title: PBMC_mort_nonagenarian 28611

description: Sample name: 28611


title: PBMC_mort_nonagenarian 28600

status: Public on Jan 22 2015

type: RNA

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

department: School of Medicine

country: Finland

institute: University of Tampere

description: Sample name: 28600

hyb_protocol: 1,500 ng of labeled cRNA was hybridized overnight according to the Illumina protocol.

scan_protocol: BeadScan

data_processing: The preprocessing, filtering and analysis of the data were performed with the Chipster v2.0 program (Kallio, M.A., et al. MBC Genomics 12, 507 (2011)). The lumi pipeline was used for data preprocessing and normalization. Array_Address_ID was used as a probe identifier, background correction was performed with the bgAdjust.affy package, and the data were log2-transformed and normalized with the quantile method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human PBMC

label_protocol: Labeled cRNA was prepared from 330 ng of total RNA using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., TX, USA) with overnight incubation according to the manufacturer's protocol.

growth_protocol: Freshly drawn blood, stored at -70 C until the analysis.

extract_protocol: RNA was purified using an miRNeasy mini kit (Qiagen, CA, USA) according to the manufacturer's protocol using on-column DNase digestion (AppliChem GmbH, Darmstadt, Germany).

treatment_protocol: Blood was collected to EDTA-containing tubes between 8 and 12 am. Leucocytes were separated with a density gradient and stored in RNAlater.

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: age

value: nonagenarian

tag: Sex

value: female

tag: status 31.1.2013 (1 died, 0 alive)

tag: follow_up_time in years_until 31.1.2013

tag: status 31.5.2014 (1 died, 0 alive)

tag: body mass index

tag: cf-dna level (µg/ml)

tag: frailty index

value: pre-frail


title: PBMC_mort_nonagenarian 28591

description: Sample name: 28591

value: non-frail


title: PBMC_mort_nonagenarian 28603

description: Sample name: 28603


title: PBMC_mort_nonagenarian 28612

description: Sample name: 28612


title: PBMC_mort_nonagenarian 28594

description: Sample name: 28594


title: HCC with lung metastasis, metastasis tumor PEM-16M

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

hyb_protocol: Labeled cRNA was hybridized onto Affymetix GeneChip HG-U133 Plus 2.0 Arrays.

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: HCC with lung metastasis

label_protocol: RNA was amplified with two linear amplification steps by in vitro transcription using the MEGAscript T7 kit (Ambion, Austin, TX) followed by the labeling step using the BioArray HighYield RNA Transcript Labeling Kit T3 from Enzo Life Sciences (Farmingdale, NY).

growth_protocol: Enriched tumor endothelium was obtained by laser capture microdissection

extract_protocol: Total RNA was isolated using the PicoPure protocol (Arcturus, Mountain View, CA)

tag: tissue

value: tumor endothelium from lung metastasis

tag: disease state

value: HCC with lung metastasis


title: HCC with lung metastasis, primary tumor PEM-12P

value: tumor endothelium from HCC tumor tissue


title: HCC with lung metastasis, metastasis tumor PEM-13M


title: PBMC_mort_nonagenarian 28588

description: Sample name: 28588


title: CC with lung metastasis, primary tumor PEM-11P

source_name: CC with lung metastasis

value: tumor endothelium from cholangiocarcinoma

value: CC with lung metastasis


title: PBMC_mort_nonagenarian 28583

description: Sample name: 28583

value: male


title: HCC with lung metastasis, metastasis tumor PEM-14M


title: PBMC_mort_nonagenarian 28807

description: Sample name: 28807


title: PBMC_mort_nonagenarian 28582

description: Sample name: 28582


title: HCC with lung metastasis, metastasis tumor PEM-12M


title: HCC with adrenal gland metastasis, primary tumor PEM-09P

source_name: HCC with adrenal gland metastasis

value: HCC with adrenal gland metastasis


title: HCC with adrenal gland metastasis, primary tumor PEM-08P


title: HCC with adrenal gland metastasis, metastasis tumor PEM-08M

value: tumor endothelium from adrenal gland metastasis


title: PBMC_mort_nonagenarian 28575

description: Sample name: 28575


title: HCC with adrenal gland metastasis, metastasis tumor PEM-07M


title: PBMC_mort_nonagenarian 28581

description: Sample name: 28581

value: frail


title: PBMC_mort_nonagenarian 28675

description: Sample name: 28675


title: HCC with adrenal gland metastasis, primary tumor PEM-07P


title: PBMC_mort_nonagenarian 28542

description: Sample name: 28542


title: PBMC_mort_nonagenarian 28544

description: Sample name: 28544


title: PBMC_mort_nonagenarian 28502

description: Sample name: 28502


title: HCC with adrenal gland metastasis, metastasis tumor PEM-09M


title: COCS exposed to RML for 45d replicate 4

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

country: Switzerland

institute: Uiversity Hospital Zurich

description: Gene expression data from cultured organotypic cerebellar slices were exposed for different time points with either prions (RML) versus non-infectious brain homogenate (NBH) or ligands to the globular domain of the prion protein (POM1) vs IgG

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

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

data_processing: The data were analyzed using the RMA method for probe set summary and normalization as implemented in the affy-package of R/Bioconductor

organism: Mus musculus

source_name: COCS exposed to RML for 45d

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

growth_protocol: Cultured organotypic cerebellar slices (COCS) were prepared and cultured as previously described (Falsig Nature Protocol 2008)

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

treatment_protocol: COCS were infected with RML prions or non-infectious brain homogenates or exposed to POM1 or IgG and harvested at different time points

tag: genotype/variation

value: Cultured organotypic cerebellar slices

tag: treatment

value: RML

tag: time period


title: CC with lymph node metastasis, metastasis tumor PEM-06M

source_name: CC with lymph node metastasis

value: tumor endothelium from lymph node metastasis

value: CC with lymph node metastasis


title: HCC/CC with lymph node metastasis, primary tumor PEM-04P

source_name: HCC/CC with lymph node metastasis

value: tumor endothelium from HCC/CC tumor tissue

value: HCC/CC with lymph node metastasis


title: PBMC_mort_nonagenarian 28559

description: Sample name: 28559

value: peripheral blood mononuclear cells (PBMCs)

value: nonagenarian

value: pre-frail


title: COCS exposed to NBH for 45d replicate 4

source_name: COCS exposed to NBH for 45d

value: NBH


title: PBMC_mort_nonagenarian 28509

description: Sample name: 28509

value: female


title: COCS exposed to RML for 45d replicate 3


title: PBMC_mort_nonagenarian 28489

description: Sample name: 28489


title: CC with lymph node metastasis, primary tumor PEM-06P

value: tumor endothelium from cholangiocarcinoma


title: COCS exposed to RML for 45d replicate 1


title: HCC/CC with lymph node metastasis, metastasis tumor PEM-04M


title: Angiosarcoma with lymph node metastasis, metastasis tumor PEM-03M

source_name: Angiosarcoma with lymph node metastasis

value: Angiosarcoma with lymph node metastasis


title: COCS exposed to NBH for 45d replicate 2


title: Angiosarcoma with lymph node metastasis, primary tumor PEM-03P

value: tumor endothelium from angiosarcoma tumor tissue


title: COCS exposed to NBH for 45d replicate 1


title: PBMC_mort_nonagenarian 28515

description: Sample name: 28515

value: male


title: PBMC_mort_nonagenarian 28501

description: Sample name: 28501


title: COCS exposed to NBH for 45d replicate 3


title: PBMC_mort_nonagenarian 28498

description: Sample name: 28498

value: non-frail


title: COCS exposed to RML for 45d replicate 2


title: PBMC_mort_nonagenarian 28472

description: Sample name: 28472


title: PBMC_mort_nonagenarian 28487

description: Sample name: 28487


title: PBMC_mort_nonagenarian 28456

description: Sample name: 28456


title: PBMC_mort_nonagenarian 28453

description: Sample name: 28453


title: COCS exposed to RML for 38d replicate 3

source_name: COCS exposed to RML for 38d


title: CC with lymph node metastasis, primary tumor PEM-02P


title: CC with lymph node metastasis, metastasis tumor PEM-02M


title: COCS exposed to RML for 38d replicate 2


title: PBMC_mort_nonagenarian 28448

description: Sample name: 28448


title: CC with lymph node metastasis, metastasis tumor PEM-01M


title: HCC without metastasis, primary tumor NM-11P

source_name: HCC without metastasis

value: tumor endothelium from HCC tumor tissue

value: HCC without metastasis


title: COCS exposed to NBH for 38d replicate 4

source_name: COCS exposed to NBH for 38d

value: Cultured organotypic cerebellar slices


title: CC with lymph node metastasis, primary tumor PEM-01P


title: COCS exposed to NBH for 38d replicate 3


title: COCS exposed to RML for 38d replicate 1

value: RML


title: COCS exposed to RML for 25d replicate 3

source_name: COCS exposed to RML for 25d


title: HCC without metastasis, primary tumor NM-10P


title: HCC without metastasis, primary tumor NM-09P


title: PBMC_mort_nonagenarian 28438

description: Sample name: 28438

value: frail


title: COCS exposed to RML for 25d replicate 4


title: COCS exposed to NBH for 38d replicate 1


title: PBMC_mort_nonagenarian 28417

description: Sample name: 28417


title: HCC without metastasis, primary tumor NM-06P


title: PBMC_mort_nonagenarian 28421

description: Sample name: 28421


title: HCC without metastasis, primary tumor NM-05P


title: COCS exposed to RML for 38d replicate 4


title: PBMC_mort_nonagenarian 28429

description: Sample name: 28429


title: HCC without metastasis, primary tumor NM-07P


title: PBMC_mort_nonagenarian 28401

description: Sample name: 28401


title: COCS exposed to NBH for 38d replicate 2


title: HCC without metastasis, primary tumor NM-04P


title: COCS exposed to RML for 25d replicate 2


title: COCS exposed to RML for 25d replicate 1


title: HCC without metastasis, primary tumor NM-02P


title: PBMC_mort_nonagenarian 28399

description: Sample name: 28399


title: COCS exposed to NBH for 25d replicate 4

source_name: COCS exposed to NBH for 25d


title: COCS exposed to NBH for 25d replicate 3


title: PBMC_mort_nonagenarian 28406

description: Sample name: 28406


title: PBMC_mort_nonagenarian 28395

description: Sample name: 28395


title: HCC without metastasis, primary tumor NM-01P


title: PBMC_mort_nonagenarian 28396

description: Sample name: 28396


title: Hemangioma of liver normal liver NL-09

source_name: Hemangioma of liver

value: tumor endothelium from normal liver

value: Hemangioma of liver


title: COCS exposed to NBH for 25d replicate 2


title: PBMC_mort_nonagenarian 28393

description: Sample name: 28393

value: peripheral blood mononuclear cells (PBMCs)


title: Hemangioma of liver normal liver NL-07


title: HCC without metastasis, primary tumor NM-03P


title: COCS exposed to NBH for 25d replicate 1


title: Hemangioma of liver normal liver NL-06


title: PBMC_mort_nonagenarian 28388

description: Sample name: 28388

value: nonagenarian


title: COCS exposed to RML for 14d replicate 3

source_name: COCS exposed to RML for 14d


title: COCS exposed to RML for 14d replicate 4


title: PBMC_mort_nonagenarian 28378

description: Sample name: 28378


title: Hemangioma of liver normal liver NL-05


title: PBMC_mort_nonagenarian 28381

description: Sample name: 28381

value: pre-frail


title: Hemangioma of liver normal liver NL-01


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-14P

value: tumor endothelium from colon adenocarcinoma tissue


title: PBMC_mort_nonagenarian 28376

description: Sample name: 28376

value: female


title: PBMC_mort_nonagenarian 28370

description: Sample name: 28370


title: COCS exposed to RML for 14d replicate 2


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-14M

value: tumor endothelium from liver metastasis


title: COCS exposed to RML for 14d replicate 1


title: PBMC_mort_nonagenarian 28372

description: Sample name: 28372


title: COCS exposed to NBH for 14d replicate 4

source_name: COCS exposed to NBH for 14d

value: NBH


title: PBMC_mort_nonagenarian 28368

description: Sample name: 28368

source_name: Human PBMC


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-12M


title: COCS exposed to NBH for 14d replicate 3


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-12P


title: COCS exposed to NBH for 14d replicate 1


title: COCS exposed to POM1 for 10d replicate 4

source_name: COCS exposed to POM1 for 10d


title: PBMC_mort_nonagenarian 28366

description: Sample name: 28366


title: PBMC_mort_nonagenarian 28358

description: Sample name: 28358


title: PBMC_mort_nonagenarian 28341

description: Sample name: 28341


title: PBMC_mort_nonagenarian 28330

description: Sample name: 28330


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-13M


title: PBMC_mort_nonagenarian 28346

description: Sample name: 28346


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-09M


title: COCS exposed to POM1 for 10d replicate 1


title: PBMC_mort_nonagenarian 28319

description: Sample name: 28319


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-09P


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-04P


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-04M


title: Gastric adenocarcinoma with liver metastasis, primary tumor GIM-11P

value: tumor endothelium from gastric adenocarcinoma tissue


title: COCS exposed to POM1 for 10d replicate 2


title: COCS exposed to IgG for 10d replicate 4

source_name: COCS exposed to IgG for 10d

value: IgG


title: COCS exposed to POM1 for 10d replicate 3


title: PBMC_mort_nonagenarian 28306

description: Sample name: 28306

value: male

value: non-frail


title: COCS exposed to IgG for 10d replicate 3


title: PBMC_mort_nonagenarian 28301

description: Sample name: 28301


title: PBMC_mort_nonagenarian 28303

description: Sample name: 28303


title: COCS exposed to NBH for 14d replicate 2


title: PBMC_mort_nonagenarian 28298

description: Sample name: 28298


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-01P


title: PBMC_mort_nonagenarian 28291

description: Sample name: 28291


title: COCS exposed to IgG for 10d replicate 2


title: PBMC_mort_nonagenarian 28290

description: Sample name: 28290


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-13P


title: COCS exposed to IgG for 10d replicate 1


title: COCS exposed to POM1 for 7d replicate 2

source_name: COCS exposed to POM1 for 7d


title: c4 vs c8 H11.14130695

city: Nouzilly

first: Rozenn

last: DALBIES-TRAN

address: Centre de Recherches INRA

country: France

institute: INRA

hyb_protocol: Probes were hybridized onto the microarray for 16h at 42°C in Advahyb buffer in a SlideBooster apparatus (Advalytix, Beckman Coulter Biomedical GmbH, Germany), then washed using the AdvaWash apparatus and buffers (Advalytix).

scan_protocol: Slides were scanned at 532nm and 635nm with a GenePix 4000B scanner. Quantitative analysis was performed using the GenePix Pro 6.0 software (Axon Molecular Devices, Sunnyvale, CA, USA).

data_processing: For each spot, the median intensity value was log 2 transformed prior to normalization step that consisted into removing from the expression measures any systematic effect. Within each array, we applied a background correction method on the foreground signal using the normexp method (Ritchie et al.,  Bioinformatics (2007) 23:2700-2707) and normalized the expression log-ratios using a loess function on the overall log ratio to remove the dye bias between the two cyanines.

organism: Bos taurus

label_protocol: 2 µg of amplified RNA were labeled with cyanine 3 or 5 using the ULS aRNA labeling kit (Kreatech, Amsterdam, The Netherlands) according to the manufacturer’s instructions, followed by incubation for 15 minutes at 70°C with RNA Fragmentation Reagent (Life Technologies, France).

growth_protocol: Animals were subjected to ovarian stimulation prior to oocyte collection.

extract_protocol: Total DNAse treated RNA was extracted from pools of 15 oocytes per stage for each animal, using Picopure RNA isolation kit (Invitrogen, Marly-le-Roi, France) according to the manufacturer’s instructions. Before extraction, 0.15 pg, 0.75 pg and 0.15 pg of luciferase RNA (Promega, Charbonnière-les-Bains, France), and alien4 and alien5 RNA (Stratagene, France) respectively had been added as external controls. Then, RNA underwent a double round amplification using the dual RiboAmp Plus kit (Invitrogen) with some modifications as compared to the manufacturer’s instructions, as in vitro transcription was run for 90 minutes and 75 minutes for the first and the second cycle respectively. The quantity and length of amplified aRNA were analysed by optical density measure and microelectrophoresis (Bionalyzer® 2100 RNA 6000 nanochip, Agilent Technologies).

treatment_protocol: Oocytes were stored frozen in RNAlater (Ambion).

value: oocyte

tag: stage of maturity

value: mature


title: PBMC_mort_nonagenarian 28288

description: Sample name: 28288


title: PBMC_mort_nonagenarian 28289

description: Sample name: 28289


title: COCS exposed to POM1 for 7d replicate 4

value: Cultured organotypic cerebellar slices


title: COCS exposed to POM1 for 7d replicate 1


title: c9 vs c8 H25.14130677


title: c9 vs c10 H31.14130671


title: c9 vs c10 H32.14130670


title: PBMC_mort_nonagenarian 28283

description: Sample name: 28283


title: COCS exposed to IgG for 7d replicate 3

source_name: COCS exposed to IgG for 7d


title: COCS exposed to IgG for 7d replicate 2


title: c9 vs c8 H26.14130676


title: COCS exposed to IgG for 7d replicate 4


title: PBMC_mort_nonagenarian 28279

description: Sample name: 28279


title: c2 vs c10 H28.14130674


title: c4 vs c8 H12.14130694


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-01M


title: PBMC_mort_nonagenarian 28284

description: Sample name: 28284


title: PBMC_mort_nonagenarian 28277

description: Sample name: 28277


title: c2 vs c10 H27.14130675


title: COCS exposed to POM1 for 3d replicate 3

source_name: COCS exposed to POM1 for 3d


title: c2 vs c5 H33.14130669


title: PBMC_mort_nonagenarian 28272

description: Sample name: 28272


title: PBMC_mort_nonagenarian 28286

description: Sample name: 28286


title: COCS exposed to IgG for 7d replicate 1


title: COCS exposed to POM1 for 3d replicate 4


title: COCS exposed to POM1 for 3d replicate 2


title: PBMC_mort_nonagenarian 28269

description: Sample name: 28269


title: COCS exposed to IgG for 3d replicate 3

source_name: COCS exposed to IgG for 3d


title: c4 vs c5 H29.14130673


title: c4 vs c5 H18x14130686

value: immature


title: PBMC_mort_nonagenarian 28247

description: Sample name: 28247


title: COCS exposed to POM1 for 3d replicate 1


title: c2 vs c5 H34.14130668


title: COCS exposed to IgG for 3d replicate 4


title: Colon adenocarcinoma with liver metastasis, metastasis tumor GIM-02M


title: PBMC_mort_nonagenarian 28242

description: Sample name: 28242


title: c4 vs c5 H30.14130672


title: COCS exposed to IgG for 3d replicate 1


title: PBMC_mort_nonagenarian 28258

description: Sample name: 28258


title: c2 vs c5 H21x14130681


title: PBMC_mort_nonagenarian 28233

description: Sample name: 28233


title: PBMC_mort_nonagenarian 28243

description: Sample name: 28243


title: PBMC_mort_nonagenarian 28237

description: Sample name: 28237


title: c4 vs c5 H17x14130687


title: PBMC_mort_nonagenarian 28232

description: Sample name: 28232


title: c2 vs c10 H15x14130689


title: COCS exposed to IgG for 3d replicate 2


title: COCS exposed to POM1 for 1d replicate 3

source_name: COCS exposed to POM1 for 1d


title: COCS exposed to POM1 for 1d replicate 4


title: PBMC_mort_nonagenarian 28223

description: Sample name: 28223


title: Mammary epithelial cells from VPA treated virgin mice replicate 1

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix GeneChip Mouse Expression Set 430A 2.0 arrays at the Microarray Core Facility (Dana-Farber Cancer Institute).

scan_protocol: Microarray gene chips were scanned using a laser, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The data was analyzed using DNA-Chip Analyzer (dChip).

source_name: mammary epithelial cells_VPA treated virgin mice

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from mRNA.

growth_protocol: Virgin and pregnant state C57BL/6 female mice were intraperitoneally injected with AzaC and VPA and maintained in the Harvard Institute of Medicine animal facility.

extract_protocol: mRNA was extracted from mouse mammary epithelial cells using μMACS™ mRNA Isolation Kits (Miltenyi Biotec) according to manufacturer instructions.

treatment_protocol: Mammary glands from mice treated with AzaC and VPA at virgin and pregnant stages  were digested to purify mouse mammary epithelial cells.

tag: strain

tag: gender

tag: Stage

value: virgin (9 week)

tag: treated with

value: VPA

value: mammary gland

value: mammary epithelial cells


title: Mammary epithelial cells from VPA treated virgin mice replicate 2

tag: cell type


title: Colon adenocarcinoma with liver metastasis, primary tumor GIM-02P


title: c2 vs c10 H16x14130688


title: c2 vs c5 H22x14130680


title: PBMC_mort_nonagenarian 28212

description: Sample name: 28212

value: peripheral blood mononuclear cells (PBMCs)

tag: age

value: nonagenarian

tag: Sex

tag: status 31.1.2013 (1 died, 0 alive)

value: pre-frail


title: Mammary epithelial cells from Aza treated virgin mice replicate 3

source_name: mammary epithelial cells_Aza treated virgin mice

value: female

value: AzaC


title: Mammary epithelial cells from Aza treated virgin mice replicate 2


title: COCS exposed to POM1 for 1d replicate 2


title: c4 vs c8 H23x14130679


title: c4 vs c8 H24x14130678


title: PBMC_mort_nonagenarian 28206

description: Sample name: 28206

tag: follow_up_time in years_until 31.1.2013

tag: status 31.5.2014 (1 died, 0 alive)

tag: body mass index


title: COCS exposed to IgG for 1d replicate 4

source_name: COCS exposed to IgG for 1d

tag: tissue


title: Mammary epithelial cells from virgin mice PBS control replicate 2

source_name: mammary epithelial cells_virgin mice PBS control

value: PBS (control)


title: PBMC_mort_nonagenarian 28204

description: Sample name: 28204

tag: cf-dna level (µg/ml)

tag: frailty index

value: frail


title: COCS exposed to POM1 for 7d replicate 3

tag: genotype/variation

tag: treatment


title: Mammary epithelial cells from virgin mice PBS control replicate 1


title: COCS exposed to IgG for 1d replicate 3

value: IgG

tag: time period


title: c9 vs c10 H19x14130683

tag: stage of maturity


title: COCS exposed to POM1 for 1d replicate 1


title: c9 vs c10 H20x14130682


title: PBMC_mort_nonagenarian 28202

description: Sample name: 28202

value: non-frail


title: PBMC_mort_nonagenarian 28200

description: Sample name: 28200

value: male


title: c9 vs c8 H14x14130690

value: oocyte


title: PBMC_mort_nonagenarian 28198

description: Sample name: 28198


title: Mammary epithelial cells from Aza treated virgin mice replicate 1

tag: strain

tag: gender


title: Mammary epithelial cells from VPA treated pregnant mice replicate 1

source_name: mammary epithelial cells_VPA treated pregnant mice

tag: Stage

value: pregnant (day 21)

tag: treated with


title: COCS exposed to POM1 for 8h replicate 3

source_name: COCS exposed to POM1 for 8h

value: Cultured organotypic cerebellar slices


title: COCS exposed to IgG for 1d replicate 1


title: Mammary epithelial cells from Aza treated pregnant mice replicate 2

source_name: mammary epithelial cells_Aza treated pregnant mice

tag: cell type


title: Mammary epithelial cells from Aza treated pregnant mice replicate 3


title: PBMC_mort_nonagenarian 28191

description: Sample name: 28191

tag: age

tag: Sex


title: Mammary epithelial cells from VPA treated pregnant mice replicate 3


title: COCS exposed to POM1 for 8h replicate 2


title: PBMC_mort_nonagenarian 28189

description: Sample name: 28189

tag: status 31.1.2013 (1 died, 0 alive)

tag: follow_up_time in years_until 31.1.2013


title: Mammary epithelial cells from VPA treated pregnant mice replicate 2


title: COCS exposed to IgG for 1d replicate 2


title: COCS exposed to POM1 for 8h replicate 4


title: c9 vs c8 H13x14130692

value: immature


title: PBMC_mort_nonagenarian 28193

description: Sample name: 28193

tag: status 31.5.2014 (1 died, 0 alive)

tag: body mass index


title: COCS exposed to IgG for 8h replicate 4

source_name: COCS exposed to IgG for 8h

tag: tissue


title: COCS exposed to POM1 for 8h replicate 1


title: PBMC_mort_nonagenarian 28182

description: Sample name: 28182

tag: cf-dna level (µg/ml)

tag: frailty index


title: COCS exposed to IgG for 8h replicate 3

tag: genotype/variation

tag: treatment


title: COCS exposed to IgG for 8h replicate 2

tag: time period


title: PBMC_mort_nonagenarian 28183

description: Sample name: 28183


title: Mammary epithelial cells from Aza treated pregnant mice replicate 1

tag: strain


title: Mammary epithelial cells from pregnant mice PBS control replicate 2

source_name: mammary epithelial cells_pregnant mice PBS control

tag: gender


title: COCS exposed to IgG for 8h replicate 1


title: PBMC_mort_nonagenarian 28179

description: Sample name: 28179

source_name: Human PBMC


title: PBMC_mort_nonagenarian 28165

description: Sample name: 28165


title: PBMC_mort_nonagenarian 28175

description: Sample name: 28175


title: PBMC_mort_nonagenarian 28172

description: Sample name: 28172


title: Mammary epithelial cells from pregnant mice PBS control replicate 1

tag: Stage


title: D10 pregnant mammary epithelial mature luminal cells replicate1

description: Gene expression data from D10 pregnant mammary epithelial mature luminal cells

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix GeneChip Mouse Expression Set 430 2.0 arrays at the Microarray Core Facility (Dana-Farber Cancer Institute).

scan_protocol: Microarray gene chips were scanned using a laser, and the positions and intensities of the fluorescent emissions are captured.

molecule: polyA RNA

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

growth_protocol: Virgin and pregnant state C57BL/6 female mice were maintained in the Harvard Institute of Medicine animal facility.

extract_protocol: mRNA was extracted from different cell types of mouse mammary epithelial cells from different reproductive stages using μMACS™ mRNA Isolation Kits (Miltenyi Biotec) according to manufacture instructions.

treatment_protocol: Mammary glands from different reproductive stages were digested to purify different cell types from the mouse epithelium.

tag: reproductive stage

value: D10 pregnant

value: mammary epithelial mature luminal cells


title: PBMC_mort_nonagenarian 28163

description: Sample name: 28163

tag: cell type


title: PBMC_mort_nonagenarian 28147

description: Sample name: 28147

tag: age


title: D10 pregnant mammary epithelial stem cells replicate1

description: Gene expression data from D10 pregnant mammary epithelial stem cells

value: mammary gland

value: mammary epithelial stem cells


title: PBMC_mort_nonagenarian 28151

description: Sample name: 28151

value: peripheral blood mononuclear cells (PBMCs)

value: nonagenarian

tag: Sex


title: PBMC_mort_nonagenarian 28148

description: Sample name: 28148

value: female

tag: status 31.1.2013 (1 died, 0 alive)


title: 9week virgin mammary epithelial stem cells replicate1

description: Gene expression data from 9week virgin mammary epithelial stem cells

value: 9 week virgin


title: PBMC_mort_nonagenarian 28140

description: Sample name: 28140

tag: follow_up_time in years_until 31.1.2013


title: 9week virgin mammary epithelial luminal progenitor cells replicate1

description: Gene expression data from 9week virgin mammary epithelial luminal progenitor cells


title: 3week virgin mammary epithelial stem cells replicate1

description: Gene expression data from 3week virgin mammary epithelial stem cells

value: 3 week virgin


title: 9week virgin mammary epithelial mature luminal cells replicate1

description: Gene expression data from 9week virgin mammary epithelial mature luminal cells


title: PBMC_mort_nonagenarian 28131

description: Sample name: 28131

tag: status 31.5.2014 (1 died, 0 alive)

value: frail


title: PBMC_mort_nonagenarian 28127

description: Sample name: 28127

tag: body mass index


title: PBMC_mort_nonagenarian 28123

description: Sample name: 28123

value: pre-frail


title: 3week virgin mammary epithelial luminal progenitor cells replicate1

description: Gene expression data from 3week virgin mammary epithelial luminal progenitor cells

tag: tissue


title: Retired breeders mammary epithelial mature luminal cells

description: Gene expression data from retired breeder mammary epithelial mature luminal cells

value: Retired Breeders


title: PBMC_mort_nonagenarian 28119

description: Sample name: 28119

tag: cf-dna level (µg/ml)


title: Retired breeders mammary epithelial luminal progenitor cells

description: Gene expression data from retired breeder mammary epithelial luminal progenitor cells


title: PBMC_mort_nonagenarian 28087

description: Sample name: 28087

value: male

tag: frailty index


description: Gene expression data from D16 pregnant mammary epithelial mature luminal cells

value: D16 pregnant


title: Retired breeders mammary epithelial stem cells

description: Gene expression data from retired breeders mammary epithelial stem cells


description: Gene expression data from D16 pregnant mammary epithelial luminal progenitor cells


title: PBMC_mort_nonagenarian 28078

description: Sample name: 28078


description: Gene expression data from D16 pregnant mammary epithelial stem cells


title: PBMC_mort_nonagenarian 28073

description: Sample name: 28073


title: PBMC_mort_nonagenarian 28062

description: Sample name: 28062


title: PBMC_mort_nonagenarian 28102

description: Sample name: 28102


description: Gene expression data from D10 pregnant mammary epithelial luminal progenitor cells


title: D10 pregnant mammary epithelial mature luminal cells replicate2


title: D10 pregnant mammary epithelial stem cells replicate2


title: PBMC_mort_nonagenarian 28059

description: Sample name: 28059


title: 9week virgin mammary epithelial mature luminal cells replicate2


title: PBMC_mort_nonagenarian 28048

description: Sample name: 28048

value: non-frail


title: PBMC_mort_nonagenarian 28058

description: Sample name: 28058


title: 9week virgin mammary epithelial luminal progenitor cells replicate2


title: 9week virgin mammary epithelial stem cells replicate2


title: PBMC_mort_nonagenarian 28032

description: Sample name: 28032


title: PBMC_mort_nonagenarian 28042

description: Sample name: 28042


title: 3week virgin mammary epithelial luminal progenitor cells replicate2


title: PBMC_mort_nonagenarian 28028

description: Sample name: 28028


title: 3week virgin mammary epithelial stem cells replicate2


title: PBMC_mort_nonagenarian 28020

description: Sample name: 28020


title: D19 pregnant mammary epithelial mature luminal cells replicate1

description: Gene expression data from D19 pregnant mammary epithelial mature luminal cells

value: D19 pregnant


title: Young foliage_1_red

status: Public on Jan 21 2015

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. Samples were hybridized with each dye as technical replicates. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next, the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution on a PowerScanner (Tecan Group Ltd., Männedorf, Switzerland) microarray scanner at 50% laser power with the autogain funtion on to automatically adjust PMT level. Image analysis was carried out using ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA).

data_processing: Median intensity and local background were obtained for each spot on the array. Bad spots resulting from dust, high local background or saturation were flagged.  Net intensity was calculated by subtracting trimmed background from median intensity. Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background-subtracted data were log2-transformed and quantile normalization was used to normalize intensity distributions between arrays.

organism: Picea glauca

source_name: Picea glauca Young foliage, 1, Cy5

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of Picea glauca, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type four biological samples were prepared from four non-related trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground using a Mixer Mill MM 300 (Retsch, Haan, Germany) and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008).

tag: biological replicate

value: Young foliage

tag: slide batch


description: Gene expression data from 3week virgin mammary epithelial mature luminal cells


title: Shoot apex_3_red

source_name: Picea glauca Shoot apex, 3, Cy5

value: Shoot apex


title: Root secondary xylem_2_red

source_name: Picea glauca Root secondary xylem, 2, Cy5

value: Root secondary xylem


title: GL10

type: genomic

city: Belmont

first: Frederik

last: van Delft

address: 15 Cotswold Road

department: Haemato-oncology

country: United Kingdom

institute: ICR

description: Hybridized to SNP 6.0

hyb_protocol: DNA was hybridised to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL and CHP (generated using Affymetrix Genotyping Console 4.0 using the birdseed-v2 algorithm) files were processed using CNAG version 3.3.0.1 (beta).

label: Biotin

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labelled as per the manufacturer (Affymetrix).

extract_protocol: The DNeasy Blood & Tissue Kit (Qiagen) was used to extract HMW DNA from peripheral blood mononuclear cells and primary GBM tumor biopsies. DNA quantity was assessed by using a NanoDrop Spectrophotometer.

tag: disease status

value: glioblastoma multiforme (GBM)

value: peripheral blood

tag: sample type

value: constitutional

tag: patient


title: GL11

description: Hybridized to SNP 6.0


title: GL12

description: Hybridized to SNP 6.0


title: Shoot apex_1_red

source_name: Picea glauca Shoot apex, 1, Cy5


title: PBMC_mort_nonagenarian 28035

description: Sample name: 28035

value: peripheral blood mononuclear cells (PBMCs)

value: nonagenarian


title: GBM11

description: Hybridized to SNP 6.0

source_name: Tumor biopsy

value: primary tumor

value: diagnosis


title: Root secondary xylem_4_red

source_name: Picea glauca Root secondary xylem, 4, Cy5


title: GBM10

description: Hybridized to SNP 6.0


title: GBM7

description: Hybridized to SNP 6.0


title: Shoot secondary xylem_4_red

source_name: Picea glauca Shoot secondary xylem, 4, Cy5

value: Shoot secondary xylem


title: Root apex_3_red

source_name: Picea glauca Root apex, 3, Cy5

value: Root apex


title: Shoot secondary xylem_2_red

source_name: Picea glauca Shoot secondary xylem, 2, Cy5


title: GBM9

description: Hybridized to SNP 6.0


title: GL8

description: Hybridized to SNP 6.0


title: GBM8

description: Hybridized to SNP 6.0


title: GBM6

description: Hybridized to SNP 6.0


title: Shoot apex_2_red

source_name: Picea glauca Shoot apex, 2, Cy5


title: Root secondary xylem_3_red

source_name: Picea glauca Root secondary xylem, 3, Cy5


title: Young foliage_3_red

source_name: Picea glauca Young foliage, 3, Cy5


title: Shoot phelloderm_1_red

source_name: Picea glauca Shoot phelloderm, 1, Cy5

value: Shoot phelloderm


title: Young foliage_2_red

source_name: Picea glauca Young foliage, 2, Cy5


title: Root apex_1_red

source_name: Picea glauca Root apex, 1, Cy5


title: Root phelloderm_4_red

source_name: Picea glauca Root phelloderm, 4, Cy5

value: Root phelloderm


title: Root phelloderm_3_red

source_name: Picea glauca Root phelloderm, 3, Cy5


title: Shoot secondary xylem_1_red

source_name: Picea glauca Shoot secondary xylem, 1, Cy5


title: Shoot apex_4_red

source_name: Picea glauca Shoot apex, 4, Cy5


title: GBM4

description: Hybridized to SNP 6.0


title: Root phelloderm_2_red

source_name: Picea glauca Root phelloderm, 2, Cy5


title: Root apex_2_red

source_name: Picea glauca Root apex, 2, Cy5


title: Shoot phelloderm_4_red

source_name: Picea glauca Shoot phelloderm, 4, Cy5


title: Root secondary xylem_1_red

source_name: Picea glauca Root secondary xylem, 1, Cy5


title: Shoot phelloderm_3_red

source_name: Picea glauca Shoot phelloderm, 3, Cy5


title: GL5

description: Hybridized to SNP 6.0

source_name: Peripheral blood


title: GBM5

description: Hybridized to SNP 6.0

source_name: Tumor biopsy


title: GL4

description: Hybridized to SNP 6.0


title: Young foliage_4_red

source_name: Picea glauca Young foliage, 4, Cy5


title: Root apex_4_green

source_name: Picea glauca Root apex, 4, Cy3


title: Shoot secondary xylem_3_red

source_name: Picea glauca Shoot secondary xylem, 3, Cy5


title: Shoot phelloderm_2_red

source_name: Picea glauca Shoot phelloderm, 2, Cy5


title: Root phelloderm_1_red

source_name: Picea glauca Root phelloderm, 1, Cy5


title: Shoot phelloderm_2_green

source_name: Picea glauca Shoot phelloderm, 2, Cy3


title: GBM2

description: Hybridized to SNP 6.0


title: GL6

description: Hybridized to SNP 6.0


title: Root apex_3_green

source_name: Picea glauca Root apex, 3, Cy3


title: GL9

description: Hybridized to SNP 6.0


title: GBM3

description: Hybridized to SNP 6.0


title: GL2

description: Hybridized to SNP 6.0


title: GL3

description: Hybridized to SNP 6.0


title: Root phelloderm_1_green

source_name: Picea glauca Root phelloderm, 1, Cy3


title: GL7

description: Hybridized to SNP 6.0


title: Root secondary xylem_1_green

source_name: Picea glauca Root secondary xylem, 1, Cy3


title: Young foliage_1_green

source_name: Picea glauca Young foliage, 1, Cy3


title: Root phelloderm_4_green

source_name: Picea glauca Root phelloderm, 4, Cy3


title: Shoot phelloderm_4_green

source_name: Picea glauca Shoot phelloderm, 4, Cy3


title: Shoot secondary xylem_2_green

source_name: Picea glauca Shoot secondary xylem, 2, Cy3


title: Young foliage_4_green

source_name: Picea glauca Young foliage, 4, Cy3


title: Shoot secondary xylem_3_green

source_name: Picea glauca Shoot secondary xylem, 3, Cy3


title: Young foliage_3_green

source_name: Picea glauca Young foliage, 3, Cy3


title: Shoot phelloderm_1_green

source_name: Picea glauca Shoot phelloderm, 1, Cy3


title: Root apex_2_green

source_name: Picea glauca Root apex, 2, Cy3


title: Young foliage_2_green

source_name: Picea glauca Young foliage, 2, Cy3


title: Shoot apex_4_green

source_name: Picea glauca Shoot apex, 4, Cy3


title: Root phelloderm_3_green

source_name: Picea glauca Root phelloderm, 3, Cy3


title: GL1

description: Hybridized to SNP 6.0

source_name: Peripheral blood


title: Root secondary xylem_4_green

source_name: Picea glauca Root secondary xylem, 4, Cy3


title: Root apex_1_green

source_name: Picea glauca Root apex, 1, Cy3


title: Shoot secondary xylem_4_green

source_name: Picea glauca Shoot secondary xylem, 4, Cy3


title: Shoot secondary xylem_1_green

source_name: Picea glauca Shoot secondary xylem, 1, Cy3


title: GBM12

description: Hybridized to SNP 6.0

source_name: Tumor biopsy


title: Shoot apex_3_green

source_name: Picea glauca Shoot apex, 3, Cy3


title: Shoot apex_2_green

source_name: Picea glauca Shoot apex, 2, Cy3


title: Shoot apex_1_green

source_name: Picea glauca Shoot apex, 1, Cy3


title: Bone Marrow_Vehicle 2_Topotecan [1344-08G_8M 93]

first: Myrtle

last: Davis Millin

address: 31 Center Drive

institute: The National Cancer Institute

hyb_protocol: 11 μg of purified cRNA was applied to Affymetrix GeneChip Rat Genome 230 2.0 Arrays, and incubated at 45°C for 16 hours. Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 using factory PMT settings. Data extraction was completed with Expression Console software using a target scaling of 500.

data_processing: Data analysis was performed with the Bioconductor R package using the affyQCReport package for array quality control followed by principal variance component based probe filtering (PVAC) where the filtering was based on a score measuring consistency among probes within a probe set (Irizarry et al., Biostatistics (2003) 4, 249-264). After one outlier sample was excluded (sample 1344-05H), the remaining Affymetrix raw CEL files were preprocessed using the robust multichip average (RMA) algorithm.

organism: Rattus norvegicus

source_name: Bone Marrow_5% Dextrose followed by Topotecan

label_protocol: Total RNA samples were converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On day 1, the rats weighed between 271.2 to 342.2 g. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

extract_protocol: RNA isolation from individual tissues was accomplished using an RNeasy microarray kit (QIAGEN Inc.). After extraction, the RNA concentration of each sample was determined using a RiboGreen assay. The RNA Integrity Number (RIN) of each sample was determined using an Agilent 2100 Bioanalyzer with 2100 Expert Software. Only samples with a RIN of 7.5 or higher were deemed acceptable for gene expression analysis.

treatment_protocol:
Rats were administered a single intravenous (IV) infusion dose, given over a 30-minute interval, of topotecan, oxaliplatin, or respective vehicle control formulation. Thirty minutes after the end of the first infusion, topotecan, oxaliplatin, or a respective vehicle control formulation was administered by IV infusion, given over a 30-minute interval.  All doses were delivered at a flow rate of approximately 4 mL/kg/30 minutes. Infusion volumes were based on the mean body weight of animals on the day prior to dosing.
At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, bone marrow from left femurs was collected for RNA isolation. Bone marrow was flushed from bone using RNAlater® and refrigerated (approximately 2-8°C) for at least 24 hours and then stored at or below -20°C.

tag: strain

value: Sprague-Dawley

value: Male

value: 8 weeks

value: Bone marrow

tag: dose 1

value: 0 mg/kg

tag: vehicle 1

value: 5% Dextrose in water

tag: compound 2

value: Topotecan

tag: dose 2

value: 4.7 mg/kg

tag: vehicle 2

value: 0.9% NaCl

tag: time

value: 6 hour

tag: route

value: intravenous (IV)


title: Bone Marrow_Vehicle 2_Topotecan [1344-08H_8M 94]

tag: Sex

tag: age


title: Root secondary xylem_3_green

source_name: Picea glauca Root secondary xylem, 3, Cy3

tag: tissue

value: Root secondary xylem


title: Bone Marrow_Vehicle 2_Topotecan [1344-06H_8M 88]


title: Bone Marrow_Vehicle 2_Topotecan [1344-06G_8M 87]


title: Root phelloderm_2_green

source_name: Picea glauca Root phelloderm, 2, Cy3


title: Root secondary xylem_2_green

source_name: Picea glauca Root secondary xylem, 2, Cy3


title: Bone Marrow_Vehicle 2_Topotecan [1346-04E_8M 95]

value: 24 hour


title: Bone Marrow_Vehicle 2_Topotecan [1346-02G_8M 90]


title: Bone Marrow_Vehicle 2_Topotecan [1344-04H_8M 92]

value: 1 hour


title: Bone Marrow_Vehicle 2_Topotecan [1346-04F_8M 96]


title: Picea abies-xylem-September-rep 3

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

label: Alexa 555

organism: Picea abies

source_name: Picea abies xylem, September

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (10 ug per sample) was labeled using Alexa Fluor 555 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: 4-year old seedlings obtained from nursery planting stock (open-pollinated seed lots) as 3-year-old seedlings of Picea glauca and Picea abies. Upon reception they were transferred to 8-inch pots and grown in a tunnel under natural light conditions for one year. Sampling of xylem was done in June, July, August and September as described (Pavy et al. 2008). 6 trees were sampled on each date, for each specie.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground using a Mixer Mill MM 300 (Retsch, Haan, Germany) and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the samples.

value: xylem

tag: month of sampling

value: September

tag: biological repetition

tag: internal ^sample


title: Picea abies-xylem-September-rep 4

tag: slide batch


title: Picea abies-xylem-September-rep 6


title: Bone Marrow_Vehicle 2_Topotecan [1344-04G_8M 91]


title: Picea abies-xylem-September-rep 5


title: Bone Marrow_Vehicle 2_Topotecan [1346-02F_8M 89]


title: Picea abies-xylem-September-rep 2


title: Picea abies-xylem-August-rep 6

source_name: Picea abies xylem, August

value: August


title: Picea abies-xylem-September-rep 1


title: Bone Marrow_Vehicle 2_Topotecan [1344-02G_8M 85]

value: Sprague-Dawley


title: Picea abies-xylem-August-rep 5


title: Bone Marrow_Vehicle 2_Topotecan [1344-02H_8M 86]

value: Male


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-08F_7M 82]

source_name: Bone Marrow_0.9% NaCl followed by Oxalipatin

value: 8 weeks

value: Oxaliplatin

value: 15 mg/kg


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-08E_7M 81]

value: Bone marrow

value: 0 mg/kg

value: 5% Dextrose in water


title: GBM1

description: Hybridized to SNP 6.0

tag: disease status

value: glioblastoma multiforme (GBM)

value: primary tumor

tag: sample type

value: diagnosis


title: Picea abies-xylem-August-rep 4


title: Bone Marrow_Vehicle 1_Oxaliplatin [1346-04D_7M 84]

tag: strain

value: 0.9% NaCl

value: intravenous (IV)


title: Picea abies-xylem-July-rep 6

source_name: Picea abies xylem, July

value: July


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-06F_7M 76]

tag: dose 1

value: 6 hour


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-06E_7M 75]

tag: vehicle 1


title: Bone Marrow_Vehicle 1_Oxaliplatin [1346-04C_7M 83]

tag: compound 2

value: 24 hour


title: Picea abies-xylem-August-rep 1

value: xylem

value: August


title: Picea abies-xylem-July-rep 5


title: Picea abies-xylem-August-rep 2


title: Shoot phelloderm_3_green

source_name: Picea glauca Shoot phelloderm, 3, Cy3

tag: biological replicate

value: Shoot phelloderm


title: Picea abies-xylem-August-rep 3


title: Root apex_4_red

source_name: Picea glauca Root apex, 4, Cy5

value: Root apex


title: Bone Marrow_Vehicle 1_Oxaliplatin [1346-02D_7M 77]

value: Sprague-Dawley

value: Male

value: 8 weeks

value: Oxaliplatin

tag: dose 2

tag: vehicle 2


title: Picea abies-xylem-July-rep 4


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-04F_7M 80]

value: Bone marrow

value: 0 mg/kg

value: 15 mg/kg

value: 5% Dextrose in water

tag: time

value: 1 hour

tag: route


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-04E_7M 79]

tag: Sex

tag: age

value: 0.9% NaCl

value: intravenous (IV)


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-02E_7M 73]

tag: tissue


title: Bone Marrow_Vehicle 1_Oxaliplatin [1344-02F_7M 74]


title: Bone Marrow_Oxaliplatin_Topotecan [1344-08D_6M 70]

source_name: Bone Marrow_Oxaliplatin followed by Topotecan

tag: compound 1

value: Topotecan

value: 4.7 mg/kg

value: 6 hour


title: Picea abies-xylem-July-rep 1

value: xylem

tag: month of sampling

value: July

tag: biological repetition

tag: internal ^sample


title: Picea abies-xylem-June-rep 6

source_name: Picea abies xylem, June

tag: slide batch

value: June


title: Picea abies-xylem-July-rep 2


title: Bone Marrow_Vehicle 1_Oxaliplatin [1346-02E_7M 78]

tag: strain

value: Sprague-Dawley

value: 24 hour


title: Bone Marrow_Oxaliplatin_Topotecan [1344-06D_6M 64]

value: Male

value: 8 weeks

tag: dose 1


title: Picea abies-xylem-June-rep 1


title: Picea abies-xylem-July-rep 3


title: Picea abies-xylem-June-rep 5


title: Bone Marrow_Oxaliplatin_Topotecan [1346-04B_6M 72]

value: Bone marrow

value: Oxaliplatin

tag: vehicle 1


title: Bone Marrow_Oxaliplatin_Topotecan [1346-02C_6M 66]

value: 15 mg/kg

tag: compound 2


title: Bone Marrow_Oxaliplatin_Topotecan [1346-04A_6M 71]

value: 5% Dextrose in water


title: Picea glauca-xylem-September-rep 6

source_name: Picea glauca xylem, September

value: September


title: Bone Marrow_Oxaliplatin_Topotecan [1346-02B_6M 65]

value: 0.9% NaCl


title: Picea abies-xylem-June-rep 3


title: Picea abies-xylem-June-rep 2


title: Picea glauca-xylem-September-rep 2


title: Picea glauca-xylem-September-rep 3


title: Bone Marrow_Oxaliplatin_Topotecan [1344-04D_6M 68]

value: 1 hour

value: intravenous (IV)


title: Bone Marrow_Oxaliplatin_Topotecan [1344-02D_6M 62]

value: Topotecan

value: 4.7 mg/kg


title: Bone Marrow_Oxaliplatin_Topotecan [1344-04C_6M 67]


title: Bone Marrow_Oxaliplatin_Topotecan [1344-02C_6M 61]


title: Picea glauca-xylem-August-rep 6

source_name: Picea glauca xylem, August

value: xylem

value: August


title: Bone Marrow_Oxaliplatin_Topotecan [1344-06C_6M 63]

value: 6 hour


title: Picea glauca-xylem-September-rep 4


title: Picea glauca-xylem-September-rep 1


title: Bone Marrow_Topotecan_Oxaliplatin [1344-08A_5M 57]

source_name: Bone Marrow_Topotecan  followed by Oxaliplatin

value: Sprague-Dawley


title: Picea glauca-xylem-August-rep 5


title: Bone Marrow_Topotecan_Oxaliplatin [1344-08B_5M 58]


title: Picea glauca-xylem-August-rep 4


title: Bone Marrow_Topotecan_Oxaliplatin [1344-06B_5M 52]


title: Bone Marrow_Topotecan_Oxaliplatin [1344-06A_5M 51]


title: Picea glauca-xylem-August-rep 3


title: Bone Marrow_Topotecan_Oxaliplatin [1346-01H_5M 53]

value: 24 hour


title: Picea glauca-xylem-August-rep 2


title: Bone Marrow_Topotecan_Oxaliplatin [1346-03G_5M 59]

value: Male


title: Picea glauca-xylem-July-rep 5

source_name: Picea glauca xylem, July

value: July


title: Picea glauca-xylem-September-rep 5


title: Picea glauca-xylem-July-rep 6


title: Bone Marrow_Topotecan_Oxaliplatin [1344-04B_5M 56]

value: 8 weeks

value: Bone marrow


title: Picea glauca-xylem-July-rep 4


title: Picea glauca-xylem-July-rep 2


title: Picea glauca-xylem-July-rep 1


title: Picea glauca-xylem-July-rep 3


title: Bone Marrow_Topotecan_Oxaliplatin [1344-04A_5M 55]

value: Oxaliplatin

value: 15 mg/kg


title: Picea glauca-xylem-August-rep 1


title: Bone Marrow_Topotecan_Oxaliplatin [1344-02A_5M 49]

value: 5% Dextrose in water


title: Bone Marrow_Topotecan_Oxaliplatin [1344-02B_5M 50]

value: 0.9% NaCl


title: Picea glauca-xylem-June-rep 6

source_name: Picea glauca xylem, June

value: June


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-07H_4M 46]

source_name: Bone Marrow_Oxaliplatin followed by 0.9% NaCl

value: intravenous (IV)


title: rnt1ts-37

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

description: rnt1ts cells grown at 37 C

hyb_protocol: Array hybridization experiment was conducted and analyzed at the Genome Quebec Innovation Center (Montreal, Quebec, Canada) according to the protocols supplied with Affymetrix GeneChip

scan_protocol: Scanning was done according to the Affymetrix tiling array manufacturer instructions

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

organism: Saccharomyces cerevisiae

source_name: rnt1ts cells grown at 37 C

label_protocol: The microarray experiment was conducted and analyzed at the Genome Quebec Innovation Center (Montreal, Quebec, Canada) according to the protocols supplied with Affymetrix GeneChip

growth_protocol: Yeast cells were grown and manipulated using standard procedures in either yeast complete (YC) medium or YC medium without leucine

extract_protocol: Cells were lysed by vortexing in presence of glass beads and phenol and the total RNA extracted using standard phenol:chloroform extraction

treatment_protocol: Exponentially growing yeast cells were collected

tag: genotype


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-05G_4M 39]


title: rnt1d-37

description: rnt1d cells grown at 37 C

source_name: rnt1d cells grown at 37 C


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-07G_4M 45]


title: WT-37

description: wild type cells grown at 37 C

source_name: wild type cells grown at 37 C

value: wild type


title: Picea glauca-xylem-June-rep 4


title: Picea glauca-xylem-June-rep 3


title: WT Smoke Sample 24

city: Boston

first: Jarrett

last: Morrow

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

description: WT Smoke

hyb_protocol: 750ng of total RNA for each sample was hybridized onto a Sentrix MouseRef-8 v2.0 Expression BeadChip Array (Illumina, San Diego, CA), based on the manufacturer's protocol.

scan_protocol: The BeadChip Array was scanned using an Illumina BeadArray Reader and quality control analysis was performed using Illumina GenomeStudio v3.1.3 software, Gene Expression Module version 1.1.1, and the statistical package R v2.15.2.

data_processing: Each of the samples and all probes passed quality control, and the data were background corrected, log2 transformed and quantile normalized.

source_name: mouse lung

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted from murine lung tissues using Allprep kit (Qiagen, Valencia, CA).

treatment_protocol: Mice were exposed to mixed main-stream and side-stream CS from 3R4F Kentucky Research cigarettes for 5 days/week for 6 months in Teague TE 10z chambers (TSP ~ 100-200 mg/m 3 and CO levels ~6 ppm).

tag: treatment

value: Smoke

value: lung

value: WT

tag: genetic background


title: Picea glauca-xylem-June-rep 2

value: xylem


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1346-03F_4M 48]

value: Sprague-Dawley

tag: vehicle 2

tag: time


title: Het Air Sample 23

description: Het Air

value: Air

value: Hhip+/-


title: rnt1d-26-2

description: rnt1d cells grown at 26 C, biological replicate 2

source_name: rnt1d cells grown at 26 C


title: rnt1ts-26

description: rnt1ts cells grown at 26 C

source_name: rnt1ts cells grown at 26 C


title: Het Smoke Sample 22

description: Het Smoke


title: WT Smoke Sample 19

description: WT Smoke


title: Picea glauca-xylem-June-rep 1


title: rnt1d-26-1

description: rnt1d cells grown at 26 C, biological replicate 1


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1346-03E_4M 47]

tag: Sex

value: Male

value: 24 hour

tag: route


title: Het Smoke Sample 21

description: Het Smoke

tag: tissue


title: Het Air Sample 20

description: Het Air


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1346-01G_4M 42]

tag: age

value: 8 weeks

value: Bone marrow

tag: compound 1


title: WT-26-2

description: wild type cells grown at 26 C, biological replicate 2

source_name: wild type cells grown at 26 C


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-03H_4M 44]

value: Oxaliplatin

value: 15 mg/kg

value: 1 hour


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1346-01F_4M 41]

value: 5% Dextrose in water

value: 0.9% NaCl


title: WT Air Sample 17

description: WT Air


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-03G_4M 43]

value: intravenous (IV)


title: Het Smoke Sample 16

description: Het Smoke

value: Smoke


title: Hela_PpIX+Xray_3

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description: Gene expression after 24hours in 3Gy-irradiated and treated with 1.0μg/ml  PpIX Hela cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent- G4112F Whole Human Genome Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. The quantile normalization method was used in our microarray analysis.

source_name: Hela cells, 24hr, 3Gy, PpIX

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: RNA was extracted using the RNeasy mini kit (Qiagen) from Hela cells. Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAlater conservation at -80ºC

tag: cell line

value: Hela

value: PpIX+Xray


title: WT Air Sample 18

description: WT Air

value: lung

value: WT


title: WT Air Sample 15

description: WT Air

value: Air


title: Picea glauca-xylem-June-rep 5

value: xylem

tag: month of sampling

value: June

tag: biological repetition

tag: internal ^sample


title: Hela_Xray_3

description: Gene expression after 24hours in 3Gy-irradiated Hela cells

source_name: Hela cells, 24hr, 3Gy

value: Xray


title: Hela_PpIX+Xray_1


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-01G_4M 37]

tag: strain

value: Sprague-Dawley

value: Male

value: 8 weeks

tag: dose 1


title: Het Air Sample 13

description: Het Air

value: Hhip+/-


title: Hela_PpIX+Xray_2


title: Bone Marrow_Topotecan_Vehicle 2 [1344-07E_3M 33]

source_name: Bone Marrow_Topotecan followed by 5% Dextrose

value: Bone marrow

value: Topotecan

value: 4.7 mg/kg

tag: vehicle 1

value: 6 hour


title: Bone Marrow_Topotecan_Vehicle 2 [1344-07F_3M 34]

value: 0.9% NaCl

value: 5% Dextrose in water

value: intravenous (IV)


title: WT Smoke Sample 12

description: WT Smoke

value: Smoke

value: lung

tag: genotype


title: Het Air Sample 14

description: Het Air

tag: treatment

value: Air


title: Bone Marrow_Oxaliplatin_Vehicle 1 [1344-01H_4M 38]

value: Oxaliplatin

value: 15 mg/kg

value: 1 hour


title: Hela_Xray_2

value: Hela

value: Xray


title: WT-26-1

description: wild type cells grown at 26 C, biological replicate 1

value: wild type


title: Bone Marrow_Topotecan_Vehicle 2 [1344-05F_3M 28]

value: Sprague-Dawley

value: Male

value: 8 weeks


title: Het Smoke Sample 10

description: Het Smoke

value: Hhip+/-

tag: genetic background


title: Bone Marrow_Oxaliplatin_Topotecan [1344-08C_6M 69]

source_name: Bone Marrow_Oxaliplatin followed by Topotecan

value: Bone marrow

tag: compound 2

value: Topotecan

tag: dose 2

value: 4.7 mg/kg

tag: vehicle 2

value: 6 hour


title: Hela_PpIX control_3

description: Gene expression after 24hours in 0 Gy-irradiated and treated with 1.0μg/ml  PpIX Hela cells

source_name: Hela cells, 24hr, 0Gy, PpIX

value: PpIX


title: Picea abies-xylem-June-rep 4

source_name: Picea abies xylem, June

value: xylem

tag: slide batch

value: June


title: Bone Marrow_Topotecan_Vehicle 2 [1346-03C_3M 35]

tag: Sex

tag: tissue

value: 0.9% NaCl

value: 5% Dextrose in water

tag: time

value: 24 hour

tag: route

value: intravenous (IV)


title: Bone Marrow_Topotecan_Vehicle 2 [1344-05E_3M 27]

tag: age

tag: compound 1


title: Bone Marrow_Topotecan_Vehicle 2 [1346-03D_3M 36]


title: Hela_control_3

description: Gene expression after 24hours in 0 Gy-irradiated Hela cells

source_name: Hela cells, 24hr, 0Gy

tag: cell line

value: Hela

value: control


title: Hela_PpIX control_1


title: WT Air Sample 9

description: WT Air

value: Air

value: lung

value: WT


title: Hela_PpIX control_2


title: Het Air Sample 5

description: Het Air

value: Hhip+/-


title: Bone Marrow_Topotecan_Vehicle 2 [1346-01E_3M 29]

tag: strain

value: Sprague-Dawley

value: Male

value: 8 weeks

value: Bone marrow


title: Bone Marrow_Topotecan_Vehicle 2 [1344-03E_3M 31]

value: Topotecan

tag: dose 1

value: 4.7 mg/kg

value: 1 hour


title: Hela_Xray_1

value: Xray


title: Hela_control_1


title: Bone Marrow_Topotecan_Oxaliplatin [1346-02A_5M 54]

source_name: Bone Marrow_Topotecan  followed by Oxaliplatin

tag: vehicle 1

value: 0.9% NaCl

value: Oxaliplatin

value: 15 mg/kg

value: 5% Dextrose in water


title: Bone Marrow_Topotecan_Oxaliplatin [1346-03H_5M 60]

value: 24 hour

value: intravenous (IV)


title: Bone Marrow_Topotecan_Vehicle 2 [1344-03F_3M 32]


title: Het Air Sample 8

description: Het Air

value: Air

value: lung

tag: genotype


title: Hela_control_2

value: Hela

tag: treatment

value: control


title: Bone Marrow_Topotecan_Vehicle 2 [1344-01F_3M 26]

value: Sprague-Dawley

value: Male


title: WT Air Sample 6

description: WT Air

value: WT

tag: genetic background


title: WT Smoke Sample 7

description: WT Smoke

value: Smoke


title: ESC-NESMC(1)

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation in package BeadArray from R/Bioconductor.

source_name: neuroectoderm-derived SMCs (NESMC)

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

growth_protocol: For neural crest differentiation, hPSCs were grown in CDM + bFGF (12 ng/ml, R&D systems) + SB431542 (10 µM, Sigma) + noggin (200 ng/ml, R&D Systems) for 10-13 days, with change of medium every 2-3 days. After which, NGFR+/ B3GAT1+ cells were isolated by FACS and re-plated for SMC induction. Sorted cells were cultured in SMC differentiation medium CDM + PDGF-BB (10 ng/ml, PeproTech) + TGF-β1 (2 ng/ml, PeproTech) for another 12 days. Derived NCSMCs could be propagated further in culture using SMC medium (SC-1101, Sciencell). All experiments were done on NCSMCs between passages 1-9. On the other hand, the other SMC subtypes (NESMC, LMSMC and PMSMC) were generated by a previously established protocol (Cheung et al., 2012).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: neuroectoderm-derived SMCs (NESMC)


title: Bone Marrow_Topotecan_Vehicle 2 [1344-01E_3M 25]

value: 8 weeks

value: Bone marrow

value: Topotecan

value: 4.7 mg/kg

value: 1 hour


title: ESC-NESMC(2)


title: WT Smoke Sample 4

description: WT Smoke


title: Het Smoke Sample 1

description: Het Smoke

value: Hhip+/-


title: Het Smoke Sample 3

description: Het Smoke


title: WT Air Sample 2

description: WT Air


title: iPSC_NESMC(2)


title: iPSC_NESMC(1)


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-07D_2M 22]

source_name: Bone Marrow_5% Dextrose followed by 0.9% NaCl

value: 5% Dextrose in water

value: 0.9% NaCl

value: 6 hour


title: WT Smoke Sample 11

description: WT Smoke

value: lung


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-05D_2M 16]

value: intravenous (IV)


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-05C_2M 15]


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-07C_2M 21]


title: 10 siAR

city: Houston

first: Nicholas

last: Mitsiades

state: Texas

address: One Baylor Plaza

department: Medicine-Hematology & Oncology

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocol

data_processing: The expression values of the samples were normalized using the oligo R package.

source_name: LNCaP

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were cultured in RPMI-1640 media with 10% FBS

extract_protocol: Total RNA was extracted witjh Trizol and purified over and RNeasy column and eluted in RNAse free water.

treatment_protocol: Cells were transfected with control siRNA or siRNA against GATA2 or AR

value: LNCaP

tag: transfection

value: AR siRNA


title: Bone Marrow_Vehicle 2_Vehicle 1 [1346-01D_2M 18]

value: Sprague-Dawley

value: Male

tag: vehicle 2

value: 24 hour


title: 9 siAR


title: 7 siAR


title: Bone Marrow_Vehicle 2_Vehicle 1 [1346-01C_2M 17]


title: ESC-NCSMC(2)

source_name: neural crest-derived SMCs (NCSMC)

value: neural crest-derived SMCs (NCSMC)


title: iPSC_NCSMC(1)


title: iPSC_NCSMC(2)


title: 8 siAR


title: HPSC(2)

source_name: human pluripotent stem cells

value: human pluripotent stem cells


title: 5 siGATA2

value: GATA2 siRNA


title: Bone Marrow_Vehicle 2_Vehicle 1 [1346-03B_2M 24]

value: 8 weeks

value: Bone marrow


title: BVSMC(1)

source_name: human brain vascular SMCs (BVSMC)

value: human brain vascular SMCs (BVSMC)


title: 3_siCon

value: control siRNA


title: 6 siGATA2


title: 2_siCon


title: ESC-NCSMC(1)


title: 1_siCon


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-03D_2M 20]

value: 5% Dextrose in water

value: 1 hour


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-01C_2M 13]

value: 0.9% NaCl


title: BVSMC(2)


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-03C_2M 19]


title: 4 siGATA2


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-05A_1M 3]

source_name: Bone Marrow_0.9% NaCl followed by 5% Dextrose

value: 6 hour


title: HPSC(1)


title: Bone Marrow_Vehicle 2_Vehicle 1 [1344-01D_2M 14]

value: intravenous (IV)


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-05B_1M 4]


title: Bone Marrow_Vehicle 1_Vehicle 2 [1346-01B_1M 6]


title: Slide 347301

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F532 Median

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown AM17 medium and harvested at OD600 of 0.15.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: ulaR2 mutant

source_name: F635 Median

value: Wild type


title: Slide 347269

description: Sample 1

growth_protocol: Cells were grown AM17 and M17 medium, and harvested at OD600 of 0.15.

tag: growth medium


title: Bone Marrow_Vehicle 1_Vehicle 2 [1346-01A_1M 5]

value: Sprague-Dawley

tag: Sex


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-07A_1M 9]

value: Male

tag: tissue


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-07B_1M 10]

tag: time


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-03A_1M 7]

tag: route


title: Slide 347303

description: Sample 2


title: Slide 347274

description: Sample 2


title: Bone Marrow_Vehicle 1_Vehicle 2 [1346-02H_1M 11]

tag: age

value: 24 hour


title: Bone Marrow_Vehicle 1_Vehicle 2 [1346-03A_1M 12]


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-01B_1M 2]


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-01A_1M 1]


title: Bone Marrow_Vehicle 1_Vehicle 2 [1344-03B_1M 8]


title: hiPSC GM4603cl27-derived Retinal Pigmented Epithelial (RPE) cells at passage 2, biological rep2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: GM04603 (Coriell)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Human iPS cells were expanded on-to mitomycin-C inactivated Zenith Mouse Embryonic Fibroblast (MEF) layer feeders (IVFonline.com). Cells were cultured using DMEM/F12 (1:1) Glutamax medium supplemented with 20% KnockOutTM SR, 1X MEM non-essential amino acids, 0.05 mM 2-mercaptoethanol (all from Invitrogen) and 10 ng.ml-1 FGF2 (PeproTech, Rocky Hill, NJ, USA). We differentiated Retinal Pigmented Epithelial (RPE) cells from iPSCs using the procedure schematically summarized. When hiPSCs on feeders reached confluence, medium was removed and cells were cultured with DMEM + GlutamaxII (High Glucose) containing 20% KnockOutTM SR (both from Invitrogen) without FGF2. Pigmented areas begun to appear within 2 weeks and allowed to expand until they reached a few millimetres (one more week). They were mechanically cut under a stereomicroscope using a needle and then placed on 1:30 Matrigel (BD Matrigel™ Basement Membrane Matrix, BD Biosciences, France) coated plate. When the confluence reached 100%, cells were dissociated in 0.05% Trypsin-EDTA and seeded on Matrigel at a density of 100,000 cells/cm2. They were then cultured in DMEM + GlutamaxII (High Glucose) containing 4% KnockOutTM SR (both from Invitrogen).

extract_protocol: Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.

treatment_protocol: Not applicable

value: wild-type

tag: gender

value: male

value: GM04603 (Coriell)

value: hiPSC-derived Retinal Pigmented Epithelial (RPE) cells

tag: passage


title: hiPSC GM4603cl27-derived Retinal Pigmented Epithelial (RPE) cells at passage 1, biological rep1

tag: cell line


title: hiPSC GM4603cl28-derived Retinal Pigmented Epithelial (RPE) cells at passage 2, biological rep1


title: hiPSC GM05300cl5-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep3

source_name: GM05300 (Coriell)

value: Leber Congenital Amaurosis

value: GM05300 (Coriell)


title: hiPSC GM05300cl5-derived Retinal Pigmented Epithelial (RPE) cells at passage 1, biological rep2


title: hiPSC GM05300cl5-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep1


title: hiPSC GM4603cl28-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep2


title: O3D

city: Yufu-city

first: Keiko

last: Matsuura

address: hasama-cho, Idaigaoka

institute: Oita University

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy3 (tumor) to Cy5 (Control) was calculated. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 7.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0., maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.163 to detect regions showing a change in the averaged copy number equal to or more than 1.12-fold (log2(1.12)=0.163).

source_name: chromophobe RCC primary tumor

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

value: chromophobe RCC primary tumor

tag: site

value: kidney

tag: phenotype

value: neuroendocrine differentiation

source_name: non-neoplastic kidney tissue from the same patient


title: K47D

value: non-neoplastic kidney tissue from the same patient


title: K1T

value: chromophobe


title: O3T


title: hiPSC GM05300cl4-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep1

tag: genotype


title: hiPSC GM05300cl4-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep2


title: hiPSC GM05300cl4-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep3


title: hiPSC GM03852cl1-derived Retinal Pigmented Epithelial (RPE) cells at passage 1, biological rep1

source_name: GM03852 (Coriell)

value: female

value: GM03852 (Coriell)


title: hiPSC FSc03-derived Neural Stem Cells at passage 7, biological rep3

source_name: CRL2097 (ATCC)

growth_protocol: Human iPS cells were expanded on-to mitomycin-C inactivated Zenith Mouse Embryonic Fibroblast (MEF) layer feeders (IVFonline.com). Cells were cultured using DMEM/F12 (1:1) Glutamax medium supplemented with 20% KnockOutTM SR, 1X MEM non-essential amino acids, 0.05 mM 2-mercaptoethanol (all from Invitrogen) and 10 ng.ml-1 FGF2 (PeproTech, Rocky Hill, NJ, USA). We differentiated neural stem cells from iPSCs using a multistage differentiation protocol. The procedure is schematically summarized. To induce Neuro EPithelial cells (NEP) formation, clumps were seeded on 0.0015% poly-L-ornithine (PO, Sigma Aldrich)/2 µg.ml-1 laminin (Invitrogen) coated culture dishes and cultured using DMEM/F12 (1:1) Glutamax medium containing Neurobasal medium (1:1) supplemented with 2% B27 supplement without vitamin A, 1% N2 supplement, 0.05 mM 2-mercaptoethanol (all from Invitrogen), 5 ng.ml-1 FGF2, 300 ng.ml 1 human Noggin (both from PeproTech) and 20 µM SB431542 (Tocris Bioscience, Bristol, United Kingdom) until appearance of NEP (8 days of differentiation). To obtain NSC, NEP were cultured using DMEM/F12 (1:1) Glutamax medium containing Neurobasal medium (1:1) supplemented with 2% B27 supplement without vitamin A, 1% N2 supplement, 0.05 mM 2-mercaptoethanol (all from Invitrogen) supplemented by 10 ng.ml-1 human EGF (Epidermal Growth Factor), 20 ng.ml-1 human BDNF (Brain-Derived Neurotrophic Factor) (both from R&D Systems, Minneapolis, MN, USA) and 10 ng.ml-1 FGF2.

value: CRL2097 (ATCC)

value: hiPS cells-derived Neural Stem Cells


title: hiPSC GM03852cl1-derived Retinal Pigmented Epithelial (RPE) cells at passage 2, biological rep2


title: hiPSC GM03852cl1-derived Retinal Pigmented Epithelial (RPE) cells at passage 3, biological rep3


title: hiPSC FSc03-derived Neural Stem Cells at passage 7, biological rep2


title: hiPSC FSc03-derived Neural Stem Cells at passage 7, biological rep1


title: hiPSC 4603cl28-derived Neural Stem Cells at passage 7, biological rep2


title: hiPSC 4603cl28-derived Neural Stem Cells at passage 7, biological rep3


title: hiPSC 4603cl28-derived Neural Stem Cells at passage 7, biological rep1


title: hiPSC 4603cl27-derived Neural Stem Cells at passage 7, biological rep3


title: hiPSC 4603cl27-derived Neural Stem Cells at passage 7, biological rep2


title: hiPSC 4603cl27-derived Neural Stem Cells at passage 7, biological rep1


title: hiPSC 46034Acl1-derived Neural Stem Cells at passage 7, biological rep3


title: hiPSC GM05300cl5-derived Neural Stem Cells at passage 7, biological rep3


title: hiPSC 46034Acl1-derived Neural Stem Cells at passage 7, biological rep2


title: hiPSC 46034Acl1-derived Neural Stem Cells at passage 7, biological rep1


title: hiPSC GM05300cl5-derived Neural Stem Cells at passage 7, biological rep2


title: Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_28_TRANS

city: Dublin 4

first: Aine

middle: C

last: Balfe

address: Belfield

department: School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

hyb_protocol: Affymetrix GeneChip WT terminal labelling and hybridisation kit- A hybridisation cocktail containing 1.7µl Control Oligonucleotide B2 (3nM), 5µl 20x Eukaroytic Hybridisation Controls, 7µl 2x Hybridisation Mix, 73µl Nuclease Free water was prepared according to manufactures instructions for 169 Format Array type. The hybridisation cocktail was incubated at 99°C for 5 minutes, cooled to 45°C for five minutes and added to 27µl of the fragmented single-strand cDNA.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Normalisation of global data was performed through RMA pre-processing, within the Bioconductor Oligo package

source_name: Human Colonic Mucin from patient with active ulcerative colitis

label_protocol: Affymetrix GeneChip WT terminal labelling and hybridisation kit- A master mix containing  5X TdTBuffer, TdT and DNA Labeling reagent was prepared and 15 μL was alliquoted into the 0.2 mL strip tubes containing the 45 μL of Fragmented Single-Stranded cDNA

extract_protocol: Qiagen Rneasy Fibrous Tissue Kit

tag: tissue source

value: Colon

tag: disease state

value: active ulcerative colitis

tag: colonic location

value: Transverse


title: hiPSC GM05300cl5-derived Neural Stem Cells at passage 7, biological rep1

value: male

tag: cell type


title: Human Colonic Mucin from patient with active ulcerative colitis AC_28_RECT

value: Rectum


title: hiPSC GM05300cl4-derived Neural Stem Cells at passage 7, biological rep3


title: hiPSC GM05300cl4-derived Neural Stem Cells at passage 7, biological rep2


title: Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_28_CAEC

value: Caecum


title: Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_26_TRANS


title: neutrophils isolated from control 15

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
Following multiple quality control measures, probe intensity values were normalized and used to determine the average methylation level on each methylation site in each sample (beta value or β). Probes that include a genetic variant within the first 10bp region of the 3’ end of the probe, and probes that had a detection P value (detection above background) of ≥0.05 were excluded from the analysis. Differentially methylated sites between groups were determined, and defined as methylation sites with an absolute difference in beta value (delta beta or Δβ) of at least 0.1 and that remained significant (P<0.01) after correction for multiple testing using a Benjamini and Hochberg false discovery rate of 0.05
Unmethylated and methylated signal intensities in Amr_raw_methylation_data_SLE_neutrophils.txt

label: Cy3 and Cy5

source_name: neutrophils

label_protocol: DNA was extracted from each sample using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), then bisulfite-converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) for DNA methylation studies.

growth_protocol: N/A (patient-derived samples)

extract_protocol: Fresh peripheral blood samples (25 ml) were collected and density gradient centrifugation (Ficoll) was used to collect PBMCs. LDGs were then isolated from PBMCs using indirect labeling and magnetic bead separation with the following antibodies: anti-CD3, anti-CD7, anti-CD19, anti-CD79b, anti-CD56, anti-MHCII, anti-CD86 and anti-CD235a. LDG purity was confirmed by flow cytometry using forward and side scatter profiles and was over 95% in all samples. Neutrophils were extracted from the granulocyte layer after Ficoll density gradient centrifugation, following previously described protocols

treatment_protocol: Bisulfite DNA sequencing on selected differentially methylated CG sites was performed to validate the results obtained from the Infinium HumanMethylation450 BeadChip arrays. One differentially methylated CG site in MX1 was selected for validation. Primers were designed using Sequenom's EpiDesigner online tool to include this CG site and an additional 20 CG sites in its vicinity. Primer quality was verified using Premier Biosoft’s Netprimer online tool (Sequenom, San Diego, CA). The following primers were used: forward 5’-TTTAGTGGATGTTATGTTTGGGGT-3’, reverse 5’-CACTACTACCTACCAAAACCCCTAAA-3’. PCR was performed on a Bio-Rad T100 (Bio-Rad, Hercules, CA) using ZymoTaq one-step master mix (Zymo, Orange, CA). The cycling conditions were as follows: 95°C for 10 min followed by 40 cycles of 95°C for 30 seconds, then 58.3°C for 40 seconds, then 72°C for 1 min, followed by 72°C for 7 min. Each PCR product was confirmed with a small aliquot by 2% agarose gel electrophoresis. The remainder of the PCR product was then purified and sequenced using an Applied Biosystems 3730 XL sequencer. Sequencing trace files were then used to calculate the percentage of cytosine methylation on each CG site using ESME software package (Epigenomics AG, Berlin).

value: control

value: normal neutrophils


title: hiPSC GM05300cl4-derived Neural Stem Cells at passage 7, biological rep1

value: Leber Congenital Amaurosis

value: GM05300 (Coriell)


title: Human Colonic Mucin from patient with active ulcerative colitis AC_28_LEFT

value: Left


title: neutrophils isolated from patient 15

value: Lupus patient

value: lupus neutrophils


title: neutrophils isolated from patient 12

value: female


title: neutrophils isolated from control 10


title: neutrophils isolated from patient 13


title: hiPSC GM03852cl1-derived Neural Stem Cells at passage 7, biological rep3

value: GM03852 (Coriell)


title: neutrophils isolated from control 14


title: neutrophils isolated from control 13


title: hiPSC GM03852cl1-derived Neural Stem Cells at passage 7, biological rep2


title: Human Colonic Mucin from patient with active ulcerative colitis AC_26_RECT


title: neutrophils isolated from patient 9


title: neutrophils isolated from patient 10


title: neutrophils isolated from patient 14


title: neutrophils isolated from control 12


title: neutrophils isolated from control 9


title: neutrophils isolated from control 11


title: Human Colonic Mucin from patient with active ulcerative colitis AC_26_LEFT


title: neutrophils isolated from control 6


title: neutrophils isolated from patient 11


title: neutrophils isolated from patient 7


title: neutrophils isolated from control 7


title: Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_21_TRANS


title: hiPSC GM03852cl1-derived Neural Stem Cells at passage 7, biological rep1


title: Human Colonic Mucin from patient with active ulcerative colitis AC_21_RECT


title: neutrophils isolated from control 8


title: Human Colonic Mucin from patient with active ulcerative colitis AC_21_LEFT


title: Human Colonic Mucin from patient with active ulcerative colitis AC_20_RECT


title: Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_21_CAEC


title: Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_20_TRANS


title: low-density granulocytes isolated from patient 6

source_name: low-density granulocytes

value: lupus low-density granulocytes


title: Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_26_CAEC


title: low-density granulocytes isolated from patient 5


title: Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_20_CAEC


title: Human Colonic Mucin from patient with active ulcerative colitis AC_20_LEFT


title: Human Colonic Mucin from Healthy controls HC31_RECT

value: Healthy controls


title: Human Colonic Mucin from the caecum of Healthy controls HC31_CAEC

source_name: Human Colonic Mucin from Healthy controls

value: Colon


title: Human Colonic Mucin from the transverse colon of Healthy controls HC31_TRANS


title: Healthy patient, Time 0 (initial), number RV30

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description:
Sample name: Healthy-RV30-I
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. control

hyb_protocol: Following fragmentation, 12 μg RNA were hybridized for 16 hr at 45ºC 60 rpm on GeneChip PrimeView Human Gene Expression Array (Affymetrix 901837) ( Hybridization Oven 645). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix Protocol FS450_0002).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with autoloader.

data_processing:
Data were analyzed with Robust MultiChip Average (RMA) using CEL files obtained from GeneChip Command Console (AGCC) and Affymetrix Expression Console Software (EC) (Affymetrix).
Stadistics and pathway analysis were generated with Partek Genomics Suite 6.6 and Partek Pathway.

source_name: Somatic cells isolated from breast-milk from healthy volunteer. control

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 0.1 μg total RNA GeneChip 3 ÍVT Express Kit (Affymetrix PN 702646 Rev 8, 2010)

growth_protocol: Female patients' breast milk was processed within 4 h after extraction and used to isolate somatic cells by centrifugation.

extract_protocol: Total RNA was isolated using the AllPrep® DNA/RNA/Protein Mini kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water and the quality and quantity were measured in a ND-1000 spectrophotometer (NanoDrop®). Samples were aliquoted and stored at –80ºC until analysis. Purity was reevaluated measuring the RNA Integrity Number (RIN) algorithm and only those with a RIN value > 6 were further selected for microarray analyses.

treatment_protocol: RNA was prepared from breast-milk isolated somatic cells obtained at day 0 (initial) and day 21 (final) following the consumption of a strain of a probiotic from the following groups:i) Mastitis, n=14 arrays (7 patients with mastitis); ii) Healthy, n=6 arrays (3 healthy volunteers)

tag: individual

value: healthy volunteer

tag: treatment

value: Somatic cells from breast milk


title: low-density granulocytes isolated from patient 8

tag: Sex


title: Human Colonic Mucin from Healthy controls HC31_LEFT


title: Healthy patient + probiotic, Time 21 days (final), number LC26

description:
Sample name: Healthy-LC26-F
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. Probiotic group. Time days (final expression levels).

source_name: Somatic cells isolated from breast-milk from healthy volunteer. Probiotic treatment. Time 21 days (final expression levels).

value: probiotic


title: low-density granulocytes isolated from patient 7


title: Healthy patient, Time 0 (initial), number LC26

description:
Sample name: Healthy-LC26-I
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. control


title: Human Colonic Mucin from the transverse colon of Healthy controls HC30_TRANS

value: Transverse


title: Healthy patient, Time 0 (initial), number EG29

description:
Sample name: Healthy-EG29-I
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. control


title: neutrophils isolated from patient 5


title: Human Colonic Mucin from Healthy controls HC30_RECT

value: Rectum


title: Human Colonic Mucin from the caecum of Healthy controls HC30_CAEC

value: Caecum


title: Healthy patient + probiotic, Time 21 days (final), number EG29

description:
Sample name: Healthy-EG29-F
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. Probiotic group. Time 21 days (final expression levels).


title: Human Colonic Mucin from Healthy controls HC30_LEFT


title: Healthy patient + probiotic, Time 21 days (final), number RV30

description:
Sample name: Healthy-RV30-F
Gene expression data from breast-milk somatic cells isolated from female healthy volunteer. Probiotic group. Time days (final expression levels).


title: Patient with Mastitis, Time 0 (initial), number TP32

description:
Sample name: Mastitis-TP32-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control

source_name: Somatic cells isolated from breast-milk from patient with mastitis. control

value: mastitis patient

value: control


title: Patient with Mastitis + probiotic, Time 21 days (final), number MR06

description:
Sample name: Mastitis-MR06-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).

source_name: Somatic cells isolated from breast-milk from patient with mastitis. Probiotic treatment. Time 21 days (final expression levels).