title: REC1-Rituximab-4h-rep2

value: Rituximab


title: REC1-LT20-4h-rep3

status: Public on Jul 23 2013

type: RNA

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

country: Germany

institute: Roche Pharma

description: Gene expression data from human cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The MAS5.0 normalized data for each unicate provided in the Sample table.
The data were further analyzed with In-house tools. We generated data sets consisting of "mean values" for the three replicates and "change factors" to the appropriate control experiment supplied in the GSE23394_Matrix_triplicates.xls file. Our in-house tool is called Race-A (Roche Affymetrix Chip Experiment - Analysis). The method is MAS5.0 and the scaling factor was adjusted for a scaling mean of 158. The CHGF=change factors are relative ratios (-1 for up regulation and +1 for down regulation to avoid the gap between -1 and +1), i.e. chgf=1 means double signal, chgf=-1 means half signal.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human cell line,  4h

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard procedures of cell culture according to the guidelines of suppliers

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

treatment_protocol: cells were treated for 4h

tag: cell line

tag: treatment

tag: dose

tag: unit

value: µg/ml


title: REC1-Rituximab-4h-rep3


title: REC1-Isotype-4h-rep1


title: REC1-Isotype-4h-rep2


title: Z138-anti-IgMFab2-4h-rep2


title: REC1-Control-4h-rep1

value: Control


title: REC1-LT20-4h-rep2


title: Z138-anti-IgMFab2-4h-rep1


title: REC1-anti-IgM-4h-rep1

value: anti-IgM


title: REC1-anti-IgM-4h-rep2


title: REC1-anti-IgM-4h-rep3


title: REC1-Control-4h-rep3


title: Z138-anti-IgMFab2-4h-rep3


title: REC1-Isotype-4h-rep3


title: REC1-Rituximab-4h-rep1


title: REC1-Control-4h-rep2


title: Z138-anti-IgM-4h-rep2


title: Z138-anti-IgM-4h-rep1


title: Z138-LT20-4h-rep1


title: Z138-anti-IgM-4h-rep3


title: Z138-LT20-4h-rep2


title: Z138-LT20-4h-rep3


title: Z138-Rituximab-4h-rep1


title: Z138-Control-4h-rep1


title: Z138-Rituximab-4h-rep2


title: OCILY18-anti-IgMFab2-4h-rep3


title: Z138-Isotype-4h-rep2


title: Z138-Isotype-4h-rep1


title: Z138-Control-4h-rep2


title: OCILY18-anti-IgM-4h-rep3


title: OCILY18-anti-IgMFab2-4h-rep1


title: OCILY18-LT20-4h-rep3


title: Z138-Rituximab-4h-rep3


title: OCILY18-LT20-4h-rep2


title: OCILY18-anti-IgM-4h-rep1


title: OCILY18-Rituximab-4h-rep2


title: Z138-Control-4h-rep3


title: OCILY18-anti-IgM-4h-rep2


title: Z138-Isotype-4h-rep3


title: OCILY18-Rituximab-4h-rep3


title: OCILY18-Isotype-4h-rep2


title: OCILY18-Isotype-4h-rep3


title: OCILY18-LT20-4h-rep1


title: OCILY18-Isotype-4h-rep1


title: OCILY18-anti-IgMFab2-4h-rep2


title: SUDHL4-anti-IgMFab2-4h-rep2


title: SUDHL4-anti-IgMFab2-4h-rep3


title: OCILY18-Rituximab-4h-rep1


title: SUDHL4-anti-IgM-4h-rep3


title: OCILY18-Control-4h-rep3


title: SUDHL4-LT20-4h-rep3


title: SUDHL4-LT20-4h-rep2


title: SUDHL4-anti-IgM-4h-rep1


title: OCILY18-Control-4h-rep1


title: SUDHL4-anti-IgM-4h-rep2


title: SUDHL4-anti-IgMFab2-4h-rep1


title: SUDHL4-LT20-4h-rep1


title: OCILY18-Control-4h-rep2


title: SUDHL4-Rituximab-4h-rep3


title: SUDHL4-Control-4h-rep2


title: SUDHL4-Rituximab-4h-rep1


title: SUDHL4-Isotype-4h-rep1


title: SUDHL4-Control-4h-rep3


title: primary CRC 6001352

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

description: A reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs.

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing:
Raw Green (ch1, sample) and Red (ch2, reference) expression levels were quantified using Agilent Feature Extraction software (version 9.5) based on MedianSignal output.  Expression levels were normalized by lowess normalization using standard Feature expression software settings (see manual for details: http://www.chem.agilent.com/Library/usermanuals/Public/ReferenceGuide_050416.pdf)
Raw Green (ch1, sample) and Red (ch2, reference) foreground and background data, and normalized 10log ratios (ch1/ch2).

source_name: primary CRC 6001352

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]  Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

extract_protocol: RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Qiazol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.

tag: gender

value: female

tag: age at diagnosis (y)

tag: tissue

value: primary CRC from rectum

tag: tumor type

value: primary CRC

tag: Stage

tag: location

value: rectum

tag: braf

value: wildtype / other

tag: kras

value: activating mutation

tag: microsattelite

value: stable

source_name: CRP

value: colon tumor

tag: sample type


title: primary CRC 6001386

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

source_name: primary CRC 6001386

value: male

value: primary CRC from colon

value: left colon

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: SUDHL4-Isotype-4h-rep3


title: SUDHL4-Control-4h-rep1


title: primary CRC 6001353

source_name: primary CRC 6001353


title: SUDHL4-Rituximab-4h-rep2


title: primary CRC 6001351

source_name: primary CRC 6001351


title: primary CRC 6001350

source_name: primary CRC 6001350


title: primary CRC 6001355

source_name: primary CRC 6001355


title: primary CRC 6001347

source_name: primary CRC 6001347


title: primary CRC 6001356

source_name: primary CRC 6001356


title: primary CRC 6001348

source_name: primary CRC 6001348


title: primary CRC 6001339

source_name: primary CRC 6001339

value: right colon


title: primary CRC 6001349

source_name: primary CRC 6001349


title: SUDHL4-Isotype-4h-rep2


title: primary CRC 6001340

source_name: primary CRC 6001340


title: primary CRC 6001374

source_name: primary CRC 6001374


title: primary CRC 7000029

source_name: primary CRC 7000029


title: primary CRC 6001344

source_name: primary CRC 6001344


title: primary CRC 6001341

source_name: primary CRC 6001341


title: primary CRC 6001385

source_name: primary CRC 6001385


title: primary CRC 6001337

source_name: primary CRC 6001337

value: instable

source_name: CRP


title: primary CRC 6001338

source_name: primary CRC 6001338


title: primary CRC 6001329

source_name: primary CRC 6001329


title: primary CRC 6001330

source_name: primary CRC 6001330


title: primary CRC 6001332

source_name: primary CRC 6001332


title: primary CRC 6001331

source_name: primary CRC 6001331


title: primary CRC 6001315

source_name: primary CRC 6001315


title: primary CRC 6001324

source_name: primary CRC 6001324


title: primary CRC 6001336

source_name: primary CRC 6001336


title: primary CRC 6001326

source_name: primary CRC 6001326


title: primary CRC 6001325

source_name: primary CRC 6001325


title: primary CRC 6001333

source_name: primary CRC 6001333


title: primary CRC 6001381

source_name: primary CRC 6001381


title: primary CRC 6001328

source_name: primary CRC 6001328


title: primary CRC 6001327

source_name: primary CRC 6001327


title: primary CRC 6001314

source_name: primary CRC 6001314


title: primary CRC 6001312

source_name: primary CRC 6001312


title: primary CRC 6001313

source_name: primary CRC 6001313

source_name: CRP


title: primary CRC 6001311

source_name: primary CRC 6001311


title: primary CRC 6001307

source_name: primary CRC 6001307


title: primary CRC 6001305

source_name: primary CRC 6001305


title: primary CRC 6001309

source_name: primary CRC 6001309


title: primary CRC 6001301

source_name: primary CRC 6001301


title: primary CRC 6001303

source_name: primary CRC 6001303


title: primary CRC 6001310

source_name: primary CRC 6001310


title: ST-HSC 2 [miRNA]

status: Public on Jul 24 2013

city: Baltimore

first: Curt

middle: I

last: Civin

state: Maryland

address: BRB 14-021, 655 W Baltimore St

department: Center for Stem Cell Biology & Regenerative Medicine

country: USA

institute: University of Maryland School of Medicine

description:
miR expression in ST-HSCs
Sample name: 251911910564_2_1

hyb_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

data_processing: normalization was performed via the quantile method in the limma bioconductor package in R

organism: Mus musculus

source_name: ST-HSC

extract_protocol: RNA was isolated from Trizol using a miRNeasy Micro kit according to manufacturer’s instructions (Qiagen)

value: Bone marrow

tag: cell type

value: ST-HSC


title: primary CRC 6001302

source_name: primary CRC 6001302


title: primary CRC 6001308

source_name: primary CRC 6001308


title: primary CRC 6001306

source_name: primary CRC 6001306


title: primary CRC 6001296

source_name: primary CRC 6001296


title: primary CRC 6001294

source_name: primary CRC 6001294


title: primary CRC 6001295

source_name: primary CRC 6001295


title: primary CRC 6001304

source_name: primary CRC 6001304


title: primary CRC 6001297

source_name: primary CRC 6001297


title: primary CRC 6001375

source_name: primary CRC 6001375

source_name: CRP


title: primary CRC 6001300

source_name: primary CRC 6001300


title: primary CRC 6001372

source_name: primary CRC 6001372


title: primary CRC 6001377

source_name: primary CRC 6001377


title: primary CRC 6001288

source_name: primary CRC 6001288


title: primary CRC 6001292

source_name: primary CRC 6001292


title: primary CRC 6001287

source_name: primary CRC 6001287


title: primary CRC 6001299

source_name: primary CRC 6001299


title: primary CRC 6001286

source_name: primary CRC 6001286


title: primary CRC 6001371

source_name: primary CRC 6001371


title: primary CRC 6001283

source_name: primary CRC 6001283


title: primary CRC 6001373

source_name: primary CRC 6001373


title: primary CRC 6001293

source_name: primary CRC 6001293


title: primary CRC 6001365

source_name: primary CRC 6001365


title: primary CRC 6001248

source_name: primary CRC 6001248


title: primary CRC 6001289

source_name: primary CRC 6001289


title: primary CRC 6001290

source_name: primary CRC 6001290


title: primary CRC 6001284

source_name: primary CRC 6001284

source_name: CRP


title: primary CRC 6001279

source_name: primary CRC 6001279


title: primary CRC 6001369

source_name: primary CRC 6001369


title: primary CRC 6001366

source_name: primary CRC 6001366


title: primary CRC 6001361

source_name: primary CRC 6001361


title: primary CRC 6001364

source_name: primary CRC 6001364


title: primary CRC 6001285

source_name: primary CRC 6001285


title: primary CRC 6001241

source_name: primary CRC 6001241


title: primary CRC 6001362

source_name: primary CRC 6001362


title: primary CRC 6001246

source_name: primary CRC 6001246


title: primary CRC 6001242

source_name: primary CRC 6001242


title: primary CRC 6001282

source_name: primary CRC 6001282


title: primary CRC 6001245

source_name: primary CRC 6001245


title: primary CRC 6001281

source_name: primary CRC 6001281


title: primary CRC 6001272

source_name: primary CRC 6001272


title: primary CRC 6001257

source_name: primary CRC 6001257


title: primary CRC 6001278

source_name: primary CRC 6001278


title: primary CRC 6001230

source_name: primary CRC 6001230

source_name: CRP


title: primary CRC 6001226

source_name: primary CRC 6001226


title: primary CRC 6001265

source_name: primary CRC 6001265


title: primary CRC 6001267

source_name: primary CRC 6001267


title: primary CRC 6001222

source_name: primary CRC 6001222


title: primary CRC 6001271

source_name: primary CRC 6001271


title: primary CRC 6001224

source_name: primary CRC 6001224


title: primary CRC 6001227

source_name: primary CRC 6001227


title: primary CRC 6001237

source_name: primary CRC 6001237


title: primary CRC 6001238

source_name: primary CRC 6001238


title: primary CRC 6001255

source_name: primary CRC 6001255


title: primary CRC 6001256

source_name: primary CRC 6001256


title: primary CRC 6001397

source_name: primary CRC 6001397


title: primary CRC 6001225

source_name: primary CRC 6001225


title: primary CRC 6001223

source_name: primary CRC 6001223


title: primary CRC 6001264

source_name: primary CRC 6001264


title: primary CRC 6001240

source_name: primary CRC 6001240


title: primary CRC 6001399

source_name: primary CRC 6001399

source_name: CRP


title: primary CRC 6001254

source_name: primary CRC 6001254


title: primary CRC 6001263

source_name: primary CRC 6001263


title: primary CRC 6001220

source_name: primary CRC 6001220


title: primary CRC 6001236

source_name: primary CRC 6001236


title: primary CRC 6001277

source_name: primary CRC 6001277


title: primary CRC 6001270

source_name: primary CRC 6001270


title: primary CRC 6001261

source_name: primary CRC 6001261


title: UESCs_42h_replicate3

city: Fukuoka

first: MASA-AKI

last: HATTORI

address: 6-10-1, Hakozaki, Higashi-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyushu University

description: Gene expression after dexamethasone synchronization

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Rat Genome Microarray Kit v3 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

organism: Rattus norvegicus

source_name: UESCs, 42h, synchronization

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The uterus endometrial stromal cells were isolated from Per2-dLuc transgenic rats on day 4.50 of gestation. The harvested cells were seeded onto 35 mm collagen-coated dishes at the density of 2×105 cells/dish with 2 mL of culture medium (phenol red-free DMEM/F12 supplemented with 10% charcoal-treated FBS and 1× PS). Then, cells were cultured in serum-free medium supplemented with 1× antibiotic–antimycotic, 1× Insulin-Transferrin-Selenium, 0.1% bovine serum albumin, and 100 nM progesterone for additional 2 days prior to other treatments. The cultured UESCs were synchronized with 100 nM dexamethasone for 2 h in the serum-free medium. RNA samples isolated from cultured cells at 30, 36, 42, and 48 h after dexamethasone synchronization.

value: uterus endometrial stromal cells


title: UESCs_48h_replicate1

source_name: UESCs, 48h, synchronization


title: UESCs_36h_replicate3

source_name: UESCs, 36h, synchronization


title: UESCs_42h_replicate1


title: UESCs_48h_replicate2


title: primary CRC 6001274

source_name: primary CRC 6001274


title: UESCs_48h_replicate3


title: primary CRC 6001253

source_name: primary CRC 6001253


title: primary CRC 6001234

source_name: primary CRC 6001234

value: female


title: primary CRC 6001259

source_name: primary CRC 6001259


title: primary CRC 6001273

source_name: primary CRC 6001273


title: primary CRC 6001233

source_name: primary CRC 6001233


title: UESCs_36h_replicate2


title: primary CRC 6001252

source_name: primary CRC 6001252

source_name: CRP


title: UESCs_42h_replicate2


title: primary CRC 6001316

source_name: primary CRC 6001316


title: UESCs_36h_replicate1


title: primary CRC 6001232

source_name: primary CRC 6001232


title: primary CRC 6001235

source_name: primary CRC 6001235


title: primary CRC 6001219

source_name: primary CRC 6001219


title: UESCs_30h_replicate2

source_name: UESCs, 30h, synchronization


title: primary CRC 6001321

source_name: primary CRC 6001321


title: UESCs_30h_replicate3


title: UESCs_30h_replicate1


title: primary CRC 6001250

source_name: primary CRC 6001250


title: primary CRC 6001269

source_name: primary CRC 6001269


title: primary CRC 7001411

source_name: primary CRC 7001411


title: primary CRC 7001409

source_name: primary CRC 7001409


title: Head 26, fished at 18:00, biological replicate 1 (H26-1)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: Gene expression of antarctit krill krill fished at 18:00 h (H26-1).

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provides spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as null. So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. 35% of null was used as threshold in the filtering process, obtaining a total of 16,396 available krill transcripts.

organism: Euphausia superba

source_name: Head of krill fished at 18:00 h

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: For each fishing, four animals were dissected individually, and total RNA was extracted from head (including brain and compound eyes), abdomen, and thoracopods as described in De Pittà et al. (2008, PMID: 1822620). All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

treatment_protocol: Antarctic krill (Euphausia  superba) were collected in the Ross Sea (longitude: 167°28'81 E – 179°54'68 W, latitude 68°40'54 S – 77°0181 S) in January 2004 during the XIX Italian Antarctic Expedition. Adult specimens were fished at different times throughout the 24 hours cycle (local times: 01:00, 06:00, 10:00, 15:00, and 18:00) and stored at -40°C in RNA stabilization solution (RNA-later, Life Technologies).

value: Head (including brain and compound eyes)

tag: time


title: primary CRC 6001231

source_name: primary CRC 6001231

value: primary CRC


title: primary CRC 7001410

source_name: primary CRC 7001410


title: Head 26, fished at 18:00, biological replicate 2 (H26-2)

description: Gene expression of antarctit krill krill fished at 18:00 h (H26-2).


title: primary CRC 6001251

source_name: primary CRC 6001251


title: primary CRC 6001249

source_name: primary CRC 6001249


title: Head 26, fished at 18:00, biological replicate 3 (H26-3)

description: Gene expression of antarctit krill krill fished at 18:00 h (H26-3).


title: Head 26, fished at 18:00, biological replicate 4 (H26-4)

description: Gene expression of antarctit krill krill fished at 18:00 h (H26-4).


title: MRC5-iPS-25 (Tic) at passage 37

type: genomic

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing: Genomic DNA extracted from breast tumors was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: iPS cells derived from MRC5 cells

label_protocol: Illumina's standard protocol

growth_protocol: All cultures were maintained at 37°C in a humidified atmosphere containing 95% air and 5% CO2. When the cultures reached subconfluence, the cells were harvested with Trypsin-EDTA Solution (cat# 23315, IBL CO., Ltd, Gunma, Japan), and re-plated at a density of 5 x 105 cells in a 100-mm dish. Medium changes were carried out twice a week thereafter.

extract_protocol: Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).

value: MRC-iPS 25 (Tic)

value: induced pluripotent stem cell


title: Head 31, fished at 15:00, biological replicate 3 (H31-3)

description: Gene expression of antarctit krill krill fished at 15:00 h (H31-3).

source_name: Head of krill fished at 15:00 h


title: primary CRC 6000961

source_name: primary CRC 6000961

value: primary CRC from rectum

value: rectum

source_name: CRP


title: Head 31, fished at 15:00, biological replicate 4 (H31-4)

description: Gene expression of antarctit krill krill fished at 15:00 h (H31-4).


title: primary CRC 7001407

source_name: primary CRC 7001407

value: wildtype / other

value: activating mutation

value: colon tumor


title: primary CRC 7001408

source_name: primary CRC 7001408

value: primary CRC from colon


title: Head 28, fished at 10:00, biological replicate 2 (H28-2)

description: Gene expression of antarctit krill krill fished at 10:00 h (H28-2).

source_name: Head of krill fished at 10:00 h


title: primary CRC 6000910

source_name: primary CRC 6000910

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: Head 28, fished at 10:00, biological replicate 3 (H28-3)

description: Gene expression of antarctit krill krill fished at 10:00 h (H28-3).


title: Head 31, fished at 15:00, biological replicate 1 (H31-1)

description: Gene expression of antarctit krill krill fished at 15:00 h (H31-1).


title: primary CRC 6001262

source_name: primary CRC 6001262

value: left colon


title: MRC5-iPS-25 (Tic) at passage 30

value: male


title: Head 28, fished at 10:00, biological replicate 1 (H28-1)

description: Gene expression of antarctit krill krill fished at 10:00 h (H28-1).


title: Head 28, fished at 10:00, biological replicate 4 (H28-4)

description: Gene expression of antarctit krill krill fished at 10:00 h (H28-4).


title: MRC5 cells

source_name: human fetal lung fibroblast cells


title: MRC5-iPS-25 (Tic) at passage 15


title: Head 30, fished at 06:00, biological replicate 1 (H30-1)

description: Gene expression of antarctit krill krill fished at 06:00 h (H30-1).

source_name: Head of krill fished at 06:00 h


title: Head 30, fished at 06:00, biological replicate 3 (H30-3)

description: Gene expression of antarctit krill krill fished at 06:00 h (H30-3).


title: Head 30, fished at 06:00, biological replicate 4 (H30-4)

description: Gene expression of antarctit krill krill fished at 06:00 h (H30-4).


title: primary CRC 6000889

description: A reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs.

source_name: primary CRC 6000889


title: Head 30, fished at 06:00, biological replicate 2 (H30-2)

description: Gene expression of antarctit krill krill fished at 06:00 h (H30-2).


title: Head 27, fished at 01:00, biological replicate 2 (H27-2)

description: Gene expression of antarctit krill krill fished at 01:00 h (H27-2).

source_name: Head of krill fished at 01:00 h


title: primary CRC 6000858

source_name: primary CRC 6000858

value: right colon


title: primary CRC 7000673

source_name: primary CRC 7000673


title: Head 27, fished at 01:00, biological replicate 4 (H27-4)

description: Gene expression of antarctit krill krill fished at 01:00 h (H27-4).


title: primary CRC 6000870

source_name: primary CRC 6000870


title: Head 27, fished at 01:00, biological replicate 3 (H27-3)

description: Gene expression of antarctit krill krill fished at 01:00 h (H27-3).


title: Head 27, fished at 01:00, biological replicate 1 (H27-1)

description: Gene expression of antarctit krill krill fished at 01:00 h (H27-1).


title: primary CRC 6000862

source_name: primary CRC 6000862


title: primary CRC 7000674

source_name: primary CRC 7000674


title: ME TT Hflu rep 9

city: Portland

first: Carol

middle: J.

last: MacArthur

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Otolaryngology

institute: Oregon Health and Science University

description:
Sample name: 031A_11H1_aff100_504DT
gene expression mouse middle ear infected

hyb_protocol: Following fragmentation and labeling, 3.4ug of cDNA were hybridized for 18 hr at 45C on the GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and AGCC version 3.2 software (Affymetrix).

data_processing: R/Bioconductor using AFFY package and RMA.  Moderated t-test (eBayes) in limma package was used and p-values were adjusted for the false discovery rate.

source_name: Mouse middle ear 6 hrs after TT inj with H flu

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation RNA Amplification System version 2 with Encore Biotin Module protocol from 50ng total RNA.  The standard input of 3.75ug was fragmented using following manufacturer’s protocol (Nugen Ovation v.2 w/ Encore Biotin Module)

growth_protocol: Housed in Animal Care Facility

extract_protocol: After isolation and removal of inner ear from middle ear in RNAlater, middle ears were stored in RNAlater at -20 degrees.  RNA was extracted using Qiagen RNAeasy Mini kit and homogenized with PowerGen 125 homogenizer.   Middle ear RNA samples  were then EtOH precipitated  for Affymetrix use.

treatment_protocol: trans-tympanically injected with H flu 10e9 for 6 hours

value: middle ear

tag: genotype

value: Balb/cJ

tag: age

value: 2.1 months


title: primary CRC 7000712

source_name: primary CRC 7000712

value: female


title: primary CRC 7000711

source_name: primary CRC 7000711

value: primary CRC

source_name: CRP


title: primary CRC 7000710

source_name: primary CRC 7000710


title: ME TT Hflu rep 7

description:
Sample name: 029A_11H1_aff111_504DT
gene expression mouse middle ear infected

tag: treatment

value: trans-tympanically injected with H flu 10e9 for 6 hours

value: 2.4 months


title: primary CRC 7000709

source_name: primary CRC 7000709


title: primary CRC 7000714

source_name: primary CRC 7000714


title: ME control rep 8

description:
Sample name: 027A_11H1_aff096_504DT
gene expression mouse middle ear control

source_name: Mouse middle ear control

value: control


title: primary CRC 6000884

source_name: primary CRC 6000884


title: MIN6 insulinoma cells_rep2

city: Sydney

first: Chris

last: O'Neill

address: Kolling Institute of Medical Research, Royal North Shore Hospital, Reserve Road, St Leonards

department: Kolling Institute of Medical Research

country: Australia

institute: University of Sydney

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with the Lumi Package in R statistical software

label: Biotin

source_name: MIN6 mouse insulinoma cell line

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

extract_protocol: RNA was extracted and DNase I treated with the Illustra RNAspin Mini RNA Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: passage


title: MIN6 insulinoma cells_rep1

description: Replicate 1


title: MIN6 insulinoma cells_rep3

description: Replicate 3


title: Head 31, fished at 15:00, biological replicate 2 (H31-2)

description: Gene expression of antarctit krill krill fished at 15:00 h (H31-2).

source_name: Head of krill fished at 15:00 h

value: Head (including brain and compound eyes)


title: D3 mouse ES cells_rep3

description: Replicate 3

source_name: D3 mouse embryonic stem cell line


title: primary CRC 6001258

source_name: primary CRC 6001258

tag: gender

value: wildtype / other


title: primary CRC 7000688

source_name: primary CRC 7000688

tag: age at diagnosis (y)


title: ME TT Hflu rep 8

description:
Sample name: 030A_11H1_aff108_504DT
gene expression mouse middle ear infected

tag: tissue


title: primary CRC 7000708

source_name: primary CRC 7000708

tag: tumor type

value: activating mutation


title: MousePCa NPK_1Month #3

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

scan_protocol: Standard Illumina scaning protocol

data_processing: Data were loaded and background corrected with BeadStudio. The resulting matrix was VST transformed and RSN normalized with lumiT and lumiN functions from lumi package in R.

source_name: anterior prostate_PCa NPK_1Month

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control of RNA samples was performed with Agilent Bioanalyser.

treatment_protocol: N/A (Not aplicable)

value: prostate tumor

tag: genotype/variation

value: NPK

tag: disease stage

value: early stage of tumorigenesis

tag: description (id)


title: D3 mouse ES cells_rep1

description: Replicate 1


title: MousePCa NPK_3Month #2

source_name: anterior prostate_PCa NPK_3Month

value: late stage of tumorigenesis


title: D3 mouse ES cells_rep2

description: Replicate 2


title: ME control rep 7

description:
Sample name: 023A_11H1_aff107_504DT
gene expression mouse middle ear control


title: ME TT Hflu rep 6

description:
Sample name: 028A_11H1_aff097_504DT
gene expression mouse middle ear infected

source_name: Mouse middle ear 6 hrs after TT inj with H flu


title: primary CRC 7000701

source_name: primary CRC 7000701

value: male

value: primary CRC from colon

tag: Stage

tag: location

tag: braf

tag: kras

value: colon tumor

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: MousePCa NPK_3Month #1


title: primary CRC 7000700

source_name: primary CRC 7000700

value: left colon

tag: sample type


title: primary CRC 7000686

source_name: primary CRC 7000686

value: female

source_name: CRP


title: ME TT Hflu rep 3

description:
Sample name: 024A_11H1_aff109_504DT
gene expression mouse middle ear infected

value: middle ear

tag: genotype

value: Balb/cJ


title: ME TT Hflu rep 4

description:
Sample name: 025A_11H1_aff106_504DT
gene expression mouse middle ear infected

value: trans-tympanically injected with H flu 10e9 for 6 hours

tag: age

value: 2.1 months


title: MousePCa NPK_1Month #2


title: MousePCa NPK_1Month #1


title: ME control rep 6

description:
Sample name: 022A_11H1_aff103_504DT
gene expression mouse middle ear control

tag: treatment

value: control


title: ME TT Hflu rep 5

description:
Sample name: 026A_11H1_aff110_504DT
gene expression mouse middle ear infected

value: 2.4 months


title: primary CRC 7000696

description: A reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs.

source_name: primary CRC 7000696

value: primary CRC

value: right colon

value: activating mutation

value: wildtype / other


title: ME control rep 5

description:
Sample name: 021A_11H1_aff095_504DT
gene expression mouse middle ear control


title: MousePCa NPK #6

source_name: anterior prostate_PCa NPK

value: prostate tumor

value: NPK


title: MousePCa NPK #5


title: MousePCa NPK #4


title: MousePCa NPK #8


title: primary CRC 7000692

source_name: primary CRC 7000692

value: primary CRC from colon


title: primary CRC 6001653

source_name: primary CRC 6001653

value: male

value: colon tumor


title: MousePCa NPK #2


title: ME control rep 4

description:
Sample name: 019A_11H1_aff102_504DT
gene expression mouse middle ear control

source_name: Mouse middle ear control


title: ME TT Hflu rep 2

description:
Sample name: 020A_11H1_aff101_504DT
gene expression mouse middle ear infected


title: Mouse PCa NP #8

source_name: anterior prostate_PCa NP

value: NP


title: MousePCa NPK #7


title: Mouse PCa NP #7


title: ME control rep 3

description:
Sample name: 018A_11H1_aff105_504DT
gene expression mouse middle ear control


title: MousePCa NPK #3


title: MousePCa NPK #1


title: Mouse PCa NP #4


title: Mouse PCa NP #6


title: Mouse PCa NP #5


title: primary CRC 7000699

source_name: primary CRC 7000699

value: left colon

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: primary CRC 7000718

source_name: primary CRC 7000718

value: female


title: ME TT Hflu rep 1

description:
Sample name: 017A_11H1_aff098_504DT
gene expression mouse middle ear infected

value: middle ear

value: trans-tympanically injected with H flu 10e9 for 6 hours

value: Balb/cJ


title: Mouse PCa NP #3


title: primary CRC 7000672

source_name: primary CRC 7000672


title: Mouse PCa NP #1


title: ME control rep 2

description:
Sample name: 016A_11H1_aff094_504DT
gene expression mouse middle ear control

value: control

value: 2.1 months


title: primary CRC 7000667

source_name: primary CRC 7000667

value: primary CRC

value: right colon


title: Mouse PCa NP #2


title: primary CRC 7000706

source_name: primary CRC 7000706

value: activating mutation


title: primary CRC 7000683

source_name: primary CRC 7000683

value: wildtype / other


title: ME control rep 1

description:
Sample name: 015A_11H1_aff104_504DT
gene expression mouse middle ear control


title: primary CRC 7000687

source_name: primary CRC 7000687


title: CD8+ T cells, placebo treatment

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent 8X60K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.

source_name: CD8+ T cells, placebo treatment

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Participants received the oral CLEAR regimen:  Levofloxacin 750 mg on day 1, then 500 mg daily, Ethambutol 1200 mg daily, Azithromycin 500 mg on day 1, then 250 mg daily, and Rifampin 300 mg daily, or a comparative placebo regimen, for a total of 8 weeks, with a 180 day follow-up.

tag: diagnosis

value: sarcoidosis

tag: cell type

value: CD8+ T cells


title: primary CRC 7000693

source_name: primary CRC 7000693

tag: gender

value: male

value: primary CRC from colon


title: IE control rep 6

description:
Sample name: 014A_11H1_aff093_504DT
gene expression mouse inner ear control

source_name: Mouse inner ear control

extract_protocol: After isolation and cleaning in RNAlater, inner ears were stored in RNAlater at -20 degrees.  RNA was extracted using Qiagen RNAeasy Mini kit and homogenized with PowerGen 125 homogenizer.   Four inner ear RNA samples were pooled and EtOH precipitated to make one sample for Affymetrix.

value: inner ear

tag: strain

value: 2.6 months


title: rsl_female_B

city: Ann Arbor

first: Christopher

middle: J

last: Krebs

state: MI

address: 1241 E. Catherine St

department: Human Genetics

institute: University of Michigan Medical School

description: rsl female, biological rep2

hyb_protocol: Following fragmentation, 400 ng of cRNA was hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 PM Array Strip. Cassettes were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Strips were scanned using the Affymetrix Scanner 3000 7G operated with the AGCC software.

data_processing: The data were analyzed with RMA and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: rsl female mouse liver RNA

label_protocol: Labeling, hybridization, scanning and data processing were performed by the University of Michigan Comprehensive Cancer Center Microarray Core facility (http://www.umich.edu/~caparray). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (GeneChip 3' IVT Express Kit, 2008, Affymetrix).

growth_protocol: Mice were fed standard laboratory chow (Purina # 5001)

extract_protocol: Total RNA was isolated using guanidinium isothiocyanate and organic extraction according to Current Protocols in Molecular Biology, Vol. 1, Supplement 36.

value: B10.D2.PL (rsl/rsl)

tag: Sex

tag: tissue

value: abdominal white adipose (WAT)


title: CD8+ T cells, baseline

source_name: CD8+ T cells, baseline


title: rsl_male_B

description: rsl male, biological rep2

source_name: rsl male mouse liver RNA


title: IE TT Hflu 6 hrs rep 8

description:
Sample name: 013A_11H1_aff085_504DT
gene expression mouse inner ear infected

source_name: Mouse inner ear 6 hrs after TT inj with H flu

value: 3.1 months


title: primary CRC 7000689

source_name: primary CRC 7000689

tag: age at diagnosis (y)

tag: tumor type

source_name: CRP

value: colon tumor

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: Wild_Type_female_B

description: wt female, biological rep2

source_name: Wild type female mouse liver RNA

value: B10.D2 (Rsl/Rsl)

value: female


title: CD4+ T cells, placebo treatment

source_name: CD4+ T cells, placebo treatment

value: CD4+ T cells


title: rsl_female_A

description: rsl female, biological rep1


title: rsl_male_A

description: rsl male, biological rep1


title: primary CRC 7000690

source_name: primary CRC 7000690

value: primary CRC

value: left colon


title: CD8+ T cells, post treatment, biological replicate 4

source_name: CD8+ T cells, post treatment


title: IE TT Hflu 6 hrs rep 6

description:
Sample name: 011A_11H1_aff080_504DT
gene expression mouse inner ear infected

value: trans-tympanically injected with H flu 10e9 for 6 hours

value: Balb/cJ

value: 2.1 months


title: Wild_Type_female_A

description: wt female, biological rep1


title: primary CRC 7000691

source_name: primary CRC 7000691

value: wildtype / other

value: activating mutation


title: Wild_Type_male_B

description: wt male, biological rep2

source_name: Wild type male mouse liver RNA

value: male


title: IE TT Hflu 6 hrs rep 7

description:
Sample name: 012A_11H1_aff086_504DT
gene expression mouse inner ear infected

value: inner ear

value: 3.3 months


title: IE TT Hflu 6 hrs rep 5

description:
Sample name: 010A_11H1_aff087_504DT_2
gene expression mouse inner ear infected


title: IE TT Hflu 6 hrs rep 4

description:
Sample name: 008A_11H1_aff082_504DT
gene expression mouse inner ear infected

value: 2.8 months


title: CD8+ T cells, baseline, biological replicate 4

value: sarcoidosis

value: CD8+ T cells


title: primary CRC 7000719

source_name: primary CRC 7000719

value: primary CRC from colon

value: colon tumor

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: IE control rep 5

description:
Sample name: 009A_11H1_aff092_504DT
gene expression mouse inner ear control

value: control

value: 2.6 months


title: CD4+ T cells, baseline

source_name: CD4+ T cells, baseline

value: CD4+ T cells


title: IE TT Hflu 6 hrs rep 3

description:
Sample name: 006A_11H1_aff081_504DT
gene expression mouse inner ear infected

value: trans-tympanically injected with H flu 10e9 for 6 hours


title: IE control rep 4

description:
Sample name: 007A_11H1_aff090_504DT
gene expression mouse inner ear control

value: Balb/cJ


title: CD8+ T cells, post treatment, biological replicate 3


title: CD4+ T cells, post treatment, biological replicate 4

source_name: CD4+ T cells, post treatment


title: CD8+ T cells, baseline, biological replicate 3


title: primary CRC 7000665

description: A reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs.

source_name: primary CRC 7000665

value: female

value: primary CRC

value: right colon


title: IE control rep 2

description:
Sample name: 003A_11H1_aff089_504DT
gene expression mouse inner ear control

source_name: Mouse inner ear control

value: 2.5 months


title: primary CRC 7000694

source_name: primary CRC 7000694

value: left colon

value: wildtype / other


title: CD8+ T cells, post treatment, biological replicate 2


title: CD4+ T cells, post treatment, biological replicate 3


title: primary CRC 7000713

source_name: primary CRC 7000713

value: activating mutation


title: primary CRC 7000666

source_name: primary CRC 7000666


title: IE TT Hflu 6 hrs rep 2

description:
Sample name: 005A_11H1_aff084_504DT
gene expression mouse inner ear infected

source_name: Mouse inner ear 6 hrs after TT inj with H flu

value: inner ear

value: 3.1 months


title: primary CRC 7000697

source_name: primary CRC 7000697

value: primary CRC from colon


title: IE control rep 3

description:
Sample name: 004A_11H1_aff088_504DT
gene expression mouse inner ear control


title: CD8+ T cells, baseline, biological replicate 2

source_name: CD8+ T cells, baseline

value: sarcoidosis

value: CD8+ T cells


title: IE TT Hflu 6 hrs rep 1

description:
Sample name: 002A_11H1_aff083_504DT
gene expression mouse inner ear infected

value: 2.8 months


title: Wild_Type_male_A

description: wt male, biological rep1

value: B10.D2 (Rsl/Rsl)

value: male

value: abdominal white adipose (WAT)


title: CD4+ T cells, baseline, biological replicate 3

value: CD4+ T cells


title: primary CRC 7000669

source_name: primary CRC 7000669

value: female

source_name: CRP

value: colon tumor

value: reference sample was made by processing of a colon cancer reference pool (BRP) that was previously generated by pooling colon tumor RNAs


title: Salmonella_typhimurium_MM-Glu_rep1

city: Stanford

first: Justin

last: Sonnenburg

state: CA

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

description: Minimal medium culture of Salmonella typhimurium SL1344 grown to mid-log phase. Replicate 1 of 2.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The raw data were RMA-MS normalized using R-2.9.1. and log2 transformed, excluding other species present on chip.

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

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Phenol-chloroform with bead-beating, Qiagen Rneasy mini column extraction, Ambion DNA free treatment


title: Salmonella_typhimurium_Sal_D5_rep3

description: Cecal contents from germ-free Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 3 of 3.


title: primary CRC 7000698

source_name: primary CRC 7000698

value: primary CRC

value: right colon


title: Salmonella_typhimurium_Sal_D5_rep2

description: Cecal contents from germ-free Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 2 of 3.


title: Salmonella_typhimurium_BTSal_D5_rep2

description: Cecal contents from Bacteroides thetaiotaomicron-monoassociated gnotobiotic Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 2 of 3.


title: Salmonella_typhimurium_Sal_D5_rep1

description: Cecal contents from germ-free Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 1 of 3.


title: Salmonella_typhimurium_BTSal_D5_rep3

description: Cecal contents from Bacteroides thetaiotaomicron-monoassociated gnotobiotic Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 3 of 3.


title: Salmonella_typhimurium_BTSal_D5_rep1

description: Cecal contents from Bacteroides thetaiotaomicron-monoassociated gnotobiotic Swiss Webster mice infected with Salmonella typhimurium for 5 days. Replicate 1 of 3.


title: CD4+ T cells, post treatment, biological replicate 2


title: CD8+ T cells, post treatment, biological replicate 1

source_name: CD8+ T cells, post treatment


title: primary CRC 7000676

source_name: primary CRC 7000676

value: left colon

value: wildtype / other


title: primary CRC 7000679

source_name: primary CRC 7000679


title: CD4+ T cells, baseline, biological replicate 2

source_name: CD4+ T cells, baseline


title: primary CRC 7000715

source_name: primary CRC 7000715


title: primary CRC 7000678

source_name: primary CRC 7000678


title: primary CRC 7000671

source_name: primary CRC 7000671


title: primary CRC 7000703

source_name: primary CRC 7000703

value: activating mutation


title: primary CRC 7000677

source_name: primary CRC 7000677


title: primary CRC 7000682

source_name: primary CRC 7000682


title: primary CRC 7000675

source_name: primary CRC 7000675


title: Salmonella_typhimurium_MM-Glu_rep2

description: Minimal medium culture of Salmonella typhimurium SL1344 grown to mid-log phase. Replicate 2 of 2.


title: IE control rep 1

description:
Sample name: 001B_11H1_aff091_504DT
gene expression mouse inner ear control

source_name: Mouse inner ear control

value: inner ear

value: control

value: Balb/cJ

value: 2.6 months


title: primary CRC 7000681

source_name: primary CRC 7000681

value: primary CRC from colon


title: CD4+ T cells, baseline, biological replicate 1

value: sarcoidosis


title: primary CRC 7000702

source_name: primary CRC 7000702

value: male


title: primary CRC 7000707

source_name: primary CRC 7000707

source_name: CRP


title: primary CRC 6001656

source_name: primary CRC 6001656


title: CD8+ T cells, baseline, biological replicate 1

source_name: CD8+ T cells, baseline

value: CD8+ T cells


title: primary CRC 7000704

source_name: primary CRC 7000704


title: CD4+ T cells, post treatment, biological replicate 1

source_name: CD4+ T cells, post treatment

value: CD4+ T cells


title: Untreated cells, biological rep2

status: Public on Jul 22 2013

city: Wageningen

first: Jia

last: Shao

address: Akkermaalsbos 2

department: TE

institute: RIKILT-Institute of food safety

hyb_protocol: cRNAs were hybridized to the arrays for 16 hours at 45 °C (GeneChip Hybridization Oven 640; Affymetrix). Washing and staining were done by using GeneChip hybridization station, Fluidics Station 450, Affymetrix.

scan_protocol: GeneChips were scanned by Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw data were extracted using GeneChip Operating Software (Affymetrix). In order to filter out probes with sub-optimal specificity for the encoding genes, custom CDF files were generated from the raw data files, by using the R package available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp. Then robust multichip average (RMA) normalization was applied to the complete dataset (Bioconductor). BioConductor packages were used for the quality control of the microarray data (www.arrayanalysis.org).

source_name: Jurkat, P17

label_protocol: cDNA synthesis and subsequent synthesis of biotin-labeled cRNA was performed using GeneChip One-Cycle Target Labeling and Control Reagents including the One-Cycle cDNA Synthesis Kit, Poly-A RNA Control Kit, Sample Cleanup Module, IVT Labeling Kit, and Hybridization Control Kit (all from Affymetrix) according to the manufacturer’s protocol.

growth_protocol: The Jurkat cells were grown in RPMI-1640 medium supplemented with 10% heat inactivated Fetal Calf Serum (FCS), 2 mM glutamine, 1 mM sodium pyruvate, 1 mM non-essential amino acids, 100 U/ml penicillin, and 100 µg/ml streptomycin. Cells were cultured at 37 °C with 5% CO2 in a humidified atmosphere. The medium was refreshed every 2 days.

extract_protocol: RNA was isolated by using Qiagen QIAshredder kit according to the manufacturer’s protocol. RNA purification was done using Qiagen miRNeasy Mini kit.

treatment_protocol: Jurkat cells (passage number 16 to 20) were seeded in 2.7 ml medium per well in 6-well plates (750,000 cells/well) . After growing the cells for 20 hours, exposure was initiated by adding 0.3 ml medium containing non-cytotoxic concentration of the compounds or vehicle controls. Subsequently, cells were exposed to the compounds for 6 h. The final DMSO concentration in the medium was 0.1%  (v/v) for all the samples. Each exposure was performed in quadruplicate at four different days.with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: passage

value: Human T cell

tag: agent

value: Untreated cells

tag: cell line

value: Jurkat, Clone E6-1


title: Ochratoxin A S9 treated 10uM, biological rep4

source_name: Jurkat, P19

value: Ochratoxin A S9 treated 10uM


title: Untreated cells, biological rep1

source_name: Jurkat, P16


title: Untreated cells, biological rep3

source_name: Jurkat, P18


title: Untreated cells, biological rep4


title: CD4+ T cells, baseline, biological replicate 4

source_name: CD4+ T cells, baseline


title: Benzo[a]pyrene S9 treated 5uM, biological rep4

value: Benzo[a]pyrene S9 treated 5uM


title: Ochratoxin A S9 treated 10uM, biological rep3


title: Cyclophosphamide S9 treated 3mM, biological rep4

value: Cyclophosphamide S9 treated 3mM


title: Ochratoxin A S9 treated 10uM, biological rep2


title: Ochratoxin A S9 treated 10uM, biological rep1


title: Cyclophosphamide S9 treated 3mM, biological rep3


title: Benzo[a]pyrene S9 treated 5uM, biological rep1


title: Benzo[a]pyrene S9 treated 5uM, biological rep2


title: Cyclophosphamide S9 treated 3mM, biological rep2


title: Sodium citrate 2mM, biological rep3

value: Sodium citrate 2mM


title: Cyclophosphamide S9 treated 3mM, biological rep1


title: Silver nitrate 1350nM, biological rep3

value: Silver nitrate 1350nM


title: Sodium citrate 2mM, biological rep2


title: Sodium citrate 2mM, biological rep4


title: Benzo[a]pyrene S9 treated 5uM, biological rep3


title: Silver nitrate 1350nM, biological rep4


title: Urethane 20mM, biological rep3

value: Urethane 20mM


title: Sodium citrate 2mM, biological rep1


title: Silver nitrate 1350nM, biological rep2


title: Silver nitrate 1350nM, biological rep1


title: Urethane 20mM, biological rep2


title: Urethane 20mM, biological rep1


title: Urethane 20mM, biological rep4


title: Tributyltin chloride 100nM, biological rep4

value: Tributyltin chloride 100nM


title: Bis(tributyltin) oxide 100nM, biological rep2

value: Bis(tributyltin) oxide 100nM


title: Tributyltin chloride 100nM, biological rep3


title: Tributyltin chloride 100nM, biological rep2


title: Bis(tributyltin) oxide 100nM, biological rep3


title: Bis(tributyltin) oxide 100nM, biological rep1


title: Bis(tributyltin) oxide 100nM, biological rep4


title: Rapamycin 20nM, biological rep4

value: Rapamycin 20nM


title: Propanil 100uM, biological rep3

value: Propanil 100uM


title: Rapamycin 20nM, biological rep2


title: Rapamycin 20nM, biological rep3


title: Rapamycin 20nM, biological rep1


title: Propanil 100uM, biological rep4


title: Tributyltin chloride 100nM, biological rep1


title: Mycophenolic acid 10uM, biological rep4

value: Mycophenolic acid 10uM


title: Propanil 100uM, biological rep1


title: Prednisolone 500uM, biological rep4

value: Prednisolone 500uM


title: Mycophenolic acid 10uM, biological rep2


title: Ochratoxin A 10uM, biological rep4

value: Ochratoxin A 10uM


title: Ochratoxin A 10uM, biological rep3


title: Mycophenolic acid 10uM, biological rep3


title: Prednisolone 500uM, biological rep1


title: Prednisolone 500uM, biological rep3


title: Propanil 100uM, biological rep2


title: Prednisolone 500uM, biological rep2


title: Ochratoxin A 10uM, biological rep1


title: Mono-2-ethylhexyl phthalate 300uM, biological rep4

value: Mono-2-ethylhexyl phthalate 300uM


title: Ochratoxin A 10uM, biological rep2

value: Human T cell


title: Mycophenolic acid 10uM, biological rep1


title: Mono-2-ethylhexyl phthalate 300uM, biological rep1


title: Mono-2-ethylhexyl phthalate 300uM, biological rep3


title: Methylmercury 1uM, biological rep4

value: Methylmercury 1uM


title: Mono-2-ethylhexyl phthalate 300uM, biological rep2

value: Jurkat, Clone E6-1


title: Mannitol 2mM, biological rep4

value: Mannitol 2mM


title: Methylmercury 1uM, biological rep3


title: Methylmercury 1uM, biological rep2


title: Mannitol 2mM, biological rep1


title: Mannitol 2mM, biological rep2


title: Mannitol 2mM, biological rep3


title: Fingolimod 4uM, biological rep4

value: Fingolimod 4uM


title: Fingolimod 4uM, biological rep2


title: Furosemide 100uM, biological rep2

value: Furosemide 100uM


title: Lindane 130uM, biological rep2

value: Lindane 130uM


title: Lindane 130uM, biological rep3


title: Furosemide 100uM, biological rep4


title: Fingolimod 4uM, biological rep3


title: Furosemide 100uM, biological rep3


title: Lindane 130uM, biological rep1


title: Methylmercury 1uM, biological rep1


title: Fluoxetine 30uM, biological rep3

value: Fluoxetine 30uM


title: Lindane 130uM, biological rep4


title: Furosemide 100uM, biological rep1


title: Fingolimod 4uM, biological rep1


title: Diazinon 200uM, biological rep4

value: Diazinon 200uM


title: Diazinon 200uM, biological rep3


title: Fluoxetine 30uM, biological rep2


title: Dichaete DamID vs control Dam rep2

city: Cambridge

first: Steve

last: Russell

address: Tennis Court Road

department: Genetics

country: United Kingdom

institute: University of Cambridge

description: Dichaete 0-12h whole embryo DamID

hyb_protocol: Combined DNA samples were loaded onto Nimblegen D.mel ChIP 2.1M tiling arrays (GEO platform GPL15057), hybridised overnight at 42˚C in a NimbleGen hyb machine, then washed and scanned the following day.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing:
NimbleScan was used for spot-finding. Scanned arrays were quantile normalised separately for samples and controls. The resulting ratios are log2 ratio of sample/control.
Peak finding was performed using RINGO to identify binding intervals at different False Discovery Rates.

organism: Drosophila melanogaster

source_name: Dichaete DamID

label_protocol: To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: Embryos collected on agar plates with yeast at 25˚C

extract_protocol: DNA was extracted from embryos using a Qiagen Dneasy Blood & Tissue kit. It then underwent a series of digestions, followed by a PCR amplification, as described in the Vogel et al. 2007 DamID protocol.

treatment_protocol: Embryos were dechorionated, followed by homogenisation and DNA extraction

tag: developmental stage

value: 0-12h embryos

tag: genotype/variation

value: Flies contain a UAS-Dichaete-Dam fusion construct

value: Whole embryos

source_name: DamID control

value: Flies contain a UAS-Dam construct


title: Fluoxetine 30uM, biological rep1


title: Dichaete DamID vs control Dam rep1

description: Dichaete 0-12h whole embryo DamID


title: Diazinon 200uM, biological rep1


title: Dichaete DamID vs control Dam rep3

description: Dichaete 0-12h whole embryo DamID


title: Deoxynivalenol 250nM, biological rep4

value: Deoxynivalenol 250nM


title: Deoxynivalenol 250nM, biological rep2


title: Diazinon 200uM, biological rep2


title: Deoxynivalenol 250nM, biological rep3


title: Bis(2-ethylhexyl) phthalate 300uM, biological rep4

value: Bis(2-ethylhexyl) phthalate 300uM


title: Bis(2-ethylhexyl) phthalate 300uM, biological rep3


title: Cyclophosphamide 5mM, biological rep4

value: Cyclophosphamide 5mM


title: Dibutyltin dichloride 100nM, biological rep3

value: Dibutyltin dichloride 100nM


title: Cyclosporine A 8uM, biological rep3

value: Human T cell

value: Cyclosporine A 8uM


title: Cyclosporine A 8uM, biological rep4

value: Jurkat, Clone E6-1


title: Cyclophosphamide 5mM, biological rep3


title: Deoxynivalenol 250nM, biological rep1


title: Dibutyltin dichloride 100nM, biological rep4


title: Bis(2-ethylhexyl) phthalate 300uM, biological rep1


title: Bis(2-ethylhexyl) phthalate 300uM, biological rep2


title: Dibutyltin dichloride 100nM, biological rep1


title: Cyclophosphamide 5mM, biological rep1


title: Cobalt(II) chloride 80uM, biological rep1

value: Cobalt(II) chloride 80uM


title: Cyclosporine A 8uM, biological rep1


title: Cyclosporine A 8uM, biological rep2


title: Cobalt(II) chloride 80uM, biological rep3


title: Dibutyltin dichloride 100nM, biological rep2


title: Cyclophosphamide 5mM, biological rep2


title: Benzo[a]pyrene 5uM, biological rep3

value: Benzo[a]pyrene 5uM


title: Cobalt(II) chloride 80uM, biological rep2


title: Benzo[a]pyrene 5uM, biological rep4


title: Azathioprine 100nM, biological rep2

value: Azathioprine 100nM


title: Benzo[a]pyrene 5uM, biological rep2


title: Azathioprine 100nM, biological rep4


title: Benzo[a]pyrene 5uM, biological rep1


title: Arsenic trioxide 3uM, biological rep2

value: Arsenic trioxide 3uM


title: Azathioprine 100nM, biological rep3


title: Arsenic trioxide 3uM, biological rep4


title: Chemicals treatment Day20

city: beijing

first: chun

last: liu

state: beijing

address: beijing

country: China

institute: Peking University

description: Mouse Whole Genome OneArray® v2 (Phalanx Biotech Group, Taiwan)

hyb_protocol: Hybridized to a mouse Oligo Microarray following the Mouse Onearray User Manual V2 (Phalanx Biotech Group).

scan_protocol: Data extracton used GenePix 4100B (Molecular Devices) scanner from molecular Devices, and measured using GenePixPro Software (Molecular Devices) .

data_processing: Primary data selected by Flags and SNRs. After selection, average or median value of each sample were normalized using matlab.

source_name: Mouse embryonic fibroblasts

label_protocol: Total mRNAs of all samples were labeled with Cy5 following the Mouse Onearray User Manual V2 (Phalanx Biotech Group).

growth_protocol: MEFs, MNFs, MAFs and ADSCs were cultured in DMEM/High Glucose (Hyclone) containing 10% fetal bovine serum (Invitrogen). Mouse ESCs (R1 and TT2), iPSCs and CiPSCs were maintained on feeder layers of mitomycin C-treated MEFs in ESC culture medium.

extract_protocol: Total RNA extracted using Trizol and purified by QIAGEN Rneasy Kit following manufacturer's instructions.

tag: development stage

value: embryo

value: fibroblast

value: D20 treatment fibroblast

tag: chemical treatment conditon


title: Ampicillin 850uM, biological rep3

value: Ampicillin 850uM


title: Chemicals treatment Day32

value: D32 treatment fibroblast


title: Azathioprine 100nM, biological rep1


title: SKM-FSK2 iPS

value: iPS

value: SKM-FSK iPS line 2

value: F


title: SKM-FSK1 iPS

value: SKM-FSK iPS line 1


title: Mouse embryonic fibroblasts3

value: MEFs line 3

value: no treatment


title: Embryonic stem cells5

source_name: Embryonic stem cell line R1

value: Embryonic stem cell

value: Embryonic stem cell line 5


title: Embryonic stem cells3

value: Embryonic stem cell line 3


title: Embryonic stem cells4

value: Embryonic stem cell line 4


title: Chemicals treatment Day12

value: D12 treatment fibroblast


title: Ampicillin 850uM, biological rep1

value: Human T cell

value: Jurkat, Clone E6-1


title: Ampicillin 850uM, biological rep4


title: Arsenic trioxide 3uM, biological rep3

value: Arsenic trioxide 3uM


title: CiPS WT1

source_name: Wildtyp mouse embryonic fibroblasts

value: embryo

value: pluripotent stem cell

value: CiPS WT line 1


title: CiPS line 58

description: CGH analysis of chemical induced pluripotent stem cells

hyb_protocol: Hybridization was processed following Roche-NimbleGen hybridization system.

scan_protocol: Data were scanned using Roche-NimbleGen MS200 scanner.

data_processing: Scaned image was transformed to digital signal by Nimblescan, and processed by segMNT algorithm to analyse. The normalized log2 signal ratio (Cy3/Cy5).

source_name: genomic DNA from CiPS58

label_protocol: Sample DNA was labeled by NimbleGen Dual-Color DNA Labeling Kit

growth_protocol: 2i ESC medium without feeder cells

extract_protocol: Genomic DNA of all samples was extracted using DNeasy Blood & Tissue Kit (QIAGEN)

tag: background strain

source_name: C57BL/6 MEFs

growth_protocol: DMEM/High Glucose (Hyclone) containing 10% fetal bovine serum (Invitrogen)

treatment_protocol: No treatment


title: CiPS line 57

source_name: genomic DNA from CiPS57


title: Mouse embryonic fibroblasts2

value: fibroblast

value: MEFs line 2


title: Ampicillin 850uM, biological rep2

value: Ampicillin 850uM


title: OSKM induced pluripotent stem cells

description: CGH analysis of OSKM-iPSC

source_name: genomic DNA from OSKM-iPSC


title: MNF CiPS1

source_name: Mouse neonatal fibroblasts

value: neonatal

value: MNF CiPS line 1


title: Wildtype mouse embryonic fibroblasts

value: WT MEFs line

value: no treatment


title: Fluoxetine 30uM, biological rep4

value: Fluoxetine 30uM


title: MAF CiPS3

source_name: Mouse adult lung fibroblasts

value: adult

value: MAF CiPS line 3


title: CiPS21

value: CiPS line 21


title: CiPS WT2

value: CiPS WT line 2


title: Adipose-derived stem cells

source_name: Adipose-derived stem cells

value: adult stem cell

value: ADSCs line


title: CiPS50

value: embryo

value: CiPS line 50


title: ADSC CiPS2

value: pluripotent stem cell

value: ADSC CiPS line 2


title: OSKM iPS2

value: iPS

value: OSKM iPS line 2


title: Mouse adult lung fibroblasts

value: fibroblast

value: MAFs line


title: SAEC-hTERT_crocidolite asbestos_6month_rep3

city: Morgantown

first: Todd

middle: A

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

description:
Genome expression after 6 month crocidolite asbestos in vitro exposure
Sample name: H-ASB 3

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on NimbleGen 12x135k Whole Human Genome Oligonucleotide Microarray (HG18) in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Axon GenePix 4000B (Molecular Devices) and uploaded into NimbleScan (v2.5), and Cy3 label intensities determined.

data_processing: GenePix data were uploaded into NimbleScan for Cy3 label intensity determination.  Intensities were quantile normalized using Robust Multichip Average method included in NimbleScan. Only genes expressing ≥50.0 normalized intensity in all 18 samples were subjected to further analysis. Gene expression text files were imported into GeneSpring GX (ver. 10.0) for further analysis.

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, crocidolite asbestos, 6 month exposed (24 passages), replicate 3

label_protocol: cDNA samples were amplified, Cy3-labeled with NimbleGen one-color DNA labeling kit following manufactorer's protocol. Microarray hybridization was performed at 65°C for 17 hours to  NimbleGen whole human genome 12x135K microarrays in NimbleGen Hybridization System.

growth_protocol: Cells were maintained in SABM medium (Lonza) supplemented with SAGM SingleQuot (Clonetics) growth factor kit and 100 U/mL penicillin and streptomycin.  Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: RNA samples from each replicate (total n=18) were collected with TRIzol (Invitrogen) post-exposure using manufactorer's protocol.  RNA quality was assessed in house using gel electrophoresis and 260/280 nm absorbance ratio.  Samples stored at -80o C were shipped to ArrayStar (Rockville, MD).  At ArrayStar, samples were treated with DNase digestion and analyzed for RNA quality using Nanodrop ND-100 and Bioanalyser 2100.

treatment_protocol: 0.1 g/mL stock solutions of SWCNT, MWCNT, crocidolite asbestos and ultrafine carbon black were prepared in sterile MilliQ water containing 150 microliters/mL of the lung surfactant Survanta®.  Each stock solution was sonicated for 20 seconds using a small sonication horn and then diluted in fresh culture medium and added to culture plates.  Saline and dispersant only containing medium served as negative passage controls.  Unexposed SAEC-hTERT cells (2x105 cells/well) were seeded to 6-well plates in triplicate per treatment (n=18).  After 24 hours, cell cultures were either exposed to 0.02 micrograms/sq. cm of each particle or saline or Survanta-dispersant only for the following 6 months.  Cells were passage matched for a total of 24 passages.  Exposed media was changed every 3 to 4 days while cells were split once every 7 days.

value: lung

tag: stress

value: crocidolite asbestos


title: CiPS34

value: CiPS line 34


title: Embryonic stem cells2

source_name: Embryonic stem cell line TT2

value: Embryonic stem cell

value: Embryonic stem cell line 2

value: no treatment


title: OSKM iPS1

value: OSKM iPS line 1


title: CiPS45

value: CiPS line 45


title: Embryonic stem cells1

value: Embryonic stem cell line 1


title: Mouse neonatal fibroblasts

value: neonatal

value: MNFs line


title: Mouse embryonic fibroblasts1

value: embryo

value: MEFs line 1


title: SAEC-hTERT_crocidolite asbestos_6month_rep2

description:
Genome expression after 6 month crocidolite asbestos in vitro exposure
Sample name: H-ASB 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, crocidolite asbestos, 6 month exposed (24 passages), replicate 2


title: SAEC-hTERT_dispersed multi wall carbon nanotube_6month_rep2

description:
Genome expression after 6 month dispersed multi wall carbon nanotube in vitro exposure
Sample name: H-D-MWCNT 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed multi wall carbon nanotube, 6 month exposed (24 passages), replicate 2

value: dispersed multi wall carbon nanotube


title: SAEC-hTERT_crocidolite asbestos_6month_rep1

description:
Genome expression after 6 month crocidolite asbestos in vitro exposure
Sample name: H-ASB 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, crocidolite asbestos, 6 month exposed (24 passages), replicate 1


title: SAEC-hTERT_dispersed ultrafine carbon black_6month_rep3

description:
Genome expression after 6 month dispersed ultrafine carbon black in vitro exposure
Sample name: H-D-UFCB 3

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed ultrafine carbon black, 6 month exposed (24 passages), replicate 3

value: dispersed ultrafine carbon black


title: SAEC-hTERT_dispersed multi wall carbon nanotube_6month_rep1

description:
Genome expression after 6 month dispersed multi wall carbon nanotube in vitro exposure
Sample name: H-D-MWCNT 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed multi wall carbon nanotube, 6 month exposed (24 passages), replicate 1


title: SAEC-hTERT_dispersed single wall carbon nanotube_6month_rep2

description:
Genome expression after 6 month dispersed single wall carbon nanotube in vitro exposure
Sample name: H-D-SWCNT 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed single wall carbon nanotube, 6 month exposed (24 passages), replicate 2

value: dispersed single wall carbon nanotube


title: SAEC-hTERT_dispersed ultrafine carbon black_6month_rep1

description:
Genome expression after 6 month dispersed ultrafine carbon black in vitro exposure
Sample name: H-D-UFCB 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed ultrafine carbon black, 6 month exposed (24 passages), replicate 1


title: MNF CiPS7

value: pluripotent stem cell

value: MNF CiPS line 7


title: Cobalt(II) chloride 80uM, biological rep4

source_name: Jurkat, P19

value: Human T cell

value: Cobalt(II) chloride 80uM

value: Jurkat, Clone E6-1


title: SAEC-hTERT_saline_6month_rep1

description:
Genome expression after 6 month saline-only in vitro exposure
Sample name: H-SAL 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, saline only, 6 month exposed (24 passages), replicate 1

value: lung

value: saline


title: SAEC-hTERT_dispersed multi wall carbon nanotube_6month_rep3

description:
Genome expression after 6 month dispersed multi wall carbon nanotube in vitro exposure
Sample name: H-D-MWCNT 3

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed multi wall carbon nanotube, 6 month exposed (24 passages), replicate 3


title: Arsenic trioxide 3uM, biological rep1

source_name: Jurkat, P16

value: Arsenic trioxide 3uM


title: SAEC-hTERT_dispersed single wall carbon nanotube_6month_rep3

description:
Genome expression after 6 month dispersed single wall carbon nanotube in vitro exposure
Sample name: H-D-SWCNT 3

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed single wall carbon nanotube, 6 month exposed (24 passages), replicate 3


title: SAEC-hTERT_dispersed single wall carbon nanotube_6month_rep1

description:
Genome expression after 6 month dispersed single wall carbon nanotube in vitro exposure
Sample name: H-D-SWCNT 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed single wall carbon nanotube, 6 month exposed (24 passages), replicate 1


title: SAEC-hTERT_dispersed ultrafine carbon black_6month_rep2

description:
Genome expression after 6 month dispersed ultrafine carbon black in vitro exposure
Sample name: H-D-UFCB 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, dispersed ultrafine carbon black, 6 month exposed (24 passages), replicate 2


title: SAEC-hTERT_saline_6month_rep2

description:
Genome expression after 6 month saline-only in vitro exposure
Sample name: H-SAL 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, saline only, 6 month exposed (24 passages), replicate 2


title: SAEC-hTERT_dispersant_6month_rep1

description:
Genome expression after 6 month dispersant-only in vitro exposure
Sample name: H-DISP 1

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, Survanta dispersant only, 6 month exposed (24 passages), replicate 1

value: dispersant


title: SAEC-hTERT_dispersant_6month_rep2

description:
Genome expression after 6 month dispersant-only in vitro exposure
Sample name: H-DISP 2

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, Survanta dispersant only, 6 month exposed (24 passages), replicate 2


title: SAEC-hTERT_dispersant_6month_rep3

description:
Genome expression after 6 month dispersant-only in vitro exposure
Sample name: H-DISP 3

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, Survanta dispersant only, 6 month exposed (24 passages), replicate 3


title: SAEC-hTERT_saline_6month_rep3

description:
Genome expression after 6 month saline-only in vitro exposure
Sample name: H-SAL 3

source_name: SAEC-hTERT immortalized human lung small airway epithelial cell, saline only, 6 month exposed (24 passages), replicate 3


title: prosGal4 UAS Dichaete WT vs UAS GFP control rep 3

description:
DWT3
Biological replicate 3 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

source_name: prosgal4 DWT

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: prosGal4 females were crossed to UAS construct carrying males. 3.5 - 4.5h Drosophila embryos (stage 8-9) grown at 25˚C were collected.

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes 4 °C to pellet debris and transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, vortex for 60 seconds. Centrifuge at 13,000 rpm for 15 minutes. Remove upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.4 µl GeneElute Linear Polyacrylamide (Sigma) (25 µg / µl stock diluted 1:10 in DEPC MilliQ water) and 0.8 volumes of isopropanol, invert and then incubate for 1 hour at -20 °C. Pellet the RNA by centrifugation at 13,000 rpm for 30 minutes. Discard the supernatant and wash the RNA pellet with 500 µl 70% ethanol/DEPC MilliQ water. Air-dry the pellet. Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 5 µl. Verify quality of RNA on a 0.8 % agarose gel stained with SYBR-gold (Molecular Probes).

treatment_protocol: The embryos were stored in Trizol.

value: Stage 8-9 (3.5-4.5h) embryos

value: The collected embryos have a prosGal4 driver and a UAS construct. Sample embryos are expressing a UAS Dichaete wild type construct.

value: Whole embryos

source_name: prosGal4 GFP

value: The collected embryos have a prosGal4 driver and a UAS construct.  The control embryos are expressing a UAS GFP construct.


title: prosGal4 UAS Dichaete WT vs UAS GFP control rep 2

description:
DWT2
Biological replicate 2 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: prosGal4 UAS HMG- vs UAS GFP control rep 2

description:
HMG2
Biological replicate 2 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.

source_name: prosgal4 HMG-

value: The collected embryos have a prosGal4 driver and a UAS construct. Sample embryos are expressing a UAS HMG- construct.


title: prosGal4 UAS HMG- vs UAS GFP control rep 4

description:
HMG4
Biological replicate 4 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: prosGal4 UAS Dichaete WT vs UAS GFP control rep 1

description:
DWT1
Biological replicate 1 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: prosGal4 UAS EnRep vs UAS GFP control rep 3

description:
EnRep3
Biological replicate 3 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.

source_name: prosgal4 En

value: The collected embryos have a prosGal4 driver and a UAS construct. Sample embryos are expressing a UAS EnRep construct.


title: prosGal4 UAS EnRep vs UAS GFP control rep 1

description:
EnRep1
Biological replicate 1 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: prosGal4 UAS HMG- vs UAS GFP control rep 3

description:
HMG3
Biological replicate 3 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: prosGal4 UAS HMG- vs UAS GFP control rep 1

description:
HMG1
Biological replicate 1 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: CiPSCs

description: Mouse Whole Genome OneArray® v2 (Phalanx Biotech Group, Taiwan)

source_name: Mouse embryonic fibroblasts

value: embryo

value: CiPS line control


title: D homozygous mutant vs heterozygous control rep 2

description:
Dmutant2
Biological replicate 2 of 4. Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked based on fluorescence, with the homozygous ones used as the sample, and the heterozygous ones used as a control.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data were then processed using the invariant normalisation method from Pradervand et al (2009). The resulting ratios are log2 ratio of sample/control.

source_name: D homozygous mutant

growth_protocol: Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked under a fluorescence dissecting microscope.  GFP negative homozygous Dichaete mutant embryos and their heterozygous single GFP positive siblings were collected. Approximately 150 embryos per sample were collected.

treatment_protocol: The embryos were stored frozen in Trizol.

value: Stage 10-11 embryos (5-7.5h)

value: Homozygous embryos from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp

source_name: D heterozygous control

value: Heterozygous embryos from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp


title: Chimpanzee [px9]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: PBMC

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

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

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference chimpanzee genome Pan_troglodytes-2.1.4 using BWA. We retained only the autosomal probes with either a perfect match, or 1 mismatch in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Quantile normalization was performed on the pooled signals from color channels and average β-values were recalculated using Genome Studio V2011.2.

label: Cy3, Cy5

organism: Pan troglodytes

source_name: Blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel.

value: Female


title: D homozygous mutant vs heterozygous control rep 1

description:
Dmutant1
Biological replicate 1 of 4. Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked based on fluorescence, with the homozygous ones used as the sample, and the heterozygous ones used as a control.


title: D homozygous mutant vs heterozygous control rep 3

description:
Dmutant3
Biological replicate 3 of 4. Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked based on fluorescence, with the homozygous ones used as the sample, and the heterozygous ones used as a control.


title: prosGal4 UAS EnRep vs UAS GFP control rep 2

description:
EnRep2
Biological replicate 2 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: Chimpanzee [px14]

description: PBMC

value: Male


title: D homozygous mutant vs heterozygous control rep 4

description:
Dmutant4
Biological replicate 4 of 4. Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked based on fluorescence, with the homozygous ones used as the sample, and the heterozygous ones used as a control.


title: Chimpanzee [A909]

description: PBMC

organism: Pan troglodytes verus


title: Chimpanzee [A913]

description: PBMC

organism: Pan troglodytes schweinfurthii


title: Chimpanzee [A958]

description: PBMC

organism: Pan troglodytes troglodytes


title: Chimpanzee [A911]

description: PBMC


title: Chimpanzee [A969]

description: PBMC


title: Chimpanzee [A965]

description: PBMC


title: Chimpanzee [A960]

description: PBMC


title: Chimpanzee [A910]

description: PBMC


title: Chimpanzee [A968]

description: PBMC


title: Chimpanzee [A957]

description: PBMC


title: Chimpanzee [A912]

description: PBMC


title: Chimpanzee [px10]

description: PBMC


title: prosGal4 UAS EnRep vs UAS GFP control rep 4

description:
EnRep4
Biological replicate 4 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a prosGal4 driver.


title: Caucasian [PBMC009]

description: healthy sample

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

data_processing: The intensities of the images were extracted using GenomeStudio (V2011.2) Methylation module (1.8.5) software. The methylation score of each CpG is represented as a beta value.

tag: health state

value: Healthy donor


title: Caucasian [PBMC001]

description: healthy sample


title: Japanese [303]

description: PBMNC


title: Caucasian [PBMC007]

description: healthy sample


title: Caucasian American [GM17291]

description: healthy sample


title: Caucasian [PBMC003]

description: healthy sample


title: Caucasian [PBMC010]

description: healthy sample


title: Japanese [301]

description: PBMNC


title: Japanese [302]

description: PBMNC


title: Caucasian [PBMC005]

description: healthy sample


title: Caucasian American [GM17293]

description: healthy sample


title: Caucasian [PBMC004]

description: healthy sample


title: Japanese [300]

description: PBMNC


title: Japanese [Blood_3_female]

description: PBMNC


title: Caucasian [PBMC006]

description: healthy sample


title: Japanese [Blood_2_female]

description: PBMNC


title: Caucasian American [GM17287]

description: healthy sample


title: Caucasian American [GM17288]

description: healthy sample


title: Caucasian American [GM17295]

description: healthy sample


title: Japanese [305]

description: PBMNC


title: Japanese [299]

description: PBMNC


title: Japanese [Blood_1_female]

description: PBMNC


title: Caucasian American [GM17296]

description: healthy sample


title: Caucasian [PBMC002]

description: healthy sample


title: Caucasian American [GM17289]

description: healthy sample


title: Caucasian [PBMC008]

description: healthy sample


title: Japanese [304]

description: PBMNC


title: Caucasian American [GM17294]

description: healthy sample


title: Caucasian American [GM17292]

description: healthy sample


title: Caucasian American [GM17290]

description: healthy sample


title: Caucasian American [GM17285]

description: healthy sample


title: Caucasian American [GM17284]

description: healthy sample


title: Caucasian American [GM17280]

description: healthy sample


title: Caucasian American [GM17276]

description: healthy sample


title: Caucasian American [GM17281]

description: healthy sample


title: Caucasian American [GM17283]

description: healthy sample


title: Caucasian American [GM17279]

description: healthy sample


title: Caucasian American [GM17260]

description: healthy sample


title: Caucasian American [GM17275]

description: healthy sample


title: Caucasian American [GM17278]

description: healthy sample


title: Caucasian American [GM17272]

description: healthy sample


title: Caucasian American [GM17267]

description: healthy sample


title: Caucasian American [GM17268]

description: healthy sample


title: Caucasian American [GM17277]

description: healthy sample


title: Caucasian American [GM17273]

description: healthy sample


title: Caucasian American [GM17286]

description: healthy sample


title: Caucasian American [GM17263]

description: healthy sample


title: Caucasian American [GM17259]

description: healthy sample


title: Caucasian American [GM17270]

description: healthy sample


title: Caucasian American [GM17274]

description: healthy sample


title: Caucasian American [GM17262]

description: healthy sample


title: Caucasian American [GM17282]

description: healthy sample


title: Caucasian American [GM17271]

description: healthy sample


title: Caucasian American [GM17261]

description: healthy sample


title: Caucasian American [GM17265]

description: healthy sample


title: Caucasian American [GM17266]

description: healthy sample


title: Caucasian American [GM17269]

description: healthy sample


title: Caucasian American [GM17264]

description: healthy sample


title: Caucasian American [GM17258]

description: healthy sample


title: Caucasian American [GM17257]

description: healthy sample


title: Caucasian American [GM17255]

description: healthy sample


title: Caucasian American [GM17256]

description: healthy sample


title: Caucasian American [GM17251]

description: healthy sample


title: Caucasian American [GM17253]

description: healthy sample


title: Caucasian American [GM17242]

description: healthy sample


title: Caucasian American [GM17246]

description: healthy sample


title: Caucasian American [GM17238]

description: healthy sample


title: Caucasian American [GM17236]

description: healthy sample


title: Caucasian American [GM17243]

description: healthy sample


title: Caucasian American [GM17245]

description: healthy sample


title: Caucasian American [GM17250]

description: healthy sample


title: Caucasian American [GM17244]

description: healthy sample


title: Caucasian American [GM17247]

description: healthy sample


title: Caucasian American [GM17241]

description: healthy sample


title: Caucasian American [GM17239]

description: healthy sample


title: Caucasian American [GM17252]

description: healthy sample


title: Caucasian American [GM17237]

description: healthy sample


title: Caucasian American [GM17248]

description: healthy sample


title: Caucasian American [GM17240]

description: healthy sample


title: Caucasian American [GM17233]

description: healthy sample


title: Caucasian American [GM17249]

description: healthy sample


title: Caucasian American [GM17229]

description: healthy sample


title: Caucasian American [GM17232]

description: healthy sample


title: Caucasian American [GM17254]

description: healthy sample


title: Caucasian American [GM17234]

description: healthy sample


title: Caucasian American [GM17230]

description: healthy sample


title: Caucasian American [GM17231]

description: healthy sample


title: Caucasian American [GM17226]

description: healthy sample


title: Caucasian American [GM17228]

description: healthy sample


title: Caucasian American [GM17227]

description: healthy sample


title: Caucasian American [GM17225]

description: healthy sample


title: Caucasian American [GM17218]

description: healthy sample


title: Caucasian American [GM17220]

description: healthy sample


title: Caucasian American [GM17213]

description: healthy sample


title: Caucasian American [GM17222]

description: healthy sample


title: Caucasian American [GM17219]

description: healthy sample


title: Caucasian American [GM17212]

description: healthy sample


title: Caucasian American [GM17215]

description: healthy sample


title: Caucasian American [GM17216]

description: healthy sample


title: Caucasian American [GM17210]

description: healthy sample


title: Caucasian American [GM17223]

description: healthy sample


title: Caucasian American [GM17235]

description: healthy sample


title: Caucasian American [GM17207]

description: healthy sample


title: Caucasian American [GM17209]

description: healthy sample


title: Caucasian American [GM17203]

description: healthy sample


title: Caucasian American [GM17224]

description: healthy sample


title: Caucasian American [GM17211]

description: healthy sample


title: Caucasian American [GM17208]

description: healthy sample


title: Caucasian American [GM17217]

description: healthy sample


title: Caucasian American [GM17205]

description: healthy sample


title: Caucasian American [GM17201]

description: healthy sample


title: Caucasian American [GM17202]

description: healthy sample


title: Caucasian American [GM17221]

description: healthy sample


title: Han Chinese American [GM17784]

description: healthy sample


title: Han Chinese American [GM17852]

description: healthy sample


title: Caucasian American [GM17204]

description: healthy sample


title: Han Chinese American [GM17847]

description: healthy sample


title: Caucasian American [GM17214]

description: healthy sample


title: Han Chinese American [GM17850]

description: healthy sample


title: Han Chinese American [GM17844]

description: healthy sample


title: Han Chinese American [GM17841]

description: healthy sample


title: Han Chinese American [GM17840]

description: healthy sample


title: Han Chinese American [GM17835]

description: healthy sample


title: Han Chinese American [GM17843]

description: healthy sample


title: Han Chinese American [GM17842]

description: healthy sample


title: Han Chinese American [GM17831]

description: healthy sample


title: Han Chinese American [GM17838]

description: healthy sample


title: Han Chinese American [GM17828]

description: healthy sample


title: Han Chinese American [GM17837]

description: healthy sample


title: Caucasian American [GM17206]

description: healthy sample


title: Han Chinese American [GM17839]

description: healthy sample


title: Han Chinese American [GM17825]

description: healthy sample


title: Han Chinese American [GM17833]

description: healthy sample


title: Han Chinese American [GM17827]

description: healthy sample


title: Han Chinese American [GM17845]

description: healthy sample


title: Han Chinese American [GM17818]

description: healthy sample