title: Lymphoblastoid cell line Down Syndrome sample279

source_name: Lymphoblastoid cell line sample279


title: Lymphoblastoid cell line Down Syndrome sample275

status: Public on Oct 24 2014

type: genomic

city: Atlanta

first: Michael

middle: Edward

last: Zwick

state: GA

address: 615 Michael Street, Suite 301

department: Human Genetics

country: USA

institute: Emory University School of Medicine

description: primary data description:  Probe ID, genomic position (Chr and base position), Copy number state and Log2 ratio for each probe.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix GeneChip 450 fluidics stations, and scanned using the Gene Chip Scanner.

data_processing: Initial QC analysis and generation of log2 files (CNCHP) were done using Affymetrix power tools (APT 1.12.0). To mimimize the issue of false positives, we used 3 algorithms to make the CNV calls from CNCHP files (BEAST, GADA and GLAD).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Lymphoblastoid cell line sample275

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was isolated using Puregene DNA purification kit from lymphoblastoid cell lines according to manufacturer's instructions. DNA quality and quantity was assessed using Nanodrop ND-1000 spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: lymphoblastoid cell line

tag: phenotype

value: Down Syndrome

tag: ethnicity

value: European Ancestry

tag: status

value: case


title: Lymphoblastoid cell line Down Syndrome sample277

source_name: Lymphoblastoid cell line sample277

value: control


title: Lymphoblastoid cell line Down Syndrome sample280

source_name: Lymphoblastoid cell line sample280


title: Lymphoblastoid cell line Down Syndrome sample278

source_name: Lymphoblastoid cell line sample278


title: Lymphoblastoid cell line Down Syndrome sample274

source_name: Lymphoblastoid cell line sample274


title: Lymphoblastoid cell line Down Syndrome sample276

source_name: Lymphoblastoid cell line sample276


title: Lymphoblastoid cell line Down Syndrome sample273

source_name: Lymphoblastoid cell line sample273


title: Lymphoblastoid cell line Down Syndrome sample268

source_name: Lymphoblastoid cell line sample268


title: Lymphoblastoid cell line Down Syndrome sample271

source_name: Lymphoblastoid cell line sample271


title: Lymphoblastoid cell line Down Syndrome sample270

source_name: Lymphoblastoid cell line sample270


title: Lymphoblastoid cell line Down Syndrome sample267

source_name: Lymphoblastoid cell line sample267


title: Lymphoblastoid cell line Down Syndrome sample281

source_name: Lymphoblastoid cell line sample281


title: Lymphoblastoid cell line Down Syndrome sample269

source_name: Lymphoblastoid cell line sample269


title: Lymphoblastoid cell line Down Syndrome sample272

source_name: Lymphoblastoid cell line sample272


title: Lymphoblastoid cell line Down Syndrome sample266

source_name: Lymphoblastoid cell line sample266


title: Lymphoblastoid cell line Down Syndrome sample265

source_name: Lymphoblastoid cell line sample265


title: Lymphoblastoid cell line Down Syndrome sample263

source_name: Lymphoblastoid cell line sample263


title: Lymphoblastoid cell line Down Syndrome sample264

source_name: Lymphoblastoid cell line sample264


title: Lymphoblastoid cell line Down Syndrome sample262

source_name: Lymphoblastoid cell line sample262


title: Lymphoblastoid cell line Down Syndrome sample258

source_name: Lymphoblastoid cell line sample258


title: Lymphoblastoid cell line Down Syndrome sample256

source_name: Lymphoblastoid cell line sample256


title: Lymphoblastoid cell line Down Syndrome sample260

source_name: Lymphoblastoid cell line sample260


title: Lymphoblastoid cell line Down Syndrome sample261

source_name: Lymphoblastoid cell line sample261


title: Lymphoblastoid cell line Down Syndrome sample259

source_name: Lymphoblastoid cell line sample259


title: Lymphoblastoid cell line Down Syndrome sample254

source_name: Lymphoblastoid cell line sample254


title: Lymphoblastoid cell line Down Syndrome sample255

source_name: Lymphoblastoid cell line sample255


title: Lymphoblastoid cell line Down Syndrome sample253

source_name: Lymphoblastoid cell line sample253


title: Lymphoblastoid cell line Down Syndrome sample252

source_name: Lymphoblastoid cell line sample252


title: Lymphoblastoid cell line Down Syndrome sample251

source_name: Lymphoblastoid cell line sample251


title: Lymphoblastoid cell line Down Syndrome sample250

source_name: Lymphoblastoid cell line sample250


title: Lymphoblastoid cell line Down Syndrome sample244

source_name: Lymphoblastoid cell line sample244


title: Lymphoblastoid cell line Down Syndrome sample248

source_name: Lymphoblastoid cell line sample248


title: Lymphoblastoid cell line Down Syndrome sample243

source_name: Lymphoblastoid cell line sample243


title: Lymphoblastoid cell line Down Syndrome sample247

source_name: Lymphoblastoid cell line sample247


title: Lymphoblastoid cell line Down Syndrome sample245

source_name: Lymphoblastoid cell line sample245


title: Lymphoblastoid cell line Down Syndrome sample249

source_name: Lymphoblastoid cell line sample249


title: Lymphoblastoid cell line Down Syndrome sample242

source_name: Lymphoblastoid cell line sample242


title: Lymphoblastoid cell line Down Syndrome sample433

source_name: Lymphoblastoid cell line sample433


title: Lymphoblastoid cell line Down Syndrome sample240

source_name: Lymphoblastoid cell line sample240


title: Lymphoblastoid cell line Down Syndrome sample237

source_name: Lymphoblastoid cell line sample237


title: Lymphoblastoid cell line Down Syndrome sample241

source_name: Lymphoblastoid cell line sample241


title: Lymphoblastoid cell line Down Syndrome sample239

source_name: Lymphoblastoid cell line sample239


title: Lymphoblastoid cell line Down Syndrome sample235

source_name: Lymphoblastoid cell line sample235


title: Lymphoblastoid cell line Down Syndrome sample236

source_name: Lymphoblastoid cell line sample236


title: Lymphoblastoid cell line Down Syndrome sample238

source_name: Lymphoblastoid cell line sample238


title: Lymphoblastoid cell line Down Syndrome sample233

source_name: Lymphoblastoid cell line sample233


title: Lymphoblastoid cell line Down Syndrome sample257

source_name: Lymphoblastoid cell line sample257


title: Lymphoblastoid cell line Down Syndrome sample228

source_name: Lymphoblastoid cell line sample228


title: Lymphoblastoid cell line Down Syndrome sample232

source_name: Lymphoblastoid cell line sample232


title: Lymphoblastoid cell line Down Syndrome sample229

source_name: Lymphoblastoid cell line sample229


title: Lymphoblastoid cell line Down Syndrome sample230

source_name: Lymphoblastoid cell line sample230


title: Lymphoblastoid cell line Down Syndrome sample227

source_name: Lymphoblastoid cell line sample227


title: Lymphoblastoid cell line Down Syndrome sample226

source_name: Lymphoblastoid cell line sample226


title: Lymphoblastoid cell line Down Syndrome sample246

source_name: Lymphoblastoid cell line sample246


title: Lymphoblastoid cell line Down Syndrome sample225

source_name: Lymphoblastoid cell line sample225


title: Lymphoblastoid cell line Down Syndrome sample223

source_name: Lymphoblastoid cell line sample223


title: Lymphoblastoid cell line Down Syndrome sample224

source_name: Lymphoblastoid cell line sample224


title: Lymphoblastoid cell line Down Syndrome sample222

source_name: Lymphoblastoid cell line sample222


title: Lymphoblastoid cell line Down Syndrome sample219

source_name: Lymphoblastoid cell line sample219


title: Lymphoblastoid cell line Down Syndrome sample217

source_name: Lymphoblastoid cell line sample217


title: Lymphoblastoid cell line Down Syndrome sample234

source_name: Lymphoblastoid cell line sample234


title: Lymphoblastoid cell line Down Syndrome sample221

source_name: Lymphoblastoid cell line sample221


title: Lymphoblastoid cell line Down Syndrome sample212

source_name: Lymphoblastoid cell line sample212


title: Lymphoblastoid cell line Down Syndrome sample213

source_name: Lymphoblastoid cell line sample213


title: Lymphoblastoid cell line Down Syndrome sample215

source_name: Lymphoblastoid cell line sample215


title: Lymphoblastoid cell line Down Syndrome sample211

source_name: Lymphoblastoid cell line sample211


title: Lymphoblastoid cell line Down Syndrome sample209

source_name: Lymphoblastoid cell line sample209


title: Lymphoblastoid cell line Down Syndrome sample216

source_name: Lymphoblastoid cell line sample216


title: Lymphoblastoid cell line Down Syndrome sample210

source_name: Lymphoblastoid cell line sample210


title: Lymphoblastoid cell line Down Syndrome sample231

source_name: Lymphoblastoid cell line sample231


title: Lymphoblastoid cell line Down Syndrome sample214

source_name: Lymphoblastoid cell line sample214


title: Lymphoblastoid cell line Down Syndrome sample208

source_name: Lymphoblastoid cell line sample208


title: Lymphoblastoid cell line Down Syndrome sample205

source_name: Lymphoblastoid cell line sample205


title: Lymphoblastoid cell line Down Syndrome sample206

source_name: Lymphoblastoid cell line sample206


title: Lymphoblastoid cell line Down Syndrome sample203

source_name: Lymphoblastoid cell line sample203


title: Lymphoblastoid cell line Down Syndrome sample207

source_name: Lymphoblastoid cell line sample207


title: Lymphoblastoid cell line Down Syndrome sample199

source_name: Lymphoblastoid cell line sample199


title: Lymphoblastoid cell line Down Syndrome sample198

source_name: Lymphoblastoid cell line sample198


title: Lymphoblastoid cell line Down Syndrome sample220

source_name: Lymphoblastoid cell line sample220


title: Lymphoblastoid cell line Down Syndrome sample218

source_name: Lymphoblastoid cell line sample218


title: Lymphoblastoid cell line Down Syndrome sample201

source_name: Lymphoblastoid cell line sample201


title: Lymphoblastoid cell line Down Syndrome sample197

source_name: Lymphoblastoid cell line sample197


title: Lymphoblastoid cell line Down Syndrome sample195

source_name: Lymphoblastoid cell line sample195


title: Lymphoblastoid cell line Down Syndrome sample196

source_name: Lymphoblastoid cell line sample196


title: Lymphoblastoid cell line Down Syndrome sample204

source_name: Lymphoblastoid cell line sample204


title: Lymphoblastoid cell line Down Syndrome sample202

source_name: Lymphoblastoid cell line sample202


title: Lymphoblastoid cell line Down Syndrome sample194

source_name: Lymphoblastoid cell line sample194


title: Lymphoblastoid cell line Down Syndrome sample189

source_name: Lymphoblastoid cell line sample189


title: Lymphoblastoid cell line Down Syndrome sample192

source_name: Lymphoblastoid cell line sample192


title: Lymphoblastoid cell line Down Syndrome sample191

source_name: Lymphoblastoid cell line sample191


title: Lymphoblastoid cell line Down Syndrome sample190

source_name: Lymphoblastoid cell line sample190


title: Lymphoblastoid cell line Down Syndrome sample186

source_name: Lymphoblastoid cell line sample186


title: Lymphoblastoid cell line Down Syndrome sample200

source_name: Lymphoblastoid cell line sample200


title: Lymphoblastoid cell line Down Syndrome sample188

source_name: Lymphoblastoid cell line sample188


title: Lymphoblastoid cell line Down Syndrome sample187

source_name: Lymphoblastoid cell line sample187


title: Lymphoblastoid cell line Down Syndrome sample182

source_name: Lymphoblastoid cell line sample182


title: Lymphoblastoid cell line Down Syndrome sample185

source_name: Lymphoblastoid cell line sample185


title: Lymphoblastoid cell line Down Syndrome sample181

source_name: Lymphoblastoid cell line sample181


title: Lymphoblastoid cell line Down Syndrome sample193

source_name: Lymphoblastoid cell line sample193


title: Lymphoblastoid cell line Down Syndrome sample180

source_name: Lymphoblastoid cell line sample180


title: Lymphoblastoid cell line Down Syndrome sample179

source_name: Lymphoblastoid cell line sample179


title: Lymphoblastoid cell line Down Syndrome sample184

source_name: Lymphoblastoid cell line sample184


title: Lymphoblastoid cell line Down Syndrome sample178

source_name: Lymphoblastoid cell line sample178


title: Lymphoblastoid cell line Down Syndrome sample177

source_name: Lymphoblastoid cell line sample177


title: Lymphoblastoid cell line Down Syndrome sample183

source_name: Lymphoblastoid cell line sample183


title: Lymphoblastoid cell line Down Syndrome sample176

source_name: Lymphoblastoid cell line sample176


title: CD8+ human naïve T cell, donor 3

type: RNA

city: Auckland

first: Vicky

last: Fan

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: University of Auckland

hyb_protocol: Hybridisation was according to the Affymetrix® GeneChip® miRNA Array Procedure

scan_protocol: Arrays were scanned using an Affymetrix® GeneChip® Scanner 7G

data_processing: The data were analysed using R and the bioconductor package limma

molecule: total RNA

source_name: CD8+ T cell

label_protocol: 100 ng Total RNA was labeled using the FlashTag™ Biotin HSR RNA Labelng Kit

extract_protocol: Total RNA was extracted from purified cells using a miRVANA kit (Ambion)

value: CD8+ T cell

tag: differentiation status

value: naïve


title: Lymphoblastoid cell line Down Syndrome sample175

source_name: Lymphoblastoid cell line sample175


title: Lymphoblastoid cell line Down Syndrome sample174

source_name: Lymphoblastoid cell line sample174


title: CD8+ human effector memory T cell, donor 2

value: effector memory


title: CD8+ human central memory T cell, donor 2

value: central memory


title: CD8+ human naïve T cell, donor 2


title: CD8+ human effector memory T cell, donor 3


title: CD8+ human central memory T cell, donor 1


title: CD8+ human naïve T cell, donor 1


title: CD8+ human central memory T cell, donor 3


title: Lymphoblastoid cell line Down Syndrome sample173

source_name: Lymphoblastoid cell line sample173


title: Lymphoblastoid cell line Down Syndrome sample172

source_name: Lymphoblastoid cell line sample172


title: CD8+ human effector memory T cell, donor 1


title: Lymphoblastoid cell line Down Syndrome sample170

source_name: Lymphoblastoid cell line sample170


title: Lymphoblastoid cell line Down Syndrome sample171

source_name: Lymphoblastoid cell line sample171


title: Lymphoblastoid cell line Down Syndrome sample166

source_name: Lymphoblastoid cell line sample166


title: Lymphoblastoid cell line Down Syndrome sample168

source_name: Lymphoblastoid cell line sample168


title: Lymphoblastoid cell line Down Syndrome sample167

source_name: Lymphoblastoid cell line sample167


title: Lymphoblastoid cell line Down Syndrome sample165

source_name: Lymphoblastoid cell line sample165


title: Lymphoblastoid cell line Down Syndrome sample169

source_name: Lymphoblastoid cell line sample169


title: Lymphoblastoid cell line Down Syndrome sample163

source_name: Lymphoblastoid cell line sample163


title: Lymphoblastoid cell line Down Syndrome sample162

source_name: Lymphoblastoid cell line sample162


title: Lymphoblastoid cell line Down Syndrome sample161

source_name: Lymphoblastoid cell line sample161


title: Lymphoblastoid cell line Down Syndrome sample160

source_name: Lymphoblastoid cell line sample160


title: Lymphoblastoid cell line Down Syndrome sample159

source_name: Lymphoblastoid cell line sample159


title: Pd-1 Intermediate H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Int

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania

description: Pd-1 Intermediate H2-Db GP33-specific CD8+ T cells 30 days p.i. with LCMV Clone 13

hyb_protocol: cDNA was amplified with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania's Microarray facility

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

label: Biotin

organism: Mus musculus

source_name: H2-Db GP33-specific CD8+ T cells

label_protocol: Microarrays were 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

growth_protocol: H2-Db GP33-specific CD8+ T cells were sorted from C57BL/6 mice 30 days p.i. with LCMV clone 13.

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

tag: time (dpi)

tag: strain

tag: infection

value: LCMV-clone 13

value: PD-1 Expression Intermediate


title: Lymphoblastoid cell line Down Syndrome sample164

source_name: Lymphoblastoid cell line sample164


title: Pd-1 Intermediate H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Int-3

treatment_protocol: H2-Db GP33-specific CD8+ T cells were sorted from C57BL/6 mice 30 days p.i. with LCMV clone 13.


title: Lymphoblastoid cell line Down Syndrome sample158

source_name: Lymphoblastoid cell line sample158


title: Pd-1 High H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Hi-2

description: Pd-1 High H2-Db GP33-specific CD8+ T cells 30 days p.i. with LCMV Clone 13

value: PD-1 Expression High


title: Pd-1 High H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Hi-1


title: Pd-1 Intermediate H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Int-2


title: Lymphoblastoid cell line Down Syndrome sample157

source_name: Lymphoblastoid cell line sample157


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Clone 13 CD4+ Chronic Day15-2

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p.i. with LCMV-Clone 13

growth_protocol: Naive CD44Lo CD4+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-IAb GP66-specific CD4+ T cells were sorted using MHC-II tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13.

value: H2-IAb GP66 specific CD4+ T cell

value: LCMV-Clone 13


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Clone 13 CD4+ Chronic Day30-3

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p.i. with LCMV-Clone 13

treatment_protocol: Naive CD44Lo CD4+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-IAb GP66-specific CD4+ T cells were sorted using MHC-II tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13.


title: Lymphoblastoid cell line Down Syndrome sample156

source_name: Lymphoblastoid cell line sample156


title: Pd-1 High H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Hi-3


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Clone 13 CD4+ Chronic Day30

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p.i. with LCMV-Clone 13


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Clone 13 CD4+ Chronic Day8-3

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p.i. with LCMV-Clone 13


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Clone 13 CD4+ Chronic Day30-1


title: Lymphoblastoid cell line Down Syndrome sample155

source_name: Lymphoblastoid cell line sample155


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Clone 13 CD4+ Chronic Day15-3

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p.i. with LCMV-Clone 13


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Clone 13 CD4+ Chronic Day8-2

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p.i. with LCMV-Clone 13


title: Pd-1 High H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Hi


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Clone 13 CD4+ Chronic Day15


title: Lymphoblastoid cell line Down Syndrome sample151

source_name: Lymphoblastoid cell line sample151


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Clone 13 CD4+ Chronic Day6-2

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p.i. with LCMV-Clone 13


title: Lymphoblastoid cell line Down Syndrome sample152

source_name: Lymphoblastoid cell line sample152


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Clone 13 CD4+ Chronic Day15-1


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Clone 13 CD4+ Chronic Day8-1


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Clone 13 CD4+ Chronic Day30-2


title: Lymphoblastoid cell line Down Syndrome sample149

source_name: Lymphoblastoid cell line sample149


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Clone 13 CD4+ Chronic Day8


title: Lymphoblastoid cell line Down Syndrome sample153

source_name: Lymphoblastoid cell line sample153


title: Lymphoblastoid cell line Down Syndrome sample150

source_name: Lymphoblastoid cell line sample150


title: Lymphoblastoid cell line Down Syndrome sample148

source_name: Lymphoblastoid cell line sample148


title: Lymphoblastoid cell line Down Syndrome sample147

source_name: Lymphoblastoid cell line sample147


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Clone 13 CD4+ Chronic Day6-3

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p.i. with LCMV-Clone 13


title: Lymphoblastoid cell line Down Syndrome sample146

source_name: Lymphoblastoid cell line sample146


title: Lymphoblastoid cell line Down Syndrome sample154

source_name: Lymphoblastoid cell line sample154


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Clone 13 CD4+ Chronic Day6-1


title: Pd-1 Intermediate H2-Db GP33-specific CD8+ T cells CD8+ Pd1 Int-1

source_name: H2-Db GP33-specific CD8+ T cells


title: Lymphoblastoid cell line Down Syndrome sample145

source_name: Lymphoblastoid cell line sample145


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Clone 13 CD4+ Chronic Day6


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Arm CD4+ Acute Day30-3

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p.i. with LCMV-Arm

value: LCMV-Arm


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Arm CD4+ Acute Day30-2

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p.i. with LCMV-Arm


title: Lymphoblastoid cell line Down Syndrome sample144

source_name: Lymphoblastoid cell line sample144


title: Lymphoblastoid cell line Down Syndrome sample143

source_name: Lymphoblastoid cell line sample143


title: Lymphoblastoid cell line Down Syndrome sample142

source_name: Lymphoblastoid cell line sample142


title: Lymphoblastoid cell line Down Syndrome sample141

source_name: Lymphoblastoid cell line sample141


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Arm CD4+ Acute Day30-1


title: Lymphoblastoid cell line Down Syndrome sample140

source_name: Lymphoblastoid cell line sample140


title: Lymphoblastoid cell line Down Syndrome sample139

source_name: Lymphoblastoid cell line sample139


title: Lymphoblastoid cell line Down Syndrome sample138

source_name: Lymphoblastoid cell line sample138


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d30 p i  with LCMV-Arm CD4+ Acute Day30


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Arm CD4+ Acute Day15-3

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p.i. with LCMV-Arm


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Arm CD4+ Acute Day15

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p.i. with LCMV-Arm


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Arm CD4+ Acute Day8-3

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p.i. with LCMV-Arm


title: Lymphoblastoid cell line Down Syndrome sample137

source_name: Lymphoblastoid cell line sample137


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Arm CD4+ Acute Day8-2

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p.i. with LCMV-Arm


title: Lymphoblastoid cell line Down Syndrome sample136

source_name: Lymphoblastoid cell line sample136


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Arm CD4+ Acute Day15-2


title: Lymphoblastoid cell line Down Syndrome sample134

source_name: Lymphoblastoid cell line sample134


title: Lymphoblastoid cell line Down Syndrome sample133

source_name: Lymphoblastoid cell line sample133


title: Lymphoblastoid cell line Down Syndrome sample132

source_name: Lymphoblastoid cell line sample132


title: Lymphoblastoid cell line Down Syndrome sample135

source_name: Lymphoblastoid cell line sample135


title: Lymphoblastoid cell line Down Syndrome sample131

source_name: Lymphoblastoid cell line sample131


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Arm CD4+ Acute Day8-1


title: Lymphoblastoid cell line Down Syndrome sample130

source_name: Lymphoblastoid cell line sample130


title: Lymphoblastoid cell line Down Syndrome sample128

source_name: Lymphoblastoid cell line sample128


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Arm CD4+ Acute Day6-2

description: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p.i. with LCMV-Arm


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d15 p i  with LCMV-Arm CD4+ Acute Day15-1


title: Lymphoblastoid cell line Down Syndrome sample129

source_name: Lymphoblastoid cell line sample129


title: Naive CD44Lo CD4+ T cells CD4+ Naive-1

description: Naive CD44Lo CD4+ T cells

source_name: Naive CD44Lo CD4+ T cells

value: Naive CD44Lo CD4+ T cell


title: Lymphoblastoid cell line Down Syndrome sample127

source_name: Lymphoblastoid cell line sample127


title: Lymphoblastoid cell line Down Syndrome sample126

source_name: Lymphoblastoid cell line sample126


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d8 p i  with LCMV-Arm CD4+ Acute Day8


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Arm CD4+ Acute Day6-1

source_name: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p.i. with LCMV-Arm


title: H2-IAb GP66 specific CD4+ T cell from C57BL/6 d6 p i  with LCMV-Arm CD4+ Acute Day6


title: Lymphoblastoid cell line Down Syndrome sample125

source_name: Lymphoblastoid cell line sample125


title: Naive CD44Lo CD4+ T cells CD4+ Naive

description: Naive CD44Lo CD4+ T cells


title: Naive CD44Lo CD4+ T cells CD4+ Naive-2

description: Naive CD44Lo CD4+ T cells


title: Lymphoblastoid cell line Down Syndrome sample124

source_name: Lymphoblastoid cell line sample124


title: Lymphoblastoid cell line Down Syndrome sample122

source_name: Lymphoblastoid cell line sample122


title: Lymphoblastoid cell line Down Syndrome sample123

source_name: Lymphoblastoid cell line sample123


title: Naive CD44Lo CD4+ T cells CD4+ Naive-3

description: Naive CD44Lo CD4+ T cells


title: Lymphoblastoid cell line Down Syndrome sample121

source_name: Lymphoblastoid cell line sample121


title: Lymphoblastoid cell line Down Syndrome sample120

source_name: Lymphoblastoid cell line sample120


title: Wildtype Villi3

city: Oxford

first: Ian

last: Tomlinson

state: England

address: WTCHG, Roosevelt Drive

country: United Kingdom

institute: Oxford University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using VSN (variance-stabilisation and normalisation) algorithm.

source_name: Small intestinal villi

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted in lysis buffer provided by Qiagen Rneasy micro kit, followed by clean-up and Dnase 1 treatment in accordance with the prescribed proctocol provided with the kit. Quality control was performed with agilent Bioanalyser.

tag: age

value: 5 months

tag: tissue

value: Small intestinal Vill

tag: genotype

value: wild type


title: Villin-Grem Villi4

value: Villin-Gremlin


title: Villin-Grem Villi3


title: Wildtype Villi4


title: Wildtype Villi2


title: Villin-Grem Villi5


title: Lymphoblastoid cell line Down Syndrome sample119

source_name: Lymphoblastoid cell line sample119

value: lymphoblastoid cell line

value: Down Syndrome

value: European Ancestry

value: case


title: Villin-Grem Villi1


title: Lymphoblastoid cell line Down Syndrome sample118

source_name: Lymphoblastoid cell line sample118

value: control


title: Wildtype Villi6


title: Lymphoblastoid cell line Down Syndrome sample117

source_name: Lymphoblastoid cell line sample117


title: Wildtype Villi5


title: Villin-Grem Villi2


title: Lymphoblastoid cell line Down Syndrome sample115

source_name: Lymphoblastoid cell line sample115


title: Lymphoblastoid cell line Down Syndrome sample114

source_name: Lymphoblastoid cell line sample114


title: Lymphoblastoid cell line Down Syndrome sample116

source_name: Lymphoblastoid cell line sample116


title: Lymphoblastoid cell line Down Syndrome sample113

source_name: Lymphoblastoid cell line sample113


title: Wildtype Villi1

description: WTV


title: 30676 [set 2]

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

hyb_protocol: Samples were hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix) in a GeneChip Hyb Oven 640 (Affymetrix) for 16 hours at 45C. Arrays were washed and stained using the GeneChip Hyb, Wash and Stain kit (Affymetrix) with a GeneChip Fluidics Station 450 (Affymetrix) according to standard protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix), and image processing was performed using AGCC version 3.1.

data_processing: Affymetrix CEL files for all samples were processed using the RMA method as implemented in the “affy” R package version 1.38.1. Probe annotations were provided by the “hugene10sttranscriptcluster.db” R package version 8.0.1.

label_protocol: Microarray target preparation from total RNA was done using Ambion WT Expression Kit from Life Technologies following standard Affymetrix protocol. Sense strand cDNA was fragmented and labeled using Genechip WT Terminal Labeling Kit from Affymetrix.

growth_protocol: Breast cancer and stromal cell lines used in this study were confirmed to be mycoplasma-free. All breast cancer and stromal cell lines were cultured at 37º C in DMEM. Media was supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin, 2 mM L-glutamine, and 10 mM HEPES. For co-cultures, breast cancer cells were labeled with 7.5 μM 5-(and-6)-carboxyfluorescein diacetate, succinimidyl ester (CFSE) and mixed 1:1 with stromal cells. All co-culture experiments were performed using EBM with 0.2% FBS.

extract_protocol: Total RNA extraction using Qiagen RNEasy

treatment_protocol: Gene knockdown by siRNA was accomplished using 15 nM siRNA and RNAiMAX (Invitrogen) transfection reagent.

tag: coculture

tag: sirna


title: 30673 [set 2]

value: cont


title: 30675 [set 2]


title: 32430 [set 2]


title: Lymphoblastoid cell line Down Syndrome sample112

source_name: Lymphoblastoid cell line sample112


title: Lymphoblastoid cell line Down Syndrome sample111

source_name: Lymphoblastoid cell line sample111


title: Lymphoblastoid cell line Down Syndrome sample109

source_name: Lymphoblastoid cell line sample109


title: 30672 [set 2]


title: Lymphoblastoid cell line Down Syndrome sample108

source_name: Lymphoblastoid cell line sample108


title: 32426 [set 2]


title: 32427 [set 2]


title: 44966


title: 44967


title: Lymphoblastoid cell line Down Syndrome sample106

source_name: Lymphoblastoid cell line sample106


title: 44968


title: Lymphoblastoid cell line Down Syndrome sample107

source_name: Lymphoblastoid cell line sample107


title: Lymphoblastoid cell line Down Syndrome sample105

source_name: Lymphoblastoid cell line sample105


title: Lymphoblastoid cell line Down Syndrome sample104

source_name: Lymphoblastoid cell line sample104


title: 44965


title: 44962


title: Lymphoblastoid cell line Down Syndrome sample110

source_name: Lymphoblastoid cell line sample110


title: 44964


title: 32429 [set 2]


title: Lymphoblastoid cell line Down Syndrome sample103

source_name: Lymphoblastoid cell line sample103


title: 44969


title: 32431


title: Lymphoblastoid cell line Down Syndrome sample102

source_name: Lymphoblastoid cell line sample102


title: Lymphoblastoid cell line Down Syndrome sample101

source_name: Lymphoblastoid cell line sample101


title: Lymphoblastoid cell line Down Syndrome sample100

source_name: Lymphoblastoid cell line sample100


title: 32432


title: Lymphoblastoid cell line Down Syndrome sample98

source_name: Lymphoblastoid cell line sample98


title: Lymphoblastoid cell line Down Syndrome sample97

source_name: Lymphoblastoid cell line sample97


title: Lymphoblastoid cell line Down Syndrome sample99

source_name: Lymphoblastoid cell line sample99


title: Lymphoblastoid cell line Down Syndrome sample95

source_name: Lymphoblastoid cell line sample95


title: 32430


title: 32429


title: Lymphoblastoid cell line Down Syndrome sample94

source_name: Lymphoblastoid cell line sample94


title: Lymphoblastoid cell line Down Syndrome sample93

source_name: Lymphoblastoid cell line sample93


title: 44963


title: Lymphoblastoid cell line Down Syndrome sample96

source_name: Lymphoblastoid cell line sample96


title: Lymphoblastoid cell line Down Syndrome sample92

source_name: Lymphoblastoid cell line sample92


title: 31310


title: Lymphoblastoid cell line Down Syndrome sample91

source_name: Lymphoblastoid cell line sample91


title: 32427


title: 32428


title: 30680


title: 31308


title: Lymphoblastoid cell line Down Syndrome sample90

source_name: Lymphoblastoid cell line sample90


title: Lymphoblastoid cell line Down Syndrome sample89

source_name: Lymphoblastoid cell line sample89


title: Lymphoblastoid cell line Down Syndrome sample87

source_name: Lymphoblastoid cell line sample87


title: 32426


title: 31309


title: 30674


title: Lymphoblastoid cell line Down Syndrome sample86

source_name: Lymphoblastoid cell line sample86


title: Lymphoblastoid cell line Down Syndrome sample85

source_name: Lymphoblastoid cell line sample85


title: 30675


title: Lymphoblastoid cell line Down Syndrome sample83

source_name: Lymphoblastoid cell line sample83


title: 30671


title: 30673


title: Lymphoblastoid cell line Down Syndrome sample84

source_name: Lymphoblastoid cell line sample84


title: 30676


title: Lymphoblastoid cell line Down Syndrome sample82

source_name: Lymphoblastoid cell line sample82


title: 30669


title: 30670


title: 30668


title: 30666


title: 30667


title: 30677


title: Lymphoblastoid cell line Down Syndrome sample78

source_name: Lymphoblastoid cell line sample78


title: 30665


title: 30672


title: Lymphoblastoid cell line Down Syndrome sample88

source_name: Lymphoblastoid cell line sample88


title: 26875


title: Lymphoblastoid cell line Down Syndrome sample81

source_name: Lymphoblastoid cell line sample81


title: 26877


title: 26876


title: Lymphoblastoid cell line Down Syndrome sample79

source_name: Lymphoblastoid cell line sample79


title: Lymphoblastoid cell line Down Syndrome sample77

source_name: Lymphoblastoid cell line sample77


title: Lymphoblastoid cell line Down Syndrome sample74

source_name: Lymphoblastoid cell line sample74


title: Lymphoblastoid cell line Down Syndrome sample80

source_name: Lymphoblastoid cell line sample80


title: Lymphoblastoid cell line Down Syndrome sample76

source_name: Lymphoblastoid cell line sample76


title: Lymphoblastoid cell line Down Syndrome sample75

source_name: Lymphoblastoid cell line sample75


title: Lymphoblastoid cell line Down Syndrome sample73

source_name: Lymphoblastoid cell line sample73


title: Lymphoblastoid cell line Down Syndrome sample72

source_name: Lymphoblastoid cell line sample72


title: Lymphoblastoid cell line Down Syndrome sample70

source_name: Lymphoblastoid cell line sample70


title: Lymphoblastoid cell line Down Syndrome sample69

source_name: Lymphoblastoid cell line sample69


title: Lymphoblastoid cell line Down Syndrome sample67

source_name: Lymphoblastoid cell line sample67


title: Lymphoblastoid cell line Down Syndrome sample65

source_name: Lymphoblastoid cell line sample65


title: 26874


title: Lymphoblastoid cell line Down Syndrome sample68

source_name: Lymphoblastoid cell line sample68


title: HEK293 2

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

description:
Control cell line
SAMPLE 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Human HT12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Probes signal value was transformed by logarithm and normalized by quantile method.All data analysis of differentially expressed genes was conducted using R 2.15.3 (www.r-project.org).

source_name: Embryonic kidney cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: HEK293 cells were maintianed in DMEM (High Glucose) supplemented with 10% Fetal Bovine Serum and 1% Pennicillin/Streptomycin.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Sodium salicylate (Sigma S3007) was dissovled in water 2.4M stock stolution, and diluted further to 50 mM final concentration. After adding salicylate, cells were incubated in 37 °C for 30, 60 min and lysed to prepare total RNA

tag: cell line

tag: salicylate treatment incubation time

value: negative control (0min)


title: Lymphoblastoid cell line Down Syndrome sample66

source_name: Lymphoblastoid cell line sample66


title: 26872


title: HEK293 treated 50 mM salicylate for 60 min 1

description:
60 min after treatment of 50 mM salicylate
SAMPLE 5

value: 60 min after treatment of sodium salicylate


title: Lymphoblastoid cell line Down Syndrome sample64

source_name: Lymphoblastoid cell line sample64


title: 26873


title: HEK293 treated 50 mM salicylate for 60 min 2

description:
60 min after treatment of 50 mM salicylate
SAMPLE 6


title: HEK293 treated 50 mM salicylate for 30 min 2

description:
30 min after treatment of 50 mM salicylate
SAMPLE 4

value: 30 min after treatment of sodium salicylate


title: HEK293 treated 50 mM salicylate for 30 min 1

description:
30 min after treatment of 50 mM salicylate
SAMPLE 3


title: 26871


title: Lymphoblastoid cell line Down Syndrome sample62

source_name: Lymphoblastoid cell line sample62


title: Lymphoblastoid cell line Down Syndrome sample71

source_name: Lymphoblastoid cell line sample71


title: Lymphoblastoid cell line Down Syndrome sample63

source_name: Lymphoblastoid cell line sample63


title: HEK293 1

description:
Control cell line
SAMPLE 1


title: HT02(6)Fluzone

city: Dallas

first: Jason

middle: A

last: Skinner

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Day 6 Post Challenge

hyb_protocol: Standard Illumina HT-12 V4 hybridization protocol

scan_protocol: Standard Illumina iScan protocol

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset.  Only probes for which pval detection  was below 0.01 in at least one sample were kept for analysis.

organism: Macaca mulatta

source_name: total RNA (globin reduced)

label_protocol: Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input

extract_protocol: RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits, Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits

tag: monkey

tag: time (day)

tag: challenge

value: Live Cal04

tag: previous vaccination

value: Fluzone

tag: dataset

value: Vaccine Assessment

value: Whole Blood


title: FT88(6)Media+PolyICLC

description: Day 6 Post Challenge

value: Media+PolyICLC


title: HF96(6)Fluzone

description: Day 6 Post Challenge


title: GB58(6)CD40-NP5+PolyICLC

description: Day 6 Post Challenge


title: Lymphoblastoid cell line Down Syndrome sample60

source_name: Lymphoblastoid cell line sample60

tag: cell type

tag: phenotype

tag: ethnicity

tag: status


title: Lymphoblastoid cell line Down Syndrome sample61

source_name: Lymphoblastoid cell line sample61


title: HD06(6)Media+PolyICLC

description: Day 6 Post Challenge


title: FM36(6)CD40-HA+PolyICLC

description: Day 6 Post Challenge


title: GP83(6)CD40-HA+PolyICLC

description: Day 6 Post Challenge


title: Lymphoblastoid cell line Down Syndrome sample59

source_name: Lymphoblastoid cell line sample59


title: HE90(6)CD40-HA+PolyICLC

description: Day 6 Post Challenge


title: GI96(6)Media+PolyICLC

description: Day 6 Post Challenge


title: FC82(6)CD40-NP5+PolyICLC

description: Day 6 Post Challenge


title: Lymphoblastoid cell line Down Syndrome sample57

source_name: Lymphoblastoid cell line sample57


title: Lymphoblastoid cell line Down Syndrome sample53

source_name: Lymphoblastoid cell line sample53


title: Lymphoblastoid cell line Down Syndrome sample52

source_name: Lymphoblastoid cell line sample52


title: Lymphoblastoid cell line Down Syndrome sample54

source_name: Lymphoblastoid cell line sample54


title: Lymphoblastoid cell line Down Syndrome sample56

source_name: Lymphoblastoid cell line sample56


title: Lymphoblastoid cell line Down Syndrome sample55

source_name: Lymphoblastoid cell line sample55


title: HP84(6)Media+PolyICLC

description: Day 6 Post Challenge


title: Lymphoblastoid cell line Down Syndrome sample58

source_name: Lymphoblastoid cell line sample58


title: EA43(6)Fluzone

description: Day 6 Post Challenge


title: HE72(6)Fluzone

description: Day 6 Post Challenge


title: FM05(6)CD40-NP5+PolyICLC

description: Day 6 Post Challenge


title: Lymphoblastoid cell line Down Syndrome sample50

source_name: Lymphoblastoid cell line sample50


title: Lymphoblastoid cell line Down Syndrome sample47

source_name: Lymphoblastoid cell line sample47


title: Lymphoblastoid cell line Down Syndrome sample48

source_name: Lymphoblastoid cell line sample48


title: Lymphoblastoid cell line Down Syndrome sample46

source_name: Lymphoblastoid cell line sample46


title: Lymphoblastoid cell line Down Syndrome sample49

source_name: Lymphoblastoid cell line sample49


title: Lymphoblastoid cell line Down Syndrome sample45

source_name: Lymphoblastoid cell line sample45


title: Lymphoblastoid cell line Down Syndrome sample51

source_name: Lymphoblastoid cell line sample51


title: Lymphoblastoid cell line Down Syndrome sample44

source_name: Lymphoblastoid cell line sample44


title: Lymphoblastoid cell line Down Syndrome sample43

source_name: Lymphoblastoid cell line sample43


title: FF91(6)CD40-HA+PolyICLC

description: Day 6 Post Challenge

source_name: total RNA (globin reduced)


title: GI96(3)Media+PolyICLC

description: Day 3 Post-Challenge


title: HT02(3)Fluzone

description: Day 3 Post-Challenge


title: HE90(3)CD40-HA+PolyICLC

description: Day 3 Post-Challenge


title: HP84(3)Media+PolyICLC

description: Day 3 Post-Challenge


title: HE72(3)Fluzone

description: Day 3 Post-Challenge


title: GP83(3)CD40-HA+PolyICLC

description: Day 3 Post-Challenge


title: FT88(3)Media+PolyICLC

description: Day 3 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample42

source_name: Lymphoblastoid cell line sample42


title: HF07(6)CD40-NP5+PolyICLC

description: Day 6 Post Challenge


title: HF96(3)Fluzone

description: Day 3 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample40

source_name: Lymphoblastoid cell line sample40


title: Lymphoblastoid cell line Down Syndrome sample39

source_name: Lymphoblastoid cell line sample39


title: Lymphoblastoid cell line Down Syndrome sample38

source_name: Lymphoblastoid cell line sample38


title: Lymphoblastoid cell line Down Syndrome sample37

source_name: Lymphoblastoid cell line sample37


title: Lymphoblastoid cell line Down Syndrome sample41

source_name: Lymphoblastoid cell line sample41


title: HD06(3)Media+PolyICLC

description: Day 3 Post-Challenge


title: HE72(20)Fluzone

description: Day 20 Post-Challenge


title: FM05(3)CD40-NP5+PolyICLC

description: Day 3 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample32

source_name: Lymphoblastoid cell line sample32


title: EA43(3)Fluzone

description: Day 3 Post-Challenge


title: FM36(3)CD40-HA+PolyICLC

description: Day 3 Post-Challenge


title: HF07(3)CD40-NP5+PolyICLC

description: Day 3 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample30

source_name: Lymphoblastoid cell line sample30


title: Lymphoblastoid cell line Down Syndrome sample36

source_name: Lymphoblastoid cell line sample36


title: FF91(3)CD40-HA+PolyICLC

description: Day 3 Post-Challenge


title: FC82(3)CD40-NP5+PolyICLC

description: Day 3 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample31

source_name: Lymphoblastoid cell line sample31


title: FM36(20)CD40-HA+PolyICLC

description: Day 20 Post-Challenge


title: FM05(20)CD40-NP5+PolyICLC

description: Day 20 Post-Challenge


title: HF07(20)CD40-NP5+PolyICLC

description: Day 20 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample28

source_name: Lymphoblastoid cell line sample28


title: Lymphoblastoid cell line Down Syndrome sample35

source_name: Lymphoblastoid cell line sample35


title: HE90(20)CD40-HA+PolyICLC

description: Day 20 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample29

source_name: Lymphoblastoid cell line sample29


title: Lymphoblastoid cell line Down Syndrome sample34

source_name: Lymphoblastoid cell line sample34


title: Lymphoblastoid cell line Down Syndrome sample33

source_name: Lymphoblastoid cell line sample33


title: Lymphoblastoid cell line Down Syndrome sample27

source_name: Lymphoblastoid cell line sample27


title: Lymphoblastoid cell line Down Syndrome sample21

source_name: Lymphoblastoid cell line sample21


title: Lymphoblastoid cell line Down Syndrome sample26

source_name: Lymphoblastoid cell line sample26


title: Lymphoblastoid cell line Down Syndrome sample25

source_name: Lymphoblastoid cell line sample25


title: Lymphoblastoid cell line Down Syndrome sample22

source_name: Lymphoblastoid cell line sample22


title: GI96(20)Media+PolyICLC

description: Day 20 Post-Challenge

source_name: total RNA (globin reduced)


title: Lymphoblastoid cell line Down Syndrome sample17

source_name: Lymphoblastoid cell line sample17


title: GB58(20)CD40-NP5+PolyICLC

description: Day 20 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample19

source_name: Lymphoblastoid cell line sample19


title: Lymphoblastoid cell line Down Syndrome sample23

source_name: Lymphoblastoid cell line sample23


title: Lymphoblastoid cell line Down Syndrome sample24

source_name: Lymphoblastoid cell line sample24


title: Lymphoblastoid cell line Down Syndrome sample18

source_name: Lymphoblastoid cell line sample18


title: Lymphoblastoid cell line Down Syndrome sample20

source_name: Lymphoblastoid cell line sample20


title: Lymphoblastoid cell line Down Syndrome sample15

source_name: Lymphoblastoid cell line sample15


title: Lymphoblastoid cell line Down Syndrome sample16

source_name: Lymphoblastoid cell line sample16


title: HP84(20)Media+PolyICLC

description: Day 20 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample14

source_name: Lymphoblastoid cell line sample14


title: FM05(14)CD40-NP5+PolyICLC

description: Day 14 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample13

source_name: Lymphoblastoid cell line sample13


title: Lymphoblastoid cell line Down Syndrome sample12

source_name: Lymphoblastoid cell line sample12


title: Lymphoblastoid cell line Down Syndrome sample11

source_name: Lymphoblastoid cell line sample11


title: FF91(20)CD40-HA+PolyICLC

description: Day 20 Post-Challenge


title: HD06(20)Media+PolyICLC

description: Day 20 Post-Challenge


title: HF96(20)Fluzone

description: Day 20 Post-Challenge


title: FC82(20)CD40-NP5+PolyICLC

description: Day 20 Post-Challenge


title: GI96(14)Media+PolyICLC

description: Day 14 Post-Challenge


title: FM36(14)CD40-HA+PolyICLC

description: Day 14 Post-Challenge


title: GP83(20)CD40-HA+PolyICLC

description: Day 20 Post-Challenge


title: FC82(14)CD40-NP5+PolyICLC

description: Day 14 Post-Challenge


title: FT88(14)Media+PolyICLC

description: Day 14 Post-Challenge


title: HE90(14)CD40-HA+PolyICLC

description: Day 14 Post-Challenge


title: FT88(20)Media+PolyICLC

description: Day 20 Post-Challenge


title: FF91(14)CD40-HA+PolyICLC

description: Day 14 Post-Challenge


title: GP83(14)CD40-HA+PolyICLC

description: Day 14 Post-Challenge


title: EA43(20)Fluzone

description: Day 20 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample7

source_name: Lymphoblastoid cell line sample7


title: Lymphoblastoid cell line Down Syndrome sample9

source_name: Lymphoblastoid cell line sample9


title: GB58(14)CD40-NP5+PolyICLC

description: Day 14 Post-Challenge


title: Lymphoblastoid cell line Down Syndrome sample6

source_name: Lymphoblastoid cell line sample6


title: Lymphoblastoid cell line Down Syndrome sample10

source_name: Lymphoblastoid cell line sample10


title: Lymphoblastoid cell line Down Syndrome sample8

source_name: Lymphoblastoid cell line sample8


title: Lymphoblastoid cell line Down Syndrome sample5

source_name: Lymphoblastoid cell line sample5


title: Lymphoblastoid cell line Down Syndrome sample4

source_name: Lymphoblastoid cell line sample4


title: Lymphoblastoid cell line Down Syndrome sample3

source_name: Lymphoblastoid cell line sample3


title: Lymphoblastoid cell line Down Syndrome sample2

source_name: Lymphoblastoid cell line sample2


title: HF96(14)Fluzone

description: Day 14 Post-Challenge

source_name: total RNA (globin reduced)


title: EA43(14)Fluzone

description: Day 14 Post-Challenge


title: HT02(14)Fluzone

description: Day 14 Post-Challenge


title: HE72(14)Fluzone

description: Day 14 Post-Challenge


title: Genomic DNA from donor 82

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

description:
Human Pancreatic Islet DNA
I_82

hyb_protocol: Illumina protocol 15019522 RevB. For XStain process only: 15019521 RevB

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing:
The GenomeStudio® methylation module software was used to calculate the raw methylation score for each DNA methylation site, which is represented as methylation β-value. The β-values are calculated as (β= intensity of the methylated allele (M) / intensity of the Unmethylated allele (U) + intensity of the Methylated allele (M) + 100). All samples passed GenomeStudio® quality control steps based on built in control probes for staining, hybridisation, extension and specificity and displayed high quality bisulfite conversion efficiency with an intensity signal above 4000. Probes were then filtered based on Illumina detection p-value, and probes with a mean detection p-value>0.01 were removed from further analysis. In total DNA methylation data were obtained for 483031 probes out of which 3039 probes are non-CpG sites. Since the cohort included islets from both males and females, Y-chromosome data were removed and subsequently DNA methylation data from 482954 probes remained for further analysis. β-values were converted to M-values for further analysis (M = log2 (β / (1 - β)) to remove heteroscedasticity in the data distribution. Background correction and quantile normalization were performed using the lumi package from bioconductor.
The signal_intensities.txt contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: female_pancreatic islet DNA

label_protocol: Bisulfite Conversion of the DNA was done with the EZ-96 DNA Methylation Kit v1.4. according to the manufacturers instructions (EZ-96 DNA Methylation Kit, cat no D5004, Zymo Research), but no labeling was done

growth_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to DNA preparation.

extract_protocol: DNA was extracted from human pancreatic islets using the AllPrep DNA/RNA kit (Qiagen, Hilding, Germany) according to the manufacturer’s instructions. Nucleic acid purity and concentration were determined using a nanodrop (NanoDrop Technologies, Wilmington, DE, USA). All DNA samples had an A260/280 ratio of 1.8-2.1, whereas the 260/280 ratios for RNA were 1.9-2.2. The integrity and quality of the RNA was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and available RIN values from the Bioanalyzer were between 8.6 and 10.

tag: donor id

value: donor 82

tag: gender

value: female

value: pancreatic islet

tag: bisuflite conversion batch

tag: illumina chip number

value: H


title: Genomic DNA from donor 53

description:
Human Pancreatic Islet DNA
I_53

source_name: male_pancreatic islet DNA

value: donor 53

value: male

tag: tissue


title: Genomic DNA from donor 113

description:
Human Pancreatic Islet DNA
I_113

value: donor 113

value: K


title: Genomic DNA from donor 70

description:
Human Pancreatic Islet DNA
I_70

value: donor 70


title: Genomic DNA from donor 112

description:
Human Pancreatic Islet DNA
I_112

value: donor 112


title: HP84(14)Media+PolyICLC

description: Day 14 Post-Challenge


title: Genomic DNA from donor 58

description:
Human Pancreatic Islet DNA
I_58

value: donor 58


title: Lymphoblastoid cell line Down Syndrome sample1

source_name: Lymphoblastoid cell line sample1

value: lymphoblastoid cell line

value: Down Syndrome

value: European Ancestry

value: case


title: HD06(14)Media+PolyICLC

description: Day 14 Post-Challenge

value: Live Cal04

value: Vaccine Assessment

value: Whole Blood


title: HF96(1)Fluzone

description: Day 1 Post-Challenge

value: Fluzone


title: Genomic DNA from donor 45

description:
Human Pancreatic Islet DNA
I_45

value: donor 45

value: female

value: pancreatic islet


title: HP84(1)Media+PolyICLC

description: Day 1 Post-Challenge

value: Media+PolyICLC


title: FM36(1)CD40-HA+PolyICLC

description: Day 1 Post-Challenge


title: HD06(1)Media+PolyICLC

description: Day 1 Post-Challenge


title: GB58(1)CD40-NP5+PolyICLC

description: Day 1 Post-Challenge


title: HF07(14)CD40-NP5+PolyICLC

description: Day 14 Post-Challenge


title: HE72(1)Fluzone

description: Day 1 Post-Challenge


title: FT88(1)Media+PolyICLC

description: Day 1 Post-Challenge


title: Genomic DNA from donor 32

description:
Human Pancreatic Islet DNA
I_32

value: donor 32

value: H


title: HF07(1)CD40-NP5+PolyICLC

description: Day 1 Post-Challenge


title: HE90(1)CD40-HA+PolyICLC

description: Day 1 Post-Challenge


title: FM05(1)CD40-NP5+PolyICLC

description: Day 1 Post-Challenge


title: EA43(1)Fluzone

description: Day 1 Post-Challenge


title: Genomic DNA from donor 5

description:
Human Pancreatic Islet DNA
I_5

value: donor 5


title: Genomic DNA from donor 19

description:
Human Pancreatic Islet DNA
I_19

value: donor 19

value: male


title: Genomic DNA from donor 39

description:
Human Pancreatic Islet DNA
I_39

value: donor 39


title: GB58(0)CD40-NP5+PolyICLC

description: Baseline 2


title: HF96(0)Fluzone

description: Baseline 2


title: Genomic DNA from donor 81

description:
Human Pancreatic Islet DNA
I_81

value: donor 81


title: FC82(1)CD40-NP5+PolyICLC

description: Day 1 Post-Challenge


title: Genomic DNA from donor 69

description:
Human Pancreatic Islet DNA
I_69

value: donor 69


title: GP83(1)CD40-HA+PolyICLC

description: Day 1 Post-Challenge


title: Genomic DNA from donor 57

description:
Human Pancreatic Islet DNA
I_57

value: donor 57


title: Genomic DNA from donor 31

description:
Human Pancreatic Islet DNA
I_31

value: donor 31

value: G


title: Genomic DNA from donor 44

description:
Human Pancreatic Islet DNA
I_44

value: donor 44


title: GI96(1)Media+PolyICLC

description: Day 1 Post-Challenge

value: Live Cal04

value: Vaccine Assessment

value: Whole Blood


title: Genomic DNA from donor 16

description:
Human Pancreatic Islet DNA
I_16

value: donor 16

value: pancreatic islet


title: Genomic DNA from donor 4

description:
Human Pancreatic Islet DNA
I_4

value: donor 4

value: female


title: Genomic DNA from donor 80

description:
Human Pancreatic Islet DNA
I_80

value: donor 80


title: Genomic DNA from donor 68

description:
Human Pancreatic Islet DNA
I_68

value: donor 68


title: Genomic DNA from donor 56

description:
Human Pancreatic Islet DNA
I_56

value: donor 56


title: Genomic DNA from donor 43

description:
Human Pancreatic Islet DNA
I_43

value: donor 43


title: HE90(0)CD40-HA+PolyICLC

description: Baseline 2


title: Genomic DNA from donor 27

description:
Human Pancreatic Islet DNA
I_27

value: donor 27


title: Genomic DNA from donor 30

description:
Human Pancreatic Islet DNA
I_30

value: donor 30

value: male


title: HP84(0)Media+PolyICLC

description: Baseline 2

value: Media+PolyICLC


title: GI96(0)Media+PolyICLC

description: Baseline 2


title: HE72(0)Fluzone

description: Baseline 2

value: Fluzone


title: HF07(0)CD40-NP5+PolyICLC

description: Baseline 2


title: HD06(0)Media+PolyICLC

description: Baseline 2


title: Genomic DNA from donor 79

description:
Human Pancreatic Islet DNA
I_79

value: donor 79

value: F


title: FF91(0)CD40-HA+PolyICLC

description: Baseline 2

value: Live Cal04

value: Vaccine Assessment


title: GI96(-7)Media+PolyICLC

description: Baseline 1

value: Whole Blood


title: FM05(0)CD40-NP5+PolyICLC

description: Baseline 2


title: GB58(-7)CD40-NP5+PolyICLC

description: Baseline 1


title: GP83(0)CD40-HA+PolyICLC

description: Baseline 2


title: HD06(-7)Media+PolyICLC

description: Baseline 1


title: FM36(0)CD40-HA+PolyICLC

description: Baseline 2


title: FT88(0)Media+PolyICLC

description: Baseline 2


title: Genomic DNA from donor 67

description:
Human Pancreatic Islet DNA
I_67

value: donor 67

value: pancreatic islet


title: HT02(0)Fluzone

description: Baseline 2


title: FC82(0)CD40-NP5+PolyICLC

description: Baseline 2


title: FF91(-7)CD40-HA+PolyICLC

description: Baseline 1


title: HT02(-7)Fluzone

description: Baseline 1


title: HF07(-7)CD40-NP5+PolyICLC

description: Baseline 1


title: Genomic DNA from donor 55

description:
Human Pancreatic Islet DNA
I_55

value: donor 55


title: EA43(-7)Fluzone

description: Baseline 1


title: Genomic DNA from donor 78

description:
Human Pancreatic Islet DNA
I_78

value: donor 78


title: Genomic DNA from donor 3

description:
Human Pancreatic Islet DNA
I_3

value: donor 3

value: female

value: G


title: Genomic DNA from donor 21

description:
Human Pancreatic Islet DNA
I_21

value: donor 21

value: D


title: Genomic DNA from donor 88

description:
Human Pancreatic Islet DNA
I_88

value: donor 88

value: male


title: Genomic DNA from donor 29

description:
Human Pancreatic Islet DNA
I_29

value: donor 29


title: Genomic DNA from donor 75

description:
Human Pancreatic Islet DNA
I_75

value: donor 75


title: Genomic DNA from donor 66

description:
Human Pancreatic Islet DNA
I_66

value: donor 66

value: F


title: Genomic DNA from donor 13

description:
Human Pancreatic Islet DNA
I_13

value: donor 13

value: E


title: EA43(0)Fluzone

description: Baseline 2

value: Live Cal04

value: Fluzone

value: Vaccine Assessment

value: Whole Blood


title: Rd6_P14_2

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.2) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.  For this experiment, six pairwise comparisons were used to statistically resolve gene expression differences between sample groups using the R/maanova analysis package.  Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova.  Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value.

source_name: whole eye

label_protocol: Fragmented biotinylated cRNA were prepared according to the standard One-Cycle cDNA synthesis Affymetrix protocol from 2 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix© 1999-2004).

tag: strain

tag: developmental stage

value: postnatal 14


title: GP83(-7)CD40-HA+PolyICLC

description: Baseline 1


title: Genomic DNA from donor 1

description:
Human Pancreatic Islet DNA
I_1

value: donor 1

value: pancreatic islet


title: Genomic DNA from donor 40

description:
Human Pancreatic Islet DNA
I_40

value: donor 40


title: Genomic DNA from donor 15

description:
Human Pancreatic Islet DNA
I_15

value: donor 15

value: G


title: FT88(-7)Media+PolyICLC

description: Baseline 1

value: Media+PolyICLC


title: Rd6_P14_3


title: HP84(-7)Media+PolyICLC

description: Baseline 1


title: HE19(20)L

description: D20 Post-Challenge

value: Model Establisment


title: HF96(-7)Fluzone

description: Baseline 1


title: Rd6_P14_1


title: HH71(14)L

description: D14 Post-Challenge


title: HE90(-7)CD40-HA+PolyICLC

description: Baseline 1


title: HH72(20)UV

description: D20 Post-Challenge

value: UV Cal04


title: HF29(8)L

description: D8 Post-Challenge


title: HH71(-7)L

description: Baseline 1


title: Genomic DNA from donor 63

description:
Human Pancreatic Islet DNA
I_63

value: donor 63

value: male

value: D


title: Genomic DNA from donor 25

description:
Human Pancreatic Islet DNA
I_25

value: donor 25

value: female


title: Genomic DNA from donor 37

description:
Human Pancreatic Islet DNA
I_37

value: donor 37


title: Genomic DNA from donor 28

description:
Human Pancreatic Islet DNA
I_28

value: donor 28

value: E


title: Genomic DNA from donor 10

description:
Human Pancreatic Islet DNA
I_10

value: donor 10


title: Genomic DNA from donor 76

description:
Human Pancreatic Islet DNA
I_76

value: donor 76


title: Genomic DNA from donor 87

description:
Human Pancreatic Islet DNA
I_87

value: donor 87

value: pancreatic islet


title: Rd6_P0_3

value: postnatal 0


title: Genomic DNA from donor 2

description:
Human Pancreatic Islet DNA
I_2

value: donor 2

value: F


title: Genomic DNA from donor 62

description:
Human Pancreatic Islet DNA
I_62

value: donor 62


title: HH72(-7)UV

description: Baseline 1

value: UV Cal04

value: Model Establisment

value: Whole Blood


title: Genomic DNA from donor 36

description:
Human Pancreatic Islet DNA
I_36

value: donor 36

value: male

value: C


title: B6_P14_2

value: postnatal 14


title: FM05(-7)CD40-NP5+PolyICLC

description: Baseline 1

value: Live Cal04

value: Vaccine Assessment


title: Rd6_P0_2


title: Rd6_P0_1


title: HE72(-7)Fluzone

description: Baseline 1

value: Fluzone


title: HF40(1)UV

description: D1 Post-Challenge


title: FC82(-7)CD40-NP5+PolyICLC

description: Baseline 1


title: Genomic DNA from donor 14

description:
Human Pancreatic Islet DNA
I_14

value: donor 14


title: HH69(8)L(Vac)

description: D8 Post-Challenge

value: Lox-1-HA and DCIR-NP with CpG-B


title: HI77(2)L(Vac)

description: D2 Post-Challenge


title: HH71(0)L

description: Baseline 2


title: B6_P14_3


title: Genomic DNA from donor 24

description:
Human Pancreatic Islet DNA
I_24

value: donor 24

value: female

value: pancreatic islet


title: B6_P0_3

value: postnatal 0


title: B6_P14_1


title: HF29(-7)L

description: Baseline 1


title: HH69(20)L(Vac)

description: D20 Post-Challenge


title: B6_P0_2


title: hmNPCs_3D_HD-CAV-2_5d_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Gene expression data from hmNPCs 3D culture transduced with HD-CAV-2 and collection at 5 days

hyb_protocol: labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's protocol.

data_processing: Expression data (CEL files) were analyzed by the Robust Multiarray Average (RMA) method of Irrizarry using the R/Bioconductor suite of packages.

source_name: hmNPCs 3D cells, transduction, HD-CAV-2, 5d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Total RNA was isolated by using the RNeasy Mini Kit (Qiagen)

value: human midbrain neuroprogenitor cells

value: embryonic midbrain tissue

tag: transduction

tag: time

value: 5 days


title: Genomic DNA from donor 9

description:
Human Pancreatic Islet DNA
I_9

value: donor 9


title: Genomic DNA from donor 86

description:
Human Pancreatic Islet DNA
I_86

value: donor 86


title: Genomic DNA from donor 73

description:
Human Pancreatic Islet DNA
I_73

value: donor 73


title: hmNPCs_3D_HD-CAV-2_5d_rep1


title: hmNPCs_3D_HD-CAV-2_5d_rep2


title: HH71(1)L

description: D1 Post-Challenge

tag: monkey

tag: time (day)

value: Model Establisment

value: Whole Blood


title: Genomic DNA from donor 23

description:
Human Pancreatic Islet DNA
I_23

value: donor 23

value: C


title: HI77(1)L(Vac)

description: D1 Post-Challenge

tag: challenge

value: Live Cal04

tag: previous vaccination


title: Genomic DNA from donor 8

description:
Human Pancreatic Islet DNA
I_8

value: donor 8

value: male


title: HF29(5)L

description: D5 Post-Challenge

tag: dataset


title: Genomic DNA from donor 52

description:
Human Pancreatic Islet DNA
I_52

value: donor 52

value: B


title: B6_P0_1


title: hmNPCs_3D_HD-CAV-2_2h_rep2

description: Gene expression data from hmNPCs 3D culture transduced with HD-CAV-2 and collection at 2 hour

source_name: hmNPCs 3D cells, transduction, HD-CAV-2, 2h

tag: cell type

value: 2 hours


title: MDX mouse treated with tadalafil 2

first: Lucia

last: Monaco

address: Piazzale Aldo Moro 5

department: Dept. di Fisiologia e Farmacologia

institute: Universita degli Studi di Roma Sapienza

hyb_protocol: Purified labeled probes were hybridized with 2X Agilent Hybridization Buffer to RNG/MRC human pangenomic microarrays in an Agilent oven at 62°C for 16 h

scan_protocol: Then microarrays were washed and scanned with a Genepix 4000B scanner

data_processing:
The TIFF images were analyzed using Genepix Pro 4.0 software, the signal intensities were log-transformed and normalization was performed by the intensity dependent Lowess method
A bioinformatics analysis was performed in the genes differentially expressed using DAVID Bioinformatics Resources 6.7

source_name: Muscles

label_protocol: Fluorescent probes were synthesized by chemical coupling of 5µg aminoallyl aRNA with cyanine Cy3 dye

extract_protocol: RNA was isolated from the quadriceps muscles. The total RNA was extracted using Trizol reagent

treatment_protocol: The treatments with tadalafil (Cialis, Ely Lilly and Company) were started before birth by oral administration through drinking water (30 mg/kg/day) and continued for four months

value: Quadriceps muscles

tag: strain/genotype

value: MDX

tag: treatment

value: tadalafil


title: MDX mouse treated with tadalafil 3


title: hmNPCs_3D_HD-CAV-2_2h_rep3

value: human midbrain neuroprogenitor cells

value: embryonic midbrain tissue


title: hmNPCs_3D_untreated_5d_rep3

description: Gene expression data from hmNPCs 3D culture without transduction and collection at 5 days

source_name: hmNPCs 3D cells, no transduction, 5d

value: control

value: 5 days


title: hmNPCs_3D_HD-CAV-2_2h_rep1


title: HH75(0)UV

description: Baseline 2

value: UV Cal04

value: Model Establisment


title: Genomic DNA from donor 85

description:
Human Pancreatic Islet DNA
I_85

tag: donor id

value: donor 85

value: pancreatic islet


title: MDX mouse 2


title: HH75(1)UV

description: D1 Post-Challenge

value: Whole Blood


title: HI77(14)L(Vac)

description: D14 Post-Challenge

value: Live Cal04

value: Lox-1-HA and DCIR-NP with CpG-B


title: HH71(8)L

description: D8 Post-Challenge


title: Genomic DNA from donor 72

description:
Human Pancreatic Islet DNA
I_72

value: donor 72

tag: gender

value: female


title: hmNPCs_3D_untreated_5d_rep2


title: MDX mouse 3


title: Genomic DNA from donor 60

description:
Human Pancreatic Islet DNA
I_60

value: donor 60

value: male

tag: bisuflite conversion batch

value: B


title: C57BL/6J WT mouse 3

value: Quadriceps muscles

value: C57BL/6J WT


title: MDX mouse treated with tadalafil 1

value: MDX

value: tadalafil


title: Genomic DNA from donor 48

description:
Human Pancreatic Islet DNA
I_48

value: donor 48

tag: illumina chip number


title: hmNPCs_3D_untreated_2h_rep3

description: Gene expression data from hmNPCs 3D culture without transduction and collection at 2 hour

source_name: hmNPCs 3D cells, no transduction, 2h

value: human midbrain neuroprogenitor cells

tag: tissue

value: embryonic midbrain tissue

value: control

value: 2 hours


title: hmNPCs_3D_untreated_5d_rep1

value: 5 days


title: HF40(14)UV

description: D14 Post-Challenge

value: UV Cal04

value: Model Establisment

value: Whole Blood


title: HF40(-7)UV

description: Baseline 1


title: Genomic DNA from donor 34

description:
Human Pancreatic Islet DNA
I_34

value: donor 34

value: pancreatic islet


title: MDX mouse 1


title: hmNPCs_3D_untreated_2h_rep2


title: Genomic DNA from donor 22

description:
Human Pancreatic Islet DNA
I_22

value: donor 22

value: male


title: Genomic DNA from donor 7

description:
Human Pancreatic Islet DNA
I_7

value: donor 7

value: B


title: Genomic DNA from donor 84

description:
Human Pancreatic Islet DNA
I_84

value: donor 84

value: female


title: HH72(5)UV

description: D5 Post-Challenge


title: hmNPCs_3D_untreated_2h_rep1


title: C57BL/6J WT mouse 1

value: Quadriceps muscles

value: C57BL/6J WT


title: Genomic DNA from donor 71

description:
Human Pancreatic Islet DNA
I_71

value: donor 71


title: HF40(5)UV

description: D5 Post-Challenge


title: HI77(5)L(Vac)

description: D8 Post-Challenge

value: Live Cal04

value: Lox-1-HA and DCIR-NP with CpG-B


title: C57BL/6J WT mouse 2


title: OCI-Ly1_ctrloverexpression

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: DLBCL_empty vector overexpression

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 200 ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Isolated human B cells were cultured on CD40L-L cells, IL-21(25 ng/ml, R&D systems, Abingdon, UK) and IL-2 (40U/ml, prospec, East Brunswick, NJ) in Iscove’s modifies Dulbecco’s medium (IMDM) containing 10% FCS, 100 units per ml of penicillin, and 100 μg per ml of glutamine (IMDM 10% FCS). DLBCL cell lines OCI-Ly1 and OCI-Ly7 were cultured in IMDM 10% FCS. OCI-Ly10 was cultured in IMDM 20% medium, supplemented with 35 μM β-mercaptoethanol.

extract_protocol: Total RNA was isolated from primary B cells using the Rneasy micro kit (Qiagen, Valencia, CA),according to the manufacturer’s protocol or from DLBCL cell lines, using using Trizol (Invitrogen) according to manufacturer’s protocol,

treatment_protocol: After culturing the primary human B cells for a minimum of 36 hours, cells were transferred to retronectin-coated plates and incubated with virus for 6-8 hours in IMDM 5% FCS medium. Thereafter, cells were cultured with CD40L-L cells in 10% FCS medium for 72 hours after which YFP positive cells were sorted and RNA was isolated. For cell line transductions, cell lines were transferred to retronectin-coated plates and incubated with virus for 24 hours. Thereafter, medium was refreshed and cells were cultured for 24 hours after which YFP positive cells were sorted and RNA was isolated. For siRNA-mediated knockdown, cells were transiently transfected using the Lonza nucleofection system. 2 days after transfection, RNA was isolated.

tag: cell line

value: diffuse large B-cell lymphoma (DLBCL)

tag: transduced with

value: LZRS-IRES-YFP

tag: genotype/variation

value: negative control


title: Genomic DNA from donor 33

description:
Human Pancreatic Islet DNA
I_33

value: donor 33

value: A


title: OCI-Ly7_ctrloverexpression


title: Genomic DNA from donor 20

description:
Human Pancreatic Islet DNA
I_20

value: donor 20

value: pancreatic islet


title: OCI-Ly7_FOXP1 overexpression

source_name: DLBCL_FOXP1 overexpression

value: FOXP1 overexpression


title: OCI-Ly10_ctrloverexpression


title: HH69(14)L(Vac)

description: D14 Post-Challenge

value: Model Establisment

value: Whole Blood


title: Genomic DNA from donor 59

description:
Human Pancreatic Islet DNA
I_59

value: donor 59

value: B


title: HE19(0)L

description: Baseline 2


title: HH75(2)UV

description: D2 Post-Challenge

value: UV Cal04


title: OCI-Ly7_siFOXP1

source_name: DLBCL_FOXP1 siRNA

value: siRNA targeting FOXP1

value: siRNA-mediated FOXP1 knockdown


title: Genomic DNA from donor 46

description:
Human Pancreatic Islet DNA
I_46

value: donor 46

value: male


title: OCI-Ly7_sictrl

source_name: DLBCL_ctrl siRNA

value: diffuse large B-cell lymphoma (DLBCL)

value: sigenome non-targeting siRNA


title: Genomic DNA from donor 26

description:
Human Pancreatic Islet DNA
I_26

value: donor 26

value: female


title: HE19(-7)L

description: Baseline 1

value: Live Cal04


title: Genomic DNA from donor 77

description:
Human Pancreatic Islet DNA
I_77

value: donor 77

value: A


title: OCI-Ly1_FOXP1 overexpression

value: FOXP1 overexpression


title: HE19(5)L

description: D5 Post-Challenge

value: Model Establisment


title: OCI-Ly10_FOXP1 overexpression


title: HH75(20)UV

description: D20 Post-Challenge

value: Whole Blood


title: HH72(2)UV

description: D2 Post-Challenge


title: OCI-Ly1_sictrl

value: negative control


title: HF29(1)L

description: D1 Post-Challenge


title: HI77(8)L(Vac)

description: D8 Post-Challenge

value: Lox-1-HA and DCIR-NP with CpG-B


title: Genomic DNA from donor 109

description:
Human Pancreatic Islet DNA
I_109

value: donor 109

value: pancreatic islet

value: J


title: HF29(14)L

description: D14 Post-Challenge


title: Genomic DNA from donor 6

description:
Human Pancreatic Islet DNA
I_6

value: donor 6


title: OCI-Ly10_siFOXP1

value: siRNA targeting FOXP1

value: siRNA-mediated FOXP1 knockdown


title: OCI-Ly1_siFOXP1

value: diffuse large B-cell lymphoma (DLBCL)


title: HH75(5)UV

description: D5 Post-Challenge

value: UV Cal04


title: OCI-Ly10_sictrl

value: sigenome non-targeting siRNA


title: Genomic DNA from donor 107

description:
Human Pancreatic Islet DNA
I_107

value: donor 107

value: male


title: Genomic DNA from donor 106

description:
Human Pancreatic Islet DNA
I_106

value: donor 106


title: Genomic DNA from donor 108

description:
Human Pancreatic Islet DNA
I_108

value: donor 108


title: HE19(2)L

description: D2 Post-Challenge

value: Live Cal04

value: Model Establisment


title: Genomic DNA from donor 110

description:
Human Pancreatic Islet DNA
I_110

value: donor 110


title: Genomic DNA from donor 101

description:
Human Pancreatic Islet DNA
I_101

value: donor 101

value: female

value: I


title: Genomic DNA from donor 100

description:
Human Pancreatic Islet DNA
I_100

value: donor 100

value: pancreatic islet


title: humanMBC_ctrl overexpression_2

source_name: human MBC_empty vector overexpression

value: human peripheral blood memory B cells (MBCs)

value: LZRS-IRES-YFP

value: negative control


title: Genomic DNA from donor 98

description:
Human Pancreatic Islet DNA
I_98

value: donor 98


title: Genomic DNA from donor 104

description:
Human Pancreatic Islet DNA
I_104

value: donor 104

value: J


title: Maturing neurons Day 8

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

hyb_protocol: Hybridization on miRCURY LNA™ Arrays, using MAUI® hybridization system.

scan_protocol: Hybridization images were scanned and digitized using InnoScan 700 microarray scanner (Innopsys, France).

data_processing: miRNA microarray data were analyzed by subtracting the background signal (B532nm) from the test signal (F532nm).

source_name: Maturing neurons Day 8

label_protocol: LNA-modified oligonucleotide (Exiqon, Denmark) probes for mouse miRNAs annotated in miRBase version 16.0 were used in the microarray. Total RNA (1 µg) was 3′-end –labeled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark).

growth_protocol: Primary cultures of cortical neurons were established from E15 Swiss albino mouse brains. The cortices were dissected from E15 mouse embryos and washed with Hanks’ balanced salt solution (HBSS, 14025-092, Gibco, Invitrogen, USA). The cortical slices was dissociated with 0.05% (w/v) trypsin in HBSS without Ca2+/Mg2+ (14175-095, Gibco, Invitrogen, USA) for 30 min at 37 °C and neutralized with 1mg/ml trypsin inhibitor (T6522, Sigma, USA). Single cells were obtained by gentle trituration in Neurobasal medium (21103-049, Gibco, Invitrogen, USA) supplemented with B27 (17504-044, Invitrogen, USA), L-glutamine and Penicillin-streptomycin (Gibco, Invitrogen, USA). The cells were counted by trypan blue exclusion and seeded on to poly-d-lysine coated 24 well plates at a density of 120, 000 cells/cm2. Cultures were maintained at 37 °C with 5% CO2 in a tissue culture incubator. Cells were harvested on Days 2, 4, 6, 8.

extract_protocol: Total RNA (+ microRNA) was extracted from cells by a single-step method using Trizol (Invitrogen, Life Technologies, USA) according to the manufacturers’ protocol. The concentration and integrity of the RNA were determined using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del) and denaturing polyacrylamide gel electrophoresis, respectively.

treatment_protocol: No treatment

tag: age

value: Gestation day 15

tag: strain

value: Swiss Albino

value: Murine primary cortical neurons

tag: age of culture

value: Day 8


title: Maturing neurons Day 4

source_name: Maturing neurons Day 4

value: Day 4


title: Maturing neurons Day 2

source_name: Maturing neurons Day 2

value: Day 2


title: humanMBC_ctrl overexpression_1


title: Genomic DNA from donor 97

description:
Human Pancreatic Islet DNA
I_97

value: donor 97

value: male


title: Genomic DNA from donor 94

description:
Human Pancreatic Islet DNA
I_94

value: donor 94

value: I


title: Genomic DNA from donor 92

description:
Human Pancreatic Islet DNA
I_92

value: donor 92

value: pancreatic islet


title: Maturing neurons Day 6

source_name: Maturing neurons Day 6

value: Day 6


title: humanMBC_FOXP1 overexpression_1

source_name: human MBC_FOXP1 overexpression

value: human peripheral blood memory B cells (MBCs)

value: FOXP1 overexpression


title: HF29(20)L

description: D20 Post-Challenge

source_name: total RNA (globin reduced)

tag: monkey

tag: time (day)

tag: challenge

value: Live Cal04

value: Model Establisment

value: Whole Blood


title: humanMBC_FOXP1 overexpression_2

tag: cell type


title: HH72(8)UV

description: D8 Post-Challenge

value: UV Cal04

tag: previous vaccination

tag: dataset


title: HI77(-7)L(Vac)

description: Baseline 1

value: Lox-1-HA and DCIR-NP with CpG-B


title: Genomic DNA from donor 102

description:
Human Pancreatic Islet DNA
I_102

source_name: male_pancreatic islet DNA

tag: donor id

value: donor 102

value: J


title: HH71(5)L

description: D5 Post-Challenge


title: HE19(8)L

description: D8 Post-Challenge


title: Genomic DNA from donor 90

description:
Human Pancreatic Islet DNA
I_90

source_name: female_pancreatic islet DNA

value: donor 90

tag: gender

value: female


title: HH75(-7)UV

description: Baseline 1


title: HH75(14)UV

description: D14 Post-Challenge


title: HF29(0)L

description: Baseline 2


title: Genomic DNA from donor 89

description:
Human Pancreatic Islet DNA
I_89

value: donor 89

value: male

tag: bisuflite conversion batch


title: HH71(20)L

description: D20 Post-Challenge


title: HF40(20)UV

description: D20 Post-Challenge


title: HI77(20)L(Vac)

description: D20 Post-Challenge


title: HF40(2)UV

description: D2 Post-Challenge


title: HH69(1)L(Vac)

description: D1 Post-Challenge


title: HH72(1)UV

description: D1 Post-Challenge


title: Pr-745#3

city: Davis

first: Takao

last: Kasuga

state: CA

address: 382 Huchison Hall

institute: USDA-ARS

hyb_protocol: NimbleGen labeling protocol version 3.1: hybridized at 42C for 12 to 16 hours on MAUI Hybridization system.  NimbleGen Hybridization and Wash Buffer kits were used.

scan_protocol: Axon GenePix 4000B, 500 to 650 PMT, single color scan (532 nm).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Phytophthora ramorum

label_protocol: NimbleGen labeling protocol version 3.1: Cy3-labeled random 9-mers were used to label double stranded cDNA.

growth_protocol: 7 days on solid CV8 medium, constant light, 21C

extract_protocol: Liquid nitrogen frozen samples were disrupted by FastPrep-24 homogenizer with Lysing Matrix A, followed by the Trizol Reagent protocol

tag: host

value: canyon live oak

tag: colony

value: nwt


title: Pr-710#2


title: HH69(-7)L(Vac)

description: Baseline 1

tag: tissue


title: HH72(0)UV

description: Baseline 2


title: G-10

city: Shantou

first: Wei

last: Gu

state: GuangDong

address: 22 Xing-Lin Road

department: Pathophysiology

country: China

institute: Shantou University Medical College

description:
SAMPLE 1
MDA231/GFP generated breast tumor, Rep1

hyb_protocol: Hybridization was  done in a Hybridization Oven 645. The experiment was performed by the 'Gene Company Limited' in Shanghai, China.

scan_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeView Human Gene expression Array. GeneChips were washed in Fluidics Station 450 and were scanned using Genechip Scanner 3000 7G.

data_processing: Data were analyzed with a commercial software Partek GS 6.5. The analysis was performed in the 'Gene Company Limited' located in Shanghai, China

source_name: Breast tumor expressing GFP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Labeling was performed by the 'Gene Company Limited' in Shanghai, China.

growth_protocol: Cultured MDA231/ZBP1-GFP and MDA231/GFP cells were resuspended in DMEM media (4x107/ml) and mixed with Matrigel at 1:1 ratio. 200 μl of cell mixture were injected into the fat pad of mammary gland of anesthesized 6-wk-old Scid/Scid mice and allowed to grow for 8 wk.

treatment_protocol: After 8 weeks, mice were sacrificed and breast tumors were removed. Total RNA was extracted from aliquots of tumor tissues

tag: host strain

value: Scid/Scid mouse

tag: injected with

value: MDA231/GFP cells

value: MDA231/GFP generated breast tumor


title: HF40(0)UV

description: Baseline 2


title: I-6-2

description:
SAMPLE 4
MDA231/ZBP1-GFP generated tumor, Rep2

source_name: Breast tumor expressing ZBP1-GFP

value: MDA231/ZBP1-GFP cells

value: MDA231/ZBP1-GFP generated tumor


title: HI77(0)L(Vac)

description: Baseline 2

value: Live Cal04

value: Model Establisment


title: I-5-2

description:
SAMPLE 3
MDA231/ZBP1-GFP generated tumor, Rep1


title: HE19(1)L

description: D1 Post-Challenge

value: Whole Blood


title: Day6neurons_OGD_6hr OGD

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software.

data_processing: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs and lncRNAs were filtered.

source_name: Day6neurons_OGD_6hr OGD

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: Total RNA was extracted from cells by a single-step method using Trizol (Invitrogen, Life Technologies, USA) according to the manufacturers’ protocol. The concentration and integrity of the RNA were determined using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del) and denaturing polyacrylamide gel electrophoresis, respectively. Thereafter, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre, USA).

treatment_protocol: Primary neuronal cultures from day 6 were subjected to oxygen-glucose deprivation (OGD) conditions as previously described (Ziu et al. 2011). Glucose-free Earle’s balanced salt solution (EBSS) was saturated with a mixture gas of 5% CO2, 95% N2, in a ProOx in vitro chamber (BioSpherix, USA) at 37ºC overnight, with O2 maintained at 0.1%. Day 6 neuronal cultures were washed twice with this medium and incubated for 2, 4, 6, 8hr in the chamber. OGD was terminated by replacing the glucose-free EBSS with reperfusion medium (Neurobasal medium with L-glutamine and Penicillin-streptomycin, without B27 supplement). Control cultures were treated identically, but without exposure to OGD conditions. During reperfusion, the cells were maintained in a regular 5% CO2 incubator for 24hrs.

tag: age

value: Gestation day 15

value: Swiss Albino Mouse

value: Murine primary cortical neurons

value: Day 6

tag: ogd treatment

tag: 24hr reperfusion


title: Pr-102

value: coast live oak


title: HH71(2)L

description: D2 Post-Challenge

tag: monkey


title: Day6neurons_OGD_4hr OGD

source_name: Day6neurons_OGD_4hr OGD

tag: strain

tag: age of culture


title: G-13

description:
SAMPLE 2
MDA231/GFP generated tumor, Rep2


title: Pr-710

value: California bay laurel

value: wt


title: Pr-745


title: Day6neurons_OGD_8hr OGD

source_name: Day6neurons_OGD_8hr OGD

tag: cell type


title: Pr-710#1

value: canyon live oak


title: HH69(0)L(Vac)

description: Baseline 2

tag: time (day)

tag: challenge

tag: previous vaccination

value: Lox-1-HA and DCIR-NP with CpG-B


title: HH75(8)UV

description: D8 Post-Challenge

value: UV Cal04

tag: dataset


title: Day6neurons_OGD_Ctrl


title: HF40(8)UV

description: D8 Post-Challenge


title: HH69(5)L(Vac)

description: D5 Post-Challenge


title: HH72(14)UV

description: D14 Post-Challenge


title: Pr-745#2

value: nwt


title: Pr-745#1


title: Maturing neurons Day 8

value: Day 8


title: HE19(14)L

description: D14 Post-Challenge


title: Day6neurons_OGD_2hr OGD

source_name: Day6neurons_OGD_2hr OGD


title: HH69(2)L(Vac)

description: D2 Post-Challenge


title: BG_21B

status: Public on Oct 23 2014

city: Düsseldorf

first: Boris

last: Goerg

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

country: Germany

institute: Heinrich-Heine Universität Düsseldorf

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 8x60K (Design ID 028004) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: post mortem tissue

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from post mortem brain tissue using the RNAeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturers protocol.

tag: diagnosis

value: healthy control

tag: tissue type

value: fisiform gyrus


title: HF29(2)L

description: D2 Post-Challenge

value: Live Cal04


title: BG_25B


title: BG_7B

value: liver cirrhosis


title: Maturing neurons Day 6


title: BG_13B

value: liver cirrhosis and hepatic encephalopathy


title: Maturing neurons Day 4

value: Gestation day 15

value: Day 4


title: BG_12B


title: BG_6B


title: BG_23B


title: BG_14B


title: BG_20B


title: Acid-Stressed K.vulgare Cell Replicate 2

city: Wuxi

first: Haoru

last: Yang

address: 1800 Lihu Road

institute: Jiangnan University

hyb_protocol: A total of 1μg of Cy3-labeled and Cy5-labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100 μl of hybridization solution was then dispensed in the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.

data_processing:
Agilent Feature Extraction Software (version 10.5.1.1) was used to analyze acquired array images. Lowess normalization and subsequent data processing was performed using the Agilent GeneSpring GX v11.5.1 software. Following Lowess normalization of the raw data, genes that at least 8 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.
The threshold we used to screen up- or downregulated genes was defined by Fold Change ≥2 and P-value <0.05.

organism: Ketogulonicigenium vulgare

source_name: Acid-stressed K.vulgare cells

label_protocol: Sample labeling and hybridization reactions were performed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA was linearly amplified and labeled with Cy5-dCTP and sample of common reference with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol Cy5/Cy3 per μg cRNA) were measured in a NanoDrop® ND-8000 spectrophotometer.

growth_protocol: The mixture of K. vulgare and B. megaterium was grown at 30 °C in the well defined chemical medium at pH 7.0 for 18 h until cells were at their mid-log phase.

extract_protocol: In order to stabilize the bacterial transcriptome profile, one-sixth of the culture volume of ice-cold 5% phenol-ethanol stop solution (v/v) was added to the culture firstly. After stabilizing the cells, the extraction of total RNA was conducted using the RNeasy Bacteria Mini kit (Qiagen) according to the manufacturer’s protocol. During the RNA extraction process, trace elements of remaining DNA were eliminated by DNase digestion using the RNase-Free DNase Set (Qiagen). The concentration and purity of the total RNA were assessed by Nanodrop® ND-8000 (Thermo Fisher), and the integrity of the RNA was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Cells were collected and shifted to the fresh chemical medium at pH 7.0 (control cells) and 4.0 (acid-stressed cells), respectively. All cultures were incubated at 30 °C for 2 h prior to RNA extraction.

tag: growth phase

value: in mid-logarithmic phase

tag: stress

value: pH 4.0 treated for 2 h

source_name: pooled 3 control and 3 acid-stressed cells

tag: reference


title: Control K.vulgare Cell Replicate 3

source_name: K.vulgare control cells

value: control

value: pooled 3 control and 3 acid-stressed cells


title: BG_5B


title: Acid-Stressed K.vulgare Cell Replicate 1


title: Control K.vulgare Cell Replicate 2


title: Acid-Stressed K.vulgare Cell Replicate 3


title: Maturing neurons Day 2

value: Swiss Albino Mouse

value: Murine primary cortical neurons

value: Day 2


title: BG_15B


title: BG_4B


title: Control K.vulgare Cell Replicate 1


title: STEMI patient, blood collected 6 months after MI (Patient 28)

city: Warsaw

first: Beata

last: Burzynska

address: Pawinskiego 5A

department: Genetics

country: Poland

institute: Institute of Biochemistry and Biophysics

description:
Sample name: Patient 28_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

hyb_protocol: Following fragmentation, 5.5 ug ssDNA were hybridized for 16 hr at 45˚C on GeneChip® Human Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 GeneArray Scanner.

data_processing: The data were analyzed with the Partek Genomics Suite software (Partek Inc, St. Louis, MO, USA) using RMA (robust multiarray average) background correction, quantile normalization, median polish method for probesets summarization, and log values of probes signals using base 2.

source_name: peripheral blood mononuclear cells

label_protocol: Biotin-labeled ssDNA were prepared from 100 ng total RNA by using the Ambion® WT Expression Kit followed by Affymetrix® GeneChip® WT Terminal Labeling Kit according to the manufacturer's instruction.

extract_protocol: Total RNA from peripheral blood mononuclear cells (PBMCs) samples was isolated using MagNA Pure Compact System (Roche Diagnostics GmbH, Germany) according to the manufacturer's recommendations. The amount of RNA was quantified by UV absorption (Nanodrop, LabTech International, UK) and its quality was determined using an Agilent 2100 Bioanalizer© and RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). For all RNA samples the RNA integrity number value was above eight.

tag: individual

value: Patient 28

tag: cardiovascular disease state

value: STEMI

tag: collection of blood samples

value: follow-up (6 months after MI)

value: PBMC


title: STEMI patient, blood collected on admission (Patient 28)

description:
Sample name: Patient 28_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: admission (on the 1st day of MI)


title: STEMI patient, blood collected 6 months after MI (Patient 27)

description:
Sample name: Patient 27_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 27