title: 1-24-2015, Mouse #510 SAMPLE 553

description: Primary tumor cell (transplanted)


title: 1-24-2015, Mouse #510 SAMPLE 554

status: Public on Jul 20 2015

type: RNA

city: San Francisco

first: Devon

last: Lawson

state: California

address: 513 Parnassus Ave Hsw 1301

department: Anatomy

country: USA

institute: UCSF

description: Primary tumor cell (transplanted)

data_processing: Data analyzed using Fluidigm real-time PCR analysis software and custom algorithms in R statistical software

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: PDX mouse

label_protocol: Single-cell gene expression using SsoFast EvaGreen SuperMix with low Rox on the BioMark system, advanced protocol 41

growth_protocol: Patient-derived xenograft model

extract_protocol: Enzymatic tissue digest

tag: model

value: Model HCI-002

tag: cell type

value: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell

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description: Primary tumor cell (transplanted)


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell (transplanted)


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description: Primary tumor cell (transplanted)


title: 11-7-2013, Mouse #22 SAMPLE 468

description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


title: 11-7-2013, Mouse #22 SAMPLE 450

description: Lung metastatic cell

value: Lung metastatic cell


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description: Primary tumor cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Primary tumor cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lymph node metastatic cell

value: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lung metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Lymph node metastatic cell


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description: Lymph node metastatic cell


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description: Primary tumor cell


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description: Lymph node metastatic cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Primary tumor cell


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description: Peripheral blood metastatic cell


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description: Bone marrow metastatic cell

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description: Bone marrow metastatic cell


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description: Primary tumor cell


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description: Bone marrow metastatic cell


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description: Primary tumor cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Bone marrow metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


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description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 233

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 252

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 230

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 228

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 229

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 232

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 239

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 227

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 225

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 223

description: Primary tumor cell

value: Model HCI-001


title: 3-13-2013, Mouse #557 SAMPLE 224

description: Primary tumor cell


title: 8-16-2013, Mouse #769 SAMPLE 226

description: Lung metastatic cell


title: 8-16-2013, Mouse #769 SAMPLE 231

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 221

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 219

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 222

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 217

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 218

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 220

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 212

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 215

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 216

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 207

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 213

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 214

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 209

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 206

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 203

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 201

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 202

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 204

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 200

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 198

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 199

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 210

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 211

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 195

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 208

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 196

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 194

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 193

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 192

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 190

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 189

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 191

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 184

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 180

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 205

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 183

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 187

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 186

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 182

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 185

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 177

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 175

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 176

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 174

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 179

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 181

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 172

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 173

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 188

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 171

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 170

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 168

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 169

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 166

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 167

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 197

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 163

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 178

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 164

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 156

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 162

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 153

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 159

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 154

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 161

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 158

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 155

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 157

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 152

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 150

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 149

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 151

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 165

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 145

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 148

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 147

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 143

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 160

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 144

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 142

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 146

description: Lung metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 141

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 140

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 139

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 134

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 136

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 135

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 138

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 132

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 133

description: Lymph node metastatic cell


title: 3-13-2013, Mouse #557 SAMPLE 131

description: Lymph node metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 129

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 125

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 126

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 130

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 127

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 128

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 124

description: Primary tumor cell


title: 3-13-2013, Mouse #557 SAMPLE 137

description: Lymph node metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 120

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 117

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 116

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 112

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 121

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 118

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 119

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 113

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 114

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 115

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 111

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 108

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 109

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 106

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 107

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 122

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 123

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 101

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 99

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 100

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 103

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 98

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 97

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 102

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 105

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 110

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 94

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 74

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 84

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 83

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 79

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 72

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 82

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 75

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 76

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 91

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 90

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 80

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 85

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 81

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 86

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 95

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 92

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 88

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 104

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 78

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 96

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 77

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 70

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 71

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 69

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 93

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 87

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 68

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 89

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 67

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 73

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 66

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 61

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 64

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 65

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 62

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 59

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 49

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 63

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 57

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 58

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 48

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 47

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 53

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 60

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 50

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 44

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 45

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 43

description: Primary tumor cell


title: 2-25-2014, Mouse #929 SAMPLE 52

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 51

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 56

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 54

description: Lung metastatic cell


title: 2-25-2014, Mouse #929 SAMPLE 55

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 41

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 39

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 46

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 40

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 31

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 37

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 36

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 32

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 42

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 30

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 34

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 35

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 28

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 27

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 26

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 25

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 29

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 24

description: Primary tumor cell


title: Adult Stomach

city: Tsukuba city

first: Takaaki

middle: K

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

country: Japan

institute: The University of Tsukuba

description: Gene expression od adult stomach

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization huffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol: GE1_1105_Oct12, and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Adult Stomach

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng-1ug RNA using the One-Color Quick amp labeling kit (Qiagen) folloowing the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic stem cells were maintained in DMEM  containing 15% FBS, Non-essential amino acids, peniciline/streptmycine, and β mercaptethanol supplemented with 1U/mL human recombinant LIF. ICR mice were grown according to the committee guidelines of the National Institute of Advanced Industrial Science and Technology for animal experiments.

extract_protocol: Total RNA was prepared using RNeasy Mini kit (Qiagen) or Isogen (Nippon Gene) following the manufacturer's instructions. The protocol of RNeasy Mini kit includes DNase digestion. Extratd RNA was qualified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Embryonic stem cells-derived stomach tissue cells were differentiated and cultured in DMEM/F12 containing N2/B27 and 50ng/mL human recombinant EGF supplemented with 100ng/mL human recombinant FGF10, Wnt3a, Noggin, and 250ng/mL R-spondin1 or 100ng/mL Shh and 10ng/mL Bmp4 for 42 days or 5 months. Adult mouse organs were freshly isolated from ICR mice, and used immediately.

tag: tissue

value: Stomach

tag: culture day/stage

value: Adult


title: Adult Lung

description: Gene expression of adult lung

source_name: Adult Lung

value: Lung


title: 3-17-2014, Mouse #202 SAMPLE 23

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 38

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 22

description: Primary tumor cell


title: 42-46days embryonic stem cells-derived stomach tissue in Shh medium

description: Gene expression of embryonic stem cells-derived stomach tissue cells cultured in Shh and Bmp4 from 42-46days after cultured in FGF10, Wnt3a, Noggin, R-spondin1 for 42days.

source_name: Embryonic stem cells-derived stomach tissue, 42-46days, Shh medium


title: Stomach Primordium

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization huffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 μm, Dye channel is set to Green).

source_name: E9.5 Stomach

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng-1 μg RNA using the One-Color Quick amp labeling kit (Qiagen) folloowing the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic stem cells were maintained in DMEM  containing 15% FBS, Non-essential amino acids, peniciline/streptmycine, and β mercaptethanol supplemented with 1 U/mL human recombinant LIF. ICR mice were grown according to the committee guidelines of the National Institute of Advanced Industrial Science and Technology for animal experiments.

treatment_protocol: Embryonic stem cells-derived stomach tissue cells were differentiated and cultured in DMEM/F12 containing N2/B27 and 50 ng/mL human recombinant EGF supplemented with 100 ng/mL human recombinant FGF10, WNT3A, NOGGIN, and 250 ng/mL R-SPONDIN1 or 100 ng/mL SHH and 10ng/mL BMP4 for 42 days or 5 months. Adult mouse organs were freshly isolated from ICR mice, and used immediately.

tag: strain background

value: ICR


title: Adult Esophagus

description: Gene expression of adult esophagus

source_name: Adult Esophagus

value: Esophagus


title: Adult Intestine

description: Gene expression of adult intestine

source_name: Adult Intestine

value: Intestine


title: 42days embryonic stem cells-derived stomach tissue in FGF medium

description: Gene expression of embryonic stem cells-derived stomach tissue cells cultured in FGF10, Wnt3a, Noggin and R-spondin1 for 42days.

source_name: Embryonic stem cells-derived stomach tissue, 42days, FGF medium


title: 3-17-2014, Mouse #202 SAMPLE 21

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 20

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 19

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 33

description: Primary tumor cell


title: 3-17-2014, Mouse #202 SAMPLE 17

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 18

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 12

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 9

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 16

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 13

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 6

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 15

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 5

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 14

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 8

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 11

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 10

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 7

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 4

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 1

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 3

description: Lung metastatic cell


title: 3-17-2014, Mouse #202 SAMPLE 2

description: Lung metastatic cell


title: Rb/Myc DKO crypts #2

city: Columbus

first: Gustavo

middle: W.

last: Leone

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

hyb_protocol: Performed at the The Ohio State University Shared Resources Microarray Core Facility

data_processing: RMAExpress was used to compute gene expression from CEL files with default settings

label: biotin

source_name: Rb/Myc DKO crypts sample #2

growth_protocol: Mice were housed under standard conditions

extract_protocol: Total RNA was isolated with TRIzol reagents and cleaned with Qiagen RNeasy Kit

treatment_protocol: Intestinal speicific inducible Cre (Ah-cre) was used to delete Rb and Myc

tag: developmental stage

value: 2 month old adult mice

value: intestinal crypts


title: Rb KO crypts #4

scan_protocol: Performed at the The Ohio State University Shared Resources Microarray Core Facility

source_name: Rb KO crypts sample #4


title: Rb/Myc DKO crypts #5

source_name: Rb/Myc DKO crypts sample #5

label_protocol: Performed at the The Ohio State University Shared Resources Microarray Core Facility


title: Rb/Myc DKO crypts #1

source_name: Rb/Myc DKO crypts sample #1


title: Rb/Myc DKO crypts #4

source_name: Rb/Myc DKO crypts sample #4


title: Rb/Myc DKO crypts #3

source_name: Rb/Myc DKO crypts sample #3


title: Rb KO crypts #2

source_name: Rb KO crypts sample #2


title: Rb KO crypts #5

source_name: Rb KO crypts sample #5


title: Rb KO crypts #1

source_name: Rb KO crypts sample #1


title: Rb KO crypts #3

source_name: Rb KO crypts sample #3


title: control crypts #4

source_name: control crypts sample #4


title: control crypts #5

source_name: control crypts sample #5


title: Rb/Myc DKO villi #2

source_name: Rb/Myc DKO villi sample #2

value: intestinal villi


title: Rb KO villi #4

source_name: Rb KO villi sample #4


title: control crypts #1

source_name: control crypts sample #1


title: Rb KO villi #1

source_name: Rb KO villi sample #1


title: Rb KO villi #3

source_name: Rb KO villi sample #3


title: Rb/Myc DKO villi #3

source_name: Rb/Myc DKO villi sample #3


title: control crypts #2

source_name: control crypts sample #2


title: Rb KO villi #5

source_name: Rb KO villi sample #5


title: Rb/Myc DKO villi #1

source_name: Rb/Myc DKO villi sample #1


title: Myc KO #4

description: gene expression from various genetic groups of crypts

source_name: Myc KO crypt sample #4

treatment_protocol: Intestinal specific inducible Cre (Ah-cre) was used to delete Myc and/or E2f alleles

value: intestinal crypt


title: E2f/Myc QKO #3

source_name: E2f/Myc QKO sample #3


title: E2f/Myc QKO #2

source_name: E2f/Myc QKO sample #2


title: control villi #2

source_name: control villi sample #2


title: E2f/Myc QKO #4

source_name: E2f/Myc QKO sample #4


title: control villi #1

source_name: control villi sample #1


title: control villi #5

source_name: control villi sample #5


title: Myc KO #3

source_name: Myc KO crypt sample #3


title: E2f/Myc QKO #1

source_name: E2f/Myc QKO sample #1


title: Rb/Myc DKO villi #4

source_name: Rb/Myc DKO villi sample #4


title: control villi #3

source_name: control villi sample #3


title: control villi #4

source_name: control villi sample #4


title: Rb KO villi #2

source_name: Rb KO villi sample #2


title: Myc KO #2

source_name: Myc KO crypt sample #2


title: Myc KO #1

source_name: Myc KO crypt sample #1


title: E2f/Myc QKO #5

source_name: E2f/Myc QKO sample #5


title: Rb/Myc DKO villi #5

source_name: Rb/Myc DKO villi sample #5


title: control crypts #3

source_name: control crypts sample #3


title: E2f TKO #3

source_name: E2f TKO crypt sample #3


title: E2f TKO #4

source_name: E2f TKO crypt sample #4


title: control #4

source_name: control crypt sample #4


title: E2f TKO #5

source_name: E2f TKO crypt sample #5


title: 2GB_B

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 h at 45 °C on GeneChip EUTOM3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF followed by batch effect removal using ComBat-n.

organism: Solanum lycopersicum

source_name: Adapted bean reared mites treatment, line B, bio rep 2

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 26 °C at 60% relative humidity with a 16:8 h (light/dark) photoperiod in controlled growth chambers.

extract_protocol: RNA samples were processed from pooled samples of two plants per treatment. 3 terminal leaflets of leaves 3 and 4 were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).

treatment_protocol: 100 adult female spider mites were applied onto terminal leaflets of leaves 3 and 4  per plant and allowed to feed for 24 hours (200 mites total).

tag: cultivar

value: Moneymaker

value: 3 terminal leaflets of leaves 3 and 4

tag: age

value: 1 month old

tag: batch

tag: treatment

value: AB mites


title: DIRC_B

source_name: Adapted tomato reared mites treatment, line C, bio rep 2

value: AT mites


title: DIRA_B

source_name: Adapted tomato reared mites treatment, line A, bio rep 2


title: 2GC_B

source_name: Adapted bean reared mites treatment, line C, bio rep 2


title: E2f TKO #2

source_name: E2f TKO crypt sample #2


title: LND_B

source_name: Ancestral mites treatment, bio rep 2

value: RB mites


title: control #2

source_name: control crypt sample #2


title: LND_C

source_name: Ancestral mites treatment, bio rep 3


title: DIRA_A

source_name: Adapted tomato reared mites treatment, line A, bio rep 1


title: DIRC_A

source_name: Adapted tomato reared mites treatment, line C, bio rep 1


title: 2GA_A

source_name: Adapted bean reared mites treatment, line A, bio rep 1


title: 2GC_A

source_name: Adapted bean reared mites treatment, line C, bio rep 1


title: DIRB_A

source_name: Adapted tomato reared mites treatment, line B, bio rep 1


title: NT_D

source_name: Control plants, bio rep 4

value: control, no treatment


title: NT_C

source_name: Control plants, bio rep 3


title: control #1

source_name: control crypt sample #1


title: LND_A

source_name: Ancestral mites treatment, bio rep 1


title: LND_D

source_name: Ancestral mites treatment, bio rep 4


title: 2GA_B

source_name: Adapted bean reared mites treatment, line A, bio rep 2


title: E2f TKO #1

source_name: E2f TKO crypt sample #1


title: 2GB_A

source_name: Adapted bean reared mites treatment, line B, bio rep 1


title: NT_B

source_name: Control plants, bio rep 2


title: NT_A

source_name: Control plants, bio rep 1


title: 210-9-2nd

city: Beijing

first: Guijie

last: Guo

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences (CAS)

description: K562 cells infected with lentivirally-expressed anti-Bcr-Abl shRNA

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. All mRNA and lncRNA level files were imported into Agilent GeneSpring Software (version 11.0) for further analysis. lncRNAs and mRNAs that at least 6 out of 6 samples have values greater than or equal to lower cut-off: 50.0 were chosen for differentially expressed lncRNAs and mRNAs screening. Differentially expressed lncRNAs and mRNAs were identified through Volcano Plot filtering.

source_name: K562 cells treated with anti-Bcr-Abl shRNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: K562 cells were maintained in RPMI1640 containing 10% fetal calf serum (FCS) supplemented with penicillin (100 U/ml) and streptomycin (100 U/ml). Cells were grown in a humidified incubator at 37℃ and 5% CO2.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: K562 cells were treated with lentivirally-expressed anti-luciferase or anti-Bcr-Abl shRNAs

tag: cell line

value: leukemia cell line K562

tag: shRNA

value: anti-Bcr-Abl


title: 210-9-3rd


title: Buffalo_F2

status: Public on Jul 19 2015

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: This sample is the second of three Buffalo_F biological replicates used in this experiment. Adult female worms were isolated from the second panel of buffalo at about 8 weeks post-infection.

hyb_protocol: Array hybridization, washing, scanning, and data acquisition were carried out according to the NimbleGen Arrays user’s guide.

scan_protocol: The arrays were scanned using MS200 scanner (NimbleGen Systems) with 2 µm resolution, and NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images.

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: Schistosoma japonicum

source_name: adult female worms from buffaloes

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) for producing higher yields of labeled cDNA.

growth_protocol: Animals were manually infected by cercariae freshly released from S. japonicum-infected Oncomelania hupensis.  At about 8 weeks post-infection, adult worm pairs were isolated from infected animals and manually separated under a light microscope. There is a one-to-one correspondence between male and female worm samples of each bioligical replicate.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (QIAGEN) and the contaminating genomic DNA were removed from RNA samples with Tubro DNA-free kit (Ambion, CA, USA).  The quantity and quality of the RNA samples were assessed by NanoDropND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and denaturing agarose gel electrophoresis.

treatment_protocol: Adult worms were soaked in RNAlater Solution (Ambion, CA, USA), and stored at -80°C until total RNA was isolated.

value: adult

tag: gender

value: female

tag: mammalian host

value: water buffalo


title: lnc3-2nd

description: K562 cells infected with lentivirally-expressed anti-luciferase shRNA

source_name: K562 cells treated with anti-luciferase shRNA

value: control


title: lnc3-3rd


title: Rabbit_F2

description: This sample is the second of three Rabbit_F biological replicates used in this experiment. Adult female worms were isolated from the second panel of rabbit at about 8 weeks post-infection.

source_name: adult female worms from rabbits

value: New Zealand white rabbit


title: Buffalo_M2

description: This sample is the second of three Buffalo_M biological replicates used in this experiment. Adult male worms were isolated from the second panel of buffalo at about 8 weeks post-infection.

source_name: adult male worms from buffaloes

value: male


title: Rabbit_M2

description: This sample is the second of three Rabbit_M biological replicates used in this experiment. Adult male worms were isolated from the second panel of rabbit at about 8 weeks post-infection.

source_name: adult male worms from rabbits


title: Buffalo_F3

description: This sample is the third of three Buffalo_F biological replicates used in this experiment. Adult female worms were isolated from the third panel of buffalo at about 8 weeks post-infection.


title: lnc3-1st


title: 210-9-1st


title: selkupFar093_1m

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Selkup

tag: region

value: Siberia

value: blood


title: Buffalo_M1

description: This sample is the first of three Buffalo_M biological replicates used in this experiment. Adult male worms were isolated from the first panel of buffalo at about 8 weeks post-infection.


title: Rabbit_F1

description: This sample is the first of three Rabbit_F biological replicates used in this experiment. Adult female worms were isolated from the first panel of rabbit at about 8 weeks post-infection.


title: Buffalo_M3

description: This sample is the third of three Buffalo_M biological replicates used in this experiment. Adult male worms were isolated from the third panel of buffalo at about 8 weeks post-infection.


title: selkupTK30_1m


title: Rabbit_F3

description: This sample is the third of three Rabbit_F biological replicates used in this experiment. Adult female worms were isolated from the third panel of rabbit at about 8 weeks post-infection.


title: C57BL/6_M1

description: This sample is the first of three C57BL/6_M biological replicates used in this experiment. Adult male worms were isolated from the first panel of C57BL/6 mice at about 8 weeks post-infection.

source_name: adult male worms from C57BL/6 mice

value: C57BL/6 mouse


title: Rabbit_M3

description: This sample is the third of three Rabbit_M biological replicates used in this experiment. Adult male worms were isolated from the third panel of rabbit at about 8 weeks post-infection.


title: C57BL/6_M2

description: This sample is the second of three C57BL/6_M biological replicates used in this experiment. Adult male worms were isolated from the second panel of C57BL/6 mice at about 8 weeks post-infection.


title: BALB/c_M3

description: This sample is the third of three BALB/c_M biological replicates used in this experiment. Adult male worms were isolated from the third panel of BALB/c mice at about 8 weeks post-infection.

source_name: adult male worms from BALB/c mice

value: BALB/c mouse


title: Rabbit_M1

description: This sample is the first of three Rabbit_M biological replicates used in this experiment. Adult male worms were isolated from the first panel of rabbit at about 8 weeks post-infection.


title: C57BL/6_M3

description: This sample is the third of three C57BL/6_M biological replicates used in this experiment. Adult male worms were isolated from the third panel of C57BL/6 mice at about 8 weeks post-infection.


title: Buffalo_F1

description: This sample is the first of three Buffalo_F biological replicates used in this experiment. Adult female worms were isolated from the first panel of buffalo at about 8 weeks post-infection.


title: BALB/c_F2

description: This sample is the second of three BALB/c_F biological replicates used in this experiment. Adult female worms were isolated from the second panel of BALB/c mice at about 8 weeks post-infection.

source_name: adult female worms from BALB/c mice


title: C57BL/6_F3

description: This sample is the third of three C57BL/6_F biological replicates used in this experiment. Adult female worms were isolated from the third panel of C57BL/6 mice at about 8 weeks post-infection.

source_name: adult female worms from C57BL/6 mice


title: C57BL/6_F1

description: This sample is the first of three C57BL/6_F biological replicates used in this experiment. Adult female worms were isolated from the first panel of C57BL/6 mice at about 8 weeks post-infection.


title: BALB/c_F3

description: This sample is the third of three BALB/c_F biological replicates used in this experiment. Adult female worms were isolated from the third panel of BALB/c mice at about 8 weeks post-infection.


title: DIRB_B

source_name: Adapted tomato reared mites treatment, line B, bio rep 2

value: Moneymaker

value: 3 terminal leaflets of leaves 3 and 4

value: 1 month old


title: C57BL/6_F2

description: This sample is the second of three C57BL/6_F biological replicates used in this experiment. Adult female worms were isolated from the second panel of C57BL/6 mice at about 8 weeks post-infection.


title: BALB/c_M1

description: This sample is the first of three BALB/c_M biological replicates used in this experiment. Adult male worms were isolated from the first panel of BALB/c mice at about 8 weeks post-infection.


title: control #3

description: gene expression from various genetic groups of crypts

source_name: control crypt sample #3

value: 2 month old adult mice

value: intestinal crypt


title: BALB/c_M2

description: This sample is the second of three BALB/c_M biological replicates used in this experiment. Adult male worms were isolated from the second panel of BALB/c mice at about 8 weeks post-infection.


title: 25487_EarlyP

status: Public on Jul 18 2015

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

country: Spain

institute: IDIBAPS / Hospital Clinic

hyb_protocol: Oligo aCGH/ChIP-on-Chip Hybridization kit (Agilent Technologies). Hybridizations were performed on SureHyb chambers on a rotator oven at 65C for 20 hours.

scan_protocol: Agilent G2565BA scanner was used for scanning and the Feature Extraction sotftware V9.1 (Agilent Technologies) was used to performed data extraction.

data_processing: Raw files were uploaded to the software Nexus Copy Number (BioDiscovery). Rank segmentation was applied and analysis was done based on log2 ratio intensities.

source_name: Spleen: B-cell lymphoma

label_protocol: BioPrime Array CGH Genomic Labeling Module (Life Technologies)

growth_protocol: Cells were grown in suspension in RPMI1640 supplemented with 2-ME, 10%FBS, NEAA, NaPy, antibiotics, and glutamine. 0.1x10^5 cells were passaged into 30ml media every 3-4 days.

tag: days in culture

value: Early Passage

tag: strain

tag: genotype/variation

tag: tissue type

value: Spleen:B-cell lymphoma

source_name: Pool DNA Normal spleens (n=5)

value: Day 0

value: Normal spleen


title: 178119_EarlyP


title: 12437_EarlyP


title: 67506_EarlyP


title: BALB/c_F1

description: This sample is the first of three BALB/c_F biological replicates used in this experiment. Adult female worms were isolated from the first panel of BALB/c mice at about 8 weeks post-infection.

value: adult

value: female


title: 12303_EarlyP


title: 16508_EarlyP


title: 39317_EarlyP


title: 47990_EarlyP


title: 161336_EarlyP


title: 141645_EarlyP


title: 180764_EarlyP


title: selkupTK07_1m

description: Genomic DNA extracted from blood was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).

tag: tissue


title: 47990_d0


title: 196303_EarlyP


title: 12437_d0


title: 67506_d0


title: 123203_d0


title: 122378_d0


title: K5-UCP3_Skin_murine 924

city: Austin

first: Edward

last: Mills

state: Texas

address: 107 W. Dean Keeton, BME 3.510D

department: Pharmacology/Toxicology

institute: University of Texas at Austin

hyb_protocol: Hybridized to the Illumina Mouse-6 v1.0-BeadChip

scan_protocol: Scanned with an Illumina Bead array reader confoal scanner

data_processing: Illumina BeadStudio Software v. 1.5.1.3. Normalization = cubic spline

source_name: Whole Skin

label_protocol: Incorporation of Biotin-16-UTP in a 1:1 ration with unlabled UTP.

extract_protocol: Trizol Reagent followed by Qiagen RNeasy clean up kit. Amplified using Illumina RNA Amplification Kit.

treatment_protocol: untreated

value: dorsal skin

value: FVB/N

value: 7 week old

tag: Sex

value: male

tag: genotype


title: K5-UCP3_Skin_murine 925


title: 161336_d0


title: 95508_KO

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies). Hybridizations were performed on SureHyb chambers on a rotator oven at 65C for 17 hours.

data_processing: Quantile normalization in R software

source_name: Spleen: Normal

label_protocol: Quick Amp Labeling Kit (Agilent Technologies), including MMLV-RT and oligo dT-Promoter primers for cDNA sinthesis, and T7 RNA Polymerase, Cy3-CTP and NTPs for labeling.

extract_protocol: Qiagen miRNeasy kit with on-column DNase treatment


title: 178119_d0


title: 141645_d0


title: K5-UCP3_Skin_murine 915


title: 102712_WT


title: 180764_d0


title: 95509_KO


title: WT FVB_Skin_murine 923

description: 923-WT FVB

value: wild type


title: 196303_d0


title: 95501_WT


title: 102713_WT


title: 102706_KO


title: 102708_WT


title: 102704_KO


title: WT FVB_Skin_murine 922

description: 922-WT FVB


title: 95506_WT


title: Slovenian321

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

value: Male

value: Slovenians

value: Europe

value: blood


title: 704405_BCL


title: 95511_KO


title: WT FVB_Skin_murine 913

description: 915-WT FVB


title: 93508_WT


title: Slovenian275


title: Slovenian299


title: 704405 (repeat)_BCL


title: 39317_BCL


title: 93511_BCL


title: 95502_WT


title: 12437_BCL


title: 16508_BCL


title: 47990_BCL


title: Slovenian271


title: Slovenian90

value: Female


title: Slovenian188


title: Slovenian241


title: Slovenian184


title: Slovenian172


title: 178119_BCL


title: 285487_BCL


title: Slovenian147


title: Slovenian137


title: Slovenian136


title: 180764_BCL


title: 95507_KO


title: Slovenian_8


title: Slovakia85

value: Slovaks


title: Slovenian_14


title: Slovakia429


title: Slovakia425


title: Slovakia96


title: Slovakia474


title: Slovakia94


title: Slovakia77


title: Slovakia235


title: Slovakia233


title: Slovakia256


title: Slovakia150


title: Slovenian237


title: latvian58C8

value: Latvians


title: 122378_EarlyP

value: Early Passage

value: Spleen:B-cell lymphoma


title: Slovakia218


title: latvian58C6


title: Slovakia222


title: latvian54A2


title: RusPinega1

source_name: Russians Northern_blood

value: Russians Northern


title: Slovakia118


title: RusPinega20


title: GreecePelop8

source_name: Greeks Peloponnese_blood

value: Greeks Peloponnese


title: RusPinega17


title: GreecePelop9


title: GreecePelop1


title: GreeceMaced8

source_name: Greeks Macedonia_blood

value: Greeks Macedonia


title: latvian22J5


title: GreecePelop7


title: Slovakia411


title: latvian54H7


title: GreecePelop10


title: RusPinega9


title: GreecePelop5


title: GreeceMaced4


title: GreeceMaced7


title: GreeceMaced6


title: GreeceMaced3


title: GreecePelop4


title: GreeceMaced2


title: GreecePelop3


title: latvian54F2


title: GreeceMaced1


title: belarusian54zp

value: Belarusians


title: GreecePelop6


title: belarusian52vp


title: belarusian47zp


title: belarusian45vp


title: belarusian32zp


title: belarusian29zp


title: belarusian50vp


title: belarusian23vp


title: wt Mound rep1

city: Pune

first: Bharat

middle: Ravi

last: Iyengar

address: Dr Homi Bhabha Road

department: Chemical Engineering and Process Development

country: India

institute: CSIR-National Chemical Laboratory

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_2_3.txt

hyb_protocol: Equal amounts of cRNA were mixed and hybridized against each microarray at 65°C for 17 hours and washed afterwards

scan_protocol: The arrays were scanned using Agilent Technologies Scanner G2505B and gene expression information was extracted from microarray scan data by Agilent Feature Extraction (FE) software

data_processing: The normalization was done using GeneSpring GX using the Per Chip and Per Gene Normalization method. Between-array quantile normalization was implemented using the Limma package in R (http://www.R-project.org/)

organism: Dictyostelium discoideum AX2

source_name: Mound

label_protocol: Samples were labeled with Cy3 (for one set of duplicates) and Cy5 (for the second set of duplicates) using Agilent’s Quick-amp labeling kit and T7 promoter based-linear amplification was used to generate labeled complementary RNA.

growth_protocol: Dictyostelium AX2 cells were used for the entire study and grown at 22ºC in HL-5 axenic medium.

extract_protocol: Total RNA and cRNA were further purified using Qiagen’s RNeasy purification kit and RNA quality was checked using Bioanalyzer.

treatment_protocol: Dictyostelium cells were collected by centrifugation at 3000 rpm for 2 min. and washed with 1X KK2 buffer thrice. The pellet was resuspended in 1X KK2 buffer and the cell suspension was poured on to non-nutrient agar (NNA) plate. After cold synchronization for 9 hrs., the plates were incubated at 22ºC for development.

value: wt


title: wt Early Culminant rep2

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_2_4.txt

source_name: Early Culminant


title: wt T0 rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_2_4.txt


title: wt Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_2_3.txt

source_name: Slug


title: wt Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_2_4.txt

source_name: Amoeboid


title: pks37 knockout Slug rep2


title: wt Loose Aggregate rep2

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_2_4.txt

source_name: Loose Aggregate


title: wt Fruiting Body rep2

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_2_4.txt

source_name: Fruiting Body


title: pks37 knockout Streaming rep2

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_2_3.txt

source_name: Streaming


title: wt Early Culminant rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_2_3.txt


title: wt Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_2_3.txt


title: wt Amoeboid rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_2_3.txt


title: wt Slug rep2

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_2_4.txt


title: pks37 knockout Mound rep2


title: wt T0 rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_1.txt


title: pks37 knockout Early Culminant rep2


title: wt Streaming rep2


title: wt Streaming rep1


title: wt Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_2_3.txt


title: wt Mound rep2

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_2_4.txt


title: pks37 knockout Fruiting Body rep2


title: pks37 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_2_2.txt


title: pks37 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_2_2.txt


title: pks37 knockout Amoeboid rep2


title: pks37 knockout Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_2_2.txt


title: pks37 knockout Loose Aggregate rep2


title: pks37 knockout Mound rep1

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_2_2.txt


title: pks37 knockout T0 rep2

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_1.txt


title: pks37 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_2_2.txt


title: pks37 knockout T0 rep1


title: pks3 knockout T0 rep2

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_1.txt


title: pks3 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_2_1.txt


title: pks3 knockout Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_2_2.txt


title: pks3 knockout Early Culminant rep2

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_2_2.txt


title: pks3 knockout Slug rep2


title: pks3 knockout T0 rep1


title: pks3 knockout Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_2_1.txt


title: pks3 knockout Mound rep1

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_2_1.txt


title: pks3 knockout Streaming rep2


title: pks2 knockout Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_2_1.txt


title: pks3 knockout Fruiting Body rep2


title: pks3 knockout Loose Aggregate rep2


title: pks2 knockout T0 rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_2_4.txt


title: pks2 knockout Loose Aggregate rep2


title: pks3 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_2_1.txt


title: pks3 knockout Mound rep2


title: pks37 knockout Amoeboid rep1


title: pks3 knockout Early Culminant rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_2_1.txt


title: pks2 knockout T0 rep2

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_1.txt


title: pks3 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_2_1.txt


title: pks2 knockout Early Culminant rep2


title: pks3 knockout Amoeboid rep1


title: pks2 knockout Slug rep2


title: pks2 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_4.txt


title: pks37 knockout Early Culminant rep1


title: pks2 knockout Mound rep2


title: pks2 knockout Streaming rep2


title: pks2 knockout Mound rep1

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_4.txt


title: pks2 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_4.txt


title: pks2 knockout Fruiting Body rep2


title: pks18 knockout Early Culminant rep2

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_4.txt


title: pks2 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_1_4.txt


title: pks2 knockout Amoeboid rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_4.txt


title: pks18 knockout Mound rep2


title: pks18 knockout Slug rep2


title: pks18 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_3.txt


title: pks18 knockout Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_3.txt


title: pks18 knockout Early Culminant rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_3.txt


title: pks18 knockout T0 rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_2_4.txt


title: pks18 knockout Ameboid rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_2.txt


title: pks18 knockout Loose Aggregate rep2

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_1_4.txt


title: pks2 knockout Loose Aggregate rep1


title: pks18 knockout T0 rep2

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_1_1.txt


title: pks18 knockout Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_1_3.txt


title: pks18 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_3.txt


title: pks18 knockout Fruiting Body rep2


title: pks18 knockout Streaming rep2


title: pks18 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_1_3.txt


title: pks2 knockout Early Culminant rep1


title: Male_liver_furan_2 mg-kg-day_ANT_replicate 5

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_ANT_S31

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE Oligo Microarrays (G4853A-028279) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

organism: Rattus norvegicus

source_name: Male_liver_furan_2 mg/kg/day_ANT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissue using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male F344 rats were treated by gavage 5 days/week with 0.92 and 2 mg furan/kg bw for 104 weeks. Experimental and control rats were euthanized by exsanguination following deep isoflurane anesthesia 24 hours after the last treatment. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

value: Fisher 344

value: 110 weeks

tag: treated with

value: 2 mg furan/kg bw for 104 weeks

value: liver

tag: tissue subtype

value: adjacent non-lesion liver tissue (ANT)


title: Male_liver_furan_2 mg-kg-day_ANT_replicate 4

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_ANT_S28

value: male

tag: age


title: Male_liver_furan_2 mg-kg-day_NT_replicate 5

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_NT_S30

source_name: Male_liver_furan_2 mg/kg/day_NT

value: non-lesion liver tissue (NT)


title: Male_liver_furan_2 mg-kg-day_TRT_replicate 4

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_TRT_S29

source_name: Male_liver_furan_2 mg/kg/day_TRT

value: cholangiofibrotic liver tissue (TRT)


title: pks14 knockout T0 rep2

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_1_1.txt


title: pks14 knockout Slug rep2


title: Male_liver_furan_2 mg-kg-day_NT_replicate 4

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_NT_S27


title: Male_liver_furan_2 mg-kg-day_ANT_replicate 3

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_ANT_S25


title: Male_liver_furan_2 mg-kg-day_TRT_replicate 3

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_TRT_S26


title: pks18 knockout Mound rep1

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_3.txt


title: Male_liver_furan_2 mg-kg-day_TRT_replicate 5

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_TRT_S32


title: pks14 knockout Mound rep2


title: pks14 knockout Loose Aggregate rep2


title: pks14 knockout T0 rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_2_4.txt


title: pks14 knockout Fruiting Body rep2


title: pks14 knockout Streaming rep2

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_3.txt


title: pks14 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_2.txt


title: pks14 knockout Mound rep1

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_2.txt


title: Male_liver_furan_2 mg-kg-day_NT_replicate 3

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_NT_S24


title: pks14 knockout Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_2.txt


title: Male_liver_furan_2 mg-kg-day_TRT_replicate 2

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_TRT_S23


title: ExVivoPlasma_Health Control_rep3

city: Nanjing

first: Juan

last: Liao

state: Jiangsu

address: No.87, Dingjiaqiao, Gulou District

institute: Southeast University

description: microRNA expression

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Plasma

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM  PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Plasma were extracted from ESCC patients' and healthy controls' peripheral blood

value: female

tag: sample type

value: plasma

tag: disease

value: control


title: ExVivoPlasma_Health Control_rep2

description: microRNA expression


title: Male_liver_furan_2 mg-kg-day_ANT_replicate 2

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_ANT_S22


title: Male_liver_furan_2 mg-kg-day_TRT_replicate 1

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_TRT_S20


title: ExVivoPlasma_Health Control_rep1

description: microRNA expression


title: Male_liver_furan_2 mg-kg-day_ANT_replicate 1

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_ANT_S19


title: pks14 knockout Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_1_2.txt


title: Male_liver_furan_2 mg-kg-day_NT_replicate 1

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_NT_S18


title: pks14 knockout Early Culminant rep2

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_3.txt


title: Male_liver_furan_2 mg-kg-day_NT_replicate 2

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 2 mg/kg/day furan for 104 weeks
2_NT_S21


title: Male_liver_furan_0.92 mg-kg-day_ANT_replicate 4

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_ANT_S16

source_name: Male_liver_furan_0.92 mg/kg/day_ANT

value: 0.92 mg furan/kg bw for 104 weeks


title: Male_liver_furan_0.92 mg-kg-day_NT_replicate 4

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_NT_S15

source_name: Male_liver_furan_0.92 mg/kg/day_NT


title: Male_liver_furan_0.92 mg-kg-day_TRT_replicate 3

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_TRT_S14

source_name: Male_liver_furan_0.92 mg/kg/day_TRT


title: Male_liver_furan_0.92 mg-kg-day_TRT_replicate 4

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_TRT_S17

value: 118 weeks


title: ExVivoPlasma_ESCC_rep3

description: microRNA expression

value: esophageal cancer


title: ExVivoPlasma_ESCC_rep2

description: microRNA expression


title: pks14 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_1_2.txt


title: ExVivoPlasma_ESCC_rep1

description: microRNA expression


title: Male_liver_furan_0.92 mg-kg-day_ANT_replicate 3

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_ANT_S13


title: pks14 knockout Early Culminant rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_2.txt


title: Male_liver_furan_0.92 mg-kg-day_NT_replicate 3

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_NT_S12


title: pks14 knockout Amoeboid rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_1.txt


title: Male_liver_furan_0.92 mg-kg-day_TRT_replicate 2

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_TRT_S11


title: pks1 knockout Slug rep2

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_2.txt


title: pks1 knockout Streaming rep2

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_2.txt


title: pks1 knockout Loose Aggregate rep2


title: pks1 knockout Mound rep2

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_2.txt


title: pks1 knockout T0 rep2

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_1.txt


title: Male_liver_furan_0.92 mg-kg-day_ANT_replicate 2

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_ANT_S10


title: pks1 knockout Early Culminant rep2


title: pks1 knockout Fruiting Body rep2


title: Male_liver_furan_0.92 mg-kg-day_ANT_replicate 1

description:
Gene expression in the ANT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_ANT_S07


title: Male_liver_furan_0.92 mg-kg-day_TRT_replicate 1

description:
Gene expression in the TRT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_TRT_S08


title: Male_liver_furan_0.92 mg-kg-day_NT_replicate 2

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_NT_S09


title: WTvsM_60minOxidation_rep3

city: Hamilton

first: Ken

last: Belanger

state: NY

address: 13 Oak Drive

institute: Colgate University

description: Biological Replicate 3 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .

hyb_protocol: RNA probes were hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC

scan_protocol: Scanned my MoGene, LC on Agilent Technologies Scanner G2505B US22502547. Protocols are GE2-v5_95_Feb07  for replicate 1/3 and GE2-v5_10_Apr08 for replicates 2/3 and 3/3

data_processing: Scanner performed background correction and linear lowess normalization. Further normalization took place by using GeneSpring GX 13.0 to perform a log2 transformation and percentile shift to the 75th percentile

organism: Saccharomyces cerevisiae

source_name: WT 60minOxidation

label_protocol: RNA generated from wild-type cell extracts was labeled with Cy3 and from ∆Kap108 cells was labeled with Cy5 by MoGene, LC

growth_protocol: Wild-type and kap108∆ cells were grown to A600 = 0.3 in 1L YPD. Two hundred ml of culture was removed, spun at 3,000rpm for 10 min, and frozen at -80 °C. This sample was used as the pre-oxidation condition.

extract_protocol: RNA from cell pellets was isolated using the RiboPure-Yeast RNA isolation kit (Ambion, Inc.)

treatment_protocol: Fresh H2O2 was added to the remaining culture (from growth protocol) to a 1.0 mM final concentration and each culture incubated for 10 min at 30 °C, after which 200 ml of culture was removed, spun, and frozen as above to generate the 10minOxidation samples. This was repeated with another 200 ml of cells 1 hr after H2O2 addition to generate the 60minOxidation samples. The remaining culture was then pelleted, YPD+H2O2 media removed, cells resuspended in 250 ml YPD, and culture incubated for 1 hr at 30 °C. Cells were then pelleted and frozen as before to generate the 120minOxidation samples, which actually are 60 min oxidative stress followed by 60 min no oxidative stress.

value: wildtype

source_name: ∆Kap108 60minOxidation


title: WTvsM_120minOxidation_rep2

description: Biological Replicate 2 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .

source_name: WT 60minPostOxidation

source_name: ∆Kap108 60minPostOxidation


title: WTvsM_120minOxidation_rep1

description: Biological Replicate 1 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .


title: WTvsM_60minOxidation_rep2


title: pks1 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_1.txt


title: Male_liver_control_replicate 5

description:
Gene expression in the livers of control male Fisher 344 rats
0_NCT_S05

value: vehicle (control)

value: 111 weeks


title: Male_liver_furan_0.92 mg-kg-day_NT_replicate 1

description:
Gene expression in the NT liver tissue of male Fisher 344 rats treated with 0.92 mg/kg/day furan for 104 weeks
0.92_NT_S06

value: Fisher 344


title: Male_liver_control_replicate 3

description:
Gene expression in the livers of control male Fisher 344 rats
0_NCT_S03

value: 110 weeks


title: Male_liver_control_replicate 2

description:
Gene expression in the livers of control male Fisher 344 rats
0_NCT_S02


title: pks1 knockout T0 rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_2_4.txt


title: WTvsM_60minOxidation_rep1


title: pks1 knockout Amoeboid rep2

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_4.txt