title: Sp_W_D2_5489x16557_109

source_name: Spleen Tissue from West Nile Virus infected Line 5489x16557 at Day 2 post infection


title: Retina, 48 hours, euglycemic clamp, replicate 1

tag: strain


title: Retina, 4 hours, euglycemic clamp, replicate 2


title: [B] DMSO 24 h

source_name: MDA-MB-468   cell lines treated with DMSO

value: [B] DMSO 24 h


title: Retina, 48 hours, hypoglycemic clamp, replicate 1


title: Sp_W_D4_5489x16557_29

tag: Sex


title: [B] OTX 8 h

value: [B] OTX 8 h


title: Retina, 48 hours, hypoglycemic clamp, replicate 3

tag: age


title: Retina, 4 hours, hypoglycemic clamp, replicate 1


title: Retina, 48 hours, hypoglycemic clamp, replicate 2


title: Sp_W_D2_5489x16557_108

tag: batch

value: m


title: Retina, 4 hours, hypoglycemic clamp, replicate 2


title: Retina, 4 hours, euglycemic clamp, replicate 1


title: [B] DMSO 8 h

value: [B] DMSO 8 h


title: Retina, 4 hours, hypoglycemic clamp, replicate 3


title: Retina, 4 hours, euglycemic clamp, replicate 3


title: [B] Control 8 h

value: [B] Control 8 h


title: Sp_W_D2_5489x16557_107

value: Spleen

tag: collaborative cross line (genetic background)

value: West Nile Virus infected


title: Sp_M_D2_5489x16557_106

source_name: Spleen Tissue from Mock infected Line 5489x16557 at Day 2 post infection

tag: animal number (rxid)

value: Mock infected


title: Sp_M_D2_5489x16557_103

tag: treatment


title: [B] OTX 4 h

value: [B] OTX 4 h


title: [A] OTX 8 h

source_name: MDA-MB-231  cell lines treated with OTX015

value: [A] OTX 8 h


title: [A] DMSO 8 h

source_name: MDA-MB-231  cell lines treated with DMSO

value: [A] DMSO 8 h


title: [B] DMSO 4 h

value: [B] DMSO 4 h


title: [A] OTX 24 h

value: [A] OTX 24 h


title: [B] Control 4 h

value: [B] Control 4 h


title: [A] DMSO 24 h

value: [A] DMSO 24 h


title: [A] Control 24 h

source_name: MDA-MB-231  cell lines untreated

value: [A] Control 24 h


title: [A] Control 8 h

value: [A] Control 8 h


title: Sp_M_D2_3154x3609_102

source_name: Spleen Tissue from Mock infected Line 3154x3609 at Day 2 post infection

tag: days post-infection


title: [A] Control 4 h

value: [A] Control 4 h


title: [A] DMSO 4 h

value: [A] DMSO 4 h


title: [A] OTX 4 h

value: [A] OTX 4 h


title: Sp_W_D12_3154x3609_74

source_name: Spleen Tissue from West Nile Virus infected Line 3154x3609 at Day 12 post infection

value: m

tag: collaborative cross line (genetic background, unc_id)


title: Sp_W_D4_5489x16557_11

tag: tissue


title: Sp_W_D12_3154x3609_78


title: Sp_W_D7_3154x3609_33

source_name: Spleen Tissue from West Nile Virus infected Line 3154x3609 at Day 7 post infection


title: Sp_W_D7_3154x3609_32


title: Sp_W_D4_3154x3609_84

source_name: Spleen Tissue from West Nile Virus infected Line 3154x3609 at Day 4 post infection


title: A549_OTX_12H

data_processing: The data were normalised using quantile method

source_name: A549 cell line treated with OTX015

tag: cell line


title: A549_DMSO_4H

source_name: A549 cell line treated with DMSO

value: DMSO


title: NCIH82_DMSO_12H

source_name: NCIH82 cell line treated with DMSO


title: A549_OTX_4H


title: Sp_W_D7_3154x3609_34

value: Spleen


title: Sp_W_D4_3154x3609_79

value: West Nile Virus infected


title: Sp_W_D4_5489x16557_12

source_name: Spleen Tissue from West Nile Virus infected Line 5489x16557 at Day 4 post infection


title: A549_DMSO_8H


title: A549_DMSO_24H


title: A549_OTX_24H


title: Sp_M_D2_3154x3609_72

value: Mock infected


title: A549_OTX_2H


title: A549_DMSO_12H


title: NCIH82_OTX_8H

source_name: NCIH82 cell line treated with OTX015


title: Sp_W_D4_3154x3609_85


title: A549_OTX_8H


title: A549_DMSO_2H


title: Sp_M_D2_16750x13421_71

source_name: Spleen Tissue from Mock infected Line 16750x13421 at Day 2 post infection


title: Sp_M_D12_16750x13421_m134

source_name: Spleen Tissue from Mock infected Line 16750x13421 at Day 12 post infection


title: A549_UNTREATED_0H

source_name: A549 cell line untreated


title: NCIH31_OTX_4H

source_name: NCIH31 cell line treated with OTX015


title: NCIH31_OTX_24H


title: NCIH31_DMSO_4H

source_name: NCIH31 cell line treated with DMSO


title: NCIH31_DMSO_8H


title: NCIH31_DMSO_24H


title: NCIH31_OTX_12H


title: NCIH31_OTX_2H


title: Sp_W_D12_16750x13421_m130

source_name: Spleen Tissue from West Nile Virus infected Line 16750x13421 at Day 12 post infection


title: Sp_W_D4_16750x13421_m107

source_name: Spleen Tissue from West Nile Virus infected Line 16750x13421 at Day 4 post infection


title: Sp_M_D12_16750x13421_m133


title: Sp_W_D7_16750x13421_m117

source_name: Spleen Tissue from West Nile Virus infected Line 16750x13421 at Day 7 post infection


title: Sp_W_D7_16750x13421_m125


title: NCIH22_OTX_4H

source_name: NCIH22 cell line treated with OTX015


title: NCIH22_DMSO_8H

source_name: NCIH22 cell line treated with DMSO


title: NCIH31_OTX_8H


title: NCIH22_OTX_12H


title: NCIH22_OTX_2H


title: NCIH31_DMSO_2H


title: Sp_W_D12_16750x13421_m129


title: NCIH82_DMSO_8H


title: NCIH22_DMSO_24H


title: Sp_W_D12_8034x8048_108

source_name: Spleen Tissue from West Nile Virus infected Line 8034x8048 at Day 12 post infection


title: NCIH31_DMSO_12H


title: NCIH22_OTX_24H


title: NCIH82_OTX_4H


title: Sp_M_D2_8034x8048_169

source_name: Spleen Tissue from Mock infected Line 8034x8048 at Day 2 post infection


title: Sp_W_D12_8034x8048_168


title: NCIH22_OTX_8H


title: DMS114_DMSO_8H

source_name: DMS114 cell line treated with DMSO


title: Sp_W_D12_8034x8048_159


title: NCIH22_UNTREATED_0H

source_name: NCIH22 cell line untreated


title: Sp_W_D12_8034x8048_160


title: NCIH22_DMSO_12H


title: NCIH31_UNTREATED_0H

source_name: NCIH31 cell line untreated


title: NCIH22_DMSO_2H


title: DMS114_OTX_24H

source_name: DMS114 cell line treated with OTX015


title: NCIH22_DMSO_4H


title: DMS114_DMSO_24H


title: DMS114_OTX_2H


title: HOP92_DMSO_8H

source_name: HOP92 cell line treated with DMSO


title: Sp_W_D2_8034x8048_158

source_name: Spleen Tissue from West Nile Virus infected Line 8034x8048 at Day 2 post infection


title: DMS114_DMSO_4H


title: DMS114_DMSO_12H


title: DMS114_OTX_12H


title: Sp_W_D2_8034x8048_137


title: NCIH82_DMSO_4H

source_name: NCIH82 cell line treated with DMSO


title: Sp_M_D2_8034x8048_144


title: Sp_M_D2_8034x8048_143


title: HOP92_OTX_4H

source_name: HOP92 cell line treated with OTX015


title: Sp_W_D7_8034x8048_124

source_name: Spleen Tissue from West Nile Virus infected Line 8034x8048 at Day 7 post infection


title: HOP92_OTX_24H


title: DMS114_UNTREATED_0H

source_name: DMS114 cell line untreated


title: Sp_W_D7_8034x8048_123


title: DMS114_OTX_8H


title: Sp_W_D4_8034x8048_122

source_name: Spleen Tissue from West Nile Virus infected Line 8034x8048 at Day 4 post infection


title: HOP92_DMSO_4H


title: HOP92_DMSO_24H


title: Sp_W_D2_8034x8048_136


title: HOP92_OTX_12H


title: Sp_W_D4_8034x8048_121


title: HOP92_OTX_2H


title: HOP92_OTX_8H


title: Sp_W_D4_8034x8048_120


title: HOP92_DMSO_2H


title: HOP92_UNTREATED_0H

source_name: HOP92 cell line untreated


title: NCIH82_UNTREATED_0H

source_name: NCIH82 cell line untreated


title: HOP92_DMSO_12H


title: Pten pc-/- GSI treated2

description: Ptenpc-/- treated with Gamma-secretase inhibitor

source_name: mouse with KO of Pten

growth_protocol: in vivo

treatment_protocol: knockdown of Pten Gene and treatment with Gamma-secretase inhibitor

value: prostate

tag: genotype/variation

value: KO of Pten


title: Sp_W_D7_3032x16188_109

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 7 post infection


title: Pten pc-/- GSI treated1


title: HOP62_DMSO_8H

source_name: HOP62 cell line treated with DMSO


title: Mouse WT prostate 4640

description: WT, Pten pc+/+

source_name: mouse Wild Type

value: Wild Type


title: Sp_W_D7_3032x16188_96


title: DMS114_DMSO_2H

source_name: DMS114 cell line treated with DMSO


title: Sp_W_D7_3032x16188_90


title: HOP62_OTX_4H

source_name: HOP62 cell line treated with OTX015


title: Mouse WT Prostate 950

description: WT, Pten pc+/+


title: Pten pc-/- ctrl3

description: Ptenpc-/-


title: HOP62_DMSO_24H


title: Pten pc-/- ctrl2

description: Ptenpc-/-


title: Sp_W_D12_3032x16188_65

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 12 post infection


title: Sp_W_D12_3032x16188_48


title: Sp_W_D12_3032x16188_47


title: Pten pc-/- ctrl1

description: Ptenpc-/-


title: Sp_W_D2_3032x16188_148

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 2 post infection


title: Sp_M_D2_3032x16188_150

source_name: Spleen Tissue from Mock infected Line 3032x16188 at Day 2 post infection


title: Sp_M_D2_3032x16188_149


title: HOP62_OTX_2H


title: HOP62_OTX_12H


title: HOP62_OTX_24H


title: HOP62_DMSO_2H


title: Sp_W_D2_3032x16188_135


title: Sp_W_D2_3032x16188_134


title: HOP62_DMSO_4H


title: HOP62_UNTREATED_0H

source_name: HOP62 cell line untreated


title: HOP62_OTX_8H


title: HOP62_DMSO_12H


title: Accessory Lacrimal Gland 1a

description: FFPE

source_name: Accessory Lacrimal gland

value: Accessory Lacrimal gland


title: Accessory Lacrimal Gland 1b

description: FFPE biologic duplicate


title: NCIH82_OTX_24H

source_name: NCIH82 cell line treated with OTX015


title: Sp_W_D4_3032x16188_126

source_name: Spleen Tissue from West Nile Virus infected Line 3032x16188 at Day 4 post infection


title: NCIH82_DMSO_24H

source_name: NCIH82 cell line treated with DMSO


title: NCIH82_OTX_12H


title: 5D4_high adipogenic

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

country: Canada

institute: Université Laval

hyb_protocol: After fragmentation and labeling, 3.5µg DNA target was hybridized on GeneChip® Mouse Gene 1.0 ST (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA, Hobbs B, Collin F, et al. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-64)

source_name: pre-confluent 3T3-L1 cells

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  Sense-strand cDNA was synthesized from 250 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Ambion® WT Expression Kit according to manufacturer’s instructions (Ambion).

growth_protocol: Proliferating Low and High 3T3-L1 cells maintained in DMEM + 10% Serum

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen, 74104)

value: pre-confluent 3T3-L1 cells

tag: adipogenic potential

value: High


title: 4D11_low adipogenic

value: Low


title: 4E3_high adipogenic


title: Sp_W_D4_3032x16188_127


title: Sp_W_D4_3032x16188_136


title: Sp_W_D7_3032x16188_119


title: 2F1_low adipogenic


title: 3F4_high adipogenic


title: Tsc2fl/fl LysM+/cre BMDM_nt_#4

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

hyb_protocol: Samples were hybridized with Affymetrix GeneChip® Mouse Gene 2.0 ST arrays

scan_protocol: standard Affymetrix protocol

data_processing:
Normalization of the data was done with the Affymetrix Expression Console. Analysis was performed with the Affymetrix Transcriptome Analysis Console (TAC) v3.0. We considered genes to be differentially regulated between Tsc2fl/fl LysM+/+ and Tsc2fl/fl LysM+/cre BMDM that were more than two-fold differently expressed with a ANOVA significance value of smaller than 0.05.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.4.0.38

source_name: Tsc2fl/fl LysM+/cre_BMDM

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and) labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Bone marrow was isolated from the indicated mice and differenciated for 6 days in 10%MΦ media [DMEM high glucose (Gibco), 10% low endotoxin FBS (Gibco), 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin, 50µg/ml β-mecaptoethanol)] supplemented with 15% L929-conditioned media. Differenciated BMDM were ≥96% positive for F4/80 and CD11b.

extract_protocol: Quiagen Rneasy Plus Micro Kit was used to isolate total RNA according to manufactures instructions.

treatment_protocol: Freshly differenciated BMDM were seeded without CSF1 in 10% MΦ media for 18 hours.

tag: strain background

value: Tsc2fl/fl LysM+/cre

tag: cell type

value: Bone marrow-derived macrophages (BMDM)


title: 5C4_high adipogenic


title: 1E7_low adipogenic


title: Tsc2fl/fl LysM+/cre BMDM_nt_#3


title: 4H4_low adipogenic


title: 2D7_low adipogenic


title: KO2-pL

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Knock Out 2

hyb_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays

scan_protocol: Illumina Scanner by Asuragen, Inc.

data_processing: The image signal quantitation results are generated by Illumina BeadStudio Software and are background-subtracted.

source_name: GFP+CD4+CD8+ bone marrow cells from T-ALL mice

tag: tumor type

value: T-ALL

tag: gender

value: Male

value: Bone marrow

value: T-ALL cells


title: KO1-pL

description: Knock Out 1

label_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays


title: 4D2_high adipogenic


title: Tsc2fl/fl LysM+/+ BMDM_nt_#4

source_name: Tsc2fl/fl LysM+/+_BMDM

value: Tsc2fl/fl LysM+/+


title: Tsc2fl/fl LysM+/+ BMDM_nt_#3


title: WT3-pL

description: Wild Type 3

extract_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays


title: Tsc2fl/fl LysM+/cre BMDM_nt_#2


title: KO3-pL

description: Knock Out 3

treatment_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays


title: WT2-pL

description: Wild Type 2


title: Tsc2fl/fl LysM+/cre BMDM_nt_#1


title: DMS114_OTX_4H

source_name: DMS114 cell line treated with OTX015


title: 800R.NH4NO3_rep3

status: Public on Jan 02 2017

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

country: Spain

institute: Universidad Pública de Navarra

description: Gene expression after 5 weeks CO2 tratment. Sample collected 4h from the beginning of the light period

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. For this study, the significant difference in gene expression was Q value < 0.05 and log2 fold change > 0.5.

organism: Arabidopsis thaliana

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana, Columbia 0 ecotype (col 0) plants grown under hydroponic conditions.

extract_protocol: Total RNA was isolated according to Liao et al.(2004).

tag: ecotype

value: Columbia 0

value: root


title: 800R.NH4NO3_rep1

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1


title: WT1-pL

description: Wild Type 1


title: 400R.NH4NO3_rep3

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3


title: 400L.NH4NO3_rep3

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3

value: leaf


title: Tsc2fl/fl LysM+/+ BMDM_nt_#2


title: 800L.NH4NO3_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1


title: 400R.NH4NO3_rep2

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2


title: Tsc2fl/fl LysM+/+ BMDM_nt_#1


title: 400R.NH4NO3_rep1

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1


title: BALB/c [A2479-3]

city: Kongens Lyngby

first: David Adrian

last: Ewald

address: Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The normalization and summarization was carried out in R, using:
- rma {affy}
- normalize.quantiles.robust {preprocessCore}
Versions: preprocessCore_1.32.0 ; affy_1.48.0

source_name: BALB/c

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: skin, ear, control

tag: condition

value: NN

tag: strain

value: BALB/c

value: Acetone Control

tag: Sex

value: female


title: 400L.NH4NO3_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2


title: BALB/c [A2479-1]

tag: age


title: Lung Shh-cre:Foxp1flox/flox:Foxp1flox/flox:Foxp4flox/flox(Mut1)

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
Sample name: TK143
Gene expression data from E14.5 lung

hyb_protocol: cDNAs  were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to  GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter.  Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Lungs were collected from E14.5 embryos

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

value: lung

value: Mix C57BL/6 and 129X1


title: 400L.NH4NO3_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1


title: Lung Shh-cre:Foxp1flox/flox:Foxp1flox/flox:Foxp4flox/flox(Mut2)

description:
Sample name: TK161
Gene expression data from E14.5 lung


title: Lung Shh-cre:Foxp1flox/flox:Foxp1flox/flox:Foxp4flox/flox(Mut3)

description:
Sample name: TK208
Gene expression data from E14.5 lung


title: BALB/c [A2479-2]


title: 800L.NH4NO3_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2


title: 800L.NH4NO3_rep3

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3


title: Lung Shh-Cre Control 2

description:
Sample name: Wt10
Gene expression data from E14.5 lung

source_name: ShhCre-Lung

value: Shh-Cre


title: Lung Shh-Cre Control 1

description:
Sample name: Wt9
Gene expression data from E14.5 lung


title: OXA 2h [A2479-4]

source_name: OXA 2h

value: skin, ear, OXA 2h

value: LS

value: OXA treated 2h


title: OXA 2h [A2479-6]


title: OXA 2h [A2479-5]


title: larger proximal  airways Scgb1a1-cre:Foxp1flox/flox:Foxp4flox/flox(Mut3)

description: Sample name: DK15L

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package (http://www.tm4.org/mev/).

source_name: Scgb1a1-cre:Foxp1flox/flox:Foxp4flox/flox-larger proximal  airways

label_protocol: After amplified, 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter.  Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Larger proximal airways were micro-dissected from  lungs of  9-week-old mice

extract_protocol: RNA was extracted using Rneasy Micro kit (Qiagene-74004)

treatment_protocol: Flash frozen Lungs were cut at -20-28oC, and mounted on membrane slides. Slides were fixed in ice-cold 75% EtOH for 2-3min, stained in 1%(w/v in 50% ETOH) Cresyl Violet (Aldrich) for 2 minutes, washed and dehydrated in ice-cold 70% EtOH,  then in 100% EtOH.  After air drying for 1-2min, larger proximal airways were Micro-dissected into RLT buffer (QIAGENE 74034) using forceps and scissors under microscope.

value: larger proximal  airways


title: Lung Shh-Cre Control 3

description:
Sample name: Wt11
Gene expression data from E14.5 lung


title: larger proximal  airways Scgb1a1-cre:Foxp1flox/flox:Foxp4flox/flox(Mut2)

description: Sample name: DK13L


title: larger proximal  airways Scgb1a1-cre:Foxp1flox/flox:Foxp4flox/flox(Mut1)

description: Sample name: DK11L


title: larger proximal  airways Scgb1a1Cre Control 3

description: Sample name: WT51L

source_name: Scgb1a1Cre-larger proximal  airways


title: Sp_M_D2_3032x16188_151

source_name: Spleen Tissue from Mock infected Line 3032x16188 at Day 2 post infection

tag: batch

value: m

value: Spleen

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

value: Mock infected


title: 400 ppm rotenone liver at day 3, biological rep2

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

hyb_protocol: Following fragmentation, 5.2 µg of biotin-labeled single-stranded copyDNA (ss-cDNA) was hybridized for 16 hr at 45C on a GeneChip® Rat Transcriptome Array 1.0. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 using the FS450_001 protocol.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Intensity values in CEL file data were first adjusted using GCCN correction to normalize the signal distribution based on the specific GC count, and then with the SST-algorithm, to expand the dynamic range of the intensity signals. Both of these algorithms are implemented in the Affymetrix® APT tool, running on an UNIX background. Further processing and quality control of the adjusted CEL files were performed with the Robust Multichip Analysis (RMA) algorithm, all implemented in the software Refiner Array (Genedata Expressionist®, current version 9), including background removal, normalization and then summarization of intensity values, to obtain a single intensity value for a transcript ID.

organism: Rattus norvegicus

source_name: 400 ppm rotenone liver at day 3

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total liver RNA (GeneChip® WT Plus Reagent Kit Version1).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals and are approved by the State Agency for Nature, Environment and Consumer Protection North Rhine-Westphalia in Germany (LANUV). Male RccHan Wistar rats at the age of 7-8 weeks were purchased from Harlan laboratories BV (Horst, Netherlands). Animals were housed under controlled standard conditions in groups with 2 or 3 animals per cage in makrolon cages type IV, with a 12h light-dark cycle at 22 ± 2°C. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from liver (70 mg) using the RNeasy Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

treatment_protocol: Male RccHan Wistar rats (7-8 weeks old) were randomly assigned to the vehicle or treatment group (n=5). 400 ppm rotenone (Sigma Aldrich, Steinheim, Germany) was administered in the diet for 1, 3 or 14 consecutive days. Control groups received untreated food.

value: Wistar (RccHan:WIST)

value: male

value: 7-8 weeks

tag: treated with

value: 400 ppm rotenone for 3 days

value: liver


title: Control liver at day 14, biological rep2

source_name: Control liver at day 14

value: none (untreated control)

tag: tissue


title: 400 ppm rotenone liver at day 14, biological rep2

source_name: 400 ppm rotenone liver at day 14

value: 400 ppm rotenone for 14 days


title: 400 ppm rotenone liver at day 14, biological rep3


title: larger proximal  airways Scgb1a1Cre Control 1

description: Sample name: W5L


title: 400 ppm rotenone liver at day 14, biological rep4


title: larger proximal  airways Scgb1a1Cre Control 2

description: Sample name: WT23L


title: 400 ppm rotenone liver at day 1, biological rep1

source_name: 400 ppm rotenone liver at day 1

value: 400 ppm rotenone for 1 day