title: MAFB_E15.5_3

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10713

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 5ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: E15.5 Podocyte Layer

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 5-10 E15.5 kidneys
Pooled sample: Yes
Dissection Method: Podocyte cells were isolated from E15.5 Mafb transgenic mice kidneys using a combination of tyrpsinization and FACS.
Mafb transgenic mice are time-mated. Pregnant Mafb transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Embryonic kidneys are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC. Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS. The dissociated cells from the kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes. The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS. Filter cells through 70 micron mesh filter and the GFP positive cells are further isolated using FACS.

tag: gene reported

value: Tg(Mafb-EGFP)79Gsat / MMRRC:011834-UCD

tag: strain

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

value: ND

tag: developmental landmark:


title: Erythroblast_SOD2+/+_repWT17

status: Public on Aug 06 2008

type: RNA

city: La Jolla

first: Florent

middle: M.

last: MARTIN

state: CA

address: 10550 North Torrey Pines Road, MEM-151

department: Department of Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

description: Gene expression data from Sod2+/+ sorted erythroblasts

hyb_protocol: The target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization on 430 2.0 arrays.  Our hybridization cocktail contained control oligo B2 and eukaryotic controls (Affymetrix), herring sperm DNA (Promega, Madison, WI), BSA (Invitrogen), hybridization buffer (Affymetrix recommended recipe) and water.  Cocktails were hybridized to GeneChip Mouse Genome 430 2.0 arrays (http://www.affymetrix.com/products/arrays/specific/mouse430_2.affx) at 45 °C for 16 hours.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned using a ScanArray 3000 running the GCOS v1.3.037 algorithm (Affymetrix), default settings and a target intensity of 250 for scaling according to the manufacturer’s protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface.  3'/5' ratios for GAPDH and β-actin were confirmed to be within acceptable limits (all but one Sod2-/- sample GAPDH 3'/5' ratios were below 2.0; the off range sample was legitimately removed from analysis), and BioB spike controls were found to be present on all chips, with BioC, BioD and CreX also present in increasing intensity.  When scaled to a target intensity of 250, scaling factors for all arrays were within acceptable limits (4.089-7.955), as were background (48-67), Q values and mean intensities.

data_processing: Arrays were scanned using GCOS v1.3.037 (Affymetrix), default settings and a target intensity of 250 for scaling.  The data was RMA-normalized and log base 2-transformed through import of .CEL files on GeneSifter Version 2.3.7.2007.05.25 (VizX Labs, Seattle, WA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Sorted erythroblasts, Sod2+/+

label_protocol: Total RNA from each sample was submitted to one-round cDNA synthesis to prepare biotinylated target RNA using standard Affymetrix protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) as previously described (Lockhart et al. Nat Biotechnol, 1996. 14(13): p. 1675-80).  Briefly, 5 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer and a SuperScript II Reverse Transcriptase (Invitrogen).  Second-strand synthesis was performed using Escherichia coli DNA ligase and polymerase I (Invitrogen); Escherichia coli RNAse H (Invitrogen) removed the remaining total RNA.  The target was amplified and biotin-labeled through in vitro transcription (IVT) with biotinylated UTP and CTP ribonucleotides (Enzo Life Sciences, Farmingdale, NY), generating a biotinylated cRNA.  Quality and amount of cRNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

growth_protocol: Heterozygous B6-Sod2tm1Cje mice were bred in timed matings to obtain Sod2-/- (KO) and Sod2+/+ (WT) littermates at E13.5-16.5 of development to serve as donors for fetal liver cell transplantation.  Embryos were harvested; fetal livers were dissected and mechanically dissociated into single cell suspensions in culture medium (RPMI, 7% FCS, glutamine, penicillin-streptomycin, 10e-5 M betamercapto-ethanol).  C57BL/6 mice congenic at the Ly5 locus (B6.SJL_PtprcaPep3b/BoyJ [Ly5.1], National Cancer Institute) were used as recipients in order to allow for differentiation of host (Ly5.1) versus donor (Ly5.2) hematopoietic cells.  11–15 week old Ly5.1 host animals were subjected to 10.50 cGy (1,050 rad) of gamma irradiation divided into two equal doses 4 h apart on the day of transplant.  10e6 fetal liver cells, prepared as above, were injected intravenously into irradiated Ly5.1 congenic recipients. Animals were maintained on chlorinated water for 21 d after irradiation.  All experiments were approved by the Animal Use Committee (Friedman et al. J. Exp. Med. 2001).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit according to the manufacturer’s suggested ‘spin’ protocol for isolation of total RNA from animal cells (Qiagen, Valencia, CA).  Briefly, we disrupted and lysed 5-10 million sorted cells in RLT Buffer, homogenized and sheared genomic DNA through centrifugation on QIAshredder spin columns; we performed on-column DNA digestion with the RNase-Free DNase Set (Qiagen) and eluted total RNA in RNase-free water (Sigma-Aldrich).  Quality and amount of starting total RNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) and on formaldehyde-containing agarose gels.

treatment_protocol: Marrow was taken from femurs, tibias, pelvic girdles and humerus after Halothane (Halocarbon Laboratories, River Edge, NJ) vapor terminal inhalation in accordance with the American Veterinary Medical Association (AVMA) Panel on Euthanasia.  All animal procedures were approved by The Scripps Research Institute (TSRI) Institutional Animal Care and Use Committee (IACUC).  Bone marrow single cell suspensions were labeled with FITC-conjugated anti-CD71 and PE-conjugated anti-TER-119 monoclonal antibodies (mAbs; Pharmingen, BD Biosciences, San Jose, CA) in ice-cold 2 mM EDTA: 0.5% BSA: PBS.  Fc-R saturation was achieved by pre-incubation with a purified anti-CD16/32 mAb.  >=92% cell viability was ensured using the Trypan blue exclusion assay.  Prior to sorting, cells were centrifuged and resuspended in 1 mM EDTA: 25 mM HEPES: 1% FCS: PBS containing 10 μg/ml propidium iodide (PI; Sigma-Aldrich, St. Louis, MO).  Pairs of Sod2+/+ and Sod2-/- samples were sorted in parallel using two FACSDiva sorters (BD Biosciences) simultaneously; sorting was operated at medium pressure (35 psi) using 80 μm nozzles.  Purity and quality of preparations were ensured by microscope examination of Wright-Giemsa-stained sorted cells cytospun onto slides and by flow cytometry analysis using a FACSCalibur cytometer running CellQuest Pro (BD Biosciences).

tag: Strain

value: C57BL/6 Ly5.1+, tissue:CD45.2+ transplanted bone marrow


title: H1299 cells transduced with TAp73beta expressing adenovirus 1

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: To identify candidate p73 target genes from this series, data can be log transformed and baseline transformed, and duplicate samples can be averaged and samples can be filtered so that the maximum number of arrays with Absent calls = 2.

hyb_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix

data_processing: Samples were processed using Stratagene ArrayAssist GC-RMA algorithm.

organism: Homo sapiens

source_name: H1299 lung carcinoma cells, transduced with pAd:p73, 5 h

growth_protocol: Cells were cultured in DMEM (Invitrogen) containing 10% Fetal Bovine Serum.

extract_protocol: Total RNA was harvested using the Aurum Total RNA Mini Kit (Bio-Rad, Richmond, CA), using lysis buffer without beta-Mercaptoethanol.

treatment_protocol: H1299 cells were infected with adenovirus expressing TAp73beta, and the cells were harvested after 80% transduction efficiency was reached, as monitored by GFP fluorescence.

tag: Lung carcinoma cell line


title: H1299 cells transduced with TAp73beta expressing adenovirus 2

description: To identify candidate p73 target genes from this series, samples can be log transformed and baseline transformed, and duplicate samples can be averaged and samples can be filtered so that the maximum number of arrays with Absent calls = 2.

scan_protocol: see Vanderbilt Microarray Shared Resource, Affymetrix


title: MAFB_E15.5_1

status: Public on Aug 04 2008

country: United Kingdom

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10711

label: Biotin

value: Tg(Mafb-EGFP)79G / MMRRC:011834-UCD


title: jurkat_rep1

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description: Jurkat cells are an immortalized line of T lymphocyte cells that are used to study acute T cell leukemia. The cell line was established from peripheral blood of a human with T cell leukemia.

hyb_protocol: GeneChip Hybridization oven 640

scan_protocol: GeneChip Scanner

source_name: Jurkat cells rep 1

label_protocol: IVT Labeling Affymetrix

growth_protocol: RPMI-1640 (Mediatech), 10% FBS (Gibco), 2mmol/L L-glutamine (Mediatech), 100IU/ml penicillin, 100 microgram/ml streptomycin, 0.25 microgram/ml amphotericin B (all from Mediatech) at 37 degrees Celsius, 5% carbon dioxide, 95% air, and 80% relative humidity.

extract_protocol: Trizol

treatment_protocol: Allowed to reach 6 X 10 5 cells/ml.

tag: Jurkat, Human T-acute lymphoblastic leukemia


title: Erythroblast_SOD2+/+_repWT29


title: MAFB_E15.5_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10712


title: BG00817_females_2

status: Public on Aug 01 2008

city: Raleigh

first: Mike

last: Magwire

state: NC

address: 3501 Gardner Hall

department: Genetics

institute: NCSU

description: Seven lines homozygous for a single P-element insertion led to an increase in life span. Two replicates of each sex and line were used to identify differences in expression from the isogenic control line. Flies were aged 6 weeks (42 days) and frozen at approximately the same time (10:30 -12:00 AM) for RNA extraction.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotinylated cRNA

organism: Drosophila melanogaster

source_name: whole bodies of 42 day old BG00817 female flies, replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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


title: BG00817_males_2

source_name: whole bodies of 42 day old BG00817 male flies, replicate 2


title: esg_females_1

source_name: whole bodies of 42 day old esg female flies, replicate 1


title: esg_males_1

source_name: whole bodies of 42 day old esg male flies, replicate 1


title: BG00817_females_1

source_name: whole bodies of 42 day old BG00817 female flies, replicate 1


title: BG00817_males_1

source_name: whole bodies of 42 day old BG00817 male flies, replicate 1


title: esg_males_2

source_name: whole bodies of 42 day old esg male flies, replicate 2


title: esg_females_2

source_name: whole bodies of 42 day old esg female flies, replicate 2


title: 1205Lu melanoma cells co-cultured with HUVEC cells

status: Public on Aug 02 2008

city: Baltimore

first: Megan

middle: Jean

last: Stine

state: MD

address: 1650 Orleans Street, CRB1 336

institute: The Johns Hopkins University School of Medicine

description: Image Analysis using GCOS 1.4, using MAS5 algorithm and manufacturer's specifications. Global scaling of images to a target intensity of 150.

hyb_protocol: 16 hrs at 45C with rotation (60 rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Affymetrix MAS5

label_protocol: One round amplification protocol for total RNA following Affymetrix specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression analysis, Technical Manual, 2003).

growth_protocol: Cells were grown in EGM-2 medium.

extract_protocol: RNeasy Kit (QIAGEN)

treatment_protocol: GFP-labeled 1205Lu melanoma cells were co-cultured with RFP-labeled HUVEC cells for 48 hours in EGM-2 medium.

tag: GFP-labeled 1205Lu melanoma cells


title: crol_females_2

source_name: whole bodies of 42 day old crol female flies, replicate 2


title: crol_females_1

source_name: whole bodies of 42 day old crol female flies, replicate 1


title: CG10990_males_1

source_name: whole bodies of 42 day old CG10990 male flies, replicate 1


title: pyd_females_1

source_name: whole bodies of 42 day old pyd female flies, replicate 1


title: CG9238_females_2

source_name: whole bodies of 42 day old CG9238 female flies, replicate 2


title: CG10990_females_1

source_name: whole bodies of 42 day old CG10990 female flies, replicate 1


title: CG9238_females_1

source_name: whole bodies of 42 day old CG9238 female flies, replicate 1


title: CG10990_females_2

source_name: whole bodies of 42 day old CG10990 female flies, replicate 2


title: pyd_females_2

source_name: whole bodies of 42 day old pyd female flies, replicate 2


title: CG10990_males_2

source_name: whole bodies of 42 day old CG10990 male flies, replicate 2


title: 1205Lu melanoma cells grown alone

source_name: 1205Lu melanoma cells grown alone

treatment_protocol: GFP-labeled 1205Lu melanoma cells were cultured for 48 hours in EGM-2 medium.


title: HUVEC cells grown alone

source_name: HUVEC cells grown alone

treatment_protocol: RFP-labeled HUVEC cells were cultured for 48 hours in EGM-2 medium.

tag: RFP-labeled HUVEC primary cells


title: crol_males_2

source_name: whole bodies of 42 day old crol male flies, replicate 2


title: mub_males_1

source_name: whole bodies of 42 day old mub male flies, replicate 1


title: mub_males_2

source_name: whole bodies of 42 day old mub male flies, replicate 2


title: HUVEC cells co-cultured with 1205Lu melanoma cells

description: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

hyb_protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

treatment_protocol: RFP-labeled HUVEC cells were co-cultured with 1205Lu melanoma cells for 48 hours in EGM-2 medium.


title: Control_F_males_2

description: Seven lines homozygous for a single P-element insertion led to an increase in life span.  Two replicates of each sex and line were used to identify differences in expression from the isogenic control line.  Flies were aged 6 weeks (42 days) and frozen at approximately the same time (10:30 -12:00 AM) for RNA extraction.

source_name: whole bodies of 42 day old control male flies, replicate 2

tag: whole bodies of 42 day old control (Canton-S strain) male flies, replicate 2


title: Control_F_females_1

source_name: whole bodies of 42 day old control female flies, replicate 1

tag: whole bodies of 42 day old control (Canton-S strain) female flies, replicate 1


title: mub_females_1

source_name: whole bodies of 42 day old mub female flies, replicate 1


title: KO TAC 3

city: Maastricht

first: Marc

last: van Bilsen

address: PO BOX 616

country: Netherlands

institute: Universiteit Maastricht

description: Gene expression data from TAC-induced PPARalpha-/- mice

hyb_protocol: Biotin labeled target complementary RNA (cRNA) was fractionated and hybridized to Affymetrix 430 2.0 Mouse Genome GeneChip according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 / 7G

data_processing: Affymetrix GeneChip Operating Software (GCOS, version 1.4) was used to analyze image data. For each transcript represented on the array by a probe set, the expression algorithm computed the detection call (present, absent, or marginal), the detection p-value, and the signal which is an average intensity value for each probe set.

source_name: TAC-induced PPARalpha-/- mice

label_protocol: One-cycle target labeling according to Affymetrix manual

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

treatment_protocol: Wild-type and PPARalpha-/- mice were sham-operated or subjected to TAC for 28 days

tag: Three-month-old male PPARa-/- mice


title: pyd_males_2

source_name: whole bodies of 42 day old pyd male flies, replicate 2


title: Control_F_males_1

source_name: whole bodies of 42 day old control male flies, replicate 1

tag: whole bodies of 42 day old control (Canton-S strain) male flies, replicate 1


title: 66cl4_II

city: Vancouver

first: Shoukat

last: Dedhar

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Hybridization and washing of gene chips were carried out according to the supplier's instructions.

scan_protocol: A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.

data_processing:
Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
library(affy)
library(maDB)
Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
+ "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
+ "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
Chips.raw <- read.affybatch(filenames = Filenames)
Chips.norm <- rma(Chips.raw)
Background correcting
Normalizing
Calculating Expression
Chips.norm <- newMadbSet(Chips.norm)

source_name: primary mammary gland tumor (66cl4 cells)

label_protocol: RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).

extract_protocol: Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

value: BALB/c

tag: Age

value: 7-9 weeks old

tag: Gender

value: female

tag: Tissue

value: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 66cl4/CMVLUC cells


title: 66cl4_III


title: 4T1_II

source_name: primary mammary gland tumor (4T1 cells)

value: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 4T1/CMVLUC cells


title: 67NR_II

data_processing:
Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
> library(affy)
> library(maDB)
> Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
+ "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
+ "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
> Chips.raw <- read.affybatch(filenames = Filenames)
> Chips.norm <- rma(Chips.raw)
Background correcting
Normalizing
Calculating Expression
> Chips.norm <- newMadbSet(Chips.norm)

source_name: primary mammary gland tumor (67NR cells)

value: 7-9 weeks


title: Control_F_females_2

source_name: whole bodies of 42 day old control female flies, replicate 2

tag: whole bodies of 42 day old control (Canton-S strain) female flies, replicate 2


title: 67NR_III


title: C3C-LU

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Microbiology Immunology

institute: Geisel School of Medicine at Dartmouth

description:
Mouse Lung AIN Diet 8hr Saline Injection, biological replicate C
AN080406_Sample 68.CEL

hyb_protocol: The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. Biotinylated cRNA (15 ug) targets were then cleaned up, fragmented, and hybridized to GeneChip® array during the overnight incubation at 45oC in rotating hybridization oven.

scan_protocol: After hybridization, the arrays were stained with streptavidin-phycoerythrin in the GeneChip Fluidics station and then scanned using Affymetrix GeneChip Scanner (laser filter set at 570 nm; pixel size 2.5 um). The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® GCOS v. 1.2 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006, Perturbation=1.1, Target Intensity=150.

data_processing: CEL file data were normalized using RMA as implented in Bioconductor simpleaffy. Genes were selected by  Rank Product (Breitling, R., 2004, FEBS Letter, 57383-92) implemented in Bioconductor RankProd at  p < .05 and by ANOVA.

source_name: Sodium arsenite added to food: None; Injection: IP 8hr saline only; Diet: AIN-76A; Sodium arsenite added to drinking water: None

label_protocol: Total RNA was first reverse-transcribed using T7-oligo(dT) promoter primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction.

growth_protocol: 6wk male C57BL/6 male mice were acclimated to their respective diets for 2 wk prior to treatments.

extract_protocol:
RNA was extracted from frozen lung samples and homogenized using QiashredderTM and RNeasy® Mini Kits (Qiagen, Valencia, CA) per manufacturer's protocol. Contaminating genomic DNA was removed using DNA-free kits
(Ambion, Austin, TX) and total RNA was quantified with a NanoDrop®ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA quality was determined with the RNA 6000 LabChip kit Nano Assay (Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: Sodium arsenite at prescribed concentrations was added to food, which was repelleted, or sodium arsenite was added to water. Injections were intraperitoneal in a normal saline solution.

tag: injection

value: IP 8hr saline only

tag: diet


title: mub_females_2

source_name: whole bodies of 42 day old mub female flies, replicate 2


title: C3D-LU

description:
Mouse Lung AIN Diet 8hr Saline Injection, biological replicate D
AN080306_Sample 64.CEL


title: C1D-LU

description:
Mouse Lung AIN Diet 5wk Control, biological replicate D
AN080806_Sample 69.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: T1C-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate C
AN080306_Sample 67.CEL

source_name: Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None

tag: sodium arsenite added to food

value: 10 ppb, 5wk


title: C1A-LU

description:
Mouse Lung AIN Diet 5wk Control, biological replicate A
AN080406_Sample 63.CEL


title: 66cl4_I


title: T9D-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate D
AN080906_Sample 61.CEL

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite, 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: T2E-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E
AN080306_Sample 66.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 10 ppb, 5wk

tag: sodium arsenite added to drinking water


title: 67NR_I

tag: Strain

value: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 67NR/CMVLUC cells


title: 4T1_III


title: C3E-LU

description:
Mouse Lung AIN Diet 8hr Saline Injection, biological replicate E
AN080906_Sample 60.CEL


title: 4T1_I


title: C1C-LU

description:
Mouse Lung AIN Diet 5wk Control, biological replicate C
AN080206_Sample 57 Lung.CEL


title: T1F-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate F
AN080806_Sample 58.CEL


title: T5D-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D
AN080906_Sample 59.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 10 ppb, 5wk


title: T2D-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D
AN080206_Sample 62 Lung.CEL


title: crol_males_1

description: Seven lines homozygous for a single P-element insertion led to an increase in life span. Two replicates of each sex and line were used to identify differences in expression from the isogenic control line. Flies were aged 6 weeks (42 days) and frozen at approximately the same time (10:30 -12:00 AM) for RNA extraction.

source_name: whole bodies of 42 day old crol male flies, replicate 1


title: biopsy20_kitB

city: Berlin

first: Jan

last: Budczies

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite - Universitaetsmedizin Berlin

description: FFPE core needle biopsy

hyb_protocol: 10 µg of biotin-labeled cRNA were hybridized to Affymetrix HG-U133 Plus 2.0 chips in a Hybridization Oven 640 (Affymetrix Inc., Santa Clara, CA). After 16 h rotation at 45°C, arrays were washed and stained with the Affymetrix Fluidics Station FS-450 using the Fluidics Protocol EukGE-WS2v4. The cRNA was stained with streptavidin-phycoerythrin conjugate (SAPE, Invitrogen, Karlsruhe, Germany), incubated with a biotinylated anti-streptavidin antibody (Axxora, Lörrach, Germany) and then stained again with SAPE.

scan_protocol: Chip scanning was done with the laser GeneChip Scanner 3000 7G equipped with AutoLoader (Affymetrix Inc.).

data_processing: Signals and detection calls were calculated with the R package affy according to the standard MAS 5.0 protocol of the chip manufacturer.

source_name: breast cancer

label_protocol: 200 ng of PCR product was transcribed into biotin-labeled cRNA using the MEGAscript T7 High Yield Transcription Kit (Ambion, UK), Biotin-11-CTP and Biotin-16-UTP (Perkin Elmer, Rodgau, Germany).

extract_protocol:
RNA was isolated using the RNeasy FFPE Kit, Quiagen (RNA extraction kit B)
RNA extracts were amplified using the Microarray Target Amplification Kit (Roche Diagnostics GmbH).

tag: tumor cells

tag: ER

value: negative

tag: PR

tag: tumor stage

tag: node stage

tag: grade


title: biopsy12_kitB

description: FFPE core needle biopsy

value: positive


title: biopsy16_kitB

description: FFPE core needle biopsy


title: biopsy8_kitB

description: FFPE core needle biopsy


title: biopsy4_kitB

description: FFPE core needle biopsy


title: T3C-LU

description:
Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C
AN080306_Sample 53.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 100 ppb, 5wk

value: 100 ppb, 5wk


title: T3B-LU

description:
Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate B
AN080906_Sample 56.CEL


title: T6D-LU

description:
Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate D
AN080806_Sample 49.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 100 ppb, 5wk


title: C3F-LU

description:
Mouse Lung AIN Diet 8hr Saline Injection, biological replicate F
AN080206_Sample 52 Lung.CEL


title: biopsy22_kitA

description: FFPE core needle biopsy

extract_protocol:
RNA was isolated using the High Pure RNA Paraffin Kit, Roche Diagnostics GmbH (RNA extraction kit A)
RNA extracts were amplified using the Microarray Target Amplification Kit (Roche Diagnostics GmbH).


title: biopsy23_kitA

description: FFPE core needle biopsy


title: biopsy1_kitB

description: FFPE core needle biopsy


title: biopsy21_kitA

description: FFPE core needle biopsy


title: T1D-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate D
AN080906_Sample 50.CEL


title: T9F-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate F
AN080306_Sample 47.CEL

value: IP 8hr 1 mg/kg sodium arsenite, 1 mg/kg Dexamethasone in saline


title: T8C-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate C
AN080906_Sample 45.CEL

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: C2F-LU

description:
Mouse Lung LRD Diet 5wk Control, biological replicate F
AN080206_Sample 48 Lung.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None


title: biopsy19_kitA

description: FFPE core needle biopsy


title: T2A-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A
AN080406_Sample 54.CEL


title: biopsy18_kitA

description: FFPE core needle biopsy


title: biopsy17_kitA

description: FFPE core needle biopsy


title: biopsy16_kitA

description: FFPE core needle biopsy


title: T5E-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E
AN080306_Sample 51.CEL


title: biopsy20_kitA

description: FFPE core needle biopsy


title: biopsy24_kitA

description: FFPE core needle biopsy


title: T6F-LU

description:
Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate F
AN080406_Sample 46.CEL


title: T9E-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate E
AN080406_Sample 43.CEL


title: T8A-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate A
AN080306_Sample 42.CEL

value: IP 8hr 1 mg/kg sodium arsenite in saline


title: T5B-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate B
AN080406_Sample 36.CEL


title: T9A-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate A
AN080206_Sample 21 Lung.CEL


title: T4B-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate B
AN080806_Sample 30.CEL

source_name: Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None


title: biopsy14_kitA

description: FFPE core needle biopsy


title: T3D-LU

description:
Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate D
AN080406_Sample 32.CEL


title: T7C-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate C
AN080206_Sample 23 Lung.CEL

source_name: Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None

value: IP 8hr 1 mg/kg Dexamethasone in saline


title: T7E-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate E
AN080806_Sample 38.CEL


title: biopsy3_kitA

description: FFPE core needle biopsy


title: T7F-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate F
AN080806_Sample 44.CEL


title: T8F-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate F
AN080906_Sample 40.CEL


title: biopsy7_kitA

description: FFPE core needle biopsy


title: T4C-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate C
AN080306_Sample 33.CEL


title: biopsy15_kitA

description: FFPE core needle biopsy


title: biopsy8_kitA

description: FFPE core needle biopsy


title: biopsy9_kitA

description: FFPE core needle biopsy


title: T8E-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate E
AN080206_Sample 24 Lung.CEL


title: biopsy6_kitA

description: FFPE core needle biopsy


title: T7B-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate B
AN080906_Sample 18.CEL


title: T4F-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate F
AN080406_Sample 19.CEL


title: C1F-LU

description:
Mouse Lung AIN Diet 5wk Control, biological replicate F
AN080906_Sample 17.CEL


title: T9C-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate C
AN080806_Sample 27.CEL


title: biopsy1_kitA

description: FFPE core needle biopsy


title: biopsy5_kitA

description: FFPE core needle biopsy


title: biopsy13_kitA

description: FFPE core needle biopsy


title: biopsy11_kitA

description: FFPE core needle biopsy


title: pyd_males_1

description: Seven lines homozygous for a single P-element insertion led to an increase in life span. Two replicates of each sex and line were used to identify differences in expression from the isogenic control line. Flies were aged 6 weeks (42 days) and frozen at approximately the same time (10:30 -12:00 AM) for RNA extraction.

source_name: whole bodies of 42 day old pyd male flies, replicate 1


title: T8B-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate B
AN080806_Sample 35.CEL


title: biopsy10_kitA

description: FFPE core needle biopsy


title: HepG2_Vector_rep3

first: Yu

last: Xia

address: 10550, N. Torrey Pines Rd.

description: Expression data from HepG2 cell line

hyb_protocol: Samples were hybridized to the Affymetrix Human Genome U133 plus 2.0 array using standard Affymetrix protocols.

scan_protocol: The chips were scanned using the Affymetrix ScanArray 3000 using default settings.

data_processing: A target intensity of 250 was used for scaling. Chips were included with a background less than 100 intensity units and a GAPDH 3':5'<3. The raw expression values were normalised using Robust Multichip Average. All further processing of the data were performed within the Bioconductor project and the R program software.

source_name: empty vector transfection

label_protocol: RNA was labeled using the MessageAmp II-Biotin Enhanced Single Round RNA Amplification Kit (Perkin-Elmer Inc.)

growth_protocol: HepG2 cells were grown in MEM (Invitrogen) supplemented with non-essential amino acids and sodium pyruvate, 10 mM HEPES and 2 mM L-glutamine and 5% FBS and 2% penicillin/streptomycin solution.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by DNase treatment and RNeasy® column clean-up.

treatment_protocol: HepG2 cells were transfected with wild type Tmprss6 cDNA, mutant version of Tmprss6 and empty vector, respectively for 36 hours.

tag: human HepG2 cells


title: T1E-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate E
AN080206_Sample 41 Lung.CEL


title: biopsy12_kitA

description: FFPE core needle biopsy


title: biopsy4_kitA

description: FFPE core needle biopsy


title: HepG2_Vector_rep2

description: Expression data from HepG2 cell line


title: biopsy2_kitA

description: FFPE core needle biopsy


title: T3A-LU

description:
Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate A
AN080206_Sample 13 Lung.CEL


title: HepG2_mutant Tmprss6_rep2

description: Expression data from HepG2 cell line

source_name: mutant Tmprss6 transfection


title: T7A-LU

description:
Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate A
AN080306_Sample 15.CEL


title: HepG2_mutant Tmprss6_rep3

description: Expression data from HepG2 cell line


title: C2C-LU

description:
Mouse Lung LRD Diet 5wk Control, biological replicate C
AN080806_Sample 11.CEL


title: HepG2_Tmprss6_rep3

description: Expression data from HepG2 cell line

source_name: wild type Tmprss6 transfection


title: T1B-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate B
AN080406_Sample 12.CEL


title: C2E-LU

description:
Mouse Lung LRD Diet 5wk Control, biological replicate E
AN080806_Sample 7.CEL


title: T4D-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate D
AN080206_Sample 10 Lung.CEL


title: HepG2_mutant Tmprss6_rep1

description: Expression data from HepG2 cell line


title: HepG2_Tmprss6_rep2

description: Expression data from HepG2 cell line


title: T6C-LU

description:
Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C
AN080206_Sample 9 Lung.CEL


title: C2A-LU

description:
Mouse Lung LRD Diet 5wk Control, biological replicate A
AN080306_Sample 5.CEL


title: T4E-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate E
AN080406_Sample 4.CEL


title: Tobacco Smoke Sample 6 6hr

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

description: In this study MSK-Leuk1 cells established from a dysplastic leukoplakia lesion adjacent to a squamous cell carcinoma of the tongue were exposed to tobacco condensate for 0.5 hr, 3 hr, 6 hr, 12 hr and 24 hr, respectively and compared to untreated controls. Six biological replicates were used at each timepoint for each condition (Control or Tobacco Smoke treated).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.

source_name: Tobacco Smoke Sample 6 6hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Cells were routinely maintained in keratinocyte growth medium supplemented with bovine pituitary extract. Cells were grown in basal medium for 24 hr before treatment

extract_protocol: Total cellular RNA was isolated from cells using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Treatment with vehicle (PBS) or Tobacco Smoke condensate was carried out under serum-free conditions. Cellular cytotoxicity was assessed by measurements of cell number, trypan blue exclusion, and release of lactate dehydrogenase. There was no evidence of cytotoxicity in our experiments.

tag: MSK-Leuk1 cells

tag: Time in hrs


title: Tobacco Smoke Sample 6 24hr

source_name: Tobacco Smoke Sample 6 24hr


title: Hepatocyte_BAF60a

city: Ann Arbor

first: Siming

last: Li

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

description: Ad-BAF60a transduced hepatocyte.

hyb_protocol: According to standard Affymetrix protocols.

data_processing: dCHIP version 2007.

source_name: Primary hepatocytes transduced with Adeno-BAF60a

extract_protocol: Trizol.

tag: Primary hepatocytes were isolated from C57/Bl6J mice (10 weeks old) and transduced with recombinant adenovirus expressing BAF60a for 40 hrs.


title: Tobacco Smoke Sample 6 3hr

source_name: Tobacco Smoke Sample 6 3hr


title: Tobacco Smoke Sample 6 30min

source_name: Tobacco Smoke Sample 6 30min


title: C3B-LU

description:
Mouse Lung AIN Diet 8hr Saline Injection, biological replicate B
AN080406_Sample 1.CEL

source_name: Sodium arsenite added to food: None; Injection: IP 8hr saline only; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: C1E-LU

description:
Mouse Lung AIN Diet 5wk Control, biological replicate E
AN080306_Sample 14.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None


title: T5A-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A
AN080906_Sample 8.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 10 ppb, 5wk


title: HepG2_Tmprss6_rep1

description: Expression data from HepG2 cell line


title: T5C-LU

description:
Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C
AN080806_Sample 3.CEL


title: Tobacco Smoke Sample 5 6hr

source_name: Tobacco Smoke Sample 5 6hr


title: Tobacco Smoke Sample 6 12hr

source_name: Tobacco Smoke Sample 6 12hr


title: Tobacco Smoke Sample 5 24hr

source_name: Tobacco Smoke Sample 5 24hr


title: Hepatocyte_GFP

description: Ad-GFP transduced hepatocyte, control.

scan_protocol: According to standard Affymetrix protocols.

source_name: Primary hepatocytes transduced with Adeno-GFP

tag: Primary hepatocytes were isolated from C57/Bl6J mice (10 weeks old) and transduced with recombinant adenovirus expressing GFP for 40 hrs.


title: Tobacco Smoke Sample 5 30min

source_name: Tobacco Smoke Sample 5 30min


title: Tobacco Smoke Sample 5 12hr

source_name: Tobacco Smoke Sample 5 12hr


title: Tobacco Smoke Sample 5 3hr

source_name: Tobacco Smoke Sample 5 3hr


title: Tobacco Smoke Sample 4 6hr

source_name: Tobacco Smoke Sample 4 6hr


title: Tobacco Smoke Sample 4 30min

source_name: Tobacco Smoke Sample 4 30min


title: Tobacco Smoke Sample 4 3hr

source_name: Tobacco Smoke Sample 4 3hr


title: Tobacco Smoke Sample 2 30min

source_name: Tobacco Smoke Sample 2 30min


title: Tobacco Smoke Sample 3 6hr

source_name: Tobacco Smoke Sample 3 6hr


title: Tobacco Smoke Sample 4 12hr

source_name: Tobacco Smoke Sample 4 12hr


title: Tobacco Smoke Sample 2 3hr

source_name: Tobacco Smoke Sample 2 3hr


title: T2C-LU

description:
Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C
AN080906_Sample 16.CEL

source_name: Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 10 ppb, 5wk


title: Tobacco Smoke Sample 3 30min

source_name: Tobacco Smoke Sample 3 30min


title: Tobacco Smoke Sample 1 30min

source_name: Tobacco Smoke Sample 1 30min


title: Tobacco Smoke Sample 4 24hr

source_name: Tobacco Smoke Sample 4 24hr


title: Tobacco Smoke Sample 2 6hr

source_name: Tobacco Smoke Sample 2 6hr


title: Tobacco Smoke Sample 1 6hr

source_name: Tobacco Smoke Sample 1 6hr


title: Tobacco Smoke Sample 2 24hr

source_name: Tobacco Smoke Sample 2 24hr


title: wildtype (GFP-negative) kidney cells, biological rep2

city: New York

first: Jonathan

last: Barasch

state: NY

address: 630 West 168th St

institute: Columbia University

description: gene expression data from wildtype (GFP-negative) kidney cells

hyb_protocol: Following fragmentation, 2.2 ?g biotinylated cDNA were hybridized in duplicate to Mouse Genome 430 2.0 Genechip arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with robust multichip analysis (RMA) using the Affymetrix microarray *.cel image file and GeneTraffic(R) (Silicon Genetics) software

source_name: wildtype (GFP-negative) kidney cells

label_protocol: Total RNA (50ng) was amplified and biotin labeled using the Ribo-SPIA isothermal linear amplification kit (Ovation Biotin system; NuGen)

extract_protocol: extraction of total RNA using Rneasy mini kit (Qiagen) was performed according to the manufacturer's instructions with on-column DNase digestion.

treatment_protocol: kidneys were microdissected on day 15.5, treated with collagenase and trypsin/EDTA followed by FACS to separate GFP-positive TFR1-negative from GFP-negative wildtype cells

tag: fluorescent activated cell sorter (FACS)-selected cells


title: Tobacco Smoke Sample 1 24hr

source_name: Tobacco Smoke Sample 1 24hr


title: Tobacco Smoke Sample 2 12hr

source_name: Tobacco Smoke Sample 2 12hr


title: Tobacco Smoke Sample 3 3hr

source_name: Tobacco Smoke Sample 3 3hr


title: Tobacco Smoke Sample 3 12hr

source_name: Tobacco Smoke Sample 3 12hr


title: Tobacco Smoke Sample 1 12hr

source_name: Tobacco Smoke Sample 1 12hr


title: Control Sample 6 3hr

source_name: Control Sample 6 3hr


title: Tobacco Smoke Sample 3 24hr

source_name: Tobacco Smoke Sample 3 24hr


title: wildtype (GFP-negative) kidney cells, biological rep1


title: Tobacco Smoke Sample 1 3hr

source_name: Tobacco Smoke Sample 1 3hr


title: Tfrc-/- (GFP-positive) kidney cells, biological rep2

description: gene expression data from Tfrc-/- (GFP-positive) kidney cells

source_name: chimeric kidneys from mouse E15.5 embryos derived from blastocysts that were injected with GFP-positive, transferrin receptor (Tfrc)-deleted embryonic stem cells


title: Control Sample 6 6hr

source_name: Control Sample 6 6hr


title: HepG2_Vector_rep1

description: Expression data from HepG2 cell line

source_name: empty vector transfection


title: Control Sample 6 30min

source_name: Control Sample 6 30min


title: Tfrc-/- (GFP-positive) kidney cells, biological rep1


title: Control Sample 6 24hr

source_name: Control Sample 6 24hr


title: Control Sample 5 30min

source_name: Control Sample 5 30min


title: Control Sample 6 12hr

source_name: Control Sample 6 12hr


title: Control Sample 5 6hr

source_name: Control Sample 5 6hr


title: Control Sample 5 12hr

source_name: Control Sample 5 12hr


title: Control Sample 5 3hr

source_name: Control Sample 5 3hr


title: Control Sample 5 24hr

source_name: Control Sample 5 24hr


title: Control Sample 4 3hr

source_name: Control Sample 4 3hr


title: Control Sample 4 24hr

source_name: Control Sample 4 24hr


title: Control Sample 3 6hr

source_name: Control Sample 3 6hr


title: Control Sample 3 3hr

source_name: Control Sample 3 3hr


title: Control Sample 4 6hr

source_name: Control Sample 4 6hr


title: Control Sample 3 24hr

source_name: Control Sample 3 24hr


title: Control Sample 3 12hr

source_name: Control Sample 3 12hr


title: Control Sample 4 30min

source_name: Control Sample 4 30min


title: Control Sample 2 30min

source_name: Control Sample 2 30min


title: Control Sample 2 6hr

source_name: Control Sample 2 6hr


title: Control Sample 1 3hr

source_name: Control Sample 1 3hr


title: Control Sample 2 3hr

source_name: Control Sample 2 3hr


title: Control Sample 1 24hr

source_name: Control Sample 1 24hr


title: Control Sample 2 12hr

source_name: Control Sample 2 12hr


title: Control Sample 1 12hr

source_name: Control Sample 1 12hr


title: Control Sample 2 24hr

source_name: Control Sample 2 24hr


title: Control Sample 1 6hr

source_name: Control Sample 1 6hr


title: Control Sample 1 30min

source_name: Control Sample 1 30min


title: alveolar macrophages, smoker 027

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: alveolar macrophages obtained from bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ancestry

value: European

tag: Smoking status

value: smoker, 45 pack-years


title: alveolar macrophages, smoker 033

value: smoker, 15 pack-years


title: alveolar macrophages, smoker 002

value: smoker, 21 pack-years


title: alveolar macrophages, smoker 044

value: smoker, 38 pack-years


title: alveolar macrophages, smoker 025

value: F

value: smoker, 30 pack-years


title: Control Sample 4 12hr

source_name: Control Sample 4 12hr


title: alveolar macrophages, smoker 057

value: African

value: smoker, 24 pack-years


title: alveolar macrophages, non-smoker 035

value: non-smoker


title: alveolar macrophages, non-smoker 006


title: alveolar macrophages, smoker 069

value: smoker, 70 pack-years


title: alveolar macrophages, non-smoker 008


title: alveolar macrophages, non-smoker 013

value: Hispanic


title: alveolar macrophages, smoker 041

value: smoker, 20 pack-years


title: Control Sample 3 30min

source_name: Control Sample 3 30min


title: alveolar macrophages, smoker 058

value: smoker, 80 pack-years


title: alveolar macrophages, smoker 040


title: alveolar macrophages, non-smoker 021


title: alveolar macrophages, non-smoker 002


title: alveolar macrophages, non-smoker 019


title: alveolar macrophages, non-smoker 001


title: alveolar macrophages, non-smoker 005


title: alveolar macrophages, smoker 063

value: smoker, 60 pack-years


title: alveolar macrophages, non-smoker 003


title: alveolar macrophages, smoker 001

value: smoker, 23 pack-years


title: Ramos_empty

status: Public on Jul 31 2008

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

hyb_protocol: Affymetrix standard protocol

data_processing: GCOS software, expression values were normalized by applying the RMA algorithm using the BRB Array Tools software package.

source_name: Burkitt lymphoma cell line, Ramos, empty

label_protocol: GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix; manufacturer’s recommendations), amount of RNA labeled: 1µg

growth_protocol: human BL cell lines were cultured in RPMI medium 1640 with 10% FCS, 1% Penicillin/Streptomycin, 1% L-Glutamin, 1% non-essential amino acids, and 0.1% b-Mercaptoethanol.

extract_protocol: Trizol (manufacturer’s recommendations)

treatment_protocol: MiRNA expression was induced in the transfected BL cell lines by Dox treatment (0.5µg/ml) for 72 hrs.

tag: Burkitt lymphoma cell line


title: Ramos_ miR26a

description: Ramos_ miR26a

source_name: Burkitt lymphoma cell line, Ramos, miR26a


title: Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days E14-2

city: Ikoma

first: Tsukasa

last: Sanosaka

state: Nara

department: bioscience

country: Japan

institute: NAIST

hyb_protocol: For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing:
Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling:All Probe Sets, Target Signal=500
Normalization value:1
Parameters: defalut settings

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

extract_protocol: The total RNA was purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) according to the manufacturer's instruction.

tag: Strain

value: ICR


title: Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day E11-2


title: ART2

city: Memphis

first: Jian

last: Yan

address: 956 Court Ave

department: Orthopedics Surgery

institute: University of Tennessee Health Science Center

description: Gene expression data

hyb_protocol: Standard Affymetrix protocol with Fluidics Station 450

scan_protocol: Standard Affymetrix protocol with GeneChip Scanner 3000

data_processing: The data were analyzed with Expressiojn Console 1.1 using default MAS5 method. The target intensity was 500.

source_name: Mouse spleen at 4 month

label_protocol: Standard Affymetrix protocol

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art2


title: ART10

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Art10


title: ART7

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art7


title: ART8

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art8


title: ART17

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art17


title: Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day E11-1


title: ART12

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art12


title: MM6 control shRNA LPS treated 2

city: Houston

first: Andrew

middle: P.

last: Rice

state: TX

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9551.

hyb_protocol: See affymetrix protocol.

scan_protocol: Affymetrix Gene Chip Scanner 3100.

source_name: Mono Mac 6 cells

label_protocol: See affymetrix protocol.

growth_protocol: MM6 cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), ), non-essential amino acids (Invitrogen), l-glutamine (Invitrogen), and OPI media supplement (Sigma) containing 0.15 mg of oxalacetate, 0.5 g of pyruvate and 8.2 mg of bovine insulin.

extract_protocol: RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's protocol and RNA quality was determined using an Agilent 2100 Bioanalyzer.

treatment_protocol: MM6 cells were transduced with a control shRNA and then treated with 10 ng/ml LPS.

tag: Monocytic cell line


title: Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days E14-1


title: MM6 control shRNA LPS treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9550.


title: Jurkat cyclin T1 knockdown PMA treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8503.

source_name: Jurkat cell line

growth_protocol: Jurkat cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone).

treatment_protocol: Jurkat cells were transduced with shRNA virus against cyclin T1 and then treated with 10 ng/ml phorbol 12-myristate 13-acetate and 1nM ionomycin..

tag: Lymphocyte cell line.


title: Raji_empty

scan_protocol: Affymetrix standard protocol

source_name: Burkitt lymphoma cell line, Raji, empty


title: NAM_miR26a

source_name: Burkitt lymphoma cell line, Namalwa, miR26a


title: ART4

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art4


title: Jurkat control shRNA PMA treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8505.

treatment_protocol: Jurkat cells were transduced with control shRNA virus and then treated with 1ng/ml phorbol 12-myristate 13-acetate and 1nM ionomycin.


title: MM6 cyclin T1 knockdown LPS treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9548.

treatment_protocol: MM6 cells were transduced with shRNA against cyclin T1 and then treated with 10 ng/ml LPS.


title: NAM_empty

source_name: Burkitt lymphoma cell line, Namalwa, empty


title: Parental MM6 cell LPS treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9547.

treatment_protocol: MM6 cells were treated with 10 ng/ml LPS.

tag: Monocytic Cell line


title: ART6

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art6


title: NON18

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non18


title: MM6 cyclin T1 knockdown LPS treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9549.


title: NON17

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non17


title: Parental MM6 cell PMA treated 3

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 7989.

treatment_protocol: MM6 cells were treated with 10 ng/ml phorbol 12-myristate 13-acetate.


title: Parental MM6 cell LPS treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 9546.

source_name: Mono Mac cells

tag: Monocytic cell line.


title: Raji_miR26a

source_name: Burkitt lymphoma cell line, Raji, miR26a


title: Parental MM6 cell Mock treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6892.

treatment_protocol: Cells were mock treated in this experiment.


title: NON15

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non15


title: MM6 control shRNA PMA treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 7987.

treatment_protocol: MM6 cells were transduced with a control shRNA and then treated with 10 ng/ml PMA.


title: alveolar macrophages, non-smoker 014

tag: Age

tag: Sex

value: M

tag: Ancestry

value: European

tag: Smoking status


title: NON16

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non16


title: MM6 control shRNA Mock treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6488.

source_name: MM6 cell line

treatment_protocol: MM6 cells were transduced with a control shRNA and then mock treated.


title: MM6 control shRNA PMA treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6489.


title: MM6 control shRNA PMA treated 3

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 7988.


title: Parental MM6 cell PMA treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6893.


title: MM6 control shRNA Mock treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6890.


title: MM6 cyclin T1 knockdown Mock treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6888.

treatment_protocol: MM6 cells were transduced with shRNA against cyclin T1 and then mock treated.


title: MM6 cyclin T1 knockdown PMA treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6487.

treatment_protocol: MM6 cells were transduced with shRNA against cyclin T1 and then treated with 10ng/ml PMA.


title: Parental MM6 cell PMA treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6490.

source_name: Mono Mac 6 cell line


title: MM6 cyclin T1 knockdown PMA treated 3

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 7986.


title: MM6 cyclin T1 knockdown PMA treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6889.


title: MM6 cyclin T1 knockdown Mock treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6486.


title: Parental MM6 cell Mock treated 1


title: NON9

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non9


title: NON10

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non10


title: Jurkat cyclin T1 knockdown PMA treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8152.


title: NON13

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non13


title: NON14

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non14


title: NON2

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non2


title: NON12

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non12


title: NON1

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non1


title: NON8

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non8


title: NON4

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non4


title: Jurkat control shRNA PMA treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8154.

growth_protocol: Jurkat cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum.

treatment_protocol: Jurkat cells were transduced with control shRNA virus and then treated  with 1ng/ml phorbol 12-myristate 13-acetate and 1nM ionomycin.

tag: Lymphocyte cell line.


title: NON3

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non3


title: Jurkat control shRNA Mock treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8504.

growth_protocol: Jurkat cells were were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone).

treatment_protocol: Jurkat cells were transduced with a control shRNA and mock treated.


title: ART18

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art18


title: NON7

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non7


title: NON11

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non11


title: ART16

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art16


title: ART15

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art15


title: Jurkat control shRNA Mock treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8153.

growth_protocol: Jurkat cells were amaintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone.

treatment_protocol: Jurkat cells were transduced with a control shRNA and then mock treated.


title: NON5

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non5


title: NON6

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 a=Non6


title: Jurkat cyclin T1 knockdown Mock treated 1

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8151.

growth_protocol: Jurkat cells were  Cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone).

treatment_protocol: Jurkat cells were transduced with shRNA against cyclin T1 and then mock treated.


title: ART14

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art14


title: Jurkat cyclin T1 knockdown Mock treated 2

description: All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 8502.

growth_protocol: Jurkat cells were a gift were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone).


title: ART13

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art13


title: MonoMac6 - lipoxin A4

first: Hartmut

last: Kühn

state: Berlin

address: Monbijoustr. 2

description: Stimulation of MonoMac6 cells with lipoxin A4

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix GCOS 1.4

label: Affymetrix protocol

source_name: human monocytic cell line MonoMac6 stimulated for 12 h with lipoxin A4

label_protocol: Affymetrix protocol

growth_protocol: cells were maintained and grown as recommended by the vendor

extract_protocol: Qiagen extraction protocol

treatment_protocol: total RNA was extracted from the cells

tag: cultured MonoMac6 cells, near confluent state, incubated for 12 h in the presence of 100 nM lipoxin A4


title: MonoMac6 - lipoxin B4

description: Expression pattern of MonoMac6 cells stimulated for 12 h with lipoxin B4

source_name: human monocytic cell line MonoMac6 stimulated for 12 h with lipoxin B4

growth_protocol: cells were grown according to vendors recommendation

tag: cultured MonoMac6 cells, near confluent state, were stimulated for 12 h in the presence of 100 nM lipoxin B4 dissolved in DMSO


title: MonoMac6 - leukotriene C4

description: Stimulation of MonoMac6 cells with leukotriene C4

source_name: human monocytic cell line MonoMac6 stimulated for 12 h with leukotriene C4

tag: cultured MonoMac6 cells, near confluent state, incubated for 12 h in the presence of 100 nM leukotriene C4 dissolved in DMSO


title: MonoMac6 - leukotriene B4

description: Expression pattern of MonoMac6 cells after stimulation with leukotriene B4

source_name: human monocytic cell line MonoMac6 stimulated for 12 h with leukotriene B4

tag: cultured MonoMac6 cells, near confluent state, incubated for 12 h in the presence of 100 nM leukotriene B4 dissolved in DMSO


title: ART11

description: Gene expression data

extract_protocol: Trizol

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art11


title: MonoMac6 - unstimulated

description: Expression pattern of unstimulated MonoMac6 cells

source_name: human monocytic cell line MonoMac6

tag: cultured MonoMac6 cells, near confluent state, solvent (12 h incubated with appropriate volume of DMSO)


title: 34079

status: Public on Jul 30 2008

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

description: Gene expression data from human ovarian tumours

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Affymetrix HG-U133 2.0plus expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GS300-7G scanner

data_processing: The data were analyzed with Gene Chip Operating Software Version 1.4 using Affymetrix default analysis settings. The CEL files generated was later normalized using the RMA method

source_name: Ovarian Tumour, Serous LMP

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

extract_protocol: Trizol extraction and column chromotogrpahy

treatment_protocol: Frozen tissue stored at -80oC taken after surgery

tag: LMP

tag: mutant KRAS

tag: Grade NA

tag: Stage IA

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: LMP Cluster

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 32066

tag: mutant ERBB2

tag: Grade High

tag: Stage IIIA

tag: Micropapillary feature Positive

tag: (LMP) implants micro-invasive


title: 41078

tag: Stage IIB

tag: (LMP) implants Non-invasive


title: 51024

tag: LMP

tag: mutant KRAS


title: 32009

tag: Stage IA

tag: (LMP) implants Negative


title: ART3

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art3


title: ART5

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art5


title: 23215

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade Low

tag: Micropapillary feature Negative

tag: Co-exhistant histology NA

tag: LMP Cluster


title: 32100

tag: mutant BRAF

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 93079


title: 91077

tag: Stage IIIC

tag: Micropapillary feature Positive


title: 92014

tag: LMP

tag: Grade NA

tag: Stage IIIB

tag: (LMP) implants Non-invasive


title: ART9

description: Gene expression data

tag: Male DBA-1/BALB/c-Il1rn -/- F2 art9


city: Cambridge

first: Whitehead

last: Institute

state: MA

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

description: mRNA expression profile comparison between wild-type cultured murine neutrophils versus miR-223 null cultured murine neutrophils during development of BM progenitors to mature neutrophils.  This data shows expression profile of mRNAs from 4 days cultured progenitors from miR-223 null mouse bone marrow.

hyb_protocol: Affy Standard Hyb Protocol

scan_protocol: Affy Scan Protocol

data_processing: GCOS and RMAExpress software

source_name: 4 days cultured BM progenitors from miR-223 null mouse bone marrow

label_protocol: Affy Standard Labeling Protocol

growth_protocol: BM-progenitors were cultured in SILAC-IMDM with G-CSF and SCF for 4 days.

extract_protocol: Tri Reagent (Ambion) followed by RNeasy Plus (Qiagen)

treatment_protocol: Cells were sorted for ckit-PE positive and Gr-1-APC negative population using FACSAria (BD Biosciences).

tag: mRNA profiling of 4 days cultures from miR-223 null mouse bone marrow progenitors - Rep 1


title: 8 days cultures from miR-223 null mouse bone marrow progenitors - Rep 2

description: mRNA expression profile comparison between wild-type cultured murine neutrophils versus miR-223 null cultured murine neutrophils during development of BM progenitors to mature neutrophils.  This data shows expression profile of mRNAs from 8 days cultured and sorted mature neutrophils from miR-223 null mouse bone marrow.

source_name: 8 day cultured and sorted mature neutrophils

growth_protocol: BM-progenitors were cultured in SILAC-IMDM with G-CSF and SCF for 6 days and subsequent culture without SCF for 42 hours.

treatment_protocol: Cells were sorted for ckit-PE negative and Gr-1-APC positive population using FACSAria (BD Biosciences).

tag: Expression profile of mRNAs of 8 days cultured and sorted mature neutrophls from miR-223 mouse bone marrow progenitors - Rep 2


title: 8 days cultures from wild-type mouse bone marrow progenitors - Rep 1

description: mRNA expression profile comparison between wild-type cultured murine neutrophils versus miR-223 null cultured murine neutrophils during development of BM progenitors to mature neutrophils.  This data shows expression profile of mRNAs from 8 days cultured and sorted mature neutrophils from wild-type mouse bone marrow.

tag: Expression profile of mRNAs of 8 days cultured and sorted mature neutrophls from wild-type mouse bone marrow progenitors - Rep 1


source_name: 4 days cultured BM progenitors from miR-223 null mouse

tag: mRNA profiling of 4 days cultures from miR-223 null mouse bone marrow progenitors - Rep 2


title: ART1

description: Gene expression data

source_name: Mouse spleen at 4 month

tag: Male art1


title: 8 days cultures from wild-type mouse bone marrow progenitors - Rep 2

tag: Expression profile of mRNAs of 8 days cultured and sorted mature neutrophls from wild-type mouse bone marrow progenitors - Rep 2


description: mRNA expression profile comparison between wild-type cultured murine neutrophils versus miR-223 null cultured murine neutrophils during development of BM progenitors to mature neutrophils.  This data shows expression profile of mRNAs from 4 days cultured progenitors from wild-type mouse bone marrow.

source_name: 4 days cultured BM progenitors from wild-type mouse bone marrow

tag: mRNA profiling of 4 days cultures from wild-type mouse bone marrow progenitors - Rep 1


title: 8 days cultures from miR-223 null mouse bone marrow progenitors - Rep 1

tag: Expression profile of mRNAs of 8 days cultured and sorted mature neutrophls from miR-223 null mouse bone marrow progenitors - Rep 1


tag: mRNA profiling of 4 days cultures from wild-type mouse bone marrow progenitors - Rep 2


title: wild-type murine neutrophils - Rep 3

description: mRNA expression profile comparison between wild-type murine neutrophils versus miR-223 null murine neutrophils.  This data shows expression profile of mRNAs from neutrophils directly isolated from wild-type mouse bone marrow.

data_processing: GCOS and RMAExpress Software

source_name: Neutrophils

growth_protocol: Samples were directly isolated from a mouse.

treatment_protocol: Neutrophils were isolated using Gr-1 antibody and MACS.

tag: Expression profile of mRNAs from neutrophils directly isolated from wild-type mouse bone marrow - Rep 3


title: miR-223 null murine neutrophils - Rep 3

description: mRNA expression profile comparison between wild-type murine neutrophils versus miR-223 null murine neutrophils.  This data shows expression profile of mRNAs from neutrophils directly isolated from miR-223 null mouse bone marrow.

tag: Expression profile of mRNAs from neutrophils directly isolated from miR-223 null mouse bone marrow - Rep 3


title: miR-223 null murine neutrophils - Rep 2

growth_protocol: samples were directly isolated from a mouse.

treatment_protocol: neutrophils were isolated using Gr-1 antibody and MACS.

tag: Expression profile of mRNAs from neutrophils directly isolated from miR-223 null mouse bone marrow - Rep 2


title: wild-type murine neutrophils - Rep 2

tag: Expression profile of mRNAs from neutrophils directly isolated from wild-type mouse bone marrow - Rep 2


title: wild-type murine neutrophils - Rep 1

tag: Expression profile of mRNAs from neutrophils directly isolated from wild-type mouse bone marrow - Rep 1


title: 579

tag: LMP

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade High

tag: Stage IC

tag: Micropapillary feature Positive

tag: (LMP) implants Negative

tag: Co-exhistant histology NA

tag: LMP Cluster

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: Neutrophils cultured from wild-type mouse bone marrow - Rep 1

description: mRNA expression profile comparison between wild-type cultured murine neutrophils versus miR-223 null cultured murine neutrophils

scan_protocol: Affy Scanner

source_name: neutrophils

label_protocol: Affy Standard labeling Protocol

growth_protocol: BM-progenitors were cultured in SILAC-IMDM with G-CSF and SCF for 6 days and subsequent culture for 42 hours without SCF.  During the time, maturation to neutrophils occurs.

treatment_protocol: Live neutrophils were isolated using MACS.

tag: mRNA profiling of neutrophils in vitro cultured from wild-type mouse bone marrow - Rep 1


title: Neutrophils cultured from miR-223 null mouse bone marrow - Rep 1

tag: mRNA profiling of neutrophils in vitro cultured from miR-223 null mouse bone marrow - Rep 1


title: Neutrophils cultured from miR-223 null mouse bone marrow - Rep 3

tag: mRNA profiling of neutrophils in vitro cultured from miR-223 null mouse bone marrow - Rep3


title: Neutrophils cultured from wild-type mouse bone marrow - Rep 2

tag: mRNA profiling of neutrophils in vitro cultured from wild-type mouse bone marrow - Rep 2


title: Neutrophils cultured from miR-223 null mouse bone marrow - Rep 2

tag: mRNA profiling of neutrophils in vitro cultured from miR-223 null mouse bone marrow - Rep2


title: miR-223 null murine neutrophils - Rep 1

tag: Expression profile of mRNAs from neutrophils directly isolated from miR-223 null mouse bone marrow - Rep 1


title: Neutrophils cultured from wild-type mouse bone marrow - Rep 3

tag: mRNA profiling of neutrophils in vitro cultured from wild-type mouse bone marrow - Rep 3


title: 23062

tag: LMP

tag: mutant KRAS

tag: Grade Low

tag: Stage IIIC

tag: Micropapillary feature Negative

tag: (LMP) implants Non-invasive


title: 24 h after differentiation medium addition patient 3206 (time course II)

status: Public on Jul 29 2008

city: Derio

first: Lourdes

last: Osaba

address: Parque Tecnologico de Bizkaia. Ed. 801

country: Spain

institute: Progenika Biopharma

description: gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human U133Plus2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with GeneSpring GX software using RMA and global median normalization method

source_name: hMSC, differentiation, 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: MNC obtained from bone marrow  were maintained in alpha MEM, supplemented with 10% FBS, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 100 μmol/L ascorbic acid-2 phosphate at 37°C in  5% CO2-humidified atmosphere. After 4 days, non-adherent cells were removed and the culture re-fed with fresh medium containing 10-8 M dexamethasone (differentiation medium).

extract_protocol: Rneasy Mini kit according to manufacturer's instructions

tag: male


title: First confluence of hMSC patient 3206 (time course II)

description: gene expression data

source_name: hMSC, differentiation, first confluence


title: Semiconfluence of hMSC patient 3206 (time course II)

description: gene expression data

source_name: hMSC, differentiation, semiconfluence


title: 10-14 days after mineralization medium addition patient 3206 (time course III)

description: gene expression data

source_name: hMSC, mineralization, 10-14 days

growth_protocol: hMSC obtained from bone marrow  were maintained in alpha MEM, supplemented with 10% FBS, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 100 μmol/L ascorbic acid-2 phosphate and 10-8 M dexamethasone  at 37°C in  5% CO2-humidified atmosphere. To obtain the formation of mineral nodules, 10 mM β-glycerophosphate was added to the hMSC cultures following the second confluence.


title: 24 h after mineralization medium addition patient 3080 (time course III)

description: gene expression data

source_name: hMSC, mineralization, 24h


title: 7 days after mineralization medium addition patient 3206 (time course III)

description: gene expression data

source_name: hMSC, mineralization, 7 days


title: 10-14 days after mineralization medium addition patient 3205 (time course III)

description: gene expression data


title: 10-14 days after mineralization medium  addition patient 3080 (time course III)

description: gene expression data


title: 24 h after mineralization medium addition patient 3206 (time course III)

description: gene expression data


title: 7 days after mineralization medium addition patient 3205 (time course III)

description: gene expression data


title: Semiconfluence of CFU patient 3205 (time course II)

description: gene expression data

source_name: hMSC, differentiation, CFU semiconfluence


title: 4 days after MNC seeding patient 3205 (time course II)

description: gene expression data

source_name: adherent MNC


title: 7 days after mineralization medium addition patient 3080 (time course III)

description: gene expression data


title: 24 h after differentiation medium addition patient 3205 (time course II)

description: gene expression data


title: Semiconfluence of hMSC patient 3205 (time course II)

description: gene expression data


title: 24 h after mineralization medium addition patient 3002 (time course III)

description: gene expression data


title: Semiconfluence of CFU patient 3206 (time course II)

description: gene expression data


title: 7 days after mineralization medium addition patient 3002 (time course III)

description: gene expression data


title: 24 h after mineralization medium addition patient 3205 (time course III)

description: gene expression data


title: First confluence of hMSC patient 3205 (time course II)

description: gene expression data


title: Semiconfluence of hMSC patient 3080 (time course II)

description: gene expression data


title: First confluence of hMSC patient 3080 (time course II)

description: gene expression data


title: 24 h after differentiation medium addition patient 3080 (time course II)

description: gene expression data


title: 4 days after MNC seeding patient 3080 (time course II)

description: gene expression data


title: Semiconfluence of CFU patient 3080 (time course II)

description: gene expression data


title: Semiconfluence of CFU patient 3002 (time course II)

description: gene expression data


title: Semiconfluence of hMSC patient 3002 (time course II)

description: gene expression data


title: 10-14 days after mineralization medium addition patient 3002 (time course III)

description: gene expression data


title: 24 h after differentiation medium addition patient 3002 (time course II)

description: gene expression data


title: 7 days after mineralization medium addition patient 3206 (time course I)

description: gene expression data

source_name: hOB, mineralization, 7 days

growth_protocol: HOB obtained from trabecular bone were maintained in alpha MEM, supplemented with 10% FBS, 100 U/mL penicillin and 0.1 mg/mL streptomycin at 37° C in 5% CO2 atmosphere. To obtain the formation of mineral nodules, 10 mM β-glycerophosphate was added to the hOB cultures following the second confluence.


title: 10-14 days after mineralization medium addition patient 3205 (time course I)

description: gene expression data

source_name: hOB, mineralization, 10-14 days


title: 24 h after mineralization medium addition patient 3206 (time course I)

description: gene expression data

source_name: hOB, mineralization, 24h


title: 7 days after mineralization medium addition patient 3205 (time course I)

description: gene expression data


title: 24 h after mineralization medium addition patient 3205 (time course I)

description: gene expression data


title: hOB culture patient 3205 (time course I)

description: gene expression data

source_name: hOB confluence


title: hOB culture patient 3206 (time course I)

description: gene expression data


title: 4 days after MNC seeding patient 3002 (time course II)

description: gene expression data


title: 7 days after mineralization medium addition patient 3080 (time course I)

description: gene expression data


title: 10-14 days after mineralization medium addition patient 3206 (time course I)

description: gene expression data


title: 24 h after mineralization medium addition patient 3080 (time course I)

description: gene expression data


title: 10-14 days after mineralization medium addition patient 3002 (time course I)

description: gene expression data


title: 24 h after mineralization medium addition patient 3002 (time course I)

description: gene expression data


title: 7 days after mineralization medium addition patient 3002 (time course I)

description: gene expression data


title: hOB culture patient 3080 (time course I)

description: gene expression data


title: hOB culture patient 3002 (time course I)

description: gene expression data


title: BM-MSC_donor3-P8

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were hybridized with 15 µg amplified RNA and washed with a fluidics station 450 (Affymetrix).

scan_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were scanned with GeneChip scanner 3000 (Affymetrix)

source_name: bone marrow mesenchymal stem cells of donor3 - passage 8

label_protocol: Two µg total RNA was amplified with GeneChip one-cycle target labeling kit (Affymetrix, High Wycombe, United Kingdom) according to the manufacturers instructions. Quality of amplified RNA was controlled by LabChip technology.

growth_protocol:
Human bone marrow (BM) samples were taken after informed consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. Mesenchymal stem cells (MSC) were isolated in the culture medium described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625).
The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548).  MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cells were harvested by trypsination after passage 8

tag: mesenchymal stem cells from human bone marrow (donor 3)

tag: (alternatively named mesenchymal stromal cells)

tag: Passage 8 (senescent passage)


title: BM-MSC_donor2(#287)-P2-55yrs

source_name: bone marrow mesenchymal stem cells of donor2 - passage 2

label_protocol: Two µg total RNA was amplified with GeneChip one-cycle target labeling kit (Affymetrix, High Wycombe, United Kingdom) according to the manufacturers instructions. Quality of amplified RNA was controlled by LabChip technology

treatment_protocol: Cells were harvested by trypsination after passage 2

tag: mesenchymal stem cells from human bone marrow (donor 2)

tag: Passage 2

tag: 55 year old donor


title: BM-MSC_donor1-P10

source_name: bone marrow mesenchymal stem cells of donor1 - passage 10

treatment_protocol: Cells were harvested by trypsination after passage 10

tag: mesenchymal stem cells from human bone marrow

tag: Passage 10


title: BM-MSC_donor1-P8

source_name: bone marrow mesenchymal stem cells of donor1 - passage 8

tag: Passage 8


title: BM-MSC_donor1-P11

source_name: bone marrow mesenchymal stem cells of donor1 - passage 11

treatment_protocol: Cells were harvested by trypsination after passage 11

tag: Passage 11


title: BM-MSC_donor2-P7

source_name: bone marrow mesenchymal stem cells of donor2 - passage 7

treatment_protocol: Cells were harvested by trypsination after passage 7

tag: Passage 7 (senescent passage)


title: BM-MSC_donor3(#288)-P2-24yrs

source_name: bone marrow mesenchymal stem cells of donor3 - passage 2

tag: 24 year old donor


title: First confluence of hMSC patient 3002 (time course II)

description: gene expression data

source_name: hMSC, differentiation, first confluence


title: BM-MSC_donor1-P4

source_name: bone marrow mesenchymal stem cells of donor1 - passage 4

treatment_protocol: Cells were harvested by trypsination after passage 4

tag: Passage 4


title: BM-MSC_donor1(#285)-P2-44yrs

source_name: bone marrow mesenchymal stem cells of donor1 - passage 2

growth_protocol:
Human bone marrow (BM) samples were taken after informed consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. Mesenchymal stem cells (MSC) were isolated in the culture medium described by M. Reyes and colleagues (Reyes et al., BLOOD, 2001).
The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use (Wagner et al., EXP HEMATOL 2005;Wagner et al., EXP HEMATOL 2006).  MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm2.

tag: 44 year old donor


title: BM-MSC_donor1-P7

source_name: bone marrow mesenchymal stem cells of donor1 - passage 7

tag: Passage 7


title: BM-MSC_donor1-P5

source_name: bone marrow mesenchymal stem cells of donor1 - passage 5

treatment_protocol: Cells were harvested by trypsination after passage 5

tag: Passage 5


title: BM-MSC_donor1-P3

source_name: bone marrow mesenchymal stem cells of donor1 - passage 3

treatment_protocol: Cells were harvested by trypsination after passage 3

tag: Passage 3


title: BM-MSC_donor1-P6

source_name: bone marrow mesenchymal stem cells of donor1 - passage 6

treatment_protocol: Cells were harvested by trypsination after passage 6

tag: Passage 6


title: wild type_female_R1

status: Public on Jul 23 2008

first: Jessica

middle: E

last: Treisman

address: 540 First Avenue

department: Cell Biology (Skirball)

institute: NYUMC

description: Wild type female Drosophila melanogaster at white prepupae stage

hyb_protocol: 10 mcg of cRNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: WT, female, 0 hr APF

label_protocol: One mcg (1 mcg) of total RNA was converted to biotinylated cRNA following the one-cycle protocol described in Affymetrix Expression Analysis Technical Manual.

growth_protocol: Flies were maintained in standard growth conditions

extract_protocol: RNA from single animals was extracted with TRIzol reagent (Invitrogen). Briefly, each sample was homogenized in 200 μl TRIzol, spun briefly, and 50 μg of glycogen were added. After 5 min at RT the samples were mixed vigorously with 40 μl chloroform and spun for 5 min. RNA was precipitated overnight with 100 μl isopropanol, washed with 70% ethanol and resuspended in water

treatment_protocol: RNAs from two males and two females for each genotype were extracted at white prepupae stage (0 hour APF)

tag: Genotype

tag: Age

value: white prepupae stage (0 hour APF)

tag: standard growth conditions


title: Primary aortic endothelial cells, transgenic_PPARG_V290M_3

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: Gene expression data from primary aortic endothelial cells.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

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

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

treatment_protocol: No treatment

tag: Mouse

value: strain C57


title: Primary aortic endothelial cells, Non_transgenic_control_2


title: wild type_female_R2


title: bap170;bap180 double mutant_female_R2

description: bap170;bap180 double mutant female Drosophila melanogaster at white prepupae stage

source_name: bap170;bap180 double mutant, female, 0 hr APF


title: Primary aortic endothelial cells, transgenic_PPARG_V290M_1


title: Primary aortic endothelial cells, Non_transgenic_control_3


title: wild type_male_R1

description: Wild type male Drosophila melanogaster at white prepupae stage

source_name: WT, male, 0 hr APF


title: Primary aortic endothelial cells, transgenic_PPARG_V290M_2


title: Primary aortic endothelial cells, Non_transgenic_control_1


title: bap170;bap180 double mutant_male_R1

description: bap170;bap180 double mutant male Drosophila melanogaster at white prepupae stage

source_name: bap170;bap180 double mutant, male, 0 hr APF


title: bap170;bap180 double mutant_male_R2


title: bap170;bap180 double mutant_female_R1


title: wild type_male_R2