title: Sez-4 cells starved of IL-2 and activated with IL-21 biological rep1

source_name: Sez-4 cell line starved of IL-2 and activated with IL-21 biological rep1


title: Normal Control C-4a

status: Public on Feb 19 2008

type: RNA

city: Baltimore

first: Ahmad

last: Sedaghat

state: MD

address: 733 North Broadway

department: School of Medicine

country: USA

institute: The Johns Hopkins University

description:
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.

hyb_protocol: 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).

data_processing: Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal Control C-4a

label_protocol: The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).

growth_protocol: RNA was isolated from fresh cells.

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).

treatment_protocol:
CD4+ T cells were positively selected to >98% purity from freshly
isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).

tag: CD4+ T-cells from normal HIV- donor


title: Sez-4 cells starved of IL-2 and activated with IL-15 biological rep1

city: Philadelphia

first: Mariusz

last: Wasik

state: PA

address: 3620 Hamilton Walk

department: Pathology

institute: University of Pennsylvania

description: Gene expression profiling of Sez-4 cell line

hyb_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

data_processing: CEL files and MAS5.0 values with global scaling set to 150 were exported from Affymetrix GCOS (v1.4) software

label: biotin

source_name: Sez-4 cell line starved of IL-2 and activated with IL-15 biological rep1

label_protocol: 3ug of input total RNA were amplified and labeled using the Affymetrix 1-cycle kit

growth_protocol: Sez-4 cell line was cultured at 37°C and 5% CO2 in the presence of 200U of IL-2 in standard RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 1% penicillin/streptomycin/fungizone mixture and 2mM L-glutamine.

extract_protocol: total RNA was isolated using a TRIZOL and Qiagen Rneasy protocols

treatment_protocol: Sez-4 cell line was starved of IL2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2 h followed by addition of IL-2 (200U), IL-15 (20ng/mL), or IL-21 (100 ng/ml) or medium alone for 4 h.

tag: Sez-4 T-cell line was derived from leukemic (Sezary) cells of a patient with a cutaneous T-cell lymphoma


title: Sez-4 cells starved of IL-2 and activated with IL-15 biological rep2

scan_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

source_name: Sez-4 cell line starved of IL-2 and activated with IL-15 biological rep2


title: Sez-4 cell line starved of IL-2, pre-treated with pan-Jak inhibitor and activated with IL-2 biological rep3

treatment_protocol: Sez-4 cell line was starved of IL-2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2h followed by pre-treating for 30’ with pan-Jak inhibitor (300 nM), Jak3 inhibitor (300 nM), or drig solvent and cultured with IL-2 (200U) or medium alone for 4 h.


title: Sez-4 cells starved of IL-2 and activated with IL-21 biological rep2

source_name: Sez-4 cell line starved of IL-2 and activated with IL-21 biological rep2


title: long 10B

status: Public on Feb 15 2008

city: Potsdam

first: Björn

last: Usadel

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description: Gene expression data from Arabidopsis rosettes 78 hours in 10C

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with RMAExpress

organism: Arabidopsis thaliana

source_name: Arabidopsis rosettes grown at 10C for 78h

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 10C 4 hours into the light period.

extract_protocol: Trizol extraction

treatment_protocol: Plants were harvested in the vegetative state with 3 rosettes per sample, and typically at least 5 replicate samples. Rosettes were transferred into liquid nitrogen 10h into the light period

tag: Genotype

tag: Age

value: 4-5 weeks

tag: Tissue

value: rosette


title: long 12B

description: Gene expression data from Arabidopsis rosettes 78 hours in 12C

source_name: Arabidopsis rosettes grown at 12C for 78h

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 12C 4 hours into the light period.


title: Sez-4 cells starved of IL-2 and activated with IL-15 biological rep3

source_name: Sez-4 cell line starved of IL-2 and activated with IL-15 biological rep3


title: control longB

description: Gene expression data from Arabidopsis rosettes, control

source_name: Arabidopsis rosettes grown at 20C, controlB for 78h

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 20C 4 hours into the light period.


title: long 8B

description: Gene expression data from Arabidopsis rosettes 78 hours in 8C

source_name: Arabidopsis rosettes grown at 8C for 78h

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 8C 4 hours into the light period.


title: long 14B

description: Gene expression data from Arabidopsis rosettes 78 hours in 14C

source_name: Arabidopsis rosettes grown at 14C for 78h

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 14C 4 hours into the light period.


title: long 17B

description: Gene expression data from Arabidopsis rosettes 78 hours in 17C

source_name: Arabidopsis rosettes grown at 17C for 78h

growth_protocol: Arabidopis thaliana ecotype Col-0 was grown on soil in a 12h light/12h dark cycle,at a light intensity of 130umol*m-2 s-1 and at a constant temperature of 20°C. At the age of 4 weeks plants were moved to 17C 4 hours into the light period.


title: short 12B

description: Gene expression data from Arabidopsis rosettes 6 hours in 12C

source_name: Arabidopsis rosettes grown at 12C for 6h


title: short 14B

description: Gene expression data from Arabidopsis rosettes 6 hours in 14C

source_name: Arabidopsis rosettes grown at 14C for 6h


title: Sez-4 cells starved of IL-2 and activated with IL-2 biological rep1

source_name: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep1


title: Sez-4 cells starved of IL-2 and activated with IL-2 biological rep3

source_name: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep3


title: Dark adapted control replicate 1

first: Amir

last: Rattner

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

description:
Dark adapted control replicate 1
contact Amir Rattner (arattne1(at)jhmi.edu) for details

hyb_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

data_processing: RMA (bioconductor)

organism: Mus musculus

source_name: BALBc mouse retina RNA, dark adapted

extract_protocol: Total RNA from retinas was extracted with Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA).

tag: Retinal RNA from BALBc mouse, dark adapted


title: short 10B

description: Gene expression data from Arabidopsis rosettes 6 hours in 10C

source_name: Arabidopsis rosettes grown at 10C for 6h


title: short 17B

description: Gene expression data from Arabidopsis rosettes 6 hours in 17C

source_name: Arabidopsis rosettes grown at 17C for 6h


title: Light damage replicate 3

description:
Light damage replicate 3
contact Amir Rattner (arattne1(at)jhmi.edu) for details

scan_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

source_name: BALBc mouse retina RNA, light damaged

tag: Retinal RNA from BALBc mice, light damaged for 6 hours under 6,000 lux white fluorescent light and allowed to recover for 24 hours in the dark.


title: long 10A


title: Dark adapted control replicate 3

description:
Dark adapted control replicate 3
contact Amir Rattner (arattne1(at)jhmi.edu) for details

label_protocol:
Affymetrix protocol
Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/


title: Light damage replicate 1

description:
Light damage replicate 1
contact Amir Rattner (arattne1(at)jhmi.edu) for details


title: Light damage replicate 2

description:
Light damage replicate 2
contact Amir Rattner (arattne1(at)jhmi.edu) for details


title: control shortB

source_name: Arabidopsis rosettes grown at 20C, controlB for 6 h


title: short 8B

description: Gene expression data from Arabidopsis rosettes 6 hours in 8C

source_name: Arabidopsis rosettes grown at 8C for 6h


title: long 8A


title: Dark adapted control replicate 2

description:
Dark adapted control replicate 2
contact Amir Rattner (arattne1(at)jhmi.edu) for details


title: long 12A


title: long 17A


title: long 14A


title: short 10A


title: short 14A


title: short 12A


title: short 8A


title: GFPTGF, rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Per Joslin Diabetes Center microarray core facility.

data_processing: RMA

source_name: Tconv cells retrovirally transduced with empty vector and activated in vitro with TGFbeta

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Genetic background

value: 4-6 wks

tag: Number of mice per chip

value: Spleen and LN (cervical, mesenteric)

tag: Sort

tag: Culture

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25ng/ml) for 24hrs, then spin infected with retrovirus (empty-GFP) and cultured for an additional 72hrs.

tag: Post-culture sort

value: GFP+ cells


title: short 17A


title: control shortA

source_name: Arabidopsis rosettes grown at 20C, controlA for 6 h


title: control longA

source_name: Arabidopsis rosettes grown at 20C, controlA for 78 h


title: Lmx1b -/- E11.5 proximal hindlimb pool 2

city: Montreal

first: dayana

last: krawchuk

state: QC

address: 110 Ave. des Pins O.

country: Canada

institute: IRCM

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45oC on GeneChips according to Affymetrix protocols.

scan_protocol: Scanning using Affymetrix protocols.

data_processing: Data processed using Robust Multi-Array Averaging (RMA) using software provided by the McGill University and Génome Québec Innovation Centre (http://www.genomequebecplatforms.com/mcgill/home/index.aspx?l=e).

molecule: polyA RNA

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols.

extract_protocol: Tissue was stored in RNAlater (Qiagen) at -20oC prior to RNA extraction.  Tissue was homogenized, extracted in Trizol reagent (Sigma), and purified on columns (Qiagen).  RNA integrity was quantified using an Agilent Bioanalyser.

tag: Proximal hindlimb bud tissue (~500um from base of limb bud) pooled from 3 embryos (6 limbs total).


title: Wild-type E11.5 proximal hindlimb pool 3

source_name: Wild-type E11.5 129Sv


title: GFPTGF, rep3

scan_protocol: Per Joslin Diabetes Center microarray core facility.


title: Lmx1b -/- E11.5 proximal hindlimb pool 3


title: Lmx1b -/- E11.5 proximal hindlimb pool 1


title: AktTGF, rep3

source_name: Tconv cells retrovirally transduced with constituatively active Akt and activated in vitro with TGFbeta

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25ng/ml) for 24hrs, then spin infected with retrovirus (Akt-GFP) and cultured for an additional 72hrs.


title: AktTGF, rep2


title: AktTGF, rep1


title: GFPTGF, rep1


title: Wild-type E11.5 proximal hindlimb pool 1


title: ex1_flu_dark 8hours/30 minute light_2

status: Public on Feb 14 2008

city: Zurich

first: Chanhong

last: Kim

address: Universitystr. 2

department: Plant Sciences

country: Switzerland

institute: ETH Zurich

description: T-DNA-line was crossed with a flu Col-0 line that had been obtained by 5 backcrosses of flu1-1 in Landsberg erecta with wild-type Columbia

hyb_protocol: Biotin-labeled cRNA samples (15 mg) were fragmented randomly to 35-200 bp at 94°C in  fragmentation buffer (P/N 900371; Affymetrix) and were mixed in 300 ml of hybridization buffer containing a  hybridization control cRNA and control oligo B2 control (P/N 900454; Affymetrix), 0.1 mg/ml herring sperm  DNA, and 0.5 mg/ml acetylated BSA in 2-(4-morpholino)-ethane sulfonic acid (Mes) buffer, pH 6.7, before  hybridization to GeneChip Arabidopsis ATH1 genome arrays for 16 h at 45°C. Arrays were then washed using  an Affymetrix Fluidics Station 450 EukGE-WS2v4_450 protocol. An Affymetrix GeneChip Scanner 3000 was  used to measure the fluorescence intensity emitted by the labeled target.

data_processing: Raw data processing was performed by using the Affymetrix GCOS 1.2 software. After  hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets  by means of the MAS5 algorithm (1). To compare the expression values of the genes from chip to chip, global  scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity  (TGT value) of 500 as detailed by Affymetrix. Quality control measures were considered before performing the  statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples), and appropriate  numbers of present calls were calculated by application of a signedrank call algorithm (2). The efficiency of the  labeling reaction and the hybridization performance were controlled with the following parameters: Present calls  and optimal 3'/5' hybridization ratios (»1) for the housekeeping genes (GAPDH and ACO7), for the poly(A)  spike in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN). After normalization, "baseline"  samples were compared (i.e., wild type after a dark/light shift versus either flu or ex1/flu or ex2/flu or ex1/ex2/flu)  and for the comparative analysis of changes in gene expression between wild type and others, only the genes that  met the following criteria were considered: (i) The genes should show a reliable level of RNA giving a detection  call of P (present in the Affymetrix nomenclature), and (ii) the signals should be changed by at least 2-fold or  greater ("difference" call) relative to the baseline sample. Based on these criteria, the remaining genes were  selected for analysis using Genespring 7.2 package. The microarray analyses were performed in duplicate using  independent samples for wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu plants.

source_name: rosette leaves from EX1/flu cross

label_protocol: Only those samples with a 260/280 nm ratio between 1.8-2.1 and a 28S/18S  ratio within 1.5-2 were further processed. Total RNA samples (5 mg) were reverse-transcribed into doublestranded  cDNA with a One-Cycle cDNA synthesis kit (P/N 900431; Affymetrix, Santa Clara, CA). The doublestranded  cDNA was purified using a Sample Cleanup Module (P/N 900371; Affymetrix). The purified doublestranded  cDNAs were in vitro-transcribed in the presence of biotin-labeled nucleotides using a IVT labeling kit  (P/N 900449; Affymetrix). The biotinylated c RNA was purified by using a Sample Cleanup Module (P/N  900371; Affymetrix), and its quality and quantity were determined with a NanoDrop ND 1000 and Bioanalyzer  2100.

growth_protocol: Two individual biological replicates, each containing material of five mature plants of wild  type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, respectively, were used for  the microarray analysis. Plants were germinated on soil and kept  under continuous light until the beginning of bolting and then  transferred to the dark for 8 h. Dark-incubated mature plants were  reilluminated for 30 min and subsequently harvested for RNA extraction.

extract_protocol: Total RNA was extracted by using an RNeasy plant mini kit (Qiagen, Hilden, Germany) and  quantified spectrophotometrically at 260 nm.

treatment_protocol: dark to light transition

tag: EX1 (At4g33630) T-DNA insertion line SALK 002088 and flu Col-0 mutant


title: ex1ex2flu_dark 8hours/30 minute light_2

description: The ex1/flu and ex2/flu mutant lines were crossed, and within the segregating F2 population triple mutants were identified by PCR-based genotyping.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.

source_name: rosette leaves from EX1/EX2/flu cross

tag: EX1 (At4g33630) T-DNA insertion line SALK 002088; EX2 (At1g27510) T-DNA insertion line SALK 012127; flu Col-0 mutant


title: ex2_flu_dark 8hours/30 minute light_2

source_name: rosette leaves from EX2/flu cross

tag: EX2 (At1g27510) T-DNA insertion line SALK 012127 and flu Col-0 mutant


title: ex1_flu_dark 8hours/30 minute light_1


title: flu_dark 8hours/30 minute light_2

description: Two individual biologica replicates, each containing material of five mature plants of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu.

source_name: rosette leaves flu Col-0 mutant

tag: flu Col-0 mutant


title: ex1ex2flu_dark 8hours/30 minute light_1


title: col_dark 8hours/30 minute light_2

source_name: rosette leaves from wild-type Columbia

tag: wild-type Columbia


title: 48h into an extended nightC

description: Gene expression data from Arabidopsis rosettes 48h into an extended night

scan_protocol: standard Affymetrix procedure

data_processing: The data were analyzed with Bioconductor using the RMA normalization procedure

source_name: Arabidopsis rosette 48h into an extended night

growth_protocol: Plants were germinated for 7 days (16 h light at 20°C, night at 6°C, 200 µE fluorescent light, 60–70% relative humidity), transferred to short-day condition (8 h light at 20°C, dark at 16°C, 180 µE fluorescent light, 60–70% relative humidity), picked after day 14 into pots and incubated under short day further 7 days. The Col-0 ecotype grew from day 22 on for 11 days in a 14-h photoperiod (20°C, 150 µE fluorescent light, 60–70% relative humidity)

treatment_protocol: Plants were harvested in the vegetative state with 3 rosettes per sample, and typically at least 5 replicate samples. Rosettes were transferred into liquid nitrogen in darkness.

value: 5-6 weeks

value: rosettes


title: 24h into an extended nightC

description: Gene expression data from Arabidopsis rosettes 24h into an extended night

source_name: Arabidopsis rosette 24h into an extended night


title: col_dark 8hours/30 minute light_1


title: 6h into an extended night

description: Gene expression data from Arabidopsis rosettes 6h into an extended night

source_name: Arabidopsis rosette 6h into an extended night


title: 4h into an extended nightA

description: Gene expression data from Arabidopsis rosettes 4h into an extended night

source_name: Arabidopsis rosette 4h into an extended night


title: flu_dark 8hours/30 minute light_1

source_name: rosette leaves from flu Col-0 mutant


title: end of the night B

description: Gene expression data from Arabidopsis rosettes at the end of the night

source_name: Arabidopsis rosette at the end of the night


title: ex2_flu_dark 8hours/30 minute light_1


title: 8h into an extended nightB

description: Gene expression data from Arabidopsis rosettes 8h into an extended night

source_name: Arabidopsis rosette 8h into an extended night


title: 4h into an extended nightB


title: end of the night C


title: 48h into an extended nightB


title: 24h into an extended nightB


title: end of the night A


title: 8h into an extended nightA


title: 2h into an extended night

description: Gene expression data from Arabidopsis rosettes 2h into an extended night

source_name: Arabidopsis rosette 2h into an extended night


title: 2h before the end of the night

description: Gene expression data from Arabidopsis rosettes 2h before the end of the night

source_name: Arabidopsis rosette 2h before the end of the night


title: Tesi plus tetracycline

city: Erlangen

first: Ralph

last: Grassmann

address: Schlossgarten 4

department: Institute of Clinical and Molecular Virology

institute: Universität Erlangen Nürnberg

description: The Tesi system allows analysis of HTLV-1 Tax's impact on the transcriptome of a human CD4+ T-cell which is not derived from leukemia but directly from normal human lymphocytes.

hyb_protocol: according to Affymetrix standard protocol

data_processing: GCOS, MAS5; mean log values of replicated samples were compared using ArrayAssist Software

source_name: Tesi, no Tax expressed

growth_protocol: Tesi cells were kept in RPMI 1640 with 50% Panserin, 20% FCS, 0.35g/l glutamine, streptomycin as antibiotic and 40U/ml interleukin-2. For repression of Tax expression, like it was done in this sample, 1µg/ml tetracycline was added for ten days.

extract_protocol: Qiagen RNeasy Kit with QIAshredder columns

treatment_protocol: For this sample, 1µg/ml tetracycline was added to the medium for ten (10) days so that Tax expression was completely repressed.

tag: Tesi, a HTLV-1 Tax-transformed T cell line with tetracycline(tet)-repressible  Tax expression. see


title: dental pulp cells (DP31) at passage 10

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

country: Japan

description: Gene expression data from samples of human dental pulp stem cells

data_processing:
Affymetrix Microarray Suite version 5.0.
The AD levels were usually normalized with a median value of the whole transcripts in each GeneChip for the comparison between passage 4 and passage 10 cells. They were normalized with the median values of the whole transcripts in each genes on GeneChip for the comparison between passage 4 and passage 10 cells.
The level of gene expression was determined as the average difference (AD) using the GeneChip software.

source_name: dental pulp cells (DP31) at passage 10

label_protocol: standard Affymetrix procedures

growth_protocol: The isolated hDPSCs were cultured in MSCGM medium (Cambrex, Walkersville, MD, USA).

extract_protocol: Total RNA was isolated from the cells with an RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA). Extraction was performed according to the manufacturer's instructions.

treatment_protocol: Normal human third molars were extracted at Gifu University Medical Hospital after informed consent had been obtained from patient, with a protocol approved by the Institutional Review Board.

tag: DP31-P10, human dental pulp stem cells (hDPSCs) (14 year-old)


title: Tesi replicate

scan_protocol: according to Affymetrix standard protocol

source_name: Tesi, Tax expressed

growth_protocol: Tesi cells were kept in RPMI 1640 with 50% Panserin, 20% FCS, 0.35g/l glutamine, streptomycin as antibiotic and 40U/ml interleukin-2.

treatment_protocol: For this sample, no tetracycline was added to the medium, so Tax is expressed.


title: dental pulp cells (DP28) at passage 4

institute: Gifu University Graduate School of Medicine

source_name: dental pulp cells (DP28) at passage 4

tag: DP28-P4, human dental pulp stem cells (hDPSCs) (14 year-old)


title: dental pulp cells (DP28) at passage 10

source_name: dental pulp cells (DP28) at passage 10

tag: DP28-P10, human dental pulp stem cells (hDPSCs) (14 year-old)


title: Tesi

label_protocol: according to Affymetrix standard protocol


title: pDC treated with IL-3+p17, biological rep2

city: Brescia

first: Simona

last: Fiorentini

address: piazzale Spedali Civili 1

department: Experimental and Applied Medicine

country: Italy

institute: University of Brescia

description: Gene expression data from pDC treated with IL-3+p17

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized on Affymetrix HG_U133 plus 2.0 Genechips according to manufacturer's protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were analyzed with RMA.

source_name: blood, pDC treated with IL-3+p17

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

growth_protocol: pDCs were cultured in 96-well flat bottom plates in RPMI 1640 culture medium supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1% nonessential amino acids plus 20 ng/ml IL-3.

extract_protocol: Total RNA was extracted using Qiagen RNA extraction easy kit according to the manufacturer's instructions.

treatment_protocol: pDCs were stimulated with 500 ng/ml of recombinant p17 or 6 µg/ml CpG type A oligonucleotides 2216 (CpG) for 18 hours.

tag: Tissue

value: human plasmacytoid dendritic cells

tag: Treatment


title: Tam-treated MCF7 xenograft, biological rep4

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Gene expression data from MCF-7 xenograft tumors that acquired resistance to E2 withdrawal plus tamoxifen.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on Human Genome U133 Plus 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-ws2v5 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10%. of intensity values

source_name: MCF7 xenografts

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

extract_protocol: Trizol extraction of total RNA was carried out using EZ1 RNA universal tissue kit with BioRobot EZ1 workstation according to the manufacturer's instructions.

tag: Tam treatment


title: pDC treated with IL-3+CpG, biological rep2

description: Gene expression data from pDC treated with IL-3+CpG

source_name: blood, pDC treated with IL-3+CpG


title: dental pulp cells (DP31) at passage 4

source_name: dental pulp cells (DP31) at passage 4

tag: DP31-P4, human dental pulp stem cells (hDPSCs) (14 year-old)


title: ERR102_Mutant_2

first: Vijay

middle: G.

last: Sankaran

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

description: ERR102 (Mutant 2)

hyb_protocol: please refer to the Microarray Core Facility website of the Dana-Farber Cancer Institute

data_processing: dChip normalization

source_name: Sorted CD71+/Ter-119+ bone marrow cells

growth_protocol: mouse model

extract_protocol: Trizol/QIAGEN columns

tag: Mutant


title: dental pulp cells (DP2) at passage 10

source_name: dental pulp cells (DP2) at passage 10

tag: DP2-P10, human dental pulp stem cells (hDPSCs) (14 year-old)


title: Tam-treated MCF7 xenograft, biological rep2

label_protocol: Biotinylated cRNA were carried out using EZ1 RNA universal tissue kit with BioRobot EZ1 workstation according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

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


title: ERR258_Control_3

description: ERR258 (Control 3)

scan_protocol: please refer to the Microarray Core Facility website of the Dana-Farber Cancer Institute

tag: Control


title: ERR262_Mutant_3

description: ERR262 (Mutant 3)

label_protocol: please refer to the Microarray Core Facility website of the Dana-Farber Cancer Institute


title: dental pulp cells (DP2) at passage 4

source_name: dental pulp cells (DP2) at passage 4

tag: DP2-P4, human dental pulp stem cells (hDPSCs) (14 year-old)


title: Tam-treated MCF7 xenograft, biological rep3


title: Tesi plus tetracycline, replicate


title: ERR67_Mutant_1

description: ERR67 (Mutant 1)


title: ERR84_Control_2

description: ERR84 (Control 2)


title: E2-treated MCF7 xenograft, biological rep3

description: Gene expression data from MCF-7 xenograft tumors supplemented with estrogen (E2).

tag: E2 treatment


title: pDC treated with IL-3+CpG, biological rep1


title: pDC treated with IL-3, biological rep2

description: Gene expression data from pDC treated with IL-3

source_name: blood, pDC treated with IL-3


title: pDC treated with IL-3, biological rep1

source_name: blood, pDC treated with IL-13


title: pDC treated with IL-3+p17, biological rep1


title: Tam-treated MCF7 xenograft, biological rep1


title: E2-treated MCF7 xenograft, biological rep2


title: E2-treated MCF7 xenograft, biological rep1


title: ERR66_Control_1

description: ERR66 (Control 1)


title: hMoDC_stim_8h_VAF347_rep2

status: Public on Feb 12 2008

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

hyb_protocol: Hybridization was carried out at 45ºC for approximately 18 hr.

scan_protocol: The arrays were stained on a GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

data_processing: The obtained signal intensities (.CEL files) were uploaded into GeneSpring (Agilent Technologies)

source_name: immature human monocyte-derived dendritic cells (MoDCs)

label_protocol:
Double-stranded cDNA synthesis was carried out with total RNA (SuperScript double-stranded cDNA synthesis kit; Invitrogen) according to the manufacturer’s instructions.
After purification (QIAquick; Qiagen), the cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High yield T7 DNA transcription kit, ENZO Life Sciences Inc.). The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen), quantified and fragmented into strands of approximately 50-200 nucleotides in length.

growth_protocol: Human peripheral blood monocytes were prepared by elutriation or by negative selection of PBMC using a monocyte isolation kit. Monocytes (typically >97% positive for CD14) were differentiated into immature DC by adding 40ng/ml IL-4 and 15ng/ml or 50ng/ml GM-CSF for 6-8 days in the absence or presence of increasing concentrations of VAF347.

extract_protocol: Absolutely RNA kit (Stratagene)

treatment_protocol: Immature monocyte-derived DC were activated with anti-CD40 antibodies for 8 hours in the absence or presence of 50nM VAF347.

tag: 8h, stimulated, treated with VAF347

tag: Donor D2_VAF347


title: hMoDC_stim_8h_VAF347_rep1

tag: Donor D1_VAF347


title: 321258

city: St Louis

first: Jacqueline

last: Payton

state: MO

address: 4320 Forest Park Avenue, Suite 211

institute: Washington University School of Medicine

description: A study that used high-throughput re-sequencing of the kinase domains of 26 Tyrosine kinase genes that are expressed in most acute myeloid leukemia patients. Used genomic DNA from bone marrow (tumor).

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data scaled to array mean of 1500

source_name: Bone marrow specimen from Tumor cells

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Bone marrow specimen from Tumor cells

extract_protocol: Trizol reagent standard protocol

tag: fab

tag: Sex

value: F

tag: race

value: C

tag: age on study

tag: cytogenetic change

tag: flt3 d835

tag: flt3 itd

tag: npm1 ins


title: 849660

value: M

value: Normal


title: 195182

value: W


title: 147796


title: hMoDC_stim_8h_ctrl_rep1

tag: 8h, stimulated, not treated

tag: Donor D1_ctrl


title: 327929

value: AA

value: ND


title: 936028


title: 412761


title: 427366


title: 986000


title: 884262


title: 730817


title: 852559


title: 957664

value: trisomy 8


title: 775109


title: 869586


title: 432398


title: 984036

value: trisomy 21  trisomy 3


title: 269542


title: 569053


title: 295


title: 380949

value: -X


title: 294154


title: 938150


title: 426980


title: Wild-type E11.5 proximal hindlimb pool 2

source_name: Wild-type E11.5 129Sv

tag: Proximal hindlimb bud tissue (~500um from base of limb bud) pooled from 3 embryos (6 limbs total).


title: 344551

value: H


title: 346190


title: 418499


title: 975684


title: 992966


title: 509754


title: 964886


title: 709968


title: 905179


title: 570755


title: 274429


title: 670224


title: 208027

value: Asian


title: 110


title: 974749


title: 318433


title: 447649


title: 863018


title: 606061


title: 633734


title: 673778


title: 399253


title: 312340


title: 275382


title: 311636


title: 269

value: trisomy Y


title: 123172


title: hMoDC_stim_8h_ctrl_rep2

tag: Donor D2_ctrl


title: 186481


title: 263578


title: 245

value: trisomy 21


title: 150951


title: 203


title: 237


title: 826984


title: 807615


title: OTSCC 20

city: Atlanta

first: Tianwei

last: Yu

state: GA

address: 1518 Clifton Rd NE

department: Biostatistics

institute: Emory University

description: This studys aim is to compare specific transcriptomic signatures that are associated with Oral Tongue Squamous Cell Carcinoma

hyb_protocol: The samples were hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays according to the Affymetrix protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000. The scanned array images were processed with GeneChip Operating software (GCOS), and the CEL files were extracted for further analysis.

source_name: Oral Tongue Squamous Cell Carcinoma

label_protocol: The Enzo BioArray High Yield RNA Transcript Labeling System (Enzo) was used for labeling the sample prior to hybridization. The biotinylated cRNA (IVT product) was purified using the RNeasy kit (Qiagen).

extract_protocol: The total RNA was isolated using RNeasy Mini kit (Qiagen), and quantified by the RiboGreen RNA Quantitation Reagent (Molecular Probes).

tag: Sex F, Age 66, pN2C


title: OTSCC normal control 9

source_name: Tongue Squamous Cells from control subjects

tag: Sex M, Age 62


title: OTSCC normal control 11

tag: Sex F, Age 70


title: OTSCC 21

tag: Sex F, Age 50, pN2C


title: OTSCC 26

tag: Sex M, Age 47, pN0


title: OTSCC 18

tag: Sex M, Age 38, pN1


title: OTSCC 14

tag: Sex M, Age 78, pN2B


title: OTSCC 25

tag: Sex F, Age 52, pN0


title: OTSCC 23

tag: Sex M, Age 37, pN2A


title: OTSCC normal control 12

tag: Sex M, Age 38


title: OTSCC 19

tag: Sex M, Age 65, pN0


title: OTSCC 16

tag: Sex M, Age 60, pN0


title: OTSCC 22

tag: Sex M, Age 74, pN2B


title: OTSCC 17

tag: Sex M, Age 67, pN0


title: OTSCC 24

tag: Sex M, Age 62, pN0


title: OTSCC normal control 10

tag: Sex M, Age 70


title: OTSCC 12

tag: Sex M, Age 47, pN2C


title: OTSCC 13


title: OTSCC 11

tag: Sex M, Age 45, pN0


title: OTSCC 9

tag: Sex F, Age 70, pN2C


title: OTSCC 10

tag: Sex F, Age 65, pN2C


title: 619751

tag: fab

tag: Sex

tag: race

tag: age on study

tag: cytogenetic change

tag: flt3 d835

tag: flt3 itd

tag: npm1 ins


title: OTSCC 8

tag: Sex M, Age 82, pN2B


title: paraquat 20mM 4h

status: Public on Feb 11 2008

first: Christophe

last: Laloi

address: Universitaetstrasse 2

department: Institute of Plant Science

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 4h after treatment with parauquat 20mM in tween 0.1%

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, protocol EukGE-WS2v4.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner

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 100.

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 4h after spray paraquat 20mM in Tween 0.1%

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Eukaryotic Target Preparation, 2002, Affymetrix).

growth_protocol: Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1

extract_protocol:
total RNA extraction was performed according to Melzer, S., Majewski, D. M. & Apel, K. (1990) Plant Cell 2, 953-961:
RNA was isolated with some modifications as described by Chirgwin et al. (1979). The plant material was ground under liquid nitrogen with a mortar and a pestle and homogenized in 4 mL of lysis buffer (4 M guanidinium isothiocyanate, 50 mM Hepes-KOH, pH 7.4, 2% Nlauroyl-sarcosin and 1 YO o-mercaptoethanol) with an Ultra Turrax (Janke and Kunkel, D7813 Stanfen, F. R. G.). Cell debris and denatured proteins were pelleted and the nucleic acids in the supernatant were precipitated overnight in the presence of 0.75 volumes of ethanol. The pellet was homogenized in 4 mL of Tes (10 mM Tris-HCI, pH 7.5, 1 mM EDTA, and 0.1% SDS) with the help of a potter, and the homogenate was extracted with phenol/chloroform and chloroform. Total RNA was precipitated overnight with 2 M LiCl at 4°C. Poly(A)-containing RNA was isolated according to Aviv and Leder (1972).

treatment_protocol: Plants were sprayed either with a solution of 20 microM paraquat (methyl viologen, Sigma) in 0.1% Tween or with Tween alone, and rosette leaves were harvested at 1, 2, and 4 h after spraying.

tag: ecotype

value: Landsberg erecta (Ler)

tag: Genotype

tag: Plant material

value: rosette leaves of 3 week-old plants grown under continuous light 90 mmol. m-2 . s-1, before bolting


title: Tween 0.1% 1h

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 1h after mock treatment with tween 0.1%

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 1h after mock spray with Tween 0.1%


title: paraquat 20mM 1h

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 1h after treatment with parauquat 20mM in tween 0.1%

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 1h after spray paraquat 20mM in Tween 0.1%


title: Tween 0.1% 2h

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 2h after mock treatment with tween 0.1%

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 2h after mock spray with Tween 0.1%


title: paraquat 20mM 2h

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 2h after treatment with parauquat 20mM in tween 0.1%

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 2h after spray paraquat 20mM in Tween 0.1%


title: OTSCC 7

tag: Sex M, Age 62, pN2B


title: OTSCC normal control 8

tag: Sex F, Age 52


title: OTSCC 5

tag: Sex M, Age 41, pN0


title: Tween 0.1% 4h

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants grown under continuous light, 4h after mock treatment with tween 0.1%

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light 4h after mock spray with Tween 0.1%


title: OTSCC 6

tag: Sex M, Age 53, pN0


title: OTSCC normal control 6

tag: Sex M, Age 65


title: OTSCC normal control 1

tag: Sex M, Age 41


title: OTSCC 4

tag: Sex M, Age 67, pN0


title: OTSCC normal control 7

tag: Sex M, Age 37


title: OTSCC normal control 4

tag: Sex F, Age 57


title: OTSCC 2

tag: Sex M, Age 44, pN0


title: CD4+ Tcell Activated T18

status: Public on Feb 09 2008

city: Bethesda

first: Dustin

middle: E

last: Schones

address: Building 10, Room 7B20A, 9000 Rockville Pike

institute: NHLBI/NIH

description:
CD4+ Tcell Activated T18
Human CD4+ T cells were prepared from crude lymphocyte fraction by negative selection using CD4+ T cell isolation kit II from Myltenyi Biotech.

hyb_protocol: 20 micrograms of biotin labeled RNA was fragmented to ~200 bp fragments by incubating in a buffer containing 200 mM Tris-Acetate pH 8.2, 500 mM Potassium Acetate and 500 Magnesium Acetate for 35 minutes at 95C.  Fragments were hybridized to Affymetrix U133A plus 2.0 chips for 16 hrs, washed and stained on an Affymetrix fluidics station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: Data processing was performed using the Affymetrix GCOS (v1.40) package with the MAS5 method.

source_name: Human CD4+ T cells, activated using anti-CD3/28 beads (Invitrogen), 18hrs

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

growth_protocol: RPMI-1640, 10% FCS, antibiotics

extract_protocol: Total RNA extraction was performed using a Qiagen RNeasy mini kit following the manufacturer's directions.

treatment_protocol: anti-CD3/28 beads (Invitrogen), 1 bead per cell, 18hrs

tag: Human CD4+ T cells


title: OTSCC normal control 2

tag: Sex M, Age 53


title: OTSCC normal control 5

tag: Sex M, Age 38


title: CD4+ Tcell Resting T0

description:
CD4+ Tcell Resting T0
Human CD4+ T cells were prepared from crude lymphocyte fraction by negative selection using CD4+ T cell isolation kit II from Myltenyi Biotech.

source_name: Human CD4+ T cells, resting


title: OTSCC normal control 3

tag: Sex M, Age 62


title: MCF7 HRG 2h

status: Public on Feb 08 2008

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

description: Gene expression induced by growth hormone (HRG) stimulation

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: breast epithelial cell, adherent, HRG, 10nM, 2h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: MCF-7 (Obtained from ATCC (American Type Culture Collection)), Organ:mammary gland; breast, Cell type:epithelial, Disease:adenocarcinoma, Derived from metastatic site:pleural effusion, Age:69 years adult, Gender:female, Ethnicity:Caucasian


title: OTSCC 1

tag: Sex

value: F, Age 57, pN0


title: CD4+ Tcell Resting M0

description:
CD4+ Tcell Resting M0
Human CD4+ T cells were prepared from crude lymphocyte fraction by negative selection using CD4+ T cell isolation kit II from Myltenyi Biotech.


title: OTSCC 3

tag: Sex M, Age 52, pN0


title: CD4+ Tcell Activated M18

description:
CD4+ Tcell Activated M18
Human CD4+ T cells were prepared from crude lymphocyte fraction by negative selection using CD4+ T cell isolation kit II from Myltenyi Biotech.


title: MCF7 Control

source_name: breast epithelial cell, adherent, without stimulus, control


title: OTSCC 15

tag: Sex M, Age 55, pN0


title: Head_group_housing_6day_male_3_2

city: Pasadena

first: Liming

last: Wang

state: CA

address: 1200 E. California Bl.

department: 216-76， Division of Biology

institute: California Institute of Technology

description: 20 group-housed males were frozen in liquid nitrogen between 5pm-6pm. Heads were separated and used for RNA extraction.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Rosetta Resolver Platform

organism: Drosophila melanogaster

label_protocol: Standard Affymetrix

extract_protocol: TriZol

treatment_protocol: new eclosion males were housed at 10 flies/vial in vials for 6 days

tag: head from 6-day-old group-housed male Canton-S


title: Head_single_housing_6day_male_3_1

description: 20 single-housed males were frozen in liquid nitrogen between 5pm-6pm. Heads were separated and used for RNA extraction.

extract_protocol: Trizol

treatment_protocol: new eclosion males were housed individually in vials for 6 days

tag: head from 6-day-old single-housed male Canton-S


title: Head_group_housing_6day_male_3_1


title: Head_group_housing_6day_male_3_3


title: Head_single_housing_6day_male_3_2


title: H133+_H448_Tri_30uM

status: Public on Feb 07 2008

city: Research Triangle Park

first: David

last: Dix

state: NC

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

hyb_protocol: cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20).  GeneChips were hybridized at 45ºC for 16 h.  After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.

scan_protocol: Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.

data_processing: To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500.  Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA.  For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics.  Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate and an absolute difference of |1.2| or greater.  Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.

label_protocol: Five micrograms or purified total RNA from each sample per treatment group was hybridized to Affymetrix GeneChip® Human Genome U133_2.0 Plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).  Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer.  Biotinylated RNA (labeled cRNA) served as the microarray target.  cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.

extract_protocol: Total RNA was extracted from primary hepatocytes using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays.  For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE).  RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).  Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays.  RNA was stored at -80ºC until labeling for microarray hybridization.

treatment_protocol: in vitro exposure, 72 hour exposure via medium

tag: primary hepatocytes


title: Head_single_housing_6day_male_3_3


title: H448 Triadimefon 100uM

description: H448 Triadimefon 100uM.CEL

source_name: H448 Triadimefon 100uM


title: H416 Triadimefon 30uM

description: H416 Triadimefon 30uM.CEL

source_name: H416 Triadimefon 30uM


title: H133+_H439_Tri_30uM


title: H438 Triadimefon 30uM

description: H438 Triadimefon 30uM.CEL

source_name: H438 Triadimefon 30uM


title: H438 Triadimefon 100uM

description: H438 Triadimefon 100uM.CEL

source_name: H438 Triadimefon 100uM


title: H416 Triadimefon 100uM

description: H416 Triadimefon 100uM.CEL

source_name: H416 Triadimefon 100uM


title: H448 Rif 30uM

description: H448 Rif 30uM.CEL

source_name: H448 Rif 30uM


title: H133+_H416_Tri_10uM


title: H439 Triadimefon 10uM

description: H439 Triadimefon 10uM.CEL

source_name: H439 Triadimefon 10uM


title: H133+_H439_Rif_30uM


title: H438 Propiconazole 100uM

description: H438 Propiconazole 100uM.CEL

source_name: H438 Propiconazole 100uM


title: H133+_H416_Propi_100uM


title: H448 Triadimefon 10uM

description: H448 Triadimefon 10uM.CEL

source_name: H448 Triadimefon 10uM


title: H448 Propiconazole 100uM

description: H448 Propiconazole 100uM.CEL

source_name: H448 Propiconazole 100uM


title: H133+_H416_Propi_30uM


title: H439 Propiconazole 30uM

description: H439 Propiconazole 30uM.CEL

source_name: H439 Propiconazole 30uM


title: H133+_H438_Tri_10uM


title: H133+_H448_Propi_30uM


title: H133+_H439_Propi_100uM


title: H416 Propiconazole 10uM

description: H416 Propiconazole 10uM.CEL

source_name: H416 Propiconazole 10uM


title: H438 Propiconazole 30uM

description: H438 Propiconazole 30uM.CEL

source_name: H438 Propiconazole 30uM


title: H133+_H416_PB_1000uM


title: H439 PB 1000uM

description: H439 PB 1000uM.CEL


title: H416 Myclobutanil 100uM

description: H416 Myclobutanil 100uM.CEL

source_name: H416 Myclobutanil 100uM


title: H416 DMSO 0.001

description: H416 DMSO 0.001.CEL


title: H439 Myclobutanil 100uM

description: H439 Myclobutanil 100uM.CEL

source_name: H439 Myclobutanil 100uM


title: H448 Myclobutanil 100uM

description: H448 Myclobutanil 100uM.CEL

source_name: H448 Myclobutanil 100uM


title: H416 Myclobutanil 10uM

description: H416 Myclobutanil 10uM.CEL

source_name: H416 Myclobutanil 10uM


title: H416 Myclobutanil 30uM

description: H416 Myclobutanil 30uM.CEL

source_name: H416 Myclobutanil 30uM


title: H133+_H448_Propi_10uM


title: H133+_H448_PB_1000uM


title: H438 PB 1000uM

description: H438 PB 1000uM.CEL


title: H133+_H439_Propi_10uM


title: H438 DMSO 0.001

description: H438 DMSO 0.001.CEL


title: H438 Myclobutanil 100uM

description: H438 Myclobutanil 100uM.CEL

source_name: H438 Myclobutanil 100uM


title: H448 DMSO 0.001

description: H448 DMSO 0.001.CEL


title: H438 Myclobutanil 10uM

description: H438 Myclobutanil 10uM.CEL

source_name: H438 Myclobutanil 10uM


title: H439 DMSO 0.001

description: H439 DMSO 0.001.CEL


title: H439 Myclobutanil 30uM

description: H439 Myclobutanil 30uM.CEL

source_name: H439 Myclobutanil 30uM


title: H438 Myclobutanil 30uM

description: H438 Myclobutanil 30uM.CEL

source_name: H438 Myclobutanil 30uM


title: H439 Myclobutanil 10uM

description: H439 Myclobutanil 10uM.CEL

source_name: H439 Myclobutanil 10uM


title: Etoh 6

status: Public on Feb 06 2008

city: philadelphia

first: Hua

last: Xu

address: 421 Curie Blvd

department: OB/GYN

institute: University of Pennsylvania

description: gene expression data from pregnant mouse cervix treated with EtOH

hyb_protocol: Following fragmentation, 2.2 ug of cDNA were hybridized for 16 hr at 45C on GeneChip mouse Genome 430V2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: gcrma calculated from cel files using Stratagene ArrayAssist Lite v3.4, producing chp files with unlogged signal levels and Affy flags

source_name: CD1, E15 pregant mouse

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT-Ovation Pico RNA Amplification System, NuGEN Technologies).

growth_protocol: CD1 mice on gestation of day 15

extract_protocol: Trizol extraction followed by Qiagen  RNeasy kit purification

treatment_protocol: MPA (1mg/dam) SubQ injection for 48 hours; or the same volume of EtOH

tag: EtOH treated, Vehicle


title: Etoh 1


title: HeLa_infected_rep3

city: Tokyo

first: Takako

last: Shigihara

address: 2-1-1, Hongo, Bunkyo-ku

department: Biomedical Research Center

institute: Juntendo University Graduate School of Medicine

description: The trypomastigotes in the medium were removed by washing the cells twice with phosphate-buffered saline (PBS) and replacing the medium 12 h before RNA isolation to remove the extracellular parasites. Using this procedure, approximately 78% of the cells were infected with T. cruzi.

hyb_protocol: Ten μg fragmented cRNA was hybridized with GeneChip Human Genome U133 plus 2.0 Array (Affymetrix) at 45℃ for 16 h.

scan_protocol: The chips were washed, stained with streptavidin phycoerythrin and scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Scanned images were converted to signal intensity using GeneChip Operating software (Affymetrix).

source_name: HeLa cell (Trypanosoma cruzi-infected)

label_protocol: Total RNA was converted to cDNA using Superscript Ⅱ reverse transcriptase, and biotin-labeled cRNA was synthesized from the cDNA by in vitro transcription as described (One-Cycle Target Labeling and Control Reagents, Affymetrix)

growth_protocol: HeLa cells were cultured in 25-cm2 flasks containing modified Eagle’s medium (MEM) supplemented with 10% heat-inactivated fetal calf serum (FCS) at 37℃ with cells passaged every 3 to 4 days.

extract_protocol: Total RNA was isolated using Agilent Total RNA Isolation Mini Kit.

treatment_protocol: Exponentially growing HeLa cells were infected with T. cruzi trypomastigotes and incubated for 3 days.

tag: HeLa cell line


title: MPA 6

description: gene expression data from pregnant mouse cervix treated with MPA

tag: MPA-treatment for 48hrs


title: Etoh 3


title: MPA 3


title: Etoh 2


title: Etoh 4


title: HeLa_infected_rep2


title: Total cellular mRNA of J774-LPS 2hr-rep1

status: Public on Feb 05 2008

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

description: Cells were washed with PBS and then directly subjected to RNA extraction.

hyb_protocol: Twenty micro gram of labeled sample was used. Hybridization was performed at 45C for 16hr with continuous rotation.

scan_protocol: Washing and streptavidin-phycoerythrin staining was done using a GeneChip Fluidics Station(Affymetrix), then scanning was performed using a GeneChip scanner 3000(Affymetrix) as the default setting.

data_processing: The value was calculated by MAS5 method using a GCOS software package(Affymetrix).

source_name: macrophage-like J774 cells, total cell, LPS 2hr

label_protocol: Labeling was performed using One-cycle target labeling kit (Affymetrix) as manufacture's indications.

growth_protocol: RPMI1649 10%FCS 37C, 5%CO2 passage:twice/week

extract_protocol: Total RNA was extracted with TRIzol reagent(Invitrogen), and subsequently poly(A) RNA was isolated using microMACS kit(Militenyi). Qulity of poly(A) RNA was checked using a bioanalyzer (Agilent).

treatment_protocol:
100ng/ml of Lipopolysaccharide from Escherichia coli (sero type 055:B5)
for 2hr.

tag: Strain:Balb/c Tissue:blood macrophage-like cell


title: trypomastigote

description: control sample to check the cross-hybridization between T.cruzi cRNA and human chip

organism: Trypanosoma cruzi

source_name: trypomastigote

growth_protocol: Trypanosoma cruzi were cultured with HeLa cell in 75-cm2 flasks containing modified Eagle’s medium (MEM) supplemented with 10% heat-inactivated fetal calf serum (FCS) at 37℃ with cells passaged every 3 to 4 days.

extract_protocol: Tropomastigote were collected from culture medium by centrifugation.Total RNA was isolated using Agilent Total RNA Isolation Mini Kit.

tag: trypomastigote (Tulahuen strain)


title: MPA 5


title: MPA 4


title: Total cellular mRNA of J774-LPS 1hr-rep1

data_processing: The value was calculated by MAS5 method using a GCOS software package(Affymetrix)

source_name: macrophage-like J774 cells, total cell, LPS 1hr

treatment_protocol:
100ng/ml of Lipopolysaccharide from Escherichia coli (sero type 055:B5)
for 1hr.

tag: Strain:Balb/c Tissue:blood macrophage-like cell.


title: HeLa_infected_rep1


title: Total cellular mRNA of J774-LPS 2hr-rep2


title: Etoh 5


title: Total cellular mRNA of J774-LPS 4hr-rep3

source_name: macrophage-like J774 cells, total cell, LPS 4hr

treatment_protocol:
100ng/ml of Lipopolysaccharide from Escherichia coli (sero type 055:B5)
for 4hr.


title: Total cellular mRNA of J774-LPS 1hr-rep2

treatment_protocol:
100ng/ml of Lipopolysaccharide from Escherichia coli (sero type 055:B5)
for 1hr


title: HeLa_uninfected_rep3

description: control sample

source_name: HeLa cell (uninfected)


title: MPA 1


title: Total cellular mRNA of J774-LPS 2hr-rep3


title: HeLa_uninfected_rep2

description: control sample

source_name: HeLa Cell (uninfected)


title: Total cellular mRNA of J774-intact-rep3

description: Cells were washed with PBS and then directly subjected to RNA extraction..

source_name: macrophage-like J774 cells, total cell, intact

treatment_protocol: intact


title: Total cellular mRNA of J774-LPS 4hr-rep2


title: Total cellular mRNA of J774-LPS 1hr-rep3

source_name: Strain:Balb/c Tissue:blood macrophage-like cell


title: Total cellular mRNA of J774-LPS 4hr-rep1


title: MPA 2


title: HeLa_uninfected_rep1

description: control sample


title: Total cellular mRNA of J774-intact-rep2


title: Total cellular mRNA of J774-intact-rep1


title: Free mRNP of J774-LPS 4hr-rep1

description: Free mRNP preparation: The cells were lysed with a solution containing 0.5%NP-40.Post-mitochondrial fraction was applied onto 15-50% sucrose gradient, and subsequently centrifuged using SW41Ti (Beckman Coulter) at 39krpm. The gradient was divided into 20 fractions from the surface. The fraction 1-5 were collected, and subjected to total RNA extraction.

source_name: macrophage-like J774 cells, free mRNP, LPS 4hr

treatment_protocol: 100ng/ml of Lipopolysaccharide from Escherichia coli (sero type 055:B5)


title: H438 Propiconazole 10uM

description: H438 Propiconazole 10uM.CEL

source_name: H438 Propiconazole 10uM


title: Free mRNP of J774-LPS 4hr-rep3


title: Polysome of J774-LPS 2hr-rep2

description: Polysome preparation: The cells were lysed with a solution containing 0.5%NP-40.Post-mitochondrial fraction was applied onto 15-50% sucrose gradient, and subsequently centrifuged using SW41Ti (Beckman Coulter) at 39krpm. The gradient was divided into 20 fractions from the surface. The fraction 11-20 were collected, and subjected to total RNA extraction.

source_name: macrophage-like J774 cells, polysome, LPS 2hr

growth_protocol: RPMI1649 10%FCS

extract_protocol: Total RNA was extracted with TRIzol reagent(Invitrogen), and subsequently poly(A) RNA was isolated using microMACS kit(Militenyi).


title: Free mRNP of J774-LPS 4hr-rep2


title: Free mRNP of J774-LPS 2hr-rep2

source_name: macrophage-like J774 cells, free mRNP, LPS 2hr


title: Free mRNP of J774-LPS 2hr-rep3


title: Polysome of J774-LPS 4hr-rep2

source_name: macrophage-like J774 cells, polysome, LPS 4hr


title: Polysome of J774-LPS 2hr-rep1


title: Free mRNP of J774-intact-rep1

source_name: macrophage-like J774 cells, free mRNP, intact


title: Polysome of J774-LPS 1hr-rep3

source_name: macrophage-like J774 cells, polysome, LPS 1hr


title: Free mRNP of J774-LPS 1hr-rep3

source_name: macrophage-like J774 cells, free mRNP, LPS 1hr


title: Polysome of J774-LPS 4hr-rep3


title: Polysome of J774-intact-rep3

source_name: macrophage-like J774 cells, polysome, intact


title: Polysome of J774-LPS 2hr-rep3


title: Polysome of J774-intact-rep2


title: Free mRNP of J774-intact-rep3


title: Free mRNP of J774-LPS 2hr-rep1


title: Polysome of J774-LPS 4hr-rep1


title: Free mRNP of J774-LPS 1hr-rep1


title: Free mRNP of J774-LPS 1hr-rep2


title: Free mRNP of J774-intact-rep2


title: Polysome of J774-LPS 1hr-rep2


title: Polysome of J774-LPS 1hr-rep1


title: Polysome of J774-intact-rep1

growth_protocol:
RPMI1649 10%FCS
37C, 5%CO2
passage:twice/week

extract_protocol:
Total RNA was extracted with TRIzol reagent(Invitrogen), and subsequently poly(A) RNA was isolated using microMACS kit(Militenyi).
Qulity of poly(A) RNA was checked using a bioanalyzer (Agilent).

tag: macrophage-like cell


title: KOPfoa4

status: Public on Feb 04 2008

city: RTP

first: Hongzu

last: Ren

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

description: gene expression data from WT and PPARalpha-null mouse liver samples

hyb_protocol: Samples were hybridized according to the Affymetrix protocol

scan_protocol: Affymetrix protocol using a GeneChip scanner 3000

data_processing: Affymetrix GeneChip microarray suite software was used for washing and scanning.  Expression summaries were calculated in Rosetta Resolver v.7 with default algorithm for normalization

label: biotin-streptavidin-R-phycoerythrin

source_name: mouse liver from wild-type and PPARalpha-null mice treated with PFOA or water.

label_protocol: Samples were labeled according to the Affymetrix protocol

growth_protocol: Mice were housed in ventilated Tecniplast cages (Tecniplast USA, Exton, PA) and provided pellet chow (LabDiet 5001, PMI Nutrition International, Brentwood, MO) and tap water ad libitum.  Animal facilities were controlled for temperature (20-24°C) and relative humidity (40-60%), and kept under a 12-h light-dark cycle.

extract_protocol: Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)

treatment_protocol: Four wild-type and PPARalpha-null male mice per group 6 months of age were dosed by gavage for 7 consecutive days with PFOA (Fluka Chemical cat#77262, Steinheim, Switzerland) in distilled water or distilled water alone.  Dose groups consisted of 1, 3 and 10 mg/kg/day PFOA.  All dosing solutions were freshly prepared each day.  At the end of the dosing period, animals were euthanized by CO2 asphyxiation and liver tissue was collected for preparation of total RNA and histopathology.

tag: Male and female 129S1/SvlmJ wild type (stock #002448) and PPARalpha-null (Ppara-tm1Gonz/J, stock #003580) mice were obtained from Jackson Laboratories, (Bar Harbor, MA).

tag: no additional


title: KOCtr5


title: KOCtr3


title: WTCtr10


title: WTPfoa9


title: KOPfoa1


title: KOPfoa2


title: KOCtr8


title: WTPfoa15


title: WTCtr11


title: KOCtr16


title: WTPfoa13


title: WTCtr14


title: WTCtr12


title: WTPfoa6


title: HOb514_dexamethasone_24h_rep1

status: Public on Feb 01 2008

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

institute: McGill University and Genome Quebec Innovation Centre

description: Primary human osteoblast like cells (HOb) were cultured in three biological replicates in cell medium containing α-MEM  supplemented with 2 mmol/l L-Glutamine, 100U/mL penicillin, 100mg/mL streptomycin, and 10% fetal bovine serum and grown at 37°C with 5% CO2 until confluence. At 70-80% confluence, each replicate was trypsinized and sub-cultured for 12 days. Prior to treatment, the cells were starved for 20h by adding complete cell medium containing 0.5% fetal bovine serum. The cells were then incubated for 2h and 24h with 10-7 M of dexamethasone and 10-4 mg/ml of rhBMP-2 with the same concentration of vehicle, respectively.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: Expression values were calculated using the Robust Multichip Average method (Irizarry RA, Hobbs B, Collin F, et al. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-64)

source_name: Primary human osteoblast like cells (HOb), dexamethasone 24h, biological replicate 1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

extract_protocol: The cells were harvested by adding 500µL of RLT buffer (Qiagen, GmbH, Germany). The cell lysates were homogenized by using QIAshredder (Qiagen, GmbH, Germany) homogenizers and stored in -70°C until RNA extraction. RNA was isolated from the cell lysates using the RNeasy® Mini Kit (Qiagen, GmbH, Germany). High RNA quality was confirmed for all samples using Agilent 2100 BioAnalyzer (Agilent technologies, Palo Alto, CA, USA) and the concentrations were determined using Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

tag: HOb derived from trabecular bone explants, Gender

value: Male, Age:64


title: KOPfoa7


title: HOb514_dexamethasone_24h_rep2

source_name: Primary human osteoblast like cells (HOb), dexamethasone 24h, biological replicate 2


title: HOb514_dexamethasone_24h_rep3

source_name: Primary human osteoblast like cells (HOb), dexamethasone 24h, biological replicate 3


title: HOb514_dexamethasone_2h_rep2

source_name: Primary human osteoblast like cells (HOb), dexamethasone 2h, biological replicate 2


title: HOb514_BMP2_24h_rep3

source_name: Primary human osteoblast like cells (HOb), BMP2 24h, biological replicate 3


title: HOb514_untreated_2h_rep1

source_name: Primary human osteoblast like cells (HOb), Untreated 2h, biological replicate 1


title: HOb514_dexamethasone_2h_rep3

source_name: Primary human osteoblast like cells (HOb), dexamethasone 2h, biological replicate 3


title: HOb514_BMP2_2h_rep3

source_name: Primary human osteoblast like cells (HOb), BMP2 2h, biological replicate 3


title: HOb514_untreated_2h_rep3

source_name: Primary human osteoblast like cells (HOb), Untreated 2h, biological replicate 3


title: HOb514_untreated_2h_rep2

source_name: Primary human osteoblast like cells (HOb), Untreated 2h, biological replicate 2


title: HOb514_BMP2_24h_rep2

source_name: Primary human osteoblast like cells (HOb), BMP2 24h, biological replicate 2


title: HOb514_dexamethasone_2h_rep1

source_name: Primary human osteoblast like cells (HOb), dexamethasone 2h, biological replicate 1


title: HOb514_BMP2_24h_rep1

source_name: Primary human osteoblast like cells (HOb), BMP2 24h, biological replicate 1


title: HOb514_BMP2_2h_rep2

source_name: Primary human osteoblast like cells (HOb), BMP2 2h, biological replicate 2


title: HOb514_untreated_24h_rep3

source_name: Primary human osteoblast like cells (HOb), untreated 24h, biological replicate 3


title: HOb506_untreated_24h_rep2

source_name: Primary human osteoblast like cells (HOb), untreated 24h, biological replicate 2

value: Male, Age:25


title: HOb514_untreated_24h_rep1

source_name: Primary human osteoblast like cells (HOb), untreated 24h, biological replicate 1


title: HOb506_untreated_24h_rep3


title: HOb506_untreated_24h_rep1


title: HOb514_BMP2_2h_rep1

source_name: Primary human osteoblast like cells (HOb), BMP2 2h, biological replicate 1


title: KO Tibialis Anterior at 4 weeks biological rep1

city: Birmingham

first: Gareth

last: Lavery

address: 2nd Floor IBR

country: United Kingdom

institute: University of Birmingham

description: Gene expression data from muscle of 4 weeks old altered in glucose and steroid metabolism

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and  as quantile normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse Tibialis Anterior 4 weeks post birth

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

tag: H6PDH knockout


title: KO Soleus at 4 weeks biological rep2

source_name: Mouse Soleus 4 weeks post birth


title: WT Soleus at 4 weeks biological rep3

tag: H6PDH WT


title: HOb514_untreated_24h_rep2


title: WT Tibialis Anterior at 4 weeks biological rep1


title: Brain_ProtocolA_rep3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

description: Samples labeling and hybridization day 2, replicate 1

hyb_protocol: Affymetrix HG-U133 Plus 2.0 arrays were hybridized with 11 mg of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: Ambion Human Brain Reference RNA (Catalog #6050)

label_protocol: 100ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791)

extract_protocol: total RNA extracted


title: WT Tibialis Anterior at 4 weeks biological rep3


title: KO Soleus at 4 weeks biological rep1


title: Universal_ProtocolN_rep1

description: Samples labeling and hybridization day 1, replicate 1

hyb_protocol: Affymetrix HG-U133 Plus 2.0 arrays were hybridized to 5 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression analysis manual (Fluidics protocol EukGeWS2v4_450)

source_name: Stratagene Universal Human Reference RNA (Catalog #740000)

label_protocol: 10 ng of total RNA were amplified and labeled using the WT-Ovation Pico RNA Amplification System V1, ( NuGen, catalog # 3300-12,) and labeling with FL-Ovation cDNA Biotin Module V2 (NuGen, catalog #4200-12)


title: Brain_ProtocolN_rep3


title: KO Tibialis Anterior at 4 weeks biological rep3


title: WT Soleus at 4 weeks biological rep1


title: Brain_ProtocolN_rep4

description: Samples labeling and hybridization day 2, replicate 2


title: KO Tibialis Anterior at 4 weeks biological rep2


title: Universal_ProtocolN_rep2

description: Samples labeling and hybridization day 1, replicate 2


title: WT Soleus at 4 weeks biological rep2


title: Brain_ProtocolN_rep1


title: Brain_ProtocolA_rep4


title: WT Tibialis Anterior at 4 weeks biological rep2


title: KO Soleus at 4 weeks biological rep3


title: Universal_ProtocolN_rep4


title: Brain_ProtocolN_rep2


title: Universal_ProtocolN_rep3


title: Universal_ProtocolA_rep4


title: Universal_ProtocolA_rep3


title: Brain_ProtocolA_rep1


title: Universal_ProtocolA_rep1


title: Universal_ProtocolA_rep2


title: UO126_3

status: Public on Jan 31 2008

city: London

first: Claudine

last: James

email: claudinegj@hotmail.com, fbeier@uwo.ca

state: Ontario

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

institute: University of Western Ontario

hyb_protocol: LRGC specifications

scan_protocol: M.A.S. 5.0-see LRGC specifications

data_processing:
Microarray data were pre-processed RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley. Background adjustment and quantile
normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA) (Subramanian et al., 2005, PNAS).

label: SAPE

source_name: UO126-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

label_protocol: Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/

growth_protocol: SEE CHARACTERISTICS

extract_protocol: Qiagen RNeasy extraction

treatment_protocol: SEE CHARACTERISTICS

tag: Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-glycerophosphate,

tag: 0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml

tag: of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells

tag: were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted.

tag: Chondrocytes were resuspended in media containing 2:3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml).

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 10 µM

tag: UO126 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: Brain_ProtocolA_rep2


title: si Control HCT116-repeat 3 - mAdbID:83284

city: gaithersburg

first: audrey

middle: n

last: player

address: 8717 grovemont circle

department: microarray facility

institute: national cancer institute

description: mAdb experiment ID: 83284

hyb_protocol: Affy Hybridization Protocol Other: The hybridization was performed as recommended in the Affymetrix GenechipTM Expression Analysis Technical Manual using fifteen micrograms each of biotin-labeled aRNA per GenechipTM, including BioB, BioC, BioD and Cre, and B2 hybridization controls, BSA, salmon sperm DNA, hybridization buffer and water; hybridizations were performed as technical replicates to U133 plus 2 GenechipsTM). GenechipsTM were washed and stained (with buffers, strepavidin phycoerythrin and biotin-antistrepavidin antibody), as recommended in the Affymetrix GenechipTM Expression Analysis Technical Manual.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
RMA Data Processing Protocol
Calculation Method: Using RMA normalization and summarization methods implemented in BioConductor.

source_name: si Control HCT116

label_protocol:
Ambion MessageAmp2 Protocol
Other: One microgram of total RNA was used to generate antisense RNA (aRNA) using the Ambion MessageAmp 2 aRNA kit as suggested by the manufacturer. Biotin-CTP and biotin-UTP were incorporated during in vitro transcription, as recommended for in the amplification protocol. A range of 10e3-3 x 10e3 fold amplification was achieved following 1 cycle of aRNA amplification. aRNA was approximately 1.5kilobases in size. Thirty micrograms of each sample was fragmented by adding 5X fragmentation buffer, water to 40ul, and heating at 95degrees as recommended in the Affymetrix GenechipTM Expression Analysis Technical Manual. Quality control and assessment of the RNA profiles were determined using the BioAnalyzer Nano6000 Assay. All samples were used for down-stream application (i.e., hybridization) within 2 days.

extract_protocol:
RNeasy Qiagen Extraction Protocol
Other: Total RNA was extracted using the RNeasy® Midi Kit and kept at -80°C. A260/280 ratios ranged from 1.8-2.0.

treatment_protocol:
Treatment type: small molecule
In-vivo treatment: To generate si Control cell lines, the plasmid pBS/U6 was cleaved with ApaI and EcoRI. Synthetic DNA oligonucleotides were then ligated into pBS/U6. A random nonsense sequence was used to produce the control siRNA (siCtrl). The siRNA-expressing cassette was removed with BamHI, and inserted into the BamHI site of the plasmid vector pRep4 (X+S). The siCtrl constructs were transfected into HCT116 and MCF-7 cells, using the Lipofectamine™ 2000 Transfection Reagent. Hygromycin B-resistant clones were selected with 600 or 400 µg/ml hygromycin B for HCT116 or MCF-7 cells, respectively. The resulting cell lines were designated as HCT116-siTop1, MCF-7-siTop1, HCT116-sictrl and MCF-7-sictrl.

tag: Tissue

value: colon

tag: Cell line

value: Colon Cancer Cell Line HCT116

tag: Cell type

value: epithelial cells

tag: Disease state

value: Colorectal carcinoma


title: SB90_2

source_name: SB90-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

tag: SB90 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: UO126_1

label: ONE COLOUR: SAPE


title: siTOP1 HCT116-repeat 3 - mAdbID:83282

description: mAdb experiment ID: 83282

source_name: siTOP1 HCT116

treatment_protocol:
Treatment type: small molecule
In-vivo treatment: To generate Top1-knockdown cell lines, the plasmid pBS/U6 was cleaved with ApaI and EcoRI. Synthetic DNA oligonucleotides were then ligated into pBS/U6. For Top1-siRNA, the core sequence of the inserted DNA oligonucleotides corresponds to a sequence from exon 17 of the TOP1 gene. The siRNA-expressing cassette was removed with BamHI, and inserted into the BamHI site of the plasmid vector pRep4 (X+S). The resulting vector corresponds to a human U6 promoter-driven DNA construct stably expressing an siRNA hairpin (shRNA) targeting human Top1 mRNA. The siTop1 constructs were transfected into HCT116 and MCF-7 cells, using the Lipofectamine™ 2000 Transfection Reagent. Hygromycin B-resistant clones were selected with 600 or 400 µg/ml hygromycin B for HCT116 or MCF-7 cells, respectively. The resulting cell lines were designated as HCT116-siTop1, MCF-7-siTop1, HCT116-sictrl and MCF-7-sictrl.

tag: genotype/variation gene knock out


title: UO126_2

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 10 uM


title: si Control HCT116-repeat 1 - mAdbID:83280

description: mAdb experiment ID: 83280


title: si Control HCT116-repeat 4 - mAdbID:83285

description: mAdb experiment ID: 83285


title: si Control MCF7-repeat 2 - mAdbID:83292

description: mAdb experiment ID: 83292

source_name: si Control MCF7

value: breast

value: Breast Cancer Cell Line MCF7

value: Adenocarcinoma


title: siTOP1 MCF7-repeat 2 - mAdbID:83287

description: mAdb experiment ID: 83287

source_name: siTOP1 MCF7


title: si Control HCT116-repeat 2 - mAdbID:83281

description: mAdb experiment ID: 83281


title: TSA_2

source_name: TSA-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 100 M

tag: TSA reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: SB90_3


title: siTOP1 HCT116-repeat 2 - mAdbID:83279

description: mAdb experiment ID: 83279


title: LY_2

source_name: LY-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 10 µM LY reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: SB90_1

tag: Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-glycerophosphate,


title: siTOP1 HCT116-repeat 1 - mAdbID:83278

description: mAdb experiment ID: 83278


title: LY_3

tag: 0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml

tag: LY reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: LY_1

tag: of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells

tag: were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted.


title: si Control MCF7-repeat 1 - mAdbID:83291

description: mAdb experiment ID: 83291


title: TSA_3

tag: Chondrocytes were resuspended in media containing 2:3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml).

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 100 µM


title: siTOP1 MCF7-repeat 1 - mAdbID:83286

description: mAdb experiment ID: 83286

tag: Tissue


title: siTOP1 HCT116-repeat 4 - mAdbID:83283

description: mAdb experiment ID: 83283

tag: Cell line


title: DMSO_2

source_name: DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with the

tag: DMSO control (vehicle) diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: TSA_1


title: DMSO_1

tag: Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with the DMSO control (vehicle) and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: DMSO_3


title: A6-LLOYD-CON_REP3

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description:
location: Growth cabinet
Atmosphere: Normal
Humidity: 60%
Temperature: 23oC
Lighting: 16h light/8h dark
Medium: 1/2 Murashige and Skoog medium (10d) followed by compost
Nutrients: 1% sucrose in Murashige and Skoog medium
Water: Twice a week
Stratification: 3d at 4oC

hyb_protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit according to guidelines set out by Affymetrix, Santa Clara, CA.

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

label_protocol: RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3') was hybridized with the Total RNA ( 8 - 12ug) at 70oC for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour. The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis. 130ul of the second strand reaction mix was added to the 20ul first strand synthesis reaction. The second strand reaction mix contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM beta-NAD+. The reaction was incubated at 16 C for 2 hours. 10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA. The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module. The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix. The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters. The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module. The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA. The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments. 15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.

extract_protocol: Qiagen / Trizol: Qiagen RNAeasy kit protocol

tag: Stock Code

tag: Developmental stage

value: Rosette leaves


title: A5-LLOYD-CON_REP2

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: A2-LLOYD-PHO_REP2

source_name: Feldmann T-DNA insert

tag: Genetic background

tag: Genetic variation

value: T-DNA insert


title: A3-LLOYD-PHO_REP3


title: YAP-overexpressing cells, biological rep2

city: Charlestown

first: Daniel

last: Haber

address: Rm.7119, Bldg.149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

description: MCF10A cells were infected with retrovirus constructs (vector or YAP) and puromycin was used to select for transduced cells. Cells were split and grown to ~60-75%% confluency at which point they were harvested for RNA.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software Ver. 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

growth_protocol: Standard MCF10A growth conditions.

extract_protocol: RNeasy miniprep columns (Qiagen) were used according to the manufacturer's instructions.

tag: MCF10A cells


title: A1-LLOYD-PHO_REP1


title: Yap_A2-AMF_Rep2

description:
location: Growth Room
Humidity: 50%-70%
Temperature: 23oC, 18oC
Lighting: 16h day/ 8h night
Medium: 1:1 Terra Green/sand
Nutrients: 0.1mM phosphate ATS
Water: 2X weekly

extract_protocol: none supplied

treatment_protocol: Inoculated with wetted sterile filter paper

value: total roots (primary and all lateral )


title: Yap_A1-AMF_Rep2

treatment_protocol: Inoculated with pre-germinated Gigaspora rosea spores


title: Yap_A1-AMF


title: Ward_A1-WARD-ax3_SLD

description:
location: Growth Room
Humidity: approx. 60% (normal)
Temperature: 21 C
Lighting: 16 hour light, 8 hour dark
Medium: compost
Treatment: Intercept WG treated soil before sowing
Water: tap water as required
Stratification: 3 days cold treatment on soil

extract_protocol: Qiagen RNEasy columns: As in manufacturers instructions including DNase treatment

value: axillary buds approx. 2 mm elongated

value: EMS


title: Yap_A2-AMF


title: YAP-overexpressing cells, biological rep1


title: vector control cells, biological rep1

source_name: vector control cells, biological rep1


title: vector control cells, biological rep2

source_name: vector control cells, biological rep2


title: A1-Greco-Bou

description:
Light: 16 hour days
Medium: compost (3 parts compost, 1 part sand, 1 part perlite)
Temperature: 23C
Location: Glasshouse

source_name: BOUNTIFUL

value: Mixture of 4 youngest rossette leaves

value: Activation Tag I/dSpm insert in BOU


title: A2-Greco-WT

value: Mixture of 4 youngest rosette leaves


title: MCF10A_Transwell-Base_1

city: Cincinnati

first: Nelson

middle: D

last: Horseman

state: OH

address: 231 Albert Sabin Way; MSB 3160

department: Molec & Cell Physiology

institute: University of Cincinnati

description:
MCF10A_Transwell-Base_1
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

hyb_protocol: The hybridization, staining, and washing are carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocols, and the arrays were hybridized for 16 hr at 45oC.   FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS and software and Affymetrix preset settings.

data_processing: Analysis was performed using R statistical software and the limma Bioconductor package 39.  All steps of data preprocessing, including background correction, normalization, and expression set summaries, were performed using RMA (Robust Multi-chip Average).  Estimated fold changes at each time point were calculated using ANOVA, and resulting t-statistics from each comparison were modified using an intensity-based empirical Bayes method (IBMT) 40 to obtain accurate significance levels.  P-values were adjusted using the False Discovery Rate (FDR) method.

source_name: Base

label_protocol: Quality of total RNA was first analyzed by Agilent Bioanalyzer 2100, and RNA samples with RIN (RNA Integrity Number) greater than 7.0 are acceptable for microarray analysis.  Total RNA samples were amplified one round, and the amplified RNA (aRNA) biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.

growth_protocol: Normal growth media for MCF10As is DMEM:F12 (Cellgro) w/ 2mM glutamine, containing 5% horse serum, insulin (10 µg ml-1) (Gibco), hydrocortisone (0.5 µg ml-1) (Sigma), EGF (20 ng ml-1) (Upstate) and 1 I.U. ml-1 penicillin, 0.1 µg ml-1 streptomysin, 0.25 µg ml-1 amphotericin B (Cellgro).

extract_protocol: Total RNA from cells grown in monolayer and Transwell® cultures were extracted using Tri reagent (MRC, Cincinnati, OH) and cleaned using DNaseI (Promega, Madison, WI) followed by standard phenol/chloroform precipitation and extraction method.

tag: MCF10A cells were plated onto polyester permeable supports from Corning (Transwells) at a density of 10^5 cells/cm^2.  Base represents those with a low trans-epithelial electrical resistance (200-300 Ohms x cm^2)


title: MCF10A_Transwell-Plateau_3

description:
MCF10A_Transwell-Plateau_3
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

source_name: Plateau

tag: MCF10A cells were plated onto polyester permeable supports from Corning (Transwells) at a density of 10^5 cells/cm^2.  Plateau represents those with a plateau trans-epithelial electrical resistance (3000-3200 Ohms x cm^2)


title: MCF10A_Transwell-Plateau_4

description:
MCF10A_Transwell-Plateau_4
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Transwell-Plateau_2

description:
MCF10A_Transwell-Plateau_2
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Transwell-Base_2

description:
MCF10A_Transwell-Base_2
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Monolayer_2

description:
MCF10A_Monolayer_2
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

source_name: monolayer

tag: MCF10A cells grown to confluency on sterile plastic from Corning Inc


title: MCF10A_Transwell-Midpoint_3

description:
MCF10A_Transwell-Midpoint_3
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

source_name: Midpoint

tag: MCF10A cells were plated onto polyester permeable supports from Corning (Transwells) at a density of 10^5 cells/cm^2.  Midpoint represents those with a mid trans-epithelial electrical resistance (1400-1600 Ohms x cm^2)


title: MCF10A_Transwell-Midpoint_1

description:
MCF10A_Transwell-Midpoint_1
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Transwell-Base_3

description:
MCF10A_Transwell-Base_3
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Transwell-Plateau_1

description:
MCF10A_Transwell-Plateau_1
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: MCF10A_Transwell-Midpoint_2

description:
MCF10A_Transwell-Midpoint_2
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).