title: Absence_of_Perineural_Invasion_13_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_13_tumor

source_name: without PNI,patient 13,tumor tissue


title: Perineural_Invasion_14_normal

status: Public on Aug 04 2017

type: RNA

city: Shanghai

first: Yongwei

last: Sun

address: 160 Pujian Rd

department: Department of Biliary-Pancreatic Surgery

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

description: Gene_expression_of_Perineural_Invasion_14_normal

hyb_protocol: Scanned on an Agilent G2565CA scanner.

scan_protocol: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

data_processing: The noromalized value of 75 percentile.

molecule: total RNA

organism: Homo sapiens

source_name: with PNI,patient 14,normal tissue

label_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

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

treatment_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: tissue

value: pancreas

tag: tumor size(≤3=0，＞3=1）

tag: t stage

tag: n stage（”n0=0,n1=1)

tag: vessel invasion(absence=0,present=1)

tag: survival time(day)

tag: survival status(alive=0,dead=1)


title: Perineural_Invasion_18_normal

description: Gene_expression_of_Perineural_Invasion_18_normal

source_name: with PNI,patient 18,normal tissue


title: Absence_of_Perineural_Invasion_10_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_10_tumor

source_name: without PNI,patient 10,tumor tissue


title: Perineural_Invasion_13_tumor

description: Gene_expression_of_Perineural_Invasion_13_tumor

source_name: with PNI,patient 13,tumor tissue


title: Perineural_Invasion_12_normal

description: Gene_expression_of_Perineural_Invasion_12_normal

source_name: with PNI,patient 12,normal tissue


title: Absence_of_Perineural_Invasion_16_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_16_tumor

source_name: without PNI,patient 16,tumor tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_12_normal

source_name: without PNI,patient 12,normal tissue


title: Perineural_Invasion_17_normal

description: Gene_expression_of_Perineural_Invasion_17_normal

source_name: with PNI,patient 17,normal tissue


title: Absence_of_Perineural_Invasion_9_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_9_tumor

source_name: without PNI,patient 9,tumor tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_14_normal

source_name: without PNI,patient 14,normal tissue


title: Perineural_Invasion_17_tumor

description: Gene_expression_of_Perineural_Invasion_17_tumor

source_name: with PNI,patient 17,tumor tissue


title: Perineural_Invasion_15_tumor

description: Gene_expression_of_Perineural_Invasion_15_tumor

source_name: with PNI,patient 15,tumor tissue


title: Perineural_Invasion_16_normal

description: Gene_expression_of_Perineural_Invasion_16_normal

source_name: with PNI,patient 16,normal tissue


title: Perineural_Invasion_11_tumor

description: Gene_expression_of_Perineural_Invasion_11_tumor

source_name: with PNI,patient 11,tumor tissue


title: Absence_of_Perineural_Invasion_12_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_12_tumor

source_name: without PNI,patient 12,tumor tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_15_normal

source_name: without PNI,patient 15,normal tissue


title: Perineural_Invasion_16_tumor

description: Gene_expression_of_Perineural_Invasion_16_tumor

source_name: with PNI,patient 16,tumor tissue


title: Absence_of_Perineural_Invasion_9_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_9_normal

source_name: without PNI,patient 9,normal tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_13_normal

source_name: without PNI,patient 13,normal tissue


title: Perineural_Invasion_13_normal

description: Gene_expression_of_Perineural_Invasion_13_normal

source_name: with PNI,patient 13,normal tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_10_normal

source_name: without PNI,patient 10,normal tissue


title: Perineural_Invasion_11_normal

description: Gene_expression_of_Perineural_Invasion_11_normal

source_name: with PNI,patient 11,normal tissue


title: Absence_of_Perineural_Invasion_8_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_8_tumor

source_name: without PNI,patient 8,tumor tissue


title: Perineural_Invasion_9_normal

description: Gene_expression_of_Perineural_Invasion_9_normal

source_name: with PNI,patient 9,normal tissue


title: Perineural_Invasion_9_tumor

description: Gene_expression_of_Perineural_Invasion_9_tumor

source_name: with PNI,patient 9,tumor tissue


description: Gene_expression_of_Absence_of_Perineural_Invasion_11_normal

source_name: without PNI,patient 11,normal tissue


title: Absence_of_Perineural_Invasion_7_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_7_tumor

source_name: without PNI,patient 7,tumor tissue


title: Perineural_Invasion_10_normal

description: Gene_expression_of_Perineural_Invasion_10_normal

source_name: with PNI,patient 10,normal tissue


title: Perineural_Invasion_8_normal

description: Gene_expression_of_Perineural_Invasion_8_normal

source_name: with PNI,patient 8,normal tissue


title: Perineural_Invasion_14_tumor

description: Gene_expression_of_Perineural_Invasion_14_tumor

source_name: with PNI,patient 14,tumor tissue


title: LP-1-HIF2A

city: Adelaide

first: Andrew

last: Zannettino

state: SA

address: SAHMRI, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

description: Gene expression data from LP-1 cells overexpressing HIF-2a

hyb_protocol: Affymetrix GeneChip Hybridisation, Wash and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix Expression Console Software

label: biotin

source_name: LP-1 human myeloma cell line

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay

extract_protocol: RNA was extracted from LP-1-pRUF and LP-1-HIF2A cell lines using TRIzol, following the manufacturer's instructions and the RNA was further purified using an RNeasy kit (Qiagen).

treatment_protocol: LP-1 cell lines stably overexpressing HIF-2α were generated by infection with the vector pRUF-IRES-GFP harbouring full-length cDNA encoding human HIF-2α and overexpression was confirmed by Western blot.

tag: vector


title: Absence_of_Perineural_Invasion_5_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_5_tumor

source_name: without PNI,patient 5,tumor tissue


title: Perineural_Invasion_6_normal

description: Gene_expression_of_Perineural_Invasion_6_normal

source_name: with PNI,patient 6,normal tissue


title: Absence_of_Perineural_Invasion_3_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_3_tumor

source_name: without PNI,patient 3,tumor tissue


title: Absence_of_Perineural_Invasion_3_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_3_normal

source_name: without PNI,patient 3,normal tissue


title: Absence_of_Perineural_Invasion_5_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_5_normal

source_name: without PNI,patient 5,normal tissue


title: Absence_of_Perineural_Invasion_8_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_8_normal

source_name: without PNI,patient 8,normal tissue


title: Absence_of_Perineural_Invasion_7_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_7_normal

source_name: without PNI,patient 7,normal tissue


title: Absence_of_Perineural_Invasion_6_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_6_tumor

source_name: without PNI,patient 6,tumor tissue


title: Perineural_Invasion_8_tumor

description: Gene_expression_of_Perineural_Invasion_8_tumor

source_name: with PNI,patient 8,tumor tissue


title: Absence_of_Perineural_Invasion_4_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_4_tumor

source_name: without PNI,patient 4,tumor tissue


title: Perineural_Invasion_10_tumor

description: Gene_expression_of_Perineural_Invasion_10_tumor

source_name: with PNI,patient 10,tumor tissue


title: Perineural_Invasion_5_normal

description: Gene_expression_of_Perineural_Invasion_5_normal

source_name: with PNI,patient 5,normal tissue


title: Perineural_Invasion_5_tumor

description: Gene_expression_of_Perineural_Invasion_5_tumor

source_name: with PNI,patient 5,tumor tissue


title: Absence_of_Perineural_Invasion_2_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_2_tumor

source_name: without PNI,patient 2,tumor tissue


title: Perineural_Invasion_7_tumor

description: Gene_expression_of_Perineural_Invasion_7_tumor

source_name: with PNI,patient 7,tumor tissue


title: Absence_of_Perineural_Invasion_1_tumor

description: Gene_expression_of_Absence_of_Perineural_Invasion_1_tumor

source_name: without PNI,patient 1,tumor tissue


title: Absence_of_Perineural_Invasion_4_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_4_normal

source_name: without PNI,patient 4,normal tissue


title: Perineural_Invasion_4_tumor

description: Gene_expression_of_Perineural_Invasion_4_tumor

source_name: with PNI,patient 4,tumor tissue


title: Absence_of_Perineural_Invasion_6_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_6_normal

source_name: without PNI,patient 6,normal tissue


title: Absence_of_Perineural_Invasion_2_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_2_normal

source_name: without PNI,patient 2,normal tissue


title: Perineural_Invasion_2_tumor

description: Gene_expression_of_Perineural_Invasion_2_tumor

source_name: with PNI,patient 2,tumor tissue


title: Perineural_Invasion_6_tumor

description: Gene_expression_of_Perineural_Invasion_6_tumor

source_name: with PNI,patient 6,tumor tissue


title: LP-1-pRUF

description: Gene expression data from vector control LP-1 cells

source_name: LP-1 human myeloma cell line

value: pRUF-IRES-GFP


title: Perineural_Invasion_7_normal

description: Gene_expression_of_Perineural_Invasion_7_normal

source_name: with PNI,patient 7,normal tissue


title: Perineural_Invasion_3_normal

description: Gene_expression_of_Perineural_Invasion_3_normal

source_name: with PNI,patient 3,normal tissue


title: Perineural_Invasion_4_normal

description: Gene_expression_of_Perineural_Invasion_4_normal

source_name: with PNI,patient 4,normal tissue


title: Perineural_Invasion_2_normal

description: Gene_expression_of_Perineural_Invasion_2_normal

source_name: with PNI,patient 2,normal tissue


title: C3_122215

status: Public on Aug 03 2017

city: Laurel

first: Atin

last: Datta

state: MD

address: 8301 Muirkirk Rd

department: CFSAN/DVA

country: USA

institute: FDA

description: Gene expression data from L. monocytogenes at stationary phase on cut cantaloupe at 10°C

hyb_protocol: Labeled cDNA was hybridized to the Listeria GeneAtlas Array strip for 17h at 45°C

scan_protocol: Array strips were scanned using the GeneAtlas instrument control software.

data_processing: Background correction nad normalization were performed using the RMA method of probe level data sumarization.

organism: Listeria monocytogenes

source_name: LS670 at stationary phase on cut cantaloupe at 10°C

label_protocol: cDNA obtained from the RNA using Superscript II Reverse Transcriptase was labeled with biotin-11-ddATP on its 3' end.

growth_protocol: Listeria monocytogenes was grown to stationary phase at 10°C

extract_protocol: Cells were pre-treated with lysocyme and proteinase K. Polyvinylpyrriodilone was added prior to RNA extraction using the RiboPure-Bacteria RNA purification kit (Thermo Fisher) with a modification to the manufacturer's protocol extending the bead beating step to 30 minutes.

treatment_protocol: Growth occurred in BHI broth (control) or cantaloupe (treatment)

tag: strain

tag: growth phase

value: stationary

tag: culture type

value: cut cantaloupe


title: Absence_of_Perineural_Invasion_1_normal

description: Gene_expression_of_Absence_of_Perineural_Invasion_1_normal

source_name: without PNI,patient 1,normal tissue


title: CP392


title: CP192


title: C3_12915


title: CP2827


title: Perineural_Invasion_1_tumor

description: Gene_expression_of_Perineural_Invasion_1_tumor

source_name: with PNI,patient 1,tumor tissue


title: Perineural_Invasion_12_tumor

description: Gene_expression_of_Perineural_Invasion_12_tumor

source_name: with PNI,patient 12,tumor tissue


title: Perineural_Invasion_3_tumor

description: Gene_expression_of_Perineural_Invasion_3_tumor

source_name: with PNI,patient 3,tumor tissue


title: CP1827


title: Perineural_Invasion_1_normal

description: Gene_expression_of_Perineural_Invasion_1_normal

source_name: with PNI,patient 1,normal tissue


title: C2_12915


title: CP492


title: C1_122215


title: C2_122215


title: C1_12915


title: B3715

description: Gene expression data from L. monocytogenes at stationary phase in BHI broth at 10°C

source_name: LS670 at stationary phase in BHI broth at 10°C

value: BHI broth


title: B3_12915


title: B2_122215


title: B2715


title: B1721


title: B1_12915


title: B1_122215


title: B1715


title: Treated group 3

city: Nanjing

first: Yabing

last: Chen

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu

institute: Nanjing University

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

organism: Mus musculus

source_name: GT1-7 treated with MC-LR

label_protocol: The miRCURY™ Hy3™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: Cell were clutured in DMEM medium with 10% FBS

extract_protocol: RNA were extracted with Trizol.

treatment_protocol: Cell were treated with or without 500 nm MC-LR.

tag: cell line

value: GT1-7 cells

tag: cell type

value: Mouse Hypothalamic GnRH Neuronal Cell Line

tag: treated with

value: MC-LR for 24 h


title: B3_122215


title: Control group 3

value: vehicle


title: Control group 2


title: Treated group 1


title: Control group 1


title: Treated group 2


title: B2721


title: B2_12915


title: Sibling 18 - GDM unexposed

type: genomic

city: Seongnam

first: Hak Chul

last: Jang

address: 82, Gumi-ro 173beon-gil, Bundang-gu

department: Department of internal medicine

country: South Korea

institute: Seoul National University Bundang Hospital

description: SAMPLE 35

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

scan_protocol: Illumina iScan standard protocol

data_processing: .idat file were loaded using RnBeads R-package. Detection p-value > 0.01, SNP-containing, outside-CpG-context and sex-chromosome-located probes were filtered and data were noralized using BMIQ.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted according to the manufacturer's instructions.

tag: gender

value: M

tag: age

tag: group

value: Non-GDM

tag: sibling


title: Sibling 16 - GDM exposed

description: SAMPLE 32

value: F

value: GDM


title: Sibling 18 - GDM exposed

description: SAMPLE 36


title: Sibling 14 - GDM unexposed

description: SAMPLE 27


title: Sibling 16 - GDM unexposed

description: SAMPLE 31


title: Sibling 8 - GDM unexposed

description: SAMPLE 15


title: Sibling 13 - GDM exposed

description: SAMPLE 26


title: Sibling 15 - GDM unexposed

description: SAMPLE 29


title: Sibling 12 - GDM exposed

description: SAMPLE 24


title: Sibling 17 - GDM unexposed

description: SAMPLE 33


title: Sibling 15 - GDM exposed

description: SAMPLE 30


title: Sibling 8 - GDM exposed

description: SAMPLE 16


title: Sibling 7 - GDM unexposed

description: SAMPLE 13


title: Sibling 11 - GDM unexposed

description: SAMPLE 21


title: Sibling 10 - GDM unexposed

description: SAMPLE 19


title: Sibling 5 - GDM unexposed

description: SAMPLE 9


title: Sibling 9 - GDM exposed

description: SAMPLE 18


title: Sibling 6 - GDM exposed

description: SAMPLE 12


title: Sibling 13 - GDM unexposed

description: SAMPLE 25


title: Sibling 14 - GDM exposed

description: SAMPLE 28


title: Sibling 12 - GDM unexposed

description: SAMPLE 23


title: Sibling 10 - GDM exposed

description: SAMPLE 20


title: Sibling 5 - GDM exposed

description: SAMPLE 10


title: WT_HCT-116_Nutreated_rep1

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

country: France

institute: CNRS

description:
Gene expression in control parental HCT-116 cells treated with 20 micromolar NU6102 for 24h
WT_NU_1

hyb_protocol: Cy3-labelled RNA was fragmented by denaturation at 60°C for 30 minutes, and 600 ng was hybridised at 65°C for 17h to SurePrint G3 Human GE v2 8x60K Microarrays

scan_protocol: Slides were scanned using the G2505C Scanner (Agilent) with the following parameters: dye channel G, Region Agilent HD (61 x 21.6mm), resolution 3µM, PMI gain 100%

data_processing: Scanned images were analyzed with Feature Extraction 11.5.1.1, with included features uniform non-outlier, non-saturated and above background

label_protocol: Labelling was performed by linear amplification on 100 ng of total RNA, using the Low Input Quick amp one-color kit (Agilent) followed by purification using the Rneasy mini kit (Qiagen). Yield of >600ng and specific activity >15pmol Cy3/µg RNA were verified using the Nanodrop ND-1000.  Analysis of size distribution uniformity was performed using the Bioanalyser 2100.

growth_protocol: Cells were grown in 10% FBS in DMEM at 37°C in a CO2 controlled incubator

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen) according to manufacturer's instructions, quantified using a Nanodrop ND-1000 and the integrity verified using a Bioanalyzer 2100. The RNA integrity number was between 9.80 and 9.90 for all samples.

treatment_protocol: Cells were untreated (WT, KO) or treated for 24h with 20 micromolar NU6102 (WT_NU) or maintained in 50 micromolar NU6102 (R50)

value: cultured HCT-116 colorectal cancer cells

tag: treatment

value: 20 micromolar NU6102 for 24h


title: Sibling 11 - GDM exposed

description: SAMPLE 22


title: Sibling 6 - GDM unexposed

description: SAMPLE 11


title: Sibling 17 - GDM exposed

description: SAMPLE 34


title: R50_HCT-116_rep2

description:
Gene expression in NU-6102-resistant R50 HCT-116 cells, exponential growth
R50_2

source_name: HCT-116 cells resistant to 50 micromolar NU6102

value: maintained in 50 micromolar NU6102


title: Sibling 4 - GDM exposed

description: SAMPLE 8


title: WT_HCT-116_Nutreated_rep2

description:
Gene expression in control parental HCT-116 cells treated with 20 micromolar NU6102 for 24h
WT_NU_2


title: Sibling 4 - GDM unexposed

description: SAMPLE 7


title: Sibling 7 - GDM exposed

description: SAMPLE 14


title: Sibling 9 - GDM unexposed

description: SAMPLE 17


title: Sibling 3 - GDM exposed

description: SAMPLE 6


title: WT_HCT-116_rep1

description:
Gene expression in control parental HCT-116 cells, exponential growth
WT_1

source_name: Parental HCT-116 cells

tag: genotype/variation

value: control parental


title: CDK2_KO_HCT-116_rep2

description:
Gene expression in CDK2 knockout HCT-116 cells, exponential growth
KO_2

source_name: CDK2 knockout HCT-116 cells

value: CDK2 knockout


title: CDK2_KO_HCT-116_rep1

description:
Gene expression in CDK2 knockout HCT-116 cells, exponential growth
KO_1


title: R50_HCT-116_rep1

description:
Gene expression in NU-6102-resistant R50 HCT-116 cells, exponential growth
R50_1


title: H9 MVs rep 3

city: Los Angeles

first: Debora

last: Farber

state: California

address: 100 Stein Plaza

department: Ophthalmology, Stein Eye Institute

institute: University of California Los Angeles

description:
Gene expression data from microvesicles derived from human H9 embryonic stem cells.
Collection protocol: After two cleaning spins at 200g for 10 min then at 2,800g for 40min, the culture medium was spun at 16,500g for 1h at 4°C. The pellet contains Microvesicles.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45 °C on Affymetrix® HG-U133 Plus 2.0 Arrays. GeneChips were washed and stained with Streptavidin Phycoerythrin (SAPE) in the Affymetrix Fluidics station (model 450).

scan_protocol: GeneChips were scanned with the Affymetrix 7G scanner. The Affymetrix GeneChip Command Console 4.0 (AGCC) was used for controlling the system and acquisition of array images.

data_processing: Data was processed with Affymetrix MAS5 with TGT500.

label_protocol: Biotin labeled aRNA were prepared according to the standard Affymetrix protocol from 12.5ug aRNA.

growth_protocol: H9 hESCs were cultured under serum-free and feeder-free conditions in mTeSR™1 medium on Matrigel-coated T75 culture flasks and kept in a humidified 37 C, 5% CO2 incubator. Culture medium was changed daily and collected every 24 hours for ESEV isolation and fractionation once cells reached 70-80% confluence.

extract_protocol: Total RNA was extracted from hESEVs, MVs and EXOs with the mirVana miRNA Isolation Kit (Ambion).

treatment_protocol: The hESC culture medium was collected after 24 hours at 80% confluence and spun for 10 minutes at 300g to pellet debris and fragmented cells. The supernatant was centrifuged at 2,800g for 40 minutes to separate the apoptotic bodies, followed by two ultracentrifugation steps using a Beckman Type 50.2 TI rotor, the first one at 16,500g for 1 hour at 4 C to pellet MVs and the last step at 120,000g for 2 hours at 4 C for pelleting the EXOs. For collecting non-fractionated hESEVs, after a spin at 300 g for 10 minutes, culture medium from H9 hESCs maintained at 80% confluence was transferred to an ultracentrifuge tube and directly spun at 120,000g for 2 hours in a Beckman Type 50.2 TI rotor at 4 C to pellet non-fractionated hESEVs.

value: microvesicles


title: H9 hESEV rep 3

description:
Gene expression data from non-fractionated extracellular vesicles derived from human H9 embryonic stem cells.
Collection protocol: After a cleaning spin at 300g for 10min, the culture medium was spun at 120,000g for 2h at 4°C. The pellet contains non-fractionated extracellular vesicles.

value: non-fractionated extracellular vesicles


title: H9 hESEV rep 1

source_name: non-fractionated extracellular vesicles derived from human H9 embryonic stem cells


title: WT_HCT-116_rep2

description:
Gene expression in control parental HCT-116 cells, exponential growth
WT_2


title: Sibling 3 - GDM unexposed

description: SAMPLE 5


title: H9 hESEV rep 2


title: H9 MVs rep 2

source_name: microvesicles derived from human H9 embryonic stem cells


title: H9 EXOs rep 1

description:
Gene expression data from exosomes derived from human H9 embryonic stem cells.
Collection protocol: The supernatant from the microvesicle collection step was spun at 120,000g for 2h at 4°C. The pellet contains exosomes.

value: exosomes


title: H9 EXOs rep 2

source_name: exosomes derived from human H9 embryonic stem cells


title: H9 MVs rep 1


title: H9 EXOs rep 3


title: Sibling 2 - GDM exposed

description: SAMPLE 4


title: Human_normal_P168

status: Public on Aug 01 2017

city: Columbus

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

description: Gene expression data

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix). Heat 65C for 5 minutes, 99C for 5 minutes, 45C for 5 minutes centrifuge top speed for 5 minutes. Hybridize 16 hours at 45°C at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and GC-RMA as normalization method.

source_name: Epithelial cells from normal breast tissue

label_protocol: 5.5 ug of single stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted using the TriplePure High Impact Zirconium beads and Rneasy Plus Mini kit according to the manufacturer's instructions.

tag: race

value: white

tag: bmi


title: Human_normal_P166

description: Gene expression data

value: black


title: Human_normal_P163

description: Gene expression data


title: Human_normal_P159

description: Gene expression data


title: Human_normal_P165

description: Gene expression data


title: Human_normal_P156

description: Gene expression data


title: Human_normal_P167

description: Gene expression data


title: Human_normal_P140

description: Gene expression data


title: Human_normal_P157

description: Gene expression data


title: Sibling 1 - GDM unexposed

description: SAMPLE 1


title: Human_normal_P155

description: Gene expression data


title: Human_normal_P130

description: Gene expression data


title: Human_normal_P131

description: Gene expression data


title: Human_normal_P158

description: Gene expression data


title: Human_normal_P126

description: Gene expression data


title: Human_normal_P161

description: Gene expression data


title: Human_normal_P139

description: Gene expression data


title: Human_normal_P121

description: Gene expression data


title: Human_normal_P127

description: Gene expression data


title: Human_normal_P123

description: Gene expression data


title: Human_normal_P162

description: Gene expression data


title: Sibling 1 - GDM exposed

description: SAMPLE 2


title: Human_normal_P125

description: Gene expression data


title: Human_normal_P138

description: Gene expression data


title: Human_normal_P119

description: Gene expression data


title: Human_normal_P124

description: Gene expression data


title: Human_normal_P113

description: Gene expression data


title: Human_normal_P115

description: Gene expression data


title: Human_normal_P116

description: Gene expression data


title: Human_normal_P111

description: Gene expression data


title: Human_normal_P90

description: Gene expression data


title: Human_normal_P105

description: Gene expression data


title: Sibling 2 - GDM unexposed

description: SAMPLE 3


title: Human_normal_P108

description: Gene expression data

value: other


title: Human_normal_P120

description: Gene expression data


title: Human_normal_P117

description: Gene expression data


title: Human_normal_P107

description: Gene expression data


title: Human_normal_P109

description: Gene expression data


title: Human_normal_P94

description: Gene expression data


title: Human_normal_P114

description: Gene expression data


title: Human_normal_P96

description: Gene expression data


title: Human_normal_P88

description: Gene expression data


title: Human_normal_P104

description: Gene expression data


title: Human_normal_P103

description: Gene expression data


title: Human_normal_P95

description: Gene expression data


title: Human_normal_P91

description: Gene expression data


title: Human_normal_P106

description: Gene expression data


title: Human_normal_P82

description: Gene expression data


title: Human_normal_P87

description: Gene expression data


title: Human_normal_P78

description: Gene expression data


title: Human_normal_P100

description: Gene expression data


title: Human_normal_P93

description: Gene expression data


title: Human_normal_P83

description: Gene expression data


title: Human_normal_P85

description: Gene expression data


title: Human_normal_P101

description: Gene expression data


title: Human_normal_P81

description: Gene expression data


title: Human_normal_P76

description: Gene expression data


title: Human_normal_P72

description: Gene expression data


title: Human_normal_P71

description: Gene expression data


title: Human_normal_P66

description: Gene expression data


title: Human_normal_P74

description: Gene expression data


title: Human_normal_P73

description: Gene expression data


title: Human_normal_P69

description: Gene expression data


title: Human_normal_P67

description: Gene expression data


title: Human_normal_P60

description: Gene expression data


title: Human_normal_P61

description: Gene expression data


title: Human_normal_P62

description: Gene expression data


title: Human_normal_P70

description: Gene expression data


title: Human_normal_P55

description: Gene expression data


title: Human_normal_P58

description: Gene expression data


title: Human_normal_P50

description: Gene expression data


title: Human_normal_P51

description: Gene expression data


title: Human_normal_P57

description: Gene expression data


title: Human_normal_P68

description: Gene expression data


title: Human_normal_P45

description: Gene expression data


title: Human_normal_P46

description: Gene expression data


title: Human_normal_P59

description: Gene expression data


title: Human_normal_P56

description: Gene expression data


title: Human_normal_P65

description: Gene expression data


title: Human_normal_P43

description: Gene expression data


title: Human_normal_P44

description: Gene expression data


title: Human_normal_P42

description: Gene expression data


title: Human_normal_P41

description: Gene expression data


title: Human_normal_P52

description: Gene expression data


title: Human_normal_P40

description: Gene expression data


title: Human_normal_P49

description: Gene expression data


title: Human_normal_P39

description: Gene expression data


title: Human_normal_P35

description: Gene expression data


title: Human_normal_P34

description: Gene expression data


title: Human_normal_P37

description: Gene expression data


title: Human_normal_P28

description: Gene expression data


title: Human_normal_P31

description: Gene expression data


title: Human_normal_P26

description: Gene expression data


title: Human_normal_P33

description: Gene expression data


title: Human_normal_P25

description: Gene expression data


title: Human_normal_P30

description: Gene expression data


title: Human_normal_P36

description: Gene expression data


title: Human_normal_P21

description: Gene expression data


title: Human_normal_P27

description: Gene expression data


title: Human_normal_P19

description: Gene expression data


title: Human_normal_P18

description: Gene expression data


title: Human_normal_P24

description: Gene expression data


title: Human_normal_P15

description: Gene expression data


title: Human_normal_P20

description: Gene expression data


title: Human_normal_P12

description: Gene expression data


title: Human_normal_P8

description: Gene expression data


title: Human_normal_P11

description: Gene expression data


title: Human_normal_P17

description: Gene expression data


title: Human_normal_P9

description: Gene expression data


title: Human_normal_P7

description: Gene expression data


title: Human_normal_P5

description: Gene expression data


title: Human_normal_P16

description: Gene expression data


title: Human_normal_P2

description: Gene expression data


title: Human_normal_P10

description: Gene expression data


title: Human_normal_P6

description: Gene expression data


title: HGSC_JH993

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

hyb_protocol: The amplified DNA is then fragmented, labeled, and hybridized to a SNP Array 6.0 containing more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation.

scan_protocol: All 96 samples were assayed at once, in a single batch

data_processing:
The Affy Power Tools (APT) copy number workflow was used to preprocess the SNP arrays and derive log R ratios representing relative copy number abundance.  A standard HapMap reference included in the APT toolbox was used to represent a diploid genome. Circular binary segmentation (CBS) as implemented in the DNAcopy  (Seshan VE and Olshen A. DNAcopy: DNA copy number data analysis. R package version 1.42.0) package from Bioconductor, using standard settings
The GISTIC2.0 algorithm was applied to the segmented data via the Genome Pattern online tool suite, using default settings, to make gene level copy number calls and identify significantly, copy number altered regions

source_name: primary ovarian tumor tissue

label_protocol: Total genomic DNA (500 ng) was collected from all 96 samples included in the study, and digested with Nsp I and Sty I restriction enzymes and ligated to adaptors.

extract_protocol: DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.).  DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.

tag: stic

value: No

value: IIIA

value: Optimal

value: Ovarian Ca

tag: platinumstatus

value: Sensitive

tag: recurrence

value: N

tag: vitalstatus

value: Alive

value: WHITE

tag: tissue

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_RG953

value: IIIC


title: HGSC_JH1075

value: Yes

value: IV

value: Suboptimal

value: Y


title: HGSC_JH1072

value: ASIAN


title: HGSC_JH1069

value: IIC

value: OTHER


title: Cre(+) VSMC KO 2

city: ANN ARBOR

first: Tae-Hwa

last: Chun

state: MI

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

institute: University of Michigan

description: Gene expressio data from MT1-MMP(−)Apoe(−) VSMCs

hyb_protocol: Following Labeling procedure, 3.75 ug of cDNA were hybridized at 48C on Mouse Gene  ST 2.1 arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267).

data_processing: Data was analyzed using the oligo bioconductor package implemented in the R-statistical environment version 3.1.1. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: VSMCs from SM22α-Cre(+)Mmp14(fl/fl)Apoe(−/− )

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6).

growth_protocol: Mouse thoracic aortas were dissected and adventitia was removed. The aorta was cut into small pieces and digested in type II collagenase. Harvested cells were cultured for five days in high glucose DMEM with 10% FBS and the identify of VSMCs was confirmed with the staining of smooth muscle alpha actin, calponin, and smoothelin.

extract_protocol: Total RNA was extracted with Rneasy Mini Kit (Qiagen)

treatment_protocol: Cre-dependent deletion of MT1-MMP in VSMCs in vivo

value: aorta

value: primary vascular smooth muscle cells (VSMCs)

tag: genotype

value: SM22α-Cre(+)Mmp14(fl/fl)Apoe(−/− )


title: Cre(−) control 2

description: Gene expressio data from MT1-MMP(+)Apoe(−) VSMCs

source_name: VSMCs from SM22α-Cre(−)Mmp14(fl/fl)Apoe(−/− )

value: SM22α-Cre(−)Mmp14(fl/fl)Apoe(−/− )


title: HGSC_JH1085

value: No

value: IA

value: Optimal

value: Ovarian Ca

value: Sensitive


title: Cre(+) VSMC KO 1


title: HGSC_JB5962

value: IIIC

value: Fallopian Tube Ca

value: Resistant

value: N

value: Alive

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5893

value: Yes

value: Fallopian tube Ca


title: HGSC_JB5861

value: IV


title: HGSC_JB5982


title: Human_normal_P4

description: Gene expression data

value: black


title: hSC-2

city: Hong Kong

first: Sally

last: Cai

address: Sassoon Road

institute: The University of Hong Kong

description:
Sample 8
replicate to Sample 4

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Human HT-12 v4.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array probes transformed by logarithm and normalized by quantile method.

source_name: human SCs

label_protocol: Total RNA was amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (EPICENTRE, Madison, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: RNA was extracted with Trizol reagent.

value: adult human Schwann cell


title: hSC-1

description:
Sample 7
Sample 4


title: hBMSC-dSC-1

description:
Sample 5
Sample 3

source_name: human bone marrow stromal cell-derived Schwann cell


title: Human_normal_P1

description: Gene expression data


title: hBMSC-dSC-2

description:
Sample 6
replicate to Sample 3

value: human bone marrow stromal cell-derived Schwann cell


title: HGSC_JH1035

value: Unknown

value: Endometrial cancer


title: HGSC_JB5567

value: No

value: Optimal

value: Ovarian Ca

value: Y


title: HGSC_JB5617

value: IIIC

value: Fallopian Tube Ca

value: Sensitive


title: HGSC_JB5585

value: Resistant

value: Dead

value: WHITE


title: HGSC_JB5615

value: Alive

value: ASIAN

value: primary tumor tissue from high grade serous ovarian tumors


title: Cre(−) control 1

value: aorta

value: primary vascular smooth muscle cells (VSMCs)

value: SM22α-Cre(−)Mmp14(fl/fl)Apoe(−/− )


title: HGSC_JB5860


title: HGSC_JB5548

value: Yes


title: SCLC_2

description:
Sample 4
replicate to Sample 2

source_name: Schwann cell-like cell

value: Schwann cell-like cell


title: hBMSC_2

description:
Sample 2
replicate to Sample 1

source_name: human bone marrow stromal cell

value: human bone marrow stromal cell


title: SCLC_1

description:
Sample 3
Sample 2


title: hBMSC_1

description:
Sample 1
Sample 1


title: HGSC_JH1066

value: No

value: Optimal

value: Ovarian Ca

value: N

value: OTHER


title: HGSC_JB5439

value: IIIC

value: Suboptimal

value: Fallopian Tube Ca

value: Sensitive

value: BLACK


title: HGSC_JB5427

value: IV

value: Y

value: Alive

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5523

value: Yes

value: Resistant

value: Dead


title: HGSC_JB5841

value: Optimal


title: HGSC_JB5287

value: Ovarian Ca


title: HGSC_JB5565


title: HGSC_JB5506

value: No


title: HGSC_JB5471


title: HGSC_JB5268

value: Not available

value: N


title: HGSC_JB5234


title: HGSC_JB5223

value: IIIC


title: HGSC_JB5214


title: HGSC_JB5087

value: Fallopian Tube Ca


title: HGSC_JB4976

value: Sensitive


title: HGSC_JB5051


title: HGSC_JB5019


title: HGSC_JB5318


title: HGSC_JH1048


title: HGSC_JB5588


title: HGSC_JB4952

value: Peritoneum Ca NOS


title: HGSC_JB5326

value: IV


title: HGSC_JB5143

value: Y


title: HGSC_JB5464

value: Alive


title: HGSC_JB4900

value: WHITE


title: HGSC_JB5537

value: Suboptimal

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB4887


title: HGSC_JB5516

value: Yes


title: HGSC_JB4904

value: Dead


title: HGSC_JB4853

value: IIC

value: Optimal


title: HGSC_JB4998

value: No

value: Ovarian Ca


title: HGSC_JB4860


title: HGSC_JB4962

value: ASIAN


title: HGSC_JB4878

value: N


title: HGSC_JB4960

value: Fallopian Tube Ca


title: HGSC_JB4912

value: IIIC

value: Sensitive


title: HGSC_JB4833


title: HGSC_JB5293


title: HGSC_JB5276

value: IV


title: HGSC_JB4744

value: OTHER


title: HGSC_JB4886

value: Alive


title: HGSC_JB4841

value: IIIB

value: WHITE


title: HGSC_JB4838

value: Y

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB4757

value: Dead


title: HGSC_JB4675

value: Yes

value: Resistant


title: HGSC_JB4442

value: Optimal


title: HGSC_JB4733


title: HGSC_JB4548

value: Ovarian Ca


title: HGSC_JB4684


title: HGSC_JB4752

value: No


title: HGSC_JB4674

value: Peritoneum Ca NOS


title: Diet enriched with beta-glukan 1 replicate 4

city: Warsaw

first: Dariusz

last: Kamola

address: Nowoursynowska 159

department: Faculty of Veterinary Medicine

country: Poland

institute: Warsaw University of Life Sciences

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_1_3

hyb_protocol: according to the Agilent manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: Diet enriched with beta-glukan 1

extract_protocol: Total RNA extracted using  RNeasy Protect Animal Blood System (Quiagen), according manufacturer's protocol

tag: strain

value: Sprague Dawley (from Charles River)

tag: diet

value: Diet enriched with beta-glukan 1 (GI)

tag: inflammation induction

value: control

value: blood

source_name: common reference sample composed of total RNAs isolated from all rats participating in the experiment (100 ng total RNA from all samples)

value: total RNAs pooled from all rats participating in the experiment


title: Diet enriched with beta-glukan 2 replicate 4

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_2_2

source_name: Diet enriched with beta-glukan 2

label_protocol: according to the Agilent manufacturer's protocol

value: Diet enriched with beta-glukan 2 (GII)


title: HGSC_JB 5768

value: IV

value: Fallopian Tube Ca

value: Sensitive

value: Alive


title: Diet enriched with beta-glukan 2 with LPS injection replicate 3

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_2_3

value: LPS injection


title: Control Diet replicate 4

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_1_1

source_name: Control Diet

value: Control Diet


title: Diet enriched with beta-glukan 2 replicate 3

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_2_1


title: Diet enriched with beta-glukan 1 with LPS injection replicate 3

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_2_2


title: Control Diet with LPS injection replicate 3

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_1_2

source_name: Control Diet with LPS injection


title: Diet enriched with beta-glukan 2 replicate 2

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_2_3


title: HGSC_JB4234

value: Yes

value: IIIC

value: Y

value: Dead

value: ASIAN

value: primary tumor tissue from high grade serous ovarian tumors


title: Diet enriched with beta-glukan 1 with LPS injection replicate 2

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_2_1

value: Sprague Dawley (from Charles River)

value: Diet enriched with beta-glukan 1 (GI)


title: Control Diet with LPS injection replicate 4

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_1_2

value: control

value: blood


title: Diet enriched with beta-glukan 2 with LPS injection replicate 4

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_2_4

value: Diet enriched with beta-glukan 2 (GII)

value: total RNAs pooled from all rats participating in the experiment


title: HGSC_JB 5727

value: Optimal

value: Ovarian Ca

value: Fallopian Tube Ca

value: N

value: HISPANIC


title: Diet enriched with beta-glukan 2 with LPS injection replicate 2

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_2_4

value: LPS injection


title: Diet enriched with beta-glukan 1 replicate 2

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_1_3


title: Diet enriched with beta-glukan 2 replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_2_3


title: HGSC_JB 5685

value: Yes

value: IIIC

value: Sensitive

value: Alive

value: WHITE


title: HGSC_GL5113

value: No

value: Y

value: primary tumor tissue from high grade serous ovarian tumors


title: Diet enriched with beta-glukan 1 with LPS injection replicate 4

description:
Biological replication
US10353831_252827910504_S01_GE2_1010_Sep10_1_4

value: Sprague Dawley (from Charles River)

value: Diet enriched with beta-glukan 1 (GI)

value: blood


title: Control Diet replicate 3

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_1_1

value: Control Diet

value: control

value: total RNAs pooled from all rats participating in the experiment


title: HGSC_40208

value: III

value: Suboptimal

value: Not available

value: Dead


title: HGSC_331T

value: IIIC

value: Optimal

value: Ovarian Ca


title: HCT116 SCD1 KO cell

city: Fujisawa

first: Akito

last: Ono

address: Muraoka-higashi 2-26-1

country: Japan

institute: Takeda Pharmaceutical company

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array.Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: HCT116 colorectal cancer cells, SCD1 was knocked-out

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HCT-116 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, and 1× penicillin/streptomycin at 37 °C and 5% CO2.

extract_protocol: Extraction of total RNA was performed using RNeasy Mini Kit (QIAGEN).

treatment_protocol: Cells were treated with DMSO or SCD1 inhibitor for 24 h.

tag: cell line

value: colon

value: SCD1 was knocked-out


title: Diet enriched with beta-glukan 1 replicate 3

description:
Biological replication
US10353831_252827910983_S01_GE2_1010_Sep10_1_4


title: HCT116 WT treated with DMSO

source_name: HCT116 colorectal cancer cells, DMSO treated, 24 h

value: DMSO treated, 24 h


title: HGSC_914T

value: No

tag: age

value: N

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: Control Diet with LPS injection replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_1_3

value: Sprague Dawley (from Charles River)

value: Control Diet

value: LPS injection

value: blood

tag: group


title: Control Diet replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_1_1

value: control

value: total RNAs pooled from all rats participating in the experiment


title: HGSC_40201

value: Not available

value: Y


title: HGSC_40202

value: III

value: Suboptimal

value: Dead


title: Diet enriched with beta-glukan 1 replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_2_1

value: Diet enriched with beta-glukan 1 (GI)


title: Diet enriched with beta-glukan 1 with LPS injection replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_2_2


title: HCT116 WT treated with SCD1 inhibitor

source_name: HCT116 colorectal cancer cells, SCD1 inhibitor treated, 24 h

value: colon

value: SCD1 inhibitor treated, 24 h


title: Control Diet with LPS injection replicate 2

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_1_4


title: HGSC_JB 5705

value: Yes

value: IIIC

value: Optimal

value: Ovarian Ca

value: Fallopian Tube Ca

value: Sensitive

value: N

value: Alive


title: Diet enriched with beta-glukan 2 with LPS injection replicate 1

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_2_4

value: Sprague Dawley (from Charles River)

value: Diet enriched with beta-glukan 2 (GII)

value: LPS injection

value: blood

value: total RNAs pooled from all rats participating in the experiment


title: HGSC_323T

value: No

value: Y

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_GL4490

value: Yes

value: BLACK


title: HGSC_40211

value: III

value: Suboptimal

value: Not available

value: Dead


title: HGSC_40207

value: Optimal


title: HGSC_GL4226

value: IIIC

value: Ovarian Ca

value: Sensitive

value: Alive


title: HGSC_222T


title: HGSC_40209


title: HGSC_40199


title: HGSC_40204


title: HGSC_40203


title: HGSC_40206


title: HGSC_40200


title: HGSC_40190


title: HGSC_40197


title: HGSC_40193

value: II

value: Unknown


title: HGSC_40191

value: No


title: HGSC_40187

value: Y


title: Control Diet replicate 2

description:
Biological replication
US10353831_252827910984_S01_GE2_1010_Sep10_1_2

value: Sprague Dawley (from Charles River)

value: Control Diet

value: control

value: blood

value: total RNAs pooled from all rats participating in the experiment


title: CD3_Transcripts-R.17Siro.F

city: Seattle

first: Victor

last: Tkachev

state: Washington

address: 1100 Olive way, suite 100

institute: Seattle Children's Research Institute Ben Towne Center for Childhood Cancer Research

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array.  GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade.

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘affy’ package).  Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package.

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of NHP received either an allogeneic or autologous HCT.  Allogeneic HCT recipients received various immunoprophylactic treatments for prevention of GVHD.  CD3 T cells were sorted by FACS from peripheral blood at various timepoints in the post transplant period and from healthy controls.

tag: ID

tag: day post hct

tag: batch


title: CD3_Transcripts-R.16Siro.F

department: Ben Towne Center for Childhood Cancer Research


title: CD3_Transcripts-R.20Tac.Mtx.F


title: CD3_Transcripts-R.221KY1005.Siro.D28


title: CD3_Transcripts-R.219KY1005.Siro.D28


title: CD3_Transcripts-R.50NoRx.F


title: CD3_Transcripts-R.20Tac.Mtx.D14


title: CD3_Transcripts-R.19Tac.Mtx.D14


title: CD3_Transcripts-R.21Tac.Mtx.F


title: CD3_Transcripts-R.221KY1005.Siro.F


title: CD3_Transcripts-R.221KY1005.Siro.D14


title: CD3_Transcripts-R.220KY1005.Siro.D14


title: CD3_Transcripts-R.52NoRx.F


title: CD3_Transcripts-R.53NoRx.F


title: CD3_Transcripts-R.217KY1005.Siro.F


title: CD3_Transcripts-R.219KY1005.Siro.F


title: CD3_Transcripts-R.219KY1005.Siro.D14


title: CD3_Transcripts-R.21Tac.Mtx.D14


title: CD3_Transcripts-R.13Siro.F


title: CD3_Transcripts-R.19Tac.Mtx.F


title: CD3_Transcripts-R.51NoRx.F


title: CD3_Transcripts-R.217KY1005.Siro.D28


title: CD3_Transcripts-R.218KY1005.Siro.D28


title: CD3_Transcripts-R.220KY1005.Siro.F


title: CD3_Transcripts-R.18Siro.F


title: CD3_Transcripts-R.220KY1005.Siro.D28


title: CD3_Transcripts-R.217KY1005.Siro.D14


title: CD3_Transcripts-R.212KY1005.F


title: CD3_Transcripts-R.206KY1005.F


title: CD3_Transcripts-R.218KY1005.Siro.D14


title: CD3_Transcripts-R.211KY1005.F


title: CD3_Transcripts-R.213Healthy.Control


title: CD3_Transcripts-R.210KY1005.D14


title: CD3_Transcripts-R.208Healthy.Control


title: CD3_Transcripts-R.215Healthy.Control


title: CD3_Transcripts-R.41Healthy.Control


title: CD3_Transcripts-R.207Healthy.Control


title: CD3_Transcripts-R.209Healthy.Control


title: CD3_Transcripts-R.216Healthy.Control


title: CD3_Transcripts-R.203Healthy.Control


title: CD3_Transcripts-R.214Healthy.Control


title: CD3_Transcripts-R.202Healthy.Control


title: CD3_Transcripts-R.205Healthy.Control


title: CD3_Transcripts-R.55Healthy.Control


title: CD3_Transcripts-R.54Healthy.Control


title: CD3_Transcripts-R.34Healthy.Control


title: CD3_Transcripts-R.204Healthy.Control


title: CD3_Transcripts-R.47Healthy.Control


title: CD3_Transcripts-R.22Healthy.Control


title: CD3_Transcripts-R.200Healthy.Control


title: CD3_Transcripts-R.49Healthy.Control


title: CD3_Transcripts-R.201Healthy.Control A


title: CD3_Transcripts-R.45Healthy.Control


title: CD3_Transcripts-R.35Healthy.Control


title: CD3_Transcripts-R.40Healthy.Control


title: CD3_Transcripts-R.201Healthy.Control B


title: CD3_Transcripts-R.43Healthy.Control


title: CD3_Transcripts-R.30Healthy.Control


title: CD3_Transcripts-R.31Healthy.Control


title: CD3_Transcripts-R.44Healthy.Control


title: CD3_Transcripts-R.60Healthy.Control


title: CD3_Transcripts-R.16Healthy.Control


title: CD3_Transcripts-R.48Healthy.Control


title: CD3_Transcripts-R.62Healthy.Control


title: CD3_Transcripts-R.39Healthy.Control


title: CD3_Transcripts-R.59Healthy.Control


title: CD3_Transcripts-R.56Healthy.Control


title: CD3_Transcripts-R.36Healthy.Control


title: CD3_Transcripts-R.32Healthy.Control


title: CD3_Transcripts-R.18Healthy.Control


title: CD3_Transcripts-R.28Healthy.Control


title: CD3_Transcripts-R.33Healthy.Control


title: CD3_Transcripts-R.13Healthy.Control


title: CD3_Transcripts-R.67Bela.Siro.F


title: CD3_Transcripts-R.70Bela.Siro.F


title: CD3_Transcripts-R.58Healthy.Control


title: CD3_Transcripts-R.206Healthy.Control


title: CD3_Transcripts-R.66Bela.Siro.F


title: CD3_Transcripts-R.53Healthy.Control


title: CD3_Transcripts-R.49Bela.Siro.F


title: CD3_Transcripts-R.68Bela.Siro.F


title: CD3_Transcripts-R.42Bela.Siro.D30


title: CD3_Transcripts-R.37Healthy.Control


title: CD3_Transcripts-R.42Bela.Siro.F


title: CD3_Transcripts-R.212KY1005.D14


title: CD3_Transcripts-R.49Bela.Siro.D14


title: CD3_Transcripts-R.38Bela.Siro.D14


title: CD3_Transcripts-R.201Auto.D100


title: OM-miRNA-1

status: Public on Jul 31 2017

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-miRNA-rep1

hyb_protocol: Labeled mRNA was hybridized to GeneChip Human Transcriptome Array 2.0 (Affymetrix) and processed with Fluidics script FS450_0001 Protocol. Labeled miRNA was hybridized to GeneChip miRNA 3.0 Array (Affymetrix)) and processed with Fluidics script FS450_0004 Protocol.

scan_protocol: Scan on Affymetrix GeneChip scanner 3000 7G.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis.

label: Biotin

source_name: LCM-derived cells from snap-frozen tissues of cancer epithelium

label_protocol: Total RNA was amplified and labeled with the WT PLUS Reagent KIT (Affymetrix). Labeling of miRNAs was performed with the FLashTag Biotin HSR RNA Labeling Kit (Affymetrix).

extract_protocol: Cells were collected from frozen sections using LCM. RNA was isolated with PicoPure RNA KIT (LifeTechnologies). miRNAs were isolated from the cells using the miRNeasy Micro KIT (Qiagen). The quality and quantity of mRNA and miRNAs were assessed on the Bioanalyzer RNA PicoChip (Agilent Technologies).

tag: cell type

value: LCM-derived

value: Metastatic ovarian cancer to omentum

tag: Stage

value: III c

tag: grade


title: CD3_Transcripts-R.42Bela.Siro.D14


title: CD3_Transcripts-R.202Auto.D36


title: OM-miRNA-3

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-miRNA-rep3


title: CD3_Transcripts-R.60Auto.D100


title: CD3_Transcripts-R.200Auto.D36


title: CD3_Transcripts-R.62Auto.D36


title: OM-miRNA-2

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-miRNA-rep2


title: CD3_Transcripts-R.201Auto.D14


title: CD3_Transcripts-R.38Bela.Siro.F


title: CD3_Transcripts-R.61Healthy.Control


title: OC-miRNA-2

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-miRNA-rep2

value: Ovarian Cancer Epithelium


title: OC-miRNA-3

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-miRNA-rep3


title: CD3_Transcripts-R.200Auto.D100


title: CD3_Transcripts-R.202Auto.D14


title: CD3_Transcripts-R.201Auto.D36


title: CD3_Transcripts-R.200Auto.D14


title: CD3_Transcripts-R.38Bela.Siro.D30


title: OC-miRNA-1

description:
miRNA expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-miRNA-rep1


title: CD3_Transcripts-R.202Auto.D100


title: WT GMP, replicate 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms (6 ug) of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip array.

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

data_processing: Signals were summarized using the Robust Multichip Algorithm (RMA) using Partek Genomics Suite software v6.6 (Partek, Inc) or or by fitting a linear model implemented in the R package “limma” (Ritchie et al., 2015)

source_name: sorted, freshly isolated GMP

label_protocol: One to five nanograms (1-5 ng) of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were freshly sorted from bone marrow of mice by FACS and only Lin– were stimulated for 12 hours in vitro

extract_protocol: RNA samples were prepared according to the manufacturer's instructions of Rneasy Micro kit from Qiagen

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen

value: C57BL/6 background

tag: gender

value: female


title: WT CMP, replicate 1

source_name: sorted, freshly isolated CMP


title: CreER-Raptor GMP, replicate 3


title: CreER-Raptor Lin– + MCSF, replicate 1

source_name: sorted Lin– stimulated with M-CSF (10 ng/ml) in vitro


title: CreER-Raptor GMP, replicate 1


title: CreER-Raptor CMP, replicate 2


title: WT CMP, replicate 2


title: WT CMP, replicate 3


title: CreER-Raptor GMP, replicate 2


title: CreER-Raptor CMP, replicate 3


title: CreER-Raptor Lin– + MCSF, replicate 2


title: CreER-Raptor Lin– + MCSF, replicate 3


title: WT GMP, replicate 1


title: OM-mRNA-2

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-mRNA-rep2


title: WT GMP, replicate 3


title: CreER-Raptor CMP, replicate 1


title: WT Lin– + MCSF, replicate 4


title: CreER-Raptor Lin– + MCSF, replicate 4


title: OM-mRNA-3

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-mRNA-rep3


title: WT Lin– + MCSF, replicate 2


title: WT Lin– + MCSF, replicate 3


title: OC-mRNA-3

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-mRNA-rep3


title: OC-mRNA-1

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-mRNA-rep1


title: Smad4 KO NK_replicate 4

city: San Francisco

middle: S

last: Cortez

state: CA

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description: gene expression data from SMAD4 KO NK cells

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression. Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data

source_name: Splenic NK cells

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

growth_protocol: Mouse spleen was made to a single cell suspension. NK cells were than enriched by positive selection via CD49b and sort purified (NK1.1+CD49b+CD3-CD19-)

extract_protocol: RNA was extracted with the RNeasy microkit from Qiagen following manufacturer's instructions.

treatment_protocol: Spleen from naïve mice were used for NK cell purificatoin.

value: Smad4F/F x Ncr1-Cre


title: WT NK_replicate 4

description: gene expression data from WT NK cells

value: WT


title: Ctrl_NK_IL-2 and TGFb1

description: gene expression data from Ctrl Blood NK cells cultured with IL-2 and TGFb1

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

source_name: Blood NK cells

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin ki

growth_protocol: CD56+ NK cells were grown in IL-2

treatment_protocol: CD56+ NK cells were cultured overnight with either IL-2 alone or IL-2 and TGFb1

value: NK cells

tag: cell population


title: Smad4 KO NK_replicate 1


title: WT NK_replicate 1

description: gene expression data from WT NK cells


title: Ctrl_NK_IL-2

description: gene expression data from Ctrl Blood NK cells cultured with IL-2


title: Smad4 KO NK_replicate 3


title: SMAD4_NK_IL-2 and TGFb1

description: gene expression data from SMAD4 mutant NK cells cultured with IL-2 and TGFb1


title: SMAD4_NK_IL-2

description: gene expression data from SMAD4 mutant NK cells cultured with IL-2


title: WT NK_replicate 3

description: gene expression data from WT NK cells


title: WT Lin– + MCSF, replicate 1


title: OC-mRNA-2

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium
Ovarian cancer patient-ovarian tumor sites-mRNA-rep2


title: Dnmt3a +/-_20679

city: St Louis

first: Timothy

middle: J

last: Ley

state: MO

address: 660 S Euclid Avenue

institute: Washington University School of Medicine

description: Dnmt3a +/- KLS

hyb_protocol: Labeled targets were hybridized to Mouse Exon 1.0 ST arrays (Affymetrix), washed, stained, and scanned using standard protocols from the Siteman Cancer Center, Molecular and Genomic Analysis Core Facility (http://pathology.wustl.edu/research/cores/lcg/index.php).

scan_protocol: Affymetrix Expression Console software was used to process array images, export signal data, and evaluate image and data quality relative to standard Affymetrix quality control metrics.

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite™ 6.6 (Partek Inc., St. Louis, MO). Probe-level data were pre-processed, including background correction, normalization, and summarization, using robust multi-array average (RMA) analysis. RMA adjusts for background noise on each array using only the PM probe intensities; and subsequently normalizes data across all arrays using quantile normalization (Bolstad et.al,; Irizarry et.al.) followed by median polish summarization to generate a single measure of expression (Irizarry et.al.). Data was filtered to include only core probesets having raw expression signal greater than 100 in all samples in order to limit the analysis within well-annotated exons.

source_name: Het1 KLS

label_protocol: Amplified cDNA was prepared from 20 ng total RNA using the whole transcript WT-Ovation RNA Amplification System and biotin-labeled using the Encore Biotin Module, both from NuGen Technologies, according to the manufacturer's instructions.

extract_protocol: For expression array profiling, total cellular RNA was purified using TRIzol reagent (Invitrogen), quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Experion Bioanalyzer.

value: KLS cells

value: Dnmt3a +/-


title: OM-mRNA-1

description:
Gene expression data of LCM-derived cells from fresh frozen tissues of metastatic ovarian cancer to omentum
Ovarian cancer patient-omentum tumor sites-mRNA-rep1


title: H1299-PD98059

city: Iowa

first: Charles

last: Brenner

address: Bowen Science Building, Newton Road

department: Biochemistry, Carver College of Medicine

institute: University of Iowa

description: miRNA profiling data from PD98059 treated H1299 cells

hyb_protocol: As per Affymetrix GeneChip™ miRNA 4.0 Assay

scan_protocol: Affymetrix GeneChip Model 3000 GeneChip Scanner was used for scanning

data_processing: Data was processed using Affymetrix Expression Console and Transcriptome Analysis Console software 3.0.

source_name: PD98059 treated H1299 cells

label_protocol: Samples were given to Genomics Division of the Iowa Institute of Human Genetics for miRNA profiling. Affymetrix GeneChip™ miRNA 4.0 Assay was utilized by the facility.

growth_protocol: Vector control and KRAS-G12V transfected HBEC3 cells were cultured in keratinocyte serum-free media supplemented with bovine pituitary extract and recombinant human EGF. H1299 cells were cultured in RPMI-1640 media supplemented with 10% FBS.

extract_protocol: RNA was isolated using the mirVANA miRNA isolation kit (Ambion, LifeTechnologies) as per manufacturer instructions.

treatment_protocol: H1299 cells were treated with either 20µM PD98059 (MEK inhibitor) or DMSO for 2 days


title: HBEC3-Vector

description: miRNA profiling data from vectrol control transfected HBEC3 cells

source_name: Vectrol control transfected HBEC3 cells


title: Wild-type_20678

description: Wild-type KLS

source_name: WT1 KLS

value: Wild-type


title: Dnmt3a +/-_20683

description: Dnmt3a +/- KLS

source_name: Het3 KLS


title: HBEC3-KRAS

description: miRNA profiling data from KRAS-G12V transfected HBEC3 cells

source_name: KRAS-G12V transfected HBEC3 cells


title: Dnmt3a +/-_20681

description: Dnmt3a +/- KLS

source_name: Het2 KLS


title: H1299-DMSO

description: miRNA profiling data from DMSO treated H1299 cells

source_name: DMSO treated H1299 cells


title: Endosalpinx-rat53, mated biological rep3

status: Public on Jul 30 2017

city: Antofagasta

first: Lidia

middle: M.

last: Zuniga

state: Antofagasta

address: Av. Universidad de Antofagasta 02800

department: Instituto Antofagasta

country: Chile

institute: Universidad de Antofagasta

hyb_protocol: The labeled samples were hybridized to the GeneChip® Rat Gene 1.0 ST Array (Affymetrix) using a GeneChip® Hybridization Kit (Applied Biosystems/Ambion) in a Gene Chip® Hybridization Oven 645. The chips were then washed and stained using the GeneChip® Wash and Stain Kit (Applied Biosystems/Ambion) in a GeneChip® Fluidics Station 450 (Affymetrix). We follow the manufacturer’s instructions.

scan_protocol: Chip scanning was performed using the GeneChip® Scanner 3000 7G (Affymetrix). Quality controls were performed using Expression Console software (Affymetrix).

data_processing:
Data were normalized using Robust Multichip Analysis (RMA) using Expression Console software (Affymetrix). Differentially expressed genes were identified using the RankProd package in the R platform (www.bioconductor.org).
The lists of up- and down-regulated genes were selected based on the estimated percentages of false positives (PFP), using a cutoff of 0.1.

source_name: Rat adult at 3 h after mating

label_protocol: We used 0.3 µg of total RNA from each sample. A whole-transcript (WT) sense target labeling assay was performed using a GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix) and a GeneChip® WT Terminal Labeling Kit (Affymetrix). We follow the manufacturer’s instructions.

growth_protocol: Animals were kept under controlled environmental conditions (temperature 21-24 °C; lights on between 0700 and 2100 h) and were provided rodent chow and water ad libitum.

extract_protocol: The total RNA from the tissue samples was purified using TRIZOL reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was assayed in 1% agarose gels, and RNA samples with an A260/A280 ratio of 2.0 were used to synthesize cDNA.

treatment_protocol: Females in pro-estrus were kept isolated (unmated rats) or were caged with fertile males at 2200 h of pro-estrus. Thirty minutes after caging with males, the presence of spermatozoa in the vaginal smear or a vaginal plug was verified. Females with spermatozoa or a vaginal plug were designated mated rats and remained caged with the males until 0130 h of estrus, 3 h after mating. Unmated and mated rats were sacrificed at 0130 h of estrus or 3 h after mating. Then, the endosalpinx was isolated from the oviducts and stored in TRIZOL reagent until processing.

value: Sprague-Dawley

tag: weight

tag: additional marker

value: Abundant semen into the uterus

value: Endosalpinx


title: Endosalpinx-rat43, mated biological rep2

tag: tissue


title: Endosalpinx-rat44, mated biological rep1

tag: strain


title: Endosalpinx-rat67, unmated biological rep3

source_name: Rat adult at 0130 h of estrus

value: Uterine edema


title: Endosalpinx-rat61, unmated biological rep2


title: Endosalpinx-rat55, unmated biological rep1


title: HepG2_Levofloxacin_6uM_with_cytokines_24h_exp3

status: Public on Jul 29 2017

city: Maastricht

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Individual samples were hybridized on Agilent 4×44K Whole Human Genome microarrays (G4112F; design ID 014850)

scan_protocol: Microarrays were scanned immediately after washing on an Agilent Technologies G2505C DNA Microarray Scanner. Raw data on pixel intensities were extracted from the scanned images using Agilent Feature Extraction Software (version 10.7.3.1; Agilent Technologies, Amstelveen, Netherlands) with default parameters (Protocol: GE1_107_Sep09; Grid 014850_D_F_20110325)

data_processing: All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transformation, and quantile normalization. Probes with less than 30% flagged bad spots were selected, missing values were imputed by k-nearest neighbors (k-NN; k-value 15) and repeated identifiers merged.

label_protocol: 0.5 ug RNA samples were labelled with Cyanine 3 (Cy3) following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands)

growth_protocol: HepG2 cells were cultured in T25 flasks in the presence of minimal essential medium supplemented with 1% nonessential amino acids, 1% sodium pyruvate, 2% penicillin/streptomycin, and 10% fetal bovine serum (all from Gibco BRL, Breda, The Netherlands) at 37°C in a humidified chamber with 95%/5% air/CO2 to reach ∼ 80% confluence.

extract_protocol: Total RNA was isolated from the cells using QIAzol reagent with the RNeasy kit according to the manufacturer’s protocol. RNA concentrations were measured on a nanodrop spectrophotometer and the quality of each RNA preparation was determined with a bio-analyzer (Agilent Technologies, The Netherlands). Only samples with a good quality (clear 18S and 28S peaks and RNA integrity number>6) were used for hybridization. Extracted RNA was stored at −80°C until it was used as the template for cDNA synthesis.

treatment_protocol: HepG2 cells were exposed to Nimesulide, Nefazodone, and Trovafloxacin (idiosyncratic compounds) and Aspirin, Buspirone, and Levofloxacin (non-idiosyncratic compounds) with or without the cytokine mix (TNF 100 ng/ml + IFNγ 100 ng/ml + IL-1α 20 ng/ml + IL-6 20 ng/ml + LPS 10 µg/ml) as described previously (Cosgrove et al., 2009) for 6, 12 or 24


title: HepG2_Trovafloxacin_3uM_without_cytokines_24h_exp3


title: HepG2_Levofloxacin_6uM_without_cytokines_24h_exp3


title: HepG2_Levofloxacin_3uM_with_cytokines_24h_exp3


title: Wild-type_20682

description: Wild-type KLS

source_name: WT3 KLS

tag: genotype


title: HepG2_Levofloxacin_6uM_with_cytokines_12h_exp3


title: HepG2_Trovafloxacin_6uM_with_cytokines_24h_exp3


title: HepG2_Trovafloxacin_6uM_without_cytokines_24h_exp3


title: HepG2_TL_DMSO_with_cytokines_24h_exp3

description:
TL_DMSO+_24h_exp3: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_TL_DMSO_with_cytokines_12h_exp3

description:
TL_DMSO+_12h_exp3: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Levofloxacin_3uM_without_cytokines_12h_exp3


title: HepG2_Trovafloxacin_3uM_with_cytokines_24h_exp3


title: HepG2_TL_DMSO_without_cytokines_24h_exp3

description:
TL_DMSO-_24h_exp3: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Levofloxacin_3uM_with_cytokines_12h_exp3


title: HepG2_Trovafloxacin_3uM_without_cytokines_12h_exp3


title: Wild-type_20680

description: Wild-type KLS

source_name: WT2 KLS


title: HepG2_TL_DMSO_without_cytokines_6h_exp3

description:
TL_DMSO-_6h_exp3: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Trovafloxacin_6uM_with_cytokines_12h_exp3


title: HepG2_TL_DMSO_without_cytokines_12h_exp3

description:
TL_DMSO-_12h_exp3: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Trovafloxacin_6uM_without_cytokines_12h_exp3


title: HepG2_Trovafloxacin_3uM_with_cytokines_12h_exp3


title: HepG2_Levofloxacin_6uM_without_cytokines_6h_exp3


title: HepG2_Levofloxacin_3uM_without_cytokines_24h_exp3


title: HepG2_Levofloxacin_6uM_with_cytokines_6h_exp3


title: HepG2_TL_DMSO_with_cytokines_6h_exp3

description:
TL_DMSO+_6h_exp3: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Levofloxacin_3uM_with_cytokines_6h_exp3


title: HepG2_Trovafloxacin_3uM_without_cytokines_6h_exp3


title: HepG2_Trovafloxacin_6uM_without_cytokines_6h_exp3


title: HepG2_Levofloxacin_6uM_without_cytokines_24h_exp2


title: HepG2_Levofloxacin_3uM_without_cytokines_24h_exp2


title: HepG2_TL_DMSO_without_cytokines_12h_exp2

description:
TL_DMSO-_12h_exp2: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Trovafloxacin_3uM_with_cytokines_24h_exp2


title: HepG2_Trovafloxacin_6uM_with_cytokines_6h_exp3


title: HepG2_Levofloxacin_3uM_without_cytokines_6h_exp3


title: HepG2_Levofloxacin_6uM_without_cytokines_12h_exp2


title: HepG2_Trovafloxacin_3uM_with_cytokines_6h_exp3


title: HepG2_Trovafloxacin_3uM_without_cytokines_24h_exp2


title: HepG2_TL_DMSO_with_cytokines_12h_exp2

description:
TL_DMSO+_12h_exp2: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Trovafloxacin_6uM_with_cytokines_24h_exp2


title: HepG2_Levofloxacin_6uM_with_cytokines_24h_exp2


title: HepG2_Levofloxacin_6uM_without_cytokines_12h_exp3


title: HepG2_TL_DMSO_without_cytokines_6h_exp2

description:
TL_DMSO-_6h_exp2: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Levofloxacin_3uM_with_cytokines_12h_exp2


title: HepG2_TL_DMSO_with_cytokines_6h_exp2

description:
TL_DMSO+_6h_exp2: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Levofloxacin_3uM_without_cytokines_12h_exp2


title: HepG2_Trovafloxacin_6uM_with_cytokines_12h_exp2


title: HepG2_Trovafloxacin_6uM_without_cytokines_24h_exp2


title: HepG2_Trovafloxacin_3uM_without_cytokines_12h_exp2


title: HepG2_Levofloxacin_6uM_with_cytokines_12h_exp2


title: HepG2_Levofloxacin_3uM_without_cytokines_6h_exp2


title: HepG2_Trovafloxacin_6uM_without_cytokines_6h_exp2


title: HepG2_Levofloxacin_3uM_with_cytokines_24h_exp2


title: HepG2_Trovafloxacin_6uM_with_cytokines_6h_exp2


title: HepG2_Trovafloxacin_6uM_without_cytokines_12h_exp2


title: HepG2_Levofloxacin_3uM_with_cytokines_6h_exp2


title: HepG2_Levofloxacin_6uM_without_cytokines_6h_exp2


title: HepG2_TL_DMSO_without_cytokines_24h_exp2

description:
TL_DMSO-_24h_exp2: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_TL_DMSO_with_cytokines_24h_exp2

description:
TL_DMSO+_24h_exp2: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Trovafloxacin_3uM_with_cytokines_12h_exp2


title: HepG2_Trovafloxacin_3uM_without_cytokines_6h_exp2


title: HepG2_Levofloxacin_6uM_with_cytokines_6h_exp2


title: HepG2_Trovafloxacin_3uM_with_cytokines_6h_exp2


title: HepG2_Levofloxacin_3uM_with_cytokines_24h_exp1


title: HepG2_Levofloxacin_6uM_without_cytokines_24h_exp1


title: HepG2_Levofloxacin_6uM_with_cytokines_24h_exp1


title: HepG2_Trovafloxacin_3uM_without_cytokines_24h_exp1


title: HepG2_Trovafloxacin_3uM_with_cytokines_24h_exp1


title: HepG2_TL_DMSO_with_cytokines_12h_exp1

description:
TL_DMSO+_12h_exp1: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_TL_DMSO_without_cytokines_24h_exp1

description:
TL_DMSO-_24h_exp1: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_TL_DMSO_without_cytokines_6h_exp1

description:
TL_DMSO-_6h_exp1: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Levofloxacin_3uM_without_cytokines_12h_exp1


title: HepG2_Trovafloxacin_3uM_without_cytokines_12h_exp1


title: HepG2_Trovafloxacin_3uM_with_cytokines_12h_exp1


title: HepG2_Levofloxacin_6uM_without_cytokines_6h_exp1


title: HepG2_Trovafloxacin_6uM_with_cytokines_24h_exp1


title: HepG2_Trovafloxacin_6uM_without_cytokines_6h_exp1


title: HepG2_Levofloxacin_3uM_without_cytokines_24h_exp1


title: HepG2_TL_DMSO_with_cytokines_24h_exp1

description:
TL_DMSO+_24h_exp1: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_TL_DMSO_without_cytokines_12h_exp1

description:
TL_DMSO-_12h_exp1: Solvent control for Trovafloxacin, Levofloxacin without cytokines
Solvent control for Trovafloxacin, Levofloxacin without cytokines


title: HepG2_Trovafloxacin_6uM_with_cytokines_12h_exp1


title: HepG2_Trovafloxacin_6uM_without_cytokines_12h_exp1


title: HepG2_Trovafloxacin_3uM_with_cytokines_6h_exp1


title: HepG2_Levofloxacin_6uM_with_cytokines_12h_exp1


title: HepG2_Levofloxacin_6uM_without_cytokines_12h_exp1


title: HepG2_Trovafloxacin_6uM_without_cytokines_24h_exp1


title: HepG2_Levofloxacin_3uM_with_cytokines_12h_exp1


title: HepG2_Levofloxacin_3uM_without_cytokines_6h_exp1


title: HepG2_DMSO_with_cytokines_24h_exp3

description:
DMSO+_24h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_DMSO_without_cytokines_12h_exp2

description:
DMSO-_12h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_DMSO_with_cytokines_6h_exp2

description:
DMSO+_6h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_Trovafloxacin_6uM_with_cytokines_6h_exp1


title: HepG2_Levofloxacin_6uM_with_cytokines_6h_exp1


title: HepG2_DMSO_without_cytokines_24h_exp3

description:
DMSO-_24h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_Buspirone_12.5uM_without_cytokines_24h_exp3


title: HepG2_Levofloxacin_3uM_with_cytokines_6h_exp1


title: HepG2_Trovafloxacin_3uM_without_cytokines_6h_exp1


title: HepG2_DMSO_with_cytokines_24h_exp2

description:
DMSO+_24h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_TL_DMSO_with_cytokines_6h_exp1

description:
TL_DMSO+_6h_exp1: Solvent control for Trovafloxacin, Levofloxacin with cytokines
Solvent control for Trovafloxacin, Levofloxacin with cytokines


title: HepG2_Nefazodone_12.5uM_with_cytokines_24h_exp3


title: HepG2_DMSO_with_cytokines_12h_exp3

description:
DMSO+_12h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_DMSO_without_cytokines_6h_exp2

description:
DMSO-_6h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_DMSO_without_cytokines_12h_exp3

description:
DMSO-_12h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_DMSO_without_cytokines_24h_exp2

description:
DMSO-_24h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_Buspirone_12.5uM_with_cytokines_24h_exp3


title: HepG2_Nefazodone_12.5uM_without_cytokines_24h_exp3


title: HepG2_Buspirone_25uM_with_cytokines_24h_exp3


title: HepG2_DMSO_with_cytokines_12h_exp2

description:
DMSO+_12h_exp2: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_Nefazodone_25uM_with_cytokines_24h_exp3


title: HepG2_Buspirone_25uM_without_cytokines_24h_exp3


title: HepG2_Nefazodone_25uM_without_cytokines_24h_exp3


title: HepG2_Aspirin_400uM_without_cytokines_24h_exp3


title: HepG2_Aspirin_400uM_with_cytokines_24h_exp3


title: HepG2_Aspirin_200uM_without_cytokines_24h_exp3


title: HepG2_Aspirin_200uM_with_cytokines_24h_exp3


title: HepG2_Nimesulide_400uM_without_cytokines_24h_exp3


title: HepG2_Buspirone_12.5uM_without_cytokines_12h_exp3


title: HepG2_Nimesulide_200uM_with_cytokines_24h_exp3


title: HepG2_Nefazodone_12.5uM_with_cytokines_12h_exp3


title: HepG2_Buspirone_25uM_with_cytokines_12h_exp3


title: HepG2_Buspirone_25uM_without_cytokines_12h_exp3


title: HepG2_Nefazodone_25uM_without_cytokines_12h_exp3


title: HepG2_Nefazodone_25uM_with_cytokines_12h_exp3


title: HepG2_Buspirone_12.5uM_with_cytokines_12h_exp3


title: HepG2_Aspirin_200uM_with_cytokines_12h_exp3


title: HepG2_Nimesulide_200uM_without_cytokines_12h_exp3


title: HepG2_Aspirin_400uM_with_cytokines_12h_exp3


title: HepG2_Buspirone_25uM_without_cytokines_6h_exp3


title: HepG2_Aspirin_400uM_without_cytokines_12h_exp3


title: HepG2_Nimesulide_200uM_without_cytokines_24h_exp3


title: HepG2_Nimesulide_400uM_with_cytokines_12h_exp3


title: HepG2_Nimesulide_400uM_with_cytokines_24h_exp3


title: HepG2_Nimesulide_400uM_without_cytokines_12h_exp3


title: HepG2_Buspirone_25uM_with_cytokines_6h_exp3


title: HepG2_Nefazodone_12.5uM_without_cytokines_12h_exp3


title: HepG2_Buspirone_12.5uM_without_cytokines_6h_exp3


title: HepG2_Aspirin_400uM_with_cytokines_6h_exp3


title: HepG2_Buspirone_12.5uM_with_cytokines_6h_exp3


title: HepG2_Nefazodone_25uM_without_cytokines_6h_exp3


title: HepG2_Nefazodone_25uM_with_cytokines_6h_exp3


title: HepG2_Nimesulide_200uM_with_cytokines_12h_exp3


title: HepG2_Nefazodone_12.5uM_without_cytokines_6h_exp3


title: HepG2_Aspirin_200uM_without_cytokines_6h_exp3


title: HepG2_Nefazodone_12.5uM_with_cytokines_6h_exp3


title: HepG2_Aspirin_400uM_without_cytokines_6h_exp3


title: HepG2_Nimesulide_400uM_with_cytokines_6h_exp3


title: HepG2_Buspirone_12.5uM_without_cytokines_24h_exp2


title: HepG2_Buspirone_12.5uM_with_cytokines_24h_exp2


title: HepG2_Nimesulide_200uM_without_cytokines_6h_exp3


title: HepG2_Nefazodone_25uM_with_cytokines_24h_exp2


title: HepG2_Aspirin_200uM_without_cytokines_12h_exp3


title: HepG2_Nefazodone_12.5uM_with_cytokines_24h_exp2


title: HepG2_Buspirone_25uM_without_cytokines_24h_exp2


title: HepG2_Nefazodone_12.5uM_without_cytokines_24h_exp2


title: HepG2_Buspirone_25uM_with_cytokines_24h_exp2


title: HepG2_Aspirin_200uM_with_cytokines_24h_exp2


title: HepG2_Aspirin_400uM_without_cytokines_24h_exp2


title: HepG2_Nimesulide_400uM_without_cytokines_24h_exp2


title: HepG2_Nefazodone_25uM_without_cytokines_24h_exp2


title: HepG2_Aspirin_200uM_with_cytokines_6h_exp3


title: HepG2_Nimesulide_200uM_with_cytokines_6h_exp3


title: HepG2_Aspirin_400uM_with_cytokines_24h_exp2


title: HepG2_Nimesulide_400uM_without_cytokines_6h_exp3


title: HepG2_Nimesulide_400uM_with_cytokines_24h_exp2


title: HepG2_Aspirin_200uM_without_cytokines_24h_exp2


title: HepG2_Nimesulide_200uM_with_cytokines_24h_exp2


title: HepG2_Nefazodone_12.5uM_without_cytokines_12h_exp2


title: HepG2_Buspirone_12.5uM_without_cytokines_12h_exp2


title: HepG2_Buspirone_25uM_with_cytokines_12h_exp2


title: HepG2_Nefazodone_12.5uM_with_cytokines_12h_exp2


title: HepG2_Nefazodone_25uM_without_cytokines_12h_exp2


title: HepG2_Buspirone_25uM_without_cytokines_12h_exp2


title: HepG2_Nefazodone_25uM_with_cytokines_12h_exp2


title: HepG2_Buspirone_12.5uM_with_cytokines_12h_exp2


title: HepG2_Nimesulide_200uM_without_cytokines_24h_exp2


title: HepG2_Aspirin_400uM_without_cytokines_12h_exp2


title: HepG2_Aspirin_400uM_with_cytokines_12h_exp2


title: Mouse lung LPS&BaP, biological rep 4

first: Quan

last: Shi

state: Limburg

address: Universiteitssingel 50

department: Pharmacology and Toxicology

hyb_protocol: Total RNA were hybridized to mouse whole-genome Affymetrix Gene 1.1 ST arrays targeting 21,115 unique genes (Affymetrix, Santa Clara, CA) using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan following the manufacturers' instructions.

data_processing: Microarrays were normalized with the robust multichip average (RMA) method and probes were annotated according to Dai et al. [1, 2]; 1 Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193. doi: 10.1093/bioinformatics/19.2.185. ; 2 Dai M, Wang P, Boyd AD, Kostov G, Athey B, et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33: e175. doi: 10.1093/nar/gni179.

source_name: mice were nasally instilled with 20 μg LPS at day 0 and after 24 hours, mice were intratracheally instilled with B[a]P (0.5 mg/mouse)

label_protocol: Total RNA (100 ng) was labelled by GeneChip Whole Transcript (WT) Sense Target Labeling Assay

growth_protocol: Animals were kept under controlled pathogen-free conditions and allowed food and water ad libitum till 8-10 weeks old, 20-25 g.

extract_protocol: Lung was collected, snap-frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA from lung (10-15 mg) was isolated using the TRIzol reagent (Invitrogen, Breda, the Netherlands) and purified on columns using Qiagen RNeasy Micro Kit (Qiagen, Venlo, the Netherlands) according to the manufacturer's instructions.

treatment_protocol: Control group: mice were instilled nasally with saline and 24 h later instilled intratracheally with vehicle, tricaprylin (25 µl/mouse). LPS group: to induce acute pulmonary inflammation mice received an intranasal dose of 20 µg LPS (Escherichia coli, serotype O55:B5; 1 mg/ml; Sigma), and 24 h later they received tricaprylin (25 µl/mouse) by intratracheal instillation. BaP group: mice were instilled nasally with saline and 24 h later instilled intratracheally with BaP (0.5 mg BaP dissolved in 25 µl tricaprylin). LPS&BaP group: mice received an intranasal administration of 20 µg LPS followed 24 h later with BaP (0.5 mg BaP/mouse) by Group I: mice were instilled nasally with saline and 24 h later instilled intratracheally with vehicle, tricaprylin (25 µl/mouse). Group II: to induce acute pulmonary inflammation mice received an intranasal dose of 20 µg LPS (Escherichia coli, serotype O55:B5; 1 mg/ml; Sigma), and 24 h later they received tricaprylin (25 µl/mouse) by intratracheal instillation. Group III: mice were instilled nasally with saline and 24 h later instilled intratracheally with BaP (0.5 mg BaP dissolved in 25 µl tricaprylin). Group IV: mice received an intranasal administration of 20 µg LPS followed 24 h later with BaP (0.5 mg BaP/mouse) by intratracheal instillation.

value: lung

value: male


title: Mouse lung BaP, biological rep 3

source_name: mice were nasally instilled with saline at day 0 and after 24 hours, mice were intratracheally instilled with B[a]P (0.5 mg in 25 μl tricaprylin/mouse)


title: Mouse lung LPS&BaP, biological rep 2


title: Mouse lung BaP, biological rep 1


title: HepG2_Nimesulide_200uM_with_cytokines_12h_exp2


title: HepG2_Buspirone_25uM_with_cytokines_6h_exp2


title: Mouse lung LPS&BaP, biological rep 1


title: Mouse lung LPS, biological rep 3

source_name: mice were nasally instilled with 20 μg LPS (Escherichia coli, serotype O55:B5; 1 mg/ml; dissolved in saline) at day 0 and after 24 hours, mice were intratracheally instilled with tricaprylin


title: HepG2_Nimesulide_400uM_with_cytokines_12h_exp2


title: HepG2_Aspirin_200uM_without_cytokines_12h_exp2


title: HepG2_Aspirin_200uM_with_cytokines_12h_exp2


title: Mouse lung BaP, biological rep 2


title: HepG2_Nefazodone_12.5uM_without_cytokines_6h_exp2


title: HepG2_Nimesulide_400uM_without_cytokines_12h_exp2


title: Mouse lung BaP, biological rep 4


title: HepG2_Nefazodone_25uM_without_cytokines_6h_exp2


title: Mouse lung LPS, biological rep 2


title: HepG2_Nimesulide_200uM_without_cytokines_12h_exp2


title: HepG2_Buspirone_25uM_without_cytokines_6h_exp2


title: HepG2_Buspirone_12.5uM_with_cytokines_6h_exp2


title: HepG2_Nefazodone_25uM_with_cytokines_6h_exp2


title: HepG2_Aspirin_400uM_without_cytokines_6h_exp2


title: HepG2_Nefazodone_12.5uM_with_cytokines_6h_exp2


title: Mouse lung control, biological rep 2

source_name: mice were nasally instilled with saline at day 0 and after 24 hours, mice were intratracheally instilled with tricaprylin (25 μl/mouse)


title: Mouse lung control, biological rep 3


title: Mouse lung LPS, biological rep 4


title: Mouse lung LPS, biological rep 1


title: Mouse lung control, biological rep 1


title: Mouse lung LPS&BaP, biological rep 3


title: HepG2_Buspirone_12.5uM_without_cytokines_6h_exp2


title: HepG2_Aspirin_200uM_without_cytokines_6h_exp2


title: HepG2_Aspirin_200uM_with_cytokines_6h_exp2


title: HepG2_Nimesulide_400uM_with_cytokines_6h_exp2


title: HepG2_Aspirin_400uM_with_cytokines_6h_exp2


title: HepG2_Nimesulide_400uM_without_cytokines_6h_exp2


title: HepG2_Nimesulide_200uM_without_cytokines_6h_exp2


title: HepG2_Nimesulide_200uM_with_cytokines_6h_exp2


title: HepG2_Buspirone_25uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_12.5uM_with_cytokines_24h_exp1


title: HepG2_Nefazodone_25uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_25uM_with_cytokines_24h_exp1


title: HepG2_Nefazodone_25uM_with_cytokines_24h_exp1


title: HepG2_Aspirin_400uM_without_cytokines_24h_exp1


title: HepG2_Nefazodone_12.5uM_with_cytokines_24h_exp1


title: HepG2_Aspirin_400uM_with_cytokines_24h_exp1


title: HepG2_Nefazodone_12.5uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_12.5uM_with_cytokines_12h_exp1


title: HepG2_Nimesulide_400uM_without_cytokines_24h_exp1


title: HepG2_Nefazodone_25uM_with_cytokines_12h_exp1


title: HepG2_Aspirin_200uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_12.5uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_25uM_with_cytokines_12h_exp1


title: HepG2_Nimesulide_200uM_with_cytokines_24h_exp1


title: HepG2_Aspirin_200uM_with_cytokines_24h_exp1


title: HepG2_Nimesulide_200uM_without_cytokines_24h_exp1


title: HepG2_Buspirone_25uM_without_cytokines_12h_exp1


title: HepG2_Nefazodone_12.5uM_with_cytokines_12h_exp1


title: HepG2_Aspirin_400uM_without_cytokines_12h_exp1


title: HepG2_Nefazodone_12.5uM_without_cytokines_12h_exp1


title: HepG2_Nefazodone_25uM_without_cytokines_12h_exp1


title: HepG2_Nimesulide_400uM_with_cytokines_24h_exp1


title: HepG2_Aspirin_200uM_without_cytokines_12h_exp1


title: HepG2_Aspirin_200uM_with_cytokines_12h_exp1


title: HepG2_Aspirin_400uM_with_cytokines_12h_exp1


title: HepG2_Buspirone_12.5uM_without_cytokines_12h_exp1


title: HepG2_Nimesulide_400uM_with_cytokines_12h_exp1


title: HepG2_Nimesulide_200uM_without_cytokines_12h_exp1


title: HepG2_Nimesulide_200uM_with_cytokines_12h_exp1


title: HepG2_Buspirone_12.5uM_with_cytokines_6h_exp1


title: HepG2_Buspirone_25uM_with_cytokines_6h_exp1


title: HepG2_Nefazodone_25uM_with_cytokines_6h_exp1


title: HepG2_Nefazodone_12.5uM_without_cytokines_6h_exp1


title: HepG2_Aspirin_200uM_without_cytokines_6h_exp1


title: HepG2_Buspirone_25uM_without_cytokines_6h_exp1


title: HepG2_Aspirin_400uM_without_cytokines_6h_exp1


title: HepG2_Buspirone_12.5uM_without_cytokines_6h_exp1


title: HepG2_Nimesulide_400uM_without_cytokines_6h_exp1


title: HepG2_Nefazodone_25uM_without_cytokines_6h_exp1


title: HepG2_Aspirin_200uM_with_cytokines_6h_exp1


title: HepG2_Nimesulide_400uM_with_cytokines_6h_exp1


title: HepG2_Nefazodone_12.5uM_with_cytokines_6h_exp1


title: HepG2_Aspirin_400uM_with_cytokines_6h_exp1


title: HepG2_DMSO_without_cytokines_6h_exp3

description:
DMSO-_6h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_DMSO_with_cytokines_24h_exp1

description:
DMSO+_24h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_DMSO_with_cytokines_12h_exp1

description:
DMSO+_12h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_Nimesulide_200uM_without_cytokines_6h_exp1