title: lung_PolyIC_96h_G3

scan_protocol: Array washing, staining and scanning was performed according to standard Affymetrix protocols.

source_name: PolyIC, 96h

tag: strain


title: lung_PolyIC_96h_G5

status: Public on Feb 27 2013

type: RNA

city: Gaithersburg

first: Sriram

last: Sridhar

state: MD

address: 1 MedImmune Way

department: Translational Medicine

country: USA

institute: MedImmune

hyb_protocol: Array washing, staining and scanning was performed according to standard Affymetrix protocols.

data_processing: Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix Mouse 430 2.0 arrays.

extract_protocol: Total RNA was isolated from the mouse lung tissue of poly I:C and saline treated mice across 7 time points (2, 6, 24, 48, 72, 96, and 168 hours, n=6 per group) and homogenized in QIAzol reagent.

treatment_protocol: Mice were intranasally treated with poly I:C or saline once prior to RNA extraction from lung tissue at subsequent timepoints.

tag: agent

value: PolyIC

tag: time point

value: BALB/cJ

tag: gender

value: Male

tag: tissue

value: lung homogenate


title: lung_PolyIC_7d_H1

source_name: PolyIC, 7d


title: Control mouse liver, 1X cDNA input, replicate 2

status: Public on Feb 28 2013

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

hyb_protocol: 1X (samples 1-8) or 1.5X (samples 9-16) cDNA was blocked with Agilent CGH-block and GE-blocking agent and hybridized to Agilent SurePrint GE 8x60 mouse microarrays for 17 hours at 65C at 20rpm

scan_protocol: Arrays were washed and scanned on an Agilent G2505B Scanner according to manufacturer’s recommendations.

data_processing: Agilent FE software, version 11 (one color protocol: GE1_1100_Jul11, or two-color protocol: GE2_1100_Jul11).

source_name: Whole liver, not-exposed, archival FFPE

label_protocol: cDNA was labeled using the KREAtech ULS genomic DNA labeling kit (Agilent)

growth_protocol: 16-year-old FFPE liver tissue blocks were used

extract_protocol: RNA was extracted using the Qiagen FFPE Rneasy kit; cDNA was synthesized using the WTA2 kit (Sigma)

treatment_protocol: Mice were exposed to PB in drinking water (or drinking water alone) for ~4 weeks

tag: age

value: 42 days

value: male

tag: organ

value: liver

tag: exposure

tag: cdna input


title: lung_PolyIC_7d_H6


title: lung_PolyIC_96h_G1


title: Control mouse liver, 1X cDNA input, replicate 1


title: lung_PolyIC_96h_G4


title: lung_PolyIC_7d_H2


title: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 1

source_name: Whole liver, 0.05% PB in drinking water, ~4 weeks, archival FFPE

value: Phenobarbital


title: lung_PolyIC_72h_F3

source_name: PolyIC, 72h


title: Rat pancreas: FeO vs. FeA

city: Gainesville

first: Richard

last: Coffey

state: Florida

address: 517 sw12th st apt 1

department: Food Science and Human Nutrition

institute: University of Florida

description: Slide 4 (FeO/FeA)

hyb_protocol: 825 ng of Cy3 labeled and 825ng of Cy5 labeled aRNA was fragmented and hybridized with rotation at 65°C for 17 hours. Samples were hybridized to rat 4x44k arrays (Agilent Technologies, Inc).

scan_protocol: The arrays were scanned on an Agilent G2505B scanner.

data_processing: Feature Extraction 10.1.1.1 software (Agilent Technologies, Inc.) was used for background subtraction, and normalization was performed by scaling the signal intensites of each data set so that the lower quartile, median, and upper quartile were comparable using MATLAB Statistical Package (MathWorks).

organism: Rattus norvegicus

source_name: pancreas of FeO rats

label_protocol: cDNA was synthesized from 200 ng of total RNA using the Quick-Amp labeling Kit (Agilent Technologies, Inc.). The cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and cyanine labeled CTP's. The amplified, labeled aRNA was purified using the RNeasy Mini Kit (Qiagen).

extract_protocol: Frozen rat pancreas was ground in liquid nitrogen using a mortar and pestle, and RNA was obtained by using the RNeasy Mini kit (Qiagen). RNA integrity was assessed by the visualization of 28s and 18s bands of individual samples subjected to denaturating agarose gel electrophoresis. In addition, integrity was also assessed by using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent).

treatment_protocol: Male Sprague-Dawley rats were fed diets containing either iron-deficient, -adequate, or -overloaded diets containing 5 ppm, 35 ppm, or 20275 ppm iron, respectively, for a duration of 3 wks before sacrificing and harvesting tissues.

value: Sprague-Dawley

value: pancreas

tag: treatment

value: iron-overload diet

source_name: pancreas of FeA rats

value: iron-adequate diet


title: Rat pancreas: FeD vs. FeA

description: Slide 2 (FeD/FeA)

source_name: pancreas of FeD rats

value: iron-deficient diet


title: lung_PolyIC_72h_F5


title: lung_PolyIC_7d_H4


title: Mouse 1 WT-AL1

city: Nagasaki

first: Isao

last: Shimokawa

address: 1-12-4 Sakamoto

department: Basic Medical Science

country: Japan

institute: Nagasaki University Graduate School of Biomedical Sciences

description: Total probes are 36227. The quality tag of probes consists of G (signal intensity was above noise levels), L (fluorescence intensity of spots is as low as noise levels), I (shape of spots is irregular), S (fluorescence intensities of most pixels in a spot is saturated), C (background area of spots is contaminated), P (spots are contaminated), and M (spots designated as "elimination from the analysis" by the maker).

hyb_protocol: After incubation, slides were washed, and stained with Cy5-streptavidin for microarray (GE Healthcara Bio-Science Corp., Piscataway, NJ).

scan_protocol: Arrays were scanned by GenePix4000B (Molecular Devices LLC., Sunnyvale, CA).

data_processing: Array images were processed using CodeLink ™ Expression Analysis v5.0 (Applied Microarray Inc.). Each slide was subjected to quantile normalization.

source_name: liver, WT, AL

label_protocol: Labeled cRNA was applied to the CodeLink Mouse Whole Genome Bioarrays (Applied Microarrays, Inc., Tempe, AZ) for 18 hours at 37°C. Individual samples from two mice of each group were run on separate microarrays.

extract_protocol: RNA, extracted from liver tissues, that passed the Agilent Technologies 2100 Bioanalyzer quality control test, was used to generate biotin-labeled cRNA with a MessageAmpTM II-Biotin Enhanced Kit (Ambion, Inc., Austin, TX ).

tag: strain/background

value: mixed (129S-Npytm1Rpa/J and 129S6/SvEvTac)

tag: genotype

value: Npy+/+

tag: feeding

value: ad libitum


title: lung_PolyIC_72h_F2


title: lung_PolyIC_7d_H3


title: lung_PolyIC_96h_G2


title: Rat pancreas: FeA vs. FeD

description: Slide 1 (FeA/FeD)


title: Rat pancreas: FeA vs. FeO

description: Slide 3 (FeA/FeO)


title: lung_PolyIC_72h_F6


title: lung_PolyIC_96h_G6


title: lung_PolyIC_72h_F4


title: lung_PolyIC_48h_E5

source_name: PolyIC, 48h


title: lung_PolyIC_48h_E6


title: lung_PolyIC_72h_F1


title: lung_PolyIC_48h_E1


title: lung_PolyIC_24h_D6

source_name: PolyIC, 24h


title: lung_PolyIC_48h_E2


title: YFPpos_5A

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: YFP-LRCs

hyb_protocol: The hybridization procedures were performed at the Paterson Institute for Cancer Research Molecular Biology Core Facility using protocols recommended by the manufacturer (Affymetrix).  The NuGEN Exon Hybridisation PICR v1.0 protocol was followed for hybridising labelled DNA to standard GeneChips with 11 micron feature size.

scan_protocol: The scanning of the arrays was performed at the Paterson Institute for Cancer Research Molecular Biology Core Facility using protocols recommended by the manufacturer (Affymetrix).  The Affymetrix GeneChip scanner 3000 running GCOS software was used, located at the PICR

data_processing:
RMA normalistion via Affymetrix Power Tools (apt-1.12.0)
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

label: Biotin

source_name: YFP-LRCs

label_protocol: 8ng of starting RNA was amplified using the NuGEN WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2.  Affymetrix PolyA controls (Part No: 900433) were included at the same concentration as the sample.

extract_protocol: After FACS sorting, RNA extraction was performed using the RNeasy Micro Kit (Qiagen) with on column DNase digestion.  RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies).

tag: litter

tag: cell type

value: YFP-LRCs


title: lung_PolyIC_24h_D3

value: PolyIC


title: YFPpos_6A

description: YFP-LRCs


title: lung_PolyIC_24h_D5

value: BALB/cJ


title: lung_PolyIC_6h_C4

source_name: PolyIC, 6h

value: Male


title: lung_PolyIC_24h_D1

value: lung homogenate


title: lung_PolyIC_6h_C5


title: lung_PolyIC_48h_E3


title: lung_PolyIC_6h_C1


title: lung_PolyIC_24h_D2


title: lung_PolyIC_6h_C2


title: lung_PolyIC_24h_D4


title: lung_PolyIC_48h_E4


title: lung_PolyIC_6h_C3


title: lung_PolyIC_6h_C6


title: lung_PolyIC_2h_B6

source_name: PolyIC, 2h


title: YFPpos_3A

description: YFP-LRCs


title: YFPpos_1A

description: YFP-LRCs


title: YFPpos_2A

description: YFP-LRCs


title: YFPneg_1B

description: LCCs

source_name: LCCs

value: LCCs


title: YFPneg_5B

description: LCCs


title: YFPneg_3B

description: LCCs


title: YFPneg_6B

description: LCCs


title: YFPneg_2B

description: LCCs


title: YFPneg_4B

description: LCCs


title: Paneth_6C

description: Paneth cells

source_name: Paneth cells

value: Paneth cells


title: YFPpos_4A

description: YFP-LRCs


title: lung_PolyIC_2h_B3


title: lung_Saline_2h_A78

source_name: Saline, 2h

value: Saline


title: lung_PolyIC_2h_B4


title: CellsHex_90 min_1.64mMOctanol_rep2

city: Frankfurt

first: Daniela

middle: Jasmin

last: Näther

address: Max-von-Laue-Str. 9

department: Molecular Biosciences

country: Germany

institute: Goethe University Frankfurt

description:
Gene expression of cells grown on hexadecane 90 min after 1-octanol addition
HEX_014

hyb_protocol: 600 ng of fluorescent labelled aRNA was hybridized to the microarray for 17h at 68 degree.

scan_protocol: Slides were scanned immediately after washing on Agilent DNA Microarray Scanner (G2565AA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default values (protocol GE1_107_Sep07 _91).

organism: Alcanivorax borkumensis SK2

source_name: Cells on hexadecane, 90 min, 1.64 mM 1-octanol, replicate 2

label_protocol: 1 µg of total RNA were Cy3-labelled with Message AmpII Bacteria Kit according to the recommendations of the supplier Ambion.

growth_protocol: Cells were grown on ONR7 medium with either pyruvate or hexadecane as carbon source to exponential growth phase.

extract_protocol: Total RNA was isolated with RiboPure Bacteria Kit following manufacturer Ambion recommendations

treatment_protocol: Samples were taken after 0 min (control/without 1-octanol), 15 min, 30min, 60min, 90min after 1-octanol addition.

tag: growth protocol (carbon source)

value: hexadecane

tag: growth phase

value: exponential

tag: stress

value: 1.64mM Octanol

tag: time

value: 90 min


title: CellsHex_90 min_1.64mMOctanol_rep1

description:
Gene expression of cells grown on hexadecane 90 min after 1-octanol addition
HEX_013

source_name: Cells on hexadecane, 90 min, 1.64 mM 1-octanol, replicate 1


title: Recipient 6 months Post-HCT GVHD

type: genomic

city: Oviedo

first: Ramon

middle: M

last: Rodriguez

state: Asturias

address: Celestino Villamil s/n

department: Department of Immunology

country: Spain

institute: Hospital Universitario del Principado de Asturias (HUCA)

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina scanner setting

data_processing: BeadStudio software v3.1.3

label: genomic DNA

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood Recipient GVHD

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit

value: Female

value: blood


title: Recipient 6 moths Post-HCT Control

source_name: Blood Recipient Control


title: lung_Saline_2h_A75

tag: agent

tag: time point

tag: strain


title: lung_Saline_2h_A74

tag: gender

tag: tissue


title: lung_Saline_2h_A77


title: Donor Blood Control

source_name: Blood Donor Control


title: CellsHex_0min_noOctanol_rep3

description:
Gene expression of cells grown on hexadecane before 1-octanol addition
HEX_012

source_name: Cells on hexadecane, 0 min, no 1-octanol, replicate 3

value: no Octanol

value: control


title: lung_PolyIC_2h_B1


title: lung_Saline_6h_A64

source_name: Saline, 6h


title: CellsHex_90 min_1.64mMOctanol_rep3

description:
Gene expression of cells grown on hexadecane 90 min after 1-octanol addition
HEX_015

source_name: Cells on hexadecane, 90 min, 1.64 mM 1-octanol, replicate 3


title: Paneth_1C

description: Paneth cells

tag: age


title: Donor Blood GVHD

source_name: Blood Donor GVHD


title: Recipient 1 month Post-HCT GVHD


title: Paneth_4C

description: Paneth cells


title: lung_Saline_6h_A65


title: lung_Saline_6h_A66


title: lung_PolyIC_2h_B2


title: lung_PolyIC_2h_B5


title: Paneth_2C

description: Paneth cells


title: lung_Saline_2h_A76


title: lung_Saline_6h_A63


title: lung_Saline_2h_A73


title: Paneth_3C

description: Paneth cells


title: Recipient 1 month Post-HCT Control


title: Paneth_5C

description: Paneth cells


title: CellsHex_60 min_1.64mMOctanol_rep2

description:
Gene expression of cells grown on hexadecane 60 min after 1-octanol addition
HEX_010

source_name: Cells on hexadecane, 60 min, 1.64 mM 1-octanol, replicate 2

value: 60 min


title: CellsHex_60 min_1.64mMOctanol_rep3

description:
Gene expression of cells grown on hexadecane 60 min after 1-octanol addition
HEX_011

source_name: Cells on hexadecane, 60 min, 1.64 mM 1-octanol, replicate 3


title: CellsHex_60 min_1.64mMOctanol_rep1

description:
Gene expression of cells grown on hexadecane 60 min after 1-octanol addition
HEX_009

source_name: Cells on hexadecane, 60 min, 1.64 mM 1-octanol, replicate 1


title: High cholesterol diet HC + RSV + EZE rep8

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

hyb_protocol: We have used standard Illumina hybridisation protocol. The amount of biotinylated cRNA that was hybridized onto the MouseRef-8 Expression BeadChip was 750 ng

scan_protocol: Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina, was used for Gene Expression analysis. All the quality control data of this BeadChip were within specifications of the microarray service provider (Service XS, Leiden, the Netherlands).

data_processing:
Probe-level, background subtracted expression values were used as input for GeneSpring GX11 software (Agilent), which was used for normalization of data; threshold signals below the value of 5 were set at 5. To be considered expressed, the signal detection p-value of the probe had to be lower than 0.01 in at least 1 of 48 experiments. 15505 probes fulfilled these criteria. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
GeneSpring GX11 software (Agilent) was used to normalize data. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch

source_name: mouse liver

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA. Concentration of the labeled cRNA was measured using the Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted from individual livers (n=8 livers per group, 48 samples in total) using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands).

value: female

value: High cholesterol diet HC+RSV+EZE

value: liver


title: High cholesterol diet HC + RSV + EZE rep4


title: CellsHex_30 min_1.64mMOctanol_rep1

description:
Gene expression of cells grown on hexadecane 30 min after 1-octanol addition
HEX_006

source_name: Cells on hexadecane, 30 min, 1.64 mM 1-octanol, replicate 1

value: 30 min


title: High cholesterol diet HC + RSV + EZE rep6


title: High cholesterol diet HC + RSV + EZE rep3


title: CellsHex_30 min_1.64mMOctanol_rep3

description:
Gene expression of cells grown on hexadecane 30 min after 1-octanol addition
HEX_008

source_name: Cells on hexadecane, 30 min, 1.64 mM 1-octanol, replicate 3


title: lung_Saline_24h_A53

source_name: Saline, 24h

value: BALB/cJ

value: Male

value: lung homogenate


title: High cholesterol diet HC + RSV + EZE rep5


title: lung_Saline_6h_A61

value: Saline


title: lung_Saline_24h_A49


title: CellsHex_15 min_1.64mMOctanol_rep2

description:
Gene expression of cells grown on hexadecane 15 min after 1-octanol addition
HEX_003

source_name: Cells on hexadecane, 15 min, 1.64 mM 1-octanol, replicate 2

value: hexadecane

value: 15 min


title: CellsHex_0min_noOctanol_rep2

description:
Gene expression of cells grown on hexadecane before 1-octanol addition
HEX_004

source_name: Cells on hexadecane, 0 min, no 1-octanol, replicate 2

value: exponential


title: lung_Saline_48h_A42

source_name: Saline, 48h


title: lung_Saline_6h_A62


title: CellsHex_15 min_1.64mMOctanol_rep1

description:
Gene expression of cells grown on hexadecane 15 min after 1-octanol addition
HEX_002

source_name: Cells on hexadecane, 15 min, 1.64 mM 1-octanol, replicate 1

value: 1.64mM Octanol


title: lung_Saline_24h_A51


title: lung_Saline_24h_A52


title: CellsHex_15 min_1.64mMOctanol_rep3

description:
Gene expression of cells grown on hexadecane 15 min after 1-octanol addition
HEX_005

source_name: Cells on hexadecane, 15 min, 1.64 mM 1-octanol, replicate 3


title: lung_Saline_24h_A54


title: High cholesterol diet HC + EZE rep8

value: High cholesterol diet HC+EZE


title: High cholesterol diet HC + RSV + EZE rep1


title: High cholesterol diet HC + RSV + EZE rep2


title: lung_Saline_24h_A50


title: lung_Saline_48h_A41


title: High cholesterol diet HC + EZE rep7


title: CellsHex_0min_noOctanol_rep1

description:
Gene expression of cells grown on hexadecane before 1-octanol addition
HEX_001

source_name: Cells on hexadecane, 0 min, no 1-octanol, replicate 1


title: High cholesterol diet HC + EZE rep5


title: lung_Saline_48h_A39


title: lung_Saline_48h_A40


title: CellsPyr_90min_0.66mMOctanol_rep2

description:
Gene expression of cells grown on pyruvate 90 min after 1-octanol addition
PYR_015

source_name: Cells on pyruvate, 90 min, 0.66 mM 1-octanol, replicate 2

value: pyruvate

value: 0.66mM Octanol

value: 90 min


title: GDF3low

city: Berlin

first: Karolina

last: Tykwinska

state: Berlin

address: Gustav-Meyer-Allee 25

institute: TU Berlin

hyb_protocol: Hybridizations were done overnight for approx. 19h at 60°C.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.6.1.1.).

data_processing: Data analysis was performed with Rosetta Informatics Platform Resolver Built 4.0. using default settings.

source_name: NCCIT cells stimulated 100ng/mL GDF3 (Intensity1)

label_protocol: 500ng of total RNA was reverse transcribed with an oligo(dT)-T7 promoter primer and Moloney murine leukaemia virus-reverse transcriptase (MMLV-RT) to synthesize first and second-strand of cDNA. Fluorescence anti-sense cRNA was synthesized with T7 RNA polymerase that simultaneoulsy incorporates either cyanine 3-cytidine 5'-triphosphate (3-CTP) or cyanine 5-CTP. Labeling efficiency was verified with a Nanodrop photometer (Kisker). Before hybridization 2µg of each labeled cRNA product were fragmented and mixed with control targets  and hybridization buffer according to the suppliers protocol (Agilent)

growth_protocol: NCCIT cells were grown in DMEM with 10%FCS and 1%PS

extract_protocol: Isolation of total RNA was performed using NucleoSpin® RNA II kit (Macherey-Nagel, Germany).

tag: cell line

value: NCCIT

source_name: Unstimulated NCCIT cells (common reference) (Intensity2)


title: High cholesterol diet HC + EZE rep6

value: female

tag: treatment


title: High cholesterol diet HC + EZE rep4


title: CellsPyr_60min_0.66mMOctanol_rep3

description:
Gene expression of cells grown on pyruvate 60 min after 1-octanol addition
PYR_012

source_name: Cells on pyruvate, 60 min, 0.66 mM 1-octanol, replicate 3

value: 60 min


title: GDF3+Nodal

source_name: NCCIT cells stimulated 100ng/mL GDF3 + 300ng/mL Nodal (Intensity1)


title: CellsPyr_90min_0.66mMOctanol_rep3

description:
Gene expression of cells grown on pyruvate 90 min after 1-octanol addition
PYR_016

source_name: Cells on pyruvate, 90 min, 0.66 mM 1-octanol, replicate 3


title: lung_Saline_72h_A30

source_name: Saline, 72h


title: GDF3high

source_name: NCCIT cells stimulated 300ng/mL GDF3 (Intensity2)


title: Nodal

source_name: NCCIT cells stimulated 300ng/mL Nodal (Intensity1)


title: High cholesterol diet HC + EZE rep3

source_name: mouse liver

value: liver


title: CellsPyr_90min_0.66mMOctanol_rep1

description:
Gene expression of cells grown on pyruvate 90 min after 1-octanol addition
PYR_014

source_name: Cells on pyruvate, 90 min, 0.66 mM 1-octanol, replicate 1


title: High cholesterol diet HC + EZE rep1


title: GDF3KD

source_name: NCCIT cells transduced with mock lentivirus (Intensity1)

source_name: NCCIT cells transduced with lentivirus with shRNA targeting GDF3 (Intensity2)


title: lung_Saline_48h_A38

source_name: Saline, 48h


title: Root_-P_PvTIFY-RNAi_rep2

city: Cuernavaca

first: Gabriel

last: Guillen

state: Morelos

address: Av. Univeridad 2001

department: Biologia Molecular de Plantas

country: Mexico

institute: IBT-UNAM

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/µl Salmon Sperm DNA, 0.05% SDS) for 30 min at 45°C. Labeled aRNA (4 µg) was fragmented by incubation with 5 µl of fragmentation solution (200mM Tris Acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc) for 20 min at 95°C. Hybridization was performed at 45°C for 16 h in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/µl Salmon Sperm DNA, 0.04% SDS).

scan_protocol: The microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a GenePix 4000B microarray scanner (Axon) and the accompanying acquisition software (CombiMatrix Microarray Imager Software). Multiple scanning at different PMT was provided for each hybridization.

data_processing: The raw intensities data were first processed using the Combimatrix Microarray Imager software. Intensity data were then exported into the Feature and Probe format of Combimatrix, where the actual raw intensity per probe and per spot is stored. Data were loaded into R and analyzed using the Limma package (47). The median value of each spot on the array was considered and the probes were filtered to remove quality and factory controls. Within-array probe replicates were defined as technical replicates, by calculating the mean intensity across the different probes. The probe intensity values of each biological condition were then normalized using the quantile function of Limma.

organism: Phaseolus vulgaris

source_name: Composite plant

label_protocol: Total RNA (1 µg) was used as a template to synthesize antisense RNA (aRNA) with Cy5-ULS using the RNA Amplification and Labelling Kit from CombiMatrix (ampULSe, Kreatech Biotechnology) according to manufacturer's instructions.

extract_protocol: Lithium Chloride (LiCl) precipitation. RNA samples were purified using a final concentration of 2.5 M LiCl. After incubation at -20°C for 2 hours the sample was centrifuged (16,000 g) at 4°C for 20 minutes (min). The pellet was then washed with 70% ethanol before drying.

treatment_protocol: The protocol used was based on the reported by Estrada-Navarrete et al.  with the following modifications. Seeds of Phaseolus vulgaris cv Negro Jamapa 81 were surface sterilized and germinated in disposable petri dishes with filter paper soaked sterile water. After 2 days the seed coat was removed and on the third day, plantlets were infected at the cotyledonary node region with the A. rhizogenes K599 strain carrying one of the constructs described above (EV, pPvTIFY-OE or pPvTIFY-RNAi). Infected plantlets were transferred to sterile assay tubes containing 15.0 ml falcon plastic tubes filled with Franco/Munns nutrient solution (42), which provided support, and a humid and sterile environment for the infected plantlets. Assay tubes containing the plantlets were covered with plastic bags to preserve humidity required for hairy root development. Fourteen days after infection, putative transgenic hairy roots were confirmed by checking for the presence of red fluorescence, resulting from the expression of the tdTomato reporter gene, using an epi-fluorescence stereo-microscope. The original root system and non-fluorescent primordia and hairy roots were excised, to avoid root chimeras, and the selected composite plants carrying only fluorescent roots were transferred to hydroponic system (described before) for growth.

tag: cv

value: Negro Jamapa 81

value: Transgenic root

tag: pvtify gene expresion

value: RNAi-silencing

tag: growth condition

value: Phosporus deficiency

value: 21 day


title: High cholesterol diet HC + EZE rep2


title: lung_Saline_72h_A29

value: Saline

value: BALB/cJ

value: Male

value: lung homogenate


title: lung_Saline_48h_A37


title: CellsPyr_0hr_noOctanol_rep4

description:
Gene expression of cells grown on pyruvate before 1-octanol addition
PYR_013

source_name: Cells on pyruvate, 0 hr, no 1-octanol, replicate 4

value: exponential

value: no Octanol

value: control


title: Root_+P_PvTIFY-RNAi_rep2


title: Root_-P_PvTIFY-RNAi_rep1


title: CellsPyr_60min_0.66mMOctanol_rep1

description:
Gene expression of cells grown on pyruvate 60 min after 1-octanol addition
PYR_010

source_name: Cells on pyruvate, 60 min, 0.66 mM 1-octanol, replicate 1

value: pyruvate

value: 0.66mM Octanol


title: CellsPyr_0hr_noOctanol_rep3

description:
Gene expression of cells grown on pyruvate before 1-octanol addition
PYR_009

source_name: Cells on pyruvate, 0 hr, no 1-octanol, replicate 3


title: CellsPyr_60min_0.66mMOctanol_rep2

description:
Gene expression of cells grown on pyruvate 60 min after 1-octanol addition
PYR_011

source_name: Cells on pyruvate, 60 min, 0.66 mM 1-octanol, replicate 2


title: lung_Saline_72h_A28


title: lung_Saline_72h_A26


title: High cholesterol diet HC + RSV rep6

value: female

value: High cholesterol diet HC+RSV


title: High cholesterol diet HC + RSV rep5

value: liver


title: High cholesterol diet HC + RSV rep8


title: CellsPyr_30min_0.66mMOctanol_rep2

description:
Gene expression of cells grown on pyruvate 30 min after 1-octanol addition
PYR_007

source_name: Cells on pyruvate, 30 min, 0.66 mM 1-octanol, replicate 2

value: 30 min


title: Root_+P_PvTIFY-RNAi_rep1

value: Negro Jamapa 81

value: Transgenic root


title: CellsPyr_30min_0.66mMOctanol_rep3

description:
Gene expression of cells grown on pyruvate 30 min after 1-octanol addition
PYR_008

source_name: Cells on pyruvate, 30 min, 0.66 mM 1-octanol, replicate 3


title: High cholesterol diet HC + RSV rep7


title: High cholesterol diet HC + RSV rep4


title: lung_Saline_96h_A18

source_name: Saline, 96h


title: CellsPyr_30min_0.66mMOctanol_rep1

description:
Gene expression of cells grown on pyruvate 30 min after 1-octanol addition
PYR_006

source_name: Cells on pyruvate, 30 min, 0.66 mM 1-octanol, replicate 1


title: lung_Saline_72h_A25

source_name: Saline, 72h


title: CellsPyr_0hr_noOctanol_rep2

description:
Gene expression of cells grown on pyruvate before 1-octanol addition
PYR_005

source_name: Cells on pyruvate, 0 hr, no 1-octanol, replicate 2


title: lung_Saline_96h_A17


title: Root_-P_PvTIFY-OE_rep1

value: Over expression

value: Phosporus deficiency


title: Root_+P_PvTIFY-OE_rep1

value: 21 day


title: lung_Saline_96h_A16

value: Saline

value: BALB/cJ


title: Root_-P_EV_rep1

value: Empty vector


title: Root_-P_PvTIFY-OE_rep2


title: lung_Saline_72h_A27

value: Male

value: lung homogenate


title: Root_-P_EV_rep2


title: High cholesterol diet HC + RSV + EZE rep7

value: High cholesterol diet HC+RSV+EZE


title: CellsPyr_15min_0.66mMOctanol_rep3

description:
Gene expression of cells grown on pyruvate 15 min after 1-octanol addition
PYR_004

source_name: Cells on pyruvate, 15 min, 0.66 mM 1-octanol, replicate 3

value: pyruvate

value: exponential

value: 15 min


title: lung_Saline_96h_A15


title: Root_+P_EV_rep1

value: control


title: High cholesterol diet HC + RSV rep3

source_name: mouse liver

value: female

value: High cholesterol diet HC+RSV

value: liver


title: CellsPyr_15min_0.66mMOctanol_rep2

description:
Gene expression of cells grown on pyruvate 15 min after 1-octanol addition
PYR_003

source_name: Cells on pyruvate, 15 min, 0.66 mM 1-octanol, replicate 2

value: 0.66mM Octanol


title: CellsHex_30 min_1.64mMOctanol_rep2

description:
Gene expression of cells grown on hexadecane 30 min after 1-octanol addition
HEX_007

source_name: Cells on hexadecane, 30 min, 1.64 mM 1-octanol, replicate 2

value: hexadecane

value: 1.64mM Octanol

value: 30 min


title: High cholesterol diet HC + RSV rep2


title: CellsPyr_15min_0.66mMOctanol_rep1

description:
Gene expression of cells grown on pyruvate 15 min after 1-octanol addition
PYR_002

source_name: Cells on pyruvate, 15 min, 0.66 mM 1-octanol, replicate 1


title: High cholesterol diet HC + RSV rep1


title: CellsPyr_0min_noOctanol_rep1

description:
Gene expression of cells grown on pyruvate before 1-octanol addition
PYR_001

source_name: Cells on pyruvate, 0 min, no 1-octanol, replicate 1

value: no Octanol


title: lung_Saline_96h_A14

value: Saline

value: BALB/cJ


title: High cholesterol diet HC rep3

value: High cholesterol diet HC


title: High cholesterol diet HC rep7


title: Root_+P_PvTIFY-OE_rep2

source_name: Composite plant

value: Negro Jamapa 81

value: Transgenic root

value: Over expression

value: 21 day


title: High cholesterol diet HC rep8


title: Caco-2_15ADON_30min_rep1

city: Yokohama

first: Tomoyuki

last: Kadota

state: Kanagawa

address: 1-13-5, Fukuura Kanazawa-ku

department: Research & Development Division

institute: Kirin Company, Limited

description:
Gene expression after 30min in 15-acetyldeoxynivalenol-exposed Caco-2 cell
7_15A30

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at  3micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1

source_name: Caco-2 cell, 15ADON, 30min, replicate1

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Caco-2 cells were harvested at 80% confluence, and seeded on collagen-coated BD FalconTM 24-Multiwell Insert Systems (BD Biosciences-Pharmingen, CA, USA) at a density of 2 × 105 cells/well. Caco-2 cells were maintained in DMEM culture medium for 1 day. DMEM was followed with EDM containing 0.08% MITO + Serum Extender, and the cells were cultured for an additional 2 days.

extract_protocol: Total RNA was isolated from the collected cells using the RNeasy kit (Qiagen, Tokyo, Japan) according to the manufacturer’s protocol.

treatment_protocol: DON and 15ADON at concentrations of 1 ug/mL were added separately to the AP chamber, and cells were harvested with 0.5% trypsin-EDTA after incubation for 0, 5, 30, and 60 min.


title: High cholesterol diet HC rep4


title: lung_Saline_96h_A13

value: Male

value: lung homogenate


title: Caco-2_15ADON_0min_rep1

description:
Gene expression after 0min in 15-acetyldeoxynivalenol-exposed Caco-2 cell
5_15A0

source_name: Caco-2 cell, 15ADON, 0min, replicate1

value: 0 min


title: Caco-2_15ADON_60min_rep1

description:
Gene expression after 60min in 15-acetyldeoxynivalenol-exposed Caco-2 cell
8_15A60

source_name: Caco-2 cell, 15ADON, 60min, replicate1

value: 60 min


title: Caco-2_DON_30min_rep1

description:
Gene expression after 30min in deoxynivalenol-exposed Caco-2 cell
3_DON30

source_name: Caco-2 cell, DON, 30min, replicate1

value: DON


title: High cholesterol diet HC rep1

value: female

value: liver


title: High cholesterol diet HC rep5


title: lung_Saline_7d_A6

source_name: Saline, 7d


title: lung_Saline_7d_A3


title: High cholesterol diet HC rep6


title: lung_Saline_7d_A1


title: lung_Saline_7d_A2


title: simulans 7

status: Public on Feb 26 2013

city: East Setauket

first: Deniz

last: Erezyilmaz

state: NY

address: CMM 440

department: Biochemistry

institute: Stony Brook University

description: individual genomic DNA

hyb_protocol: 65C for 40 hours, as described in Agilent CGH micrarray protocol

scan_protocol: Slides were scanned using Agilent Tech Scanner Model G2505B using software version A.7.0.1

data_processing: To compare hyb values between indel probe pairs, we used the final processed Green or Red intensity (separately) without filters or flags. Excel files were generated that contain final processed <color> intensity, the seq description, chromosome, begin coordinate and end coordinate, sorted by SUID. These individual excel files were processed using the custom python script described in Erezyilmaz and Stern 3013.

organism: Drosophila simulans

source_name: Drosophila simulans standard

label_protocol: 50 ng of individual genomic DNA was amplified using Agilent CGH protocol and kit.

growth_protocol: Larvae were grown to L2 or L3.

extract_protocol: Purgene protocol for single Drosophila, followed by Sigma WGA

treatment_protocol: Wandering larvae were tested for pupariation site preference.

tag: sample type

value: control


title: sechellia 2

description: individual genomic DNA

organism: Drosophila sechellia

source_name: Drosophila sechellia standard


title: lung_Saline_7d_A5


title: simulans 8

description: individual genomic DNA


title: simulans 6

description: individual genomic DNA


title: D. simulans/D. sechellia 1

description: individual genomic DNA

organism: Drosophila sechellia x Drosophila simulans

source_name: F1 Hybrid


title: lung_Saline_7d_A4


title: D. simulans/D. sechellia 2

description: individual genomic DNA


title: simulans 5

description: individual genomic DNA


title: simulans 4

description: individual genomic DNA


title: High cholesterol diet HC rep2


title: sechellia 3

description: individual genomic DNA


title: sechellia 1

description: individual genomic DNA


title: Caco-2_DON_0min_rep1

description:
Gene expression after 0min in deoxynivalenol-exposed Caco-2 cell
1_DON0

source_name: Caco-2 cell, DON, 0min, replicate1


title: Caco-2_DON_5min_rep1

description:
Gene expression after 5min in deoxynivalenol-exposed Caco-2 cell
2_DON5

source_name: Caco-2 cell, DON, 5min, replicate1

value: 5 min


title: Caco-2_15ADON_5min_rep1

description:
Gene expression after 5min in 15-acetyldeoxynivalenol-exposed Caco-2 cell
6_15A5

source_name: Caco-2 cell, 15ADON, 5min, replicate1


title: P.iv

description: individual genomic DNA

source_name: Drosophila sechellia backcross

tag: site preference

value: substrate pupariation


title: N.v

description: individual genomic DNA


title: H.v

description: individual genomic DNA


title: O.v

description: individual genomic DNA


title: G.i

description: individual genomic DNA


title: M.iii

description: individual genomic DNA


title: F.v

description: individual genomic DNA


title: E.v

description: individual genomic DNA


title: D.v

description: individual genomic DNA


title: L.iv

description: individual genomic DNA


title: K.v

description: individual genomic DNA


title: C.v

description: individual genomic DNA


title: J.iv

description: individual genomic DNA


title: B.v

description: individual genomic DNA


title: F.iv

description: individual genomic DNA


title: D.iv

description: individual genomic DNA


title: A.iv

description: individual genomic DNA


title: O.iii

description: individual genomic DNA


title: G

description: individual genomic DNA


title: O'.iv

description: individual genomic DNA


title: H.

description: individual genomic DNA


title: E.iv

description: individual genomic DNA


title: N.iv

description: individual genomic DNA


title: I.iv

description: individual genomic DNA


title: M.ii

description: individual genomic DNA


title: J.iii

description: individual genomic DNA


title: I.iii 2

description: individual genomic DNA


title: B.iv

description: individual genomic DNA


title: O.ii

description: individual genomic DNA


title: A.iii

description: individual genomic DNA


title: H.iv

description: individual genomic DNA


title: G.ii

description: individual genomic DNA


title: F.iii

description: individual genomic DNA


title: P.iii

description: individual genomic DNA


title: N.iii

description: individual genomic DNA


title: M.i

description: individual genomic DNA


title: L.iii

description: individual genomic DNA


title: C.iv

description: individual genomic DNA


title: L.ii

description: individual genomic DNA


title: D.iii

description: individual genomic DNA


title: K.iv

description: individual genomic DNA


title: J.ii

description: individual genomic DNA


title: C.iii

description: individual genomic DNA


title: B.iii

description: individual genomic DNA


title: High Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 3 - mAdbID:38415

city: Bethesda

first: Kathryn

middle: E

last: King

address: 29 Lincoln Drive, HFD-123

department: Division of Monoclonal Antibodies

institute: FDA/CDER

description: mAdb experiment ID: 38415

hyb_protocol: Hybridization Protocol Other: Hybridization was carried out using a Genisphere sub-Micro labeling kit according to instructions (Genisphere, Hatfield, PA).

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 870;; 710 ScanPower: 100;; 100 LaserPower: 4.09;; 3.74 Temperature: 31.36 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.

data_processing: Calculation Method: Scanned images were then processed with Genepix 4.0 software to quantitate spot intensities for each label. Spots with high artifactual background or no signal were flagged for exclusion. The intensity files were uploaded and analyzed with the mAdb software suite (CIT, NCI, NIH, Bethesda, MD). The following parameters were set for analysis: Target spot size 100-400 mm and 2-fold difference in four of six arrays (66%). Values for the reverse labeling were reciprocated. Default Ratio: ChanB/ChanA (Cy5/Cy3)Signal calculation: Mean Intensity minus Median Background Any Features designated Control were excluded. Normalization method: 50th Percentile (Median) using all spot filtered Genes Spot Filter Options: Include Spots not flagged BAD or Not Found  AND Target diameter >= 100 um AND Target diameter <= 400 um  AND Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% Data was extracted and aligned by the Inventory Well ID Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B)Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5.

source_name: High Calcium beta-gal keratinocytes - Cy5 (control)

label_protocol:
Cy5 Labeling Protocol
Other: Labeling was carried out using a Genisphere sub-Micro labeling kit according to instructions (Genisphere, Hatfield, PA).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was isolated 41h post-adenoviral transduction from deltaNp63alpha- or beta-gal-overexpressing keratinocytes at 7-8 days post-plating using TRIzol (LifeTechnologies).

treatment_protocol:
Treatment type: compound
Agent: Calcium
Treatment dose: 0.12 mM
Treatment time: 24 hours
In-vitro treatment: Keratinocytes were induced to differentiate by elevating [Ca2+] to 0.12 mM 24 hours prior to harvest.

tag: transduction

value: beta-gal

value: high calcium

value: skin

tag: cell type

value: keratinocytes

tag: other

value: Primary keratinocytes isolated from C57Bl/6NCr mice were maintained in 0.05 mM Ca2+-containing medium. Keratinocytes were transduced with adenoviruses encoding beta-galactosidase 41 hours prior to harvest.

source_name: High Calcium deltaNp63alpha keratinocytes - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Labeling was carried out using a Genisphere sub-Micro labeling kit according to instructions (Genisphere, Hatfield, PA).

value: Primary keratinocytes isolated from C57Bl/6NCr mice were maintained in 0.05 mM Ca2+-containing medium. Keratinocytes were transduced with adenoviruses encoding deltaNp63alpha 41 hours prior to harvest.


title: I.iii

description: individual genomic DNA


title: E.iii

description: individual genomic DNA


title: G.iii

description: individual genomic DNA

value: wall pupariation


title: A.ii

description: individual genomic DNA


title: H.ii

description: individual genomic DNA


title: P.ii

description: individual genomic DNA


title: High Calcium - deltaNp63alpha vs beta-gal - repeat 3 - mAdbID:38410

description: mAdb experiment ID: 38410

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 870;; 710 ScanPower: 100;; 100 LaserPower: 4.06;; 3.73 Temperature: 31.76 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.

source_name: High Calcium beta-gal keratinocytes - Cy3 (control)

source_name: High Calcium deltaNp63alpha keratinocytes - Cy5


title: N.ii

description: individual genomic DNA


title: Low Calcium - deltaNp63alpha vs beta-gal - repeat 3 - mAdbID:38407

description: mAdb experiment ID: 38407

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 860;; 730 ScanPower: 100;; 100 LaserPower: 4.14;; 3.78 Temperature: 29.2 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.

source_name: Low Calcium beta-gal keratinocytes - Cy3 (control)

treatment_protocol:
Treatment type: compound
Agent: Calcium
Treatment dose: 0.05 mM
Treatment time: 24 hours
In-vitro treatment: Keratinocytes remained in 0.05 mM Ca2+-containing medium for 24 hours prior to harvest.

value: low calcium

source_name: Low Calcium deltaNp63alpha keratinocytes - Cy5


title: High Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 1 - mAdbID:38233

description: mAdb experiment ID: 38233

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.5;; 3.98 Temperature: 28.8 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: F.ii

description: individual genomic DNA


title: High Calcium - deltaNp63alpha vs beta-gal - repeat 1 - mAdbID:38232

description: mAdb experiment ID: 38232

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.52;; 3.99 Temperature: 29.04 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: Low Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 1 - mAdbID:38231

description: mAdb experiment ID: 38231

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.5;; 3.95 Temperature: 28.01 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.

source_name: Low Calcium beta-gal keratinocytes - Cy5 (control)

source_name: Low Calcium deltaNp63alpha keratinocytes - Cy3


title: E.ii

description: individual genomic DNA


title: Low Calcium - deltaNp63alpha vs beta-gal - repeat 2 - mAdbID:38395

description: mAdb experiment ID: 38395

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 740;; 660 ScanPower: 100;; 100 LaserPower: 4.61;; 3.35 Temperature: 30.05 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: High Calcium - deltaNp63alpha vs beta-gal - repeat 2 - mAdbID:38238

description: mAdb experiment ID: 38238

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.62;; 3.97 Temperature: 29.71 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: D.ii

description: individual genomic DNA


title: Low Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 3 - mAdbID:38408

description: mAdb experiment ID: 38408

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 880;; 730 ScanPower: 100;; 100 LaserPower: 4.14;; 3.73 Temperature: 29.74 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: H.iii

description: individual genomic DNA


title: K.iii

description: individual genomic DNA


title: High Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 2 - mAdbID:38244

description: mAdb experiment ID: 38244

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.65;; 3.97 Temperature: 29.93 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: Low Calcium - deltaNp63alpha vs beta-gal - repeat 1 - mAdbID:38230

description: mAdb experiment ID: 38230

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.48;; 3.97 Temperature: 28.43 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: Low Calcium - deltaNp63alpha vs beta-gal - rev. fluor. - repeat 2 - mAdbID:38397

description: mAdb experiment ID: 38397

scan_protocol: Creator: GenePix Pro 3.0.6.53 Scanner: GenePix 4000B [84573] PMTVolts: 760;; 670 ScanPower: 100;; 100 LaserPower: 4.64;; 3.38 Temperature: 30.97 Scanning Protocol Other: Slides were scanned on an Axon 4000B scanner and PMT voltage levels were adjusted to obtain an equivalent overall intensity for Cy3 and Cy5.


title: C.ii

description: individual genomic DNA


title: B.ii

description: individual genomic DNA


title: M

description: individual genomic DNA


title: I.ii

description: individual genomic DNA


title: A.i

description: individual genomic DNA


title: P.i

description: individual genomic DNA


title: K.ii

description: individual genomic DNA


title: O.i

description: individual genomic DNA


title: N.i

description: individual genomic DNA


title: G.iv

description: individual genomic DNA


title: F.i

description: individual genomic DNA


title: [mDCs]_[Ro+LPS]_[2]

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning. The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

label: Biotin (as a biotinylated nucleotide)

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences Intl. Plymouth Meeting, PA).

extract_protocol: Trizol Qiagen Total RNA isolation kit

treatment_protocol:
LPS added at 1ug/ml
Ro41-5253 added 100nmol/ml

value: 6-8 weeks

value: bone marrow

value: dendritic cells


title: M.iv

description: individual genomic DNA


title: Adult mouse control smooth muscle beta1 integrin wild type mesenteric arteries, 74M_ctrl

city: Los Angeles

first: Kirsten

middle: Ann

last: Turlo

state: CA

address: 621 Charles E Young Dr

department: Molecular Cell and Developmental Biology

institute: UCLA

description:
74M ctrl
Control mesenteric arteries from a cre negative beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.

hyb_protocol: Affymetrix 645 hybridization oven for 16h.

scan_protocol: Affymetrix 3000 7G scanner.

data_processing: The data was processed using D-Chip. Normalized to Control 75M.

source_name: Adult mouse mesentery arteries, 7 weeks, control

label_protocol: Ambion MessageAMO Premier kit, biotin labeled.

growth_protocol: Animals were aged to 5 weeks before beginning induced deletion of beta1 integrin and aged an additional 2 weeks after initiation of deletion.

extract_protocol: RNA was extracted using the Roche MagNA Pure System.

treatment_protocol: Animals were administered 1mg of tamoxifen per day for 14 days, after which mesenteric arteries were isolated and cleared of adipose and lymph tissue.

tag: strain/background

value: mixed (including but not limited to FVB, SVJ129 and C57BL/6)

tag: genotype

value: loxP flanked beta1 integrin

value: mesenteric arteries

value: 7 weeks

value: 14 doses of 1mg tamoxifen


title: Adult mouse smooth muscle beta1 integrin null mesenteric arteries, 86F_exp

description:
86F exp
Induced beta1 integrin null smooth muscle mesenteric arteries from induced beta1 integrin null smooth muscle sm22alphaCRE positive and beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.

source_name: Adult mouse mesentery arteries, 7 weeks, beta1 integrin knockout

value: sm22alphaCRE-positive loxP flanked beta1 integrin


title: [mDCs]_[control+LPS]_[2]

treatment_protocol: LPS added at 1ug/ml


title: E.i

description: individual genomic DNA


title: [mDCs]_[RA+LPS]_[2]

source_name: mDCs_Retinoic Acid_LPS

treatment_protocol:
LPS added at 1ug/ml
All-trans Retinoic Acid added 10nmol/ml


title: [mDCs]_[Ro]_[2]

treatment_protocol: Ro41-5253 added 100nmol/ml


title: H.i

description: individual genomic DNA


title: Adult mouse smooth muscle beta1 integrin null mesenteric arteries, 73M_exp

description:
73M exp
Induced beta1 integrin null smooth muscle mesenteric arteries from induced beta1 integrin null smooth muscle sm22alphaCRE positive and beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.


title: [mDCs]_[Ro]_[1]

extract_protocol: Trizol and Qiagen Total RNA isolation kit

value: BALB/c


title: Bladder_HG8

first: Hellmuth-A

last: Meyer

address: Charitéplatz 1

department: Department of Urology

institute: Charite

description:
URO100_024
total microRNA profiling

hyb_protocol: Labeled samples were hybridized on Agilent-019118 Human miRNA Microarray 2.0 from Agilent Technologies encoding probes for 723 human and 76 human viral microRNAs from the Sanger database v.10.1. Microarrays were washed according to the supplier’s protocol.

scan_protocol: Microarrays were scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.

data_processing:
GeneView files were generated using Agilent's Genespring GX including Feature Extractor software
Normalized signal intensity (persentile 90 shift, no baseline transformation)

source_name: high-grade papillary urothelial carcinoma

label_protocol: 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase, denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3', 5'-cytidine bisphosphate having a single Cy3 label attached to the 3' phosphate of the nucleotide (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: MiRNAs were isolated using the miRNAeasy Mini Kit (Qiagen, Hilden, Germany) following manufacturer´s instructions. An additional DNase I digestion step on the RNA binding silica gel membrane of the spin column was performed. RNA concentration and the absorbance ratio of 260 nm to 280 nm were measured on the NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of isolated RNA was determined by the RNA integrity number (RIN) with an Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

tag: tumor stage

value: male


title: Adult mouse smooth muscle beta1 integrin null mesenteric arteries, 72M_exp

description:
72M exp
Induced beta1 integrin null smooth muscle mesenteric arteries from induced beta1 integrin null smooth muscle sm22alphaCRE positive and beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.


title: K.i

description: individual genomic DNA


title: D.i

description: individual genomic DNA


title: Adult mouse control smooth muscle beta1 integrin wild type mesenteric arteries, 30M_ctrl

description:
30M ctrl
Control mesenteric arteries from a cre negative beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.


title: Bladder_HG7

description:
URO100_023
total microRNA profiling

value: high-grade papillary urothelial carcinoma


title: [mDCs]_[control]_[2]

tag: strain


title: Adult mouse control smooth muscle beta1 integrin wild type mesenteric arteries, 75M_ctrl

description:
75M ctrl
Control mesenteric arteries from a cre negative beta1 integrin floxed mouse at 7 weeks of age after 14 doses of tamoxifen administered at 24h intervals from 5 weeks.


title: [mDCs]_[RA]_[2]

source_name: mDCs_Retinoic Acid

treatment_protocol: All-trans Retinoic Acid added 10nmol/ml


title: Bladder_HG6

description:
URO100_022
total microRNA profiling

tag: gender


title: [mDCs]_[Ro+LPS]_[1]

tag: tissue


title: [mDCs]_[RA]_[1]

tag: age


title: C.i

description: individual genomic DNA


title: L.i

description: individual genomic DNA


title: B.i

description: individual genomic DNA


title: [mDCs]_[control+LPS]_[1]


title: [mDCs]_[control]_[1]


title: Bladder_HG3

description:
URO100_019
total microRNA profiling


title: Bladder_HG4

description:
URO100_020
total microRNA profiling

value: femal


title: J.i

description: individual genomic DNA


title: Bladder_HG5

description:
URO100_021
total microRNA profiling


title: [mDCs]_[RA+LPS]_[1]


title: Bladder_HG2

description:
URO100_018
total microRNA profiling


title: I.i

description: individual genomic DNA


title: P

description: individual genomic DNA


title: Bladder_HG1

description:
URO100_017
total microRNA profiling


title: N

description: individual genomic DNA


title: Bladder_LG7

description:
URO100_015
total microRNA profiling

source_name: low-grade papillary urothelial carcinoma


title: O

description: individual genomic DNA


title: Bladder_LG6

description:
URO100_014
total microRNA profiling

value: low-grade papillary urothelial carcinoma


title: Bladder_LG8

description:
URO100_016
total microRNA profiling


title: M.v

description: individual genomic DNA


title: Bladder_LG5

description:
URO100_013
total microRNA profiling


title: Bladder_LG4

description:
URO100_012
total microRNA profiling


title: Bladder_LG3

description:
URO100_011
total microRNA profiling


title: E

description: individual genomic DNA


title: H

description: individual genomic DNA


title: D

description: individual genomic DNA


title: Bladder_LG2

description:
URO100_010
total microRNA profiling


title: K

description: individual genomic DNA


title: Caco-2_DON_60min_rep1

description:
Gene expression after 60min in deoxynivalenol-exposed Caco-2 cell
4_DON60

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at  3micron resolution.

source_name: Caco-2 cell, DON, 60min, replicate1

tag: cell line

tag: agent

value: DON

tag: time

value: 60 min


title: G.v

description: individual genomic DNA

scan_protocol: Slides were scanned using Agilent Tech Scanner Model G2505B using software version A.7.0.1

value: wall pupariation


title: J2

description: individual genomic DNA


title: B

description: individual genomic DNA


title: F

description: individual genomic DNA


title: J

description: individual genomic DNA


title: E7M4

description: individual genomic DNA

value: substrate pupariation


title: Bladder_LG1

description:
URO100_009
total microRNA profiling


title: Bladder_N4

description:
URO100_004
total microRNA profiling

source_name: nonmaligant bladder

value: nonmaligant bladder


title: Bladder_N5

description:
URO100_005
total microRNA profiling


title: Bladder_N6

description:
URO100_006
total microRNA profiling


title: Bladder_N8

description:
URO100_008
total microRNA profiling


title: E7M2

description: individual genomic DNA

source_name: Drosophila sechellia backcross


title: E7M3

description: individual genomic DNA


title: Bladder_N3

description:
URO100_003
total microRNA profiling


title: Bladder_N1

description:
URO100_001
total microRNA profiling


title: Bladder_N2

description:
URO100_002
total microRNA profiling


title: E7M

description: individual genomic DNA


title: Malignant 14C

description:
Same sample as GSM303561.
Total microRNA.

hyb_protocol: Labeled samples were hybridized on Agilent-016436 Human miRNA Microarray 1.0 from Agilent Technologies and washed according to the supplier's protocol.

scan_protocol: Microarrays were scanned at 5 µm resolution with a DNA microarray laser scanner (Agilent Technologies) using recommended settings, and features were extracted with the Agilent FE 9.05 software using the recommended protocol according to the supplier's instructions.

data_processing: Expression files were generated using Agilent's GeneSpring GX including Feature Extractor software. Normalized signal intensities were generated using percentile 90 shift and no baseline transformation.

source_name: kidney, malignant ccRCC

label_protocol: RNA labeling was done using the miRNA Labeling and Hyb Kit from Agilent Technologies using recommended settings. In brief, 100 ng of total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase, denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3', 5'-cytidine bisphosphate having a single Cy3 label attached to the 3' phosphate of the nucleotide (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: Total RNA including miRNAs was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. DNase digestion of the RNA preparation was accomplished by on-column digestion with DNase I according to supplier's instructions. RNA concentration was measured by the absorbance ratio of 260 nm to 280 nm with a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA degradation and quality were determined by the RNA integrity number (RIN) with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

value: malignant ccRCC

value: 74 yrs


title: C

description: individual genomic DNA


title: E43M2

description: individual genomic DNA


title: Bladder_N7

description:
URO100_007
total microRNA profiling


title: 27M3

description: individual genomic DNA


title: E43M

description: individual genomic DNA


title: Malignant 12NC

description:
Same sample as GSM303559.
Total microRNA.

value: 62 yrs


title: E138f

description: individual genomic DNA


title: Non-malignant 11NN

description:
Same sample as GSM303558.
Total microRNA.

source_name: kidney, non-malignant ccRCC

value: non-malignant ccRCC


title: Malignant 6NC

description:
Same sample as GSM303557.
Total microRNA.

value: 63 yrs


title: E138pupa

description: individual genomic DNA


title: Non-malignant 5NN

description:
Same sample as GSM303556.
Total microRNA.


title: A4M4

description: individual genomic DNA


title: Malignant 4NC

description:
Same sample as GSM303555.
Total microRNA.

value: female

value: 92 yrs


title: Non-malignant 3NN

description:
Same sample as GSM303554.
Total microRNA.


title: A5M3

description: individual genomic DNA


title: A4M3

description: individual genomic DNA


title: A5F

description: individual genomic DNA


title: Malignant 42NC

description:
Same sample as GSM303553.
Total microRNA.

value: 55 yrs


title: A5M2

description: individual genomic DNA


title: A4M2

description: individual genomic DNA


title: E38M7

description: individual genomic DNA


title: Non-malignant 13NN

description:
Same sample as GSM303560.
Total microRNA.

value: male


title: A4M

description: individual genomic DNA


title: A3F

description: individual genomic DNA


title: Non-malignant 41NN

description:
Same sample as GSM303552.
Total microRNA.


title: A5M

description: individual genomic DNA


title: Non-malignant 39NN

description:
Same sample as GSM303546.
Total microRNA.

value: 65 yrs


title: Malignant 34NC

description:
Same sample as GSM303545.
Total microRNA.

value: 64 yrs


title: Non-malignant 33NN

description:
Same sample as GSM303544.
Total microRNA.


title: 12

description: individual genomic DNA


title: 2

description: individual genomic DNA


title: Malignant 28NC

description:
Same sample as GSM303543.
Total microRNA.

value: 56 yrs


title: Non-malignant 27NN

description:
Same sample as GSM303542.
Total microRNA.


title: Non-malignant 23NN

description:
Same sample as GSM303540.
Total microRNA.

value: 57 yrs


title: Malignant 24NC

description:
Same sample as GSM303541.
Total microRNA.


title: Malignant 18NC

description:
Same sample as GSM303539.
Total microRNA.

value: 67 yrs


title: 14

description: individual genomic DNA


title: Malignant 40NC

description:
Same sample as GSM303551.
Total microRNA.


title: Malignant 10NC

description:
Same sample as GSM303537.
Total microRNA.


title: M7

description: individual genomic DNA


title: A

description: individual genomic DNA


title: E38M5

description: individual genomic DNA


title: F9

description: individual genomic DNA


title: Non-malignant 9NN

description:
Same sample as GSM303536.
Total microRNA.


title: E38F10

description: individual genomic DNA


title: Non-malignant 1NN

description:
Same sample as GSM303535.
Total microRNA.


title: Pool non-malignant prostate

description: Total microRNA.

source_name: prostate, non-malignant

value: pool non-malignant prostate

value: non-malignant prostate

value: 12 males


title: Malignant 2NC

description:
Same sample as GSM298369.
Total microRNA.

value: malignant ccRCC


title: E38F9

description: individual genomic DNA

value: substrate pupariation


title: Pool malignant prostate

description: Total microRNA.

source_name: prostate, malignant

value: pool malignant prostate

value: malignant prostate


title: E38M6

description: individual genomic DNA


title: Pool malignant ccRCC NC2

description: Total microRNA.

value: pool malignant ccRCC

value: 9 males and 2 females


title: 5

description: individual genomic DNA


title: Pool malignant ccRCC NC1

description: Total microRNA.


title: Non-malignant 17NN

description:
Same sample as GSM303538.
Total microRNA.

value: non-malignant ccRCC

value: female


title: Pool non-malignant ccRCC

description: Total microRNA.

value: pool non-malignant ccRCC


title: Renal metastases O8

description: Total microRNA.

source_name: bone, metastases of ccRCC

value: bone metastases of ccRCC

value: metastasis

value: male

value: 61 yrs


title: Renal metastases O12

description: Total microRNA.

value: 89 yrs


title: Renal metastases O9

description: Total microRNA.

value: 59 yrs


title: Renal metastases O10

description: Total microRNA.

value: 74 yrs


title: Renal metastases O7

description: Total microRNA.

value: 66 yrs


title: Prostate metastases O6

description: Total microRNA.

source_name: bone, metastases of prostate

value: bone metastases of prostate

value: 55 yrs


title: E38M3

description: individual genomic DNA

value: substrate pupariation


title: Renal metastases O5

description: Total microRNA.

value: 70 yrs


title: Renal metastases O4

description: Total microRNA.

value: 69 yrs


title: Renal metastases O2

description: Total microRNA.

value: 72 yrs


title: Renal metastases O3

description: Total microRNA.

value: 60 yrs


title: Prostate metastases O1

description: Total microRNA.


title: Oral neutrophils [20]

city: Toronto

first: Flavia

last: Lakschevitz

state: ON

address: 150 College st room 221

department: Faculty of Dentistry

institute: University of Toronto

description:
replicate 6
Array barcode number: 5662468027
Location of sample: J 20

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was pre-processed using lumi R package.  Background correction was done in Genomestudio. The quantile normalization method implemented in lumi R package was used to normalize the data

source_name: Saliva

label_protocol: Biotinylated cRNA were prepared with the Ambion Amplification kit:  - Illumina TotalPrep-96 RNA Amplification Kit cat# 4393543

extract_protocol: Following neutrophil isolation, total RNA was extracted with mirVANA kit from Ambion, followed by clean-up and DNase I treatment with Ambion kit in accordance with protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: Chronic Periodontits

value: Female

value: 50 - 60 years

value: Neutrophils


title: Blood neutrophils [15]

description:
replicate 5
Array barcode number: 5662468025
Location of sample: I 15

source_name: Blood

value: 60 - 70 years


title: Blood neutrophils [22]

description:
replicate 4
Array barcode number: 5662468027
Location of sample: K 22

value: Refractory Periodontits

value: Male

value: 40 - 50 years


title: Blood neutrophils [19]

description:
replicate 5
Array barcode number: 5662468027
Location of sample: I 19


title: Oral neutrophils [18]

description:
replicate 6
Array barcode number: 5662468027
Location of sample: H 18


title: Oral neutrophils [16]

description:
replicate 6
Array barcode number: 5662468025
Location of sample: J 16


title: Oral neutrophils [14]

description:
replicate 6
Array barcode number: 5662468025
Location of sample: H 14


title: Blood neutrophils [21n-54B]

description:
replicate 4
Array barcode number: 5662468025
Location of sample: K 21n-54B

value: 30 - 40 years


title: Oral neutrophils [11]

description:
replicate 3
Array barcode number: 5662468027
Location of sample: E 11

value: 20 - 30 years


title: Blood neutrophils [24]

description:
replicate 2
Array barcode number: 5662468027
Location of sample: L 24

value: Control


title: Blood neutrophils [12]

description:
replicate 4
Array barcode number: 5662468027
Location of sample: F 12


title: Oral neutrophils [9n-53S]

description:
replicate 3
Array barcode number: 5662468027
Location of sample: C 9n-53S


title: Blood neutrophils [8]

description:
replicate 4
Array barcode number: 5662468025
Location of sample: F 8


title: Blood neutrophils [17]

description:
replicate 5
Array barcode number: 5662468027
Location of sample: G 17


title: Blood neutrophils [10n-53B]

description:
replicate 4
Array barcode number: 5662468027
Location of sample: D 10n-53B


title: Oral neutrophils [7]

description:
replicate 3
Array barcode number: 5662468025
Location of sample: E 7


title: Ptr_HRSP27-5-rep2

city: Vancouver

first: Ilga

last: Porth

address: 2424 Main Mall

institute: University of British Columbia

description: wildtype

hyb_protocol: 4ug of each Cy3-labeled sample was hybridized on Roche Nimblegen poplar gene expression microarrays (Design Name Populus 135K EXP HX12 090828). Microarray hybridizations and basic bioinformatics analysis were carried out at the NimbleGen processing site (Jack Bell Research Centre, Prostate Centre, Vancouver, BC).

scan_protocol: Arrays were scanned at a 5um resolution with the Molecular Devices GenePix 4200AL scanner.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). Agilent’s GeneSpring 7.3.1 was used to analyze the normalized data.

organism: Populus trichocarpa

source_name: Populus trichocarpa HRSP27-5 wt

label_protocol: Samples were prepared following NimbleGen’s Arrays User Guide Gene Expression Analysis version 3.2.  10ug of each total RNA was converted to ds cDNA with the Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit, 1ug of each ds cDNA was fluorescently labeled using the NimbleGen One-Color DNA Labeling Kit.

growth_protocol: Nine-year-old P. trichocarpa trees grown in the common-garden plot (located 49.18°N and 122.85°W, Surrey, BC, Canada) representing populations that span a latitudinal range of 44°N to 58.6°N

extract_protocol: RNA extractions and quality control of the extracted RNA was carried out as described previously (Geraldes et al., 2011, Molecular Ecology Res.). Total RNA quality was assessed with the Agilent 2100 Bioanalyzer prior to microarray analysis.  Samples with a RIN value of greater than or equal to 8.0 were deemed to be acceptable for microarray analysis.

treatment_protocol: Natural accessions were used throughout the study. We used a subset of the P. trichocarpa genotypes from the population with contrasting wood chemical composition and wood average density for gene expression profiling.

tag: phenotype (density)

value: high

tag: phenotype (alpha cellulose)

tag: phenotype (hemicellulose (xylose))

tag: phenotype (lignin)

value: low

tag: phenotype (glucose)

tag: phenotype (density-alpha cellulose)

value: high/high

tag: phenotype (hemicellulose-lignin)

value: low/low

tag: phenotype (density-lignin)

value: high/low

tag: phenotype (alpha cellulose-hemicellulose (glucose-xylose))

tag: phenotype (alpha cellulose-lignin)


title: Blood neutrophils [13]

description:
replicate 5
Array barcode number: 5662468025
Location of sample: G 13

tag: gender

tag: cell type


title: Blood neutrophils [6]

description:
replicate 2
Array barcode number: 5662468027
Location of sample: B 6

tag: age


title: Oral neutrophils [5]

description:
replicate 1
Array barcode number: 5662468027
Location of sample: A 5


title: Blood neutrophils [4]

description:
replicate 2
Array barcode number: 5662468025
Location of sample: D 4


title: Oral neutrophils [1]

description:
replicate 1
Array barcode number: 5662468025
Location of sample: A 1


title: Ptr_LILC26-2-rep2

description: wildtype

source_name: Populus trichocarpa LILC26-2 wt

tag: genotype

value: low/high


title: Ptr_HRSO27-1-rep1

description: wildtype

source_name: Populus trichocarpa HRSO27-1 wt


title: Ptr_QLKE16-3-rep1

description: wildtype

source_name: Populus trichocarpa QLKE16-3 wt


title: Oral neutrophils [3]

description:
replicate 1
Array barcode number: 5662468025
Location of sample: C 3


title: Ptr_SQMC25-2-rep1

description: wildtype

source_name: Populus trichocarpa SQMC25-2 wt


title: Blood neutrophils [2]

description:
replicate 2
Array barcode number: 5662468025
Location of sample: B 2


title: Ptr_SKNP10-8-rep2

description: wildtype

source_name: Populus trichocarpa SKNP10-8 wt


title: Ptr_HRSO27-1-rep2

description: wildtype


title: Ptr_HRSP27-5-rep1

description: wildtype


title: Ptr_SKNP10-8-rep1

description: wildtype


title: Ptr_LILC26-2-rep1

description: wildtype


title: Ptr_HOMA21-4-rep2

description: wildtype

source_name: Populus trichocarpa HOMA21-4 wt


title: Ptr_HOMB21-2-rep2

description: wildtype

source_name: Populus trichocarpa HOMB21-2 wt


title: Ptr_LAFY30-1-rep1

description: wildtype

source_name: Populus trichocarpa LAFY30-1 wt


title: Ptr_LILA26-3-rep1

description: wildtype

source_name: Populus trichocarpa LILA26-3 wt


title: Mock_vs_treated_MCF7_KD_rep1

city: Tehran

first: Mohammadreza

last: Zamanian

state: Tehran

address: Hafez al., Bani Hashem st., Resalat Highway

department: Genetics

country: Iran

institute: Royan Institute

description: Biological replicate 1

hyb_protocol: Manufacturer protocol, see manufacturer's web site at http://www.agilent.com/, Catalog number G4112F

data_processing:
Data Sourcing: Primary data were obtained from Dr. Volker Brenner, Oxford Gene Technology. Quality Control: The arrays used in the experiment were 512_SEN (Agilent), each comprising 45015 features.  Normalization: The data were normalised within arrays using lowess, followed by normalisation between arrays using the Aquantile method, which ensures that A-values (average intensities) have the same empirical distribution across arrays leaving the M-values (log-ratios) unchanged.
The output is log2 ratios of Cy5 relative to Cy3. The gene lists which result are fully annotated, and are sorted in order of decreasing significance [gene_lists_data.txt available on Series records].

source_name: Mock Control_MCF7 Cells

growth_protocol: MCF7 cells were grown in Dulbecco’s modified eagle’s medium (DMEM) high glucose (Sigma, MO, USA) supplemented with 7.5% fetal bovine serum and were kept at 37°C and 5% CO₂ pressure.

extract_protocol: RNA extraction performed using RNeasy mini kit (Qiagen). The quality of RNA was checked by nanodrop. The acceptable quality of RNA was determined by the proportions of A260/A280 and A260/230, which were set as ≥1.8 and ≥1.5 in respect.

treatment_protocol: MCF7 cells were diluted in an antibiotic free medium with a plating density of 1 X 10⁵ cells/mL. For 12 wells plate, one mL of the cell dilution was applied into each well and incubated at 37 °C, and 5% CO₂ overnight. On the following day, two tubes were prepared for each group of study. In tube A, 50 μl of 2mM siRNA targeting pool against calreticulin was mixed with 50 μl of serum and antibiotic free media for the test group (Treated). In tube B, 1.5 μl  of DharmaFECT 1 was mixed with 98.5 μl of serum and antibiotic free media. The contents of each tube were mixed and homogenized by pipetting up and down carefully and incubated at room temperature for 5 minutes. Then, the content of tube A was added into tube B, mixed carefully and incubated at room temperature for 20 minutes. In the next step, 800 μl of antiobitic free complete media was added into the tube, mixed gently and finally added to the well of the plate after removing the culture medium. The reaction was prepared in triplicates and all the volumes multiplied by 3.5 to account for loss during pipetting. In mock control, ON-TARGETplus SMARTpool was replaced by equal amount of antibiotic and serum free media. The plates were kept at 37° C and 5% CO₂.

value: MCF7 breast cancer cells

tag: transfected with

value: transfection reagent (mock control)

source_name: Calreticulin-siRNA_MCF7 Cells

value: transfection reagent + siRNA against calreticulin


title: Mock_vs_treated_MCF7_KD_rep2

description: Biological replicate 2

scan_protocol: Manufacturer protocol, see manufacturer's web site at http://www.agilent.com/, Catalog number G4112F


title: Ptr_HOMB21-1-rep1

description: wildtype

source_name: Populus trichocarpa HOMB21-1 wt


title: THz-irradiated skin, biological rep3

city: Seoul

first: Kyu-Tae

address: Irwon-Ro 81

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

description: Gene expression data from 1 hour of fs-THz irradiated mouse skin at post-24 hours

hyb_protocol: Labeled RNAs were hybridized according to the standard Affymetrix protocol for the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on the GenePix 4000B (Molecular Devices, Sunnyvale, CA).

data_processing: The levels of hybridization were determined using GenePix Pro 6.0 software as recommended by the manufacturer. The background-adjusted intensity was corrected by Robust Multichip Average (RMA).

source_name: THz-targeted skin at post-24 hours

label_protocol: Biotinylated cRNAs were prepared from 100 ng total RNA, according to the standard Affymetrix protocol for the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

extract_protocol: Targeted dorsal skin tissue was promptly lysed with TissueLyser II (Quiagen, Hilden, Germany) and isolated into total RNA using TRiZol (Invitrogen, Carlsbad, CA).

treatment_protocol: Anesthetized mice were hair-clipped and prepared to get sham or THz irradiation in the targeted restrainer.

tag: strain

value: male

value: 6-8 weeks-old

tag: tissue

value: full-thickness dorsal skin

tag: stress

value: THz-irradiated


title: THz-irradiated skin, biological rep2


title: Mock_vs_treated_MCF7_KD_rep3

description: Biological replicate 3

label_protocol: Manufacturer protocol, see manufacturer's web site at http://www.agilent.com/, Catalog number G4112F


title: Ptr_NBON29-4-rep1

description: wildtype

source_name: Populus trichocarpa NBON29-4 wt

tag: phenotype (density)

tag: phenotype (alpha cellulose)


title: THz-irradiated skin, biological rep1


title: sham-irradiated skin, biological rep3

description: Gene expression data from 1 hour of sham irradiated mouse skin at post-24 hours

source_name: sham-targeted skin at post-24 hours

value: control


title: Ptr_PHLC22-4-rep2

description: wildtype

source_name: Populus trichocarpa PHLC22-4 wt

tag: phenotype (hemicellulose (xylose))

tag: phenotype (lignin)


title: sham-irradiated skin, biological rep2


title: Ptr_DEND17-5-rep1

description: wildtype

source_name: Populus trichocarpa DEND17-5 wt

tag: phenotype (glucose)

tag: phenotype (density-alpha cellulose)


title: Ptr_PHLC22-4-rep1

description: wildtype

tag: phenotype (hemicellulose-lignin)

tag: phenotype (density-lignin)


title: sham-irradiated skin, biological rep1


title: Ptr_HOMB21-2-rep1

description: wildtype

tag: phenotype (alpha cellulose-hemicellulose (glucose-xylose))

tag: phenotype (alpha cellulose-lignin)


title: Ptr_JASP30-4-rep1

description: wildtype

source_name: Populus trichocarpa JASP30-4 wt


title: Ptr_SQMC25-2-rep2

description: wildtype


title: bic_activated_3

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania

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

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

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

source_name: bic activated

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

growth_protocol: CD8 T cells were purified by negative selection with magnetic beads (EasySep, Stemcell Technologies) from uninfected wild-type or miR-155 deficient (bic-/-) C57BL/6 mice and stimulated in vitro with 1microgram/ml plate-bound anti-CD3 and 5microgram/ml plate-bound anti-CD28 for 48hrs. Unstimulated, purified CD8 T cells from the same mice were used as control.

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

tag: stimulation

value: stimulated

value: bic-/-

tag: genetic background

tag: cell type

value: CD8 T cell


title: Ptr_QLKE16-3-rep2

description: wildtype

source_name: Populus trichocarpa QLKE16-3 wt

tag: genotype

value: high


title: bic_activated_2

treatment_protocol: CD8 T cells were purified by negative selection with magnetic beads (EasySep, Stemcell Technologies) from uninfected wild-type or miR-155 deficient (bic-/-) C57BL/6 mice and stimulated in vitro with 1microgram/ml plate-bound anti-CD3 and 5microgram/ml plate-bound anti-CD28 for 48hrs. Unstimulated, purified CD8 T cells from the same mice were used as control.


title: bic_activated_1


title: bic_unstimulated_3

source_name: bic unstimulated

value: unstimulated


title: male brain 105, selenium

city: Moscow

first: Maia

middle: J

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Affymetrix Zebrafish Genome Arrays (~14,900 transcripts) were hybridized with fragmented biotinylated cRNA for 16 h at 45 °C with constant rotation (45 rpm), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.

scan_protocol: Another round of SAPE was performed prior to scanning using a GeneChip Scanner 3000 (Affymetrix). All microarray procedures were performed at the Genomics Core Facility of the Center for Reproductive Biology at Washington State University (Pullman, WA).

data_processing: CEL files containing raw data were processed and analyzed using R software and Bioconductor packages. Microarray data were examined for physical anomalies on the chip by pseudo chip and residual error visualizations. Quality Assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport. The arrays were pre-processed using the Robust Multi-array Average (RMA) procedure using the affy package. Next, unexpressed and low variability genes were removed by unbiased filtering. Probesets with less than a median log2 signal value of 5.00 were removed from further analysis. A filter on interquartile range was also applied to remove low variability genes. Genes with an interquartile range of less than 0.5 across all chips in the experiment were excluded. We performed an additional filtration step to reduce the genes down to annotated Ensembl genes.

organism: Danio rerio

source_name: Zebrafish male adult brain selenium supplemented

label_protocol: For each array, 10 μg of total RNA were converted to cDNA. Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix, Santa Clara, CA, USA).

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

treatment_protocol: 1 year old sexually mature adult zebrafish were fed diets with either control levels of selenium (1.4ppmSe) or supplemented with sodium selenite (5.6ppmSe) for 14 days.

value: whole brain

tag: strain

value: Transgenic Mosaic 1

tag: age

value: 1 year old (sexually mature adult)

tag: Sex

tag: treatment

value: selenium supplemented


title: male brain 121, control

source_name: Zebrafish male adult brain control

tag: tissue


title: Ptr_KLNE20-5-rep2

description: wildtype

source_name: Populus trichocarpa KLNE20-5 wt

tag: phenotype (density)

tag: phenotype (alpha cellulose)

tag: phenotype (hemicellulose (xylose))

value: low

value: high/high

value: low/low

value: high/low


title: Ptr_LONG29-3-rep1

description: wildtype

source_name: Populus trichocarpa LONG29-3 wt

tag: phenotype (lignin)

tag: phenotype (glucose)

tag: phenotype (density-alpha cellulose)

value: low/high


title: male brain 101, selenium

value: male


title: bic_unstimulated_2


title: male brain 98, selenium


title: Ptr_NBON29-4-rep2

description: wildtype

tag: phenotype (hemicellulose-lignin)

tag: phenotype (density-lignin)

tag: phenotype (alpha cellulose-hemicellulose (glucose-xylose))


title: Ptr_DEND17-5-rep2

description: wildtype

tag: phenotype (alpha cellulose-lignin)


title: Ptr_LILA26-3-rep2

description: wildtype

source_name: Populus trichocarpa LILA26-3 wt


title: Ptr_BELA18-4-rep2

description: wildtype

source_name: Populus trichocarpa BELA18-4 wt


title: Ptr_LAFY30-1-rep2

description: wildtype

source_name: Populus trichocarpa LAFY30-1 wt


title: Ptr_HOMA21-4-rep1

description: wildtype

source_name: Populus trichocarpa HOMA21-4 wt


title: Ptr_LONG29-3-rep2

description: wildtype


title: Ptr_KLNE20-5-rep1

description: wildtype


title: Ptr_LONG29-2-rep1

description: wildtype

source_name: Populus trichocarpa LONG29-2 wt


title: male brain 99, control


title: wt_activated_4

source_name: wt activated

tag: stimulation

value: wild-type

tag: genetic background

tag: cell type


title: male brain 111, control

tag: strain

tag: age

value: control


title: female brain 136, selenium

source_name: Zebrafish female adult brain selenium supplemented

tag: Sex

value: female

tag: treatment


title: female brain 129, selenium

tag: tissue


title: LIN28B_knockdown_rep2 [Affymetrix]

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B after knockdown with siRNA

hyb_protocol: 3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC

scan_protocol: Genechips scanned on Affymetrix Genechip 300 7G scanner

data_processing: We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 2

label_protocol: 2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).

growth_protocol: HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking.  Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

treatment_protocol: siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

tag: cell line


title: wt_activated_2

value: stimulated

tag: genotype


title: LIN28B_knockdown_rep1 [Affymetrix]

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 1


title: male brain 108, control


title: wt_unstimulated_3

source_name: wt unstimulated

value: CD8 T cell


title: wt_activated_1


title: wt_unstimulated_2


title: Ptr_LONG29-2-rep2

description: wildtype

tag: phenotype (density)

value: high

tag: phenotype (alpha cellulose)

tag: phenotype (hemicellulose (xylose))

tag: phenotype (lignin)


title: female brain 120, selenium


title: wt_activated_3


title: wt_unstimulated_1

value: unstimulated


title: LIN28B_induced_rep2 [Affymetrix]

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B  induced

source_name: HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 2


title: female brain 122, selenium

value: whole brain


title: female brain 102, control

source_name: Zebrafish female adult brain control

value: Transgenic Mosaic 1


title: LIN28B_not_induced_rep1 [Affymetrix]

description: Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B not induced

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 1


title: female brain 124, control

value: 1 year old (sexually mature adult)


title: LIN28B_not_induced_rep2 [Affymetrix]

source_name: HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 2


title: famale brain 133, control


title: wt_unstimulated_4


title: LIN28B_induced_rep1 [Affymetrix]

source_name: HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 1


title: HealthyDonor_1-18h

status: Public on Feb 25 2013

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

institute: Munich University Hospital

hyb_protocol: The hybridization was done using the Affy Hybridization, wash and stain kit according to the manufacturers protocol.

scan_protocol: The arrays were scanned using the GeneChip 3000 7G Scanner with AGCC software version 3.0

data_processing:
The were processed with various packages from Bioconductor suite. The intensities were background corrected, normalized, and the expression values computed by Robust Microchip Average methodology (package oligo). hours) were identified.
probe group file: Bioconductor package pd.hugene.1.0.st.v1 (v. 3.0.2) was used
meta-probeset file: Bioconductor package pd.hugene.1.0.st.v1 (v. 3.0.2) was used

source_name: PBMC

label_protocol: The labeled target was prepared from 100ng total RNA using Ambion WT Expression kit and the Affymetrix terminal labeling kit.

growth_protocol: PBMC separated on Ficoll gradient

extract_protocol: Ethanol extraction of total RNA.

treatment_protocol: Stimulation with anti-CD3 and anti-CD28 antibodies for 6h, 12h, 18h. Unstimulated samples as a controls.

tag: patient status

value: Healthy Donor

tag: time


title: HealthyDonor_2-18h


title: HealthyDonor_1-12h


title: Patient-12h

value: Patient


title: Day10 MDI repl1 vs MDI repl3

city: Antwerp

first: Anna

last: Pereira-Fernandes

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

hyb_protocol: 825 ng of both Cy3 and Cy5 labelled cRNA were co-hybridized on a 44K Whole Rat Genome Oligo Microarray (G4131F, Agilent) for 17h at 60°C in a continuous rotation Agilent hybridization oven. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies, Diegem, Belgium) to prevent ozone-induced Cy5-degradation. A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias.

scan_protocol: Arrays were scanned at 532 and 635 nm using a Genetix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing:
The images were analysed using the Genepix Pro software 4.1 (Axon Instruments) for spot identification and for quantification of the fluorescent signal intensities. Statistical analysis of microarray data was performed with the R package limma. Briefly, spots for which red or green FG < BG + 2SD on all arrays were deleted before analysis (FG: medium foreground intensity; BG: average local background intensity calculated over the full microarray; SD: standard deviation of local background intensities). After background correction (backgroundCorrect, method “normexp”, offset = 50) of the median intensity data, loess normalisation (normalizeWithinArrays) was applied. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Exposure versus control contrasts were fitted to the linear models and considered significant if p<0.05 and ǀlog2FCǀ>0.75 (log2 fold change).
Since a loop design was used for this microarray design, the final contrasts between the conditions (DMSO vs MDI; DMSO vs TBT 10 nM and DMSO vs TBT 50 nM) were added in separate .txt sheets with the log2 based FC values and the adjusted p-value for each ID.  The .txt files are linked as supplementary files on the Series record.
The .txt files report loess normalized log2 based fold-change Cy5/Cy3.

source_name: Day10 MDI repl1

label_protocol: Low Input Quick Amplification Labeling Kit (LIQA, Agilent, Diegem, Belgium), according to the protocol of the manufacturers. Briefly, starting from 200 ng of total RNA, poly-A RNA was reverse transcribed using a poly dT-T7 primer. The resulting cDNA was used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP or Cyanine 5-CTP. The amplified and labelled RNA samples were purified separately on an RNeasy purification column (Qiagen).

growth_protocol: 3T3-L1 murine cell line (ATCC CRL-173) were cultured in 75 cm2 Nunc cell culture flasks in standard growth medium (DMEM high glucose, Gibco BRL, 31885-023) supplemented with 10% heat inactivated Newborn Calf serum, 100 U/mL Penicillin, 100 µg/mL Streptomycin (Life Technologies) and 1 mM sodium pyruvate  and phenol red as pH indicator. Cells were grown in a 37°C incubator under a 5% CO2 atmosphere and cultures were routinely verified as mycoplasma free with the PCR-based VenorTM GeM Mycoplasma Detection kit (Sigma-Aldrich, Bornem, Belgium). At 70-90% confluence, cells were detached with 0.25% tryspin/EDTA during 3 min (37°C). The  trypsin was neutralized with growth medium and cells were split, with a maximum of 12 passages. Every 2-3 days, medium was refreshed.

extract_protocol: Total RNA extracted using the Qiagen RNeasy mini kit

treatment_protocol: Cells were seeded in 6- well plates at a density of 200,000 cells/well and grown until confluence. Standard medium of 2 days post-confluent cells was replaced by mature medium containing 10% Heat Inactivated Foetal Bovine Serum (FBS, Life Technologies) instead of Newborn Calf Serum and the test compound, Tributyltin Chloride (TBT-Cl, Acros Chemicals, Geel, Belgium), was added for 10 days, changing the medium every 2-3 days. TBT was dissolved in DMSO with a final maximal concentration of 0.1%. Therefore, a solvent control (0.1% DMSO) was included in each experiment. As positive control, 2 days post-confluent cells were stimulated for 48h in mature medium containing a MDI hormonal cocktail (0.5 mM isobutyl methylxanthine, 0.25 µM dexamethasone and 10 µg/mL insulin) and another 8 days in mature medium containing only insulin (10 µg/mL) and changed every 3 days. In the following experiments and results, 2 days post-confluent cells are indicated by the ‘day 0’ time point. After exposure, cells were harvested for RNA extraction at day1 and day10.

tag: agent

value: MDI

source_name: Day10 MDI repl3


title: Patient-6h


title: HealthyDonor_1-6h


title: Patient-18h


title: Day10 MDI repl2 vs MDI repl1

source_name: Day10 MDI repl2


title: HealthyDonor_2-6h


title: Patient-0h