title: PP149_unifected_Skin biopsy

description: Gene expression data from biopsy of PBS treated skin of subject with pustule-former phenotype. (control)

treatment_protocol: Control treated with sterile PBS only.

tag: PBS treated skin (control) from pustule former, id 149


title: RR200_uninfected_DC

status: Public on Sep 13 2007

type: RNA

city: Indianapolis

first: Stanley

middle: M.

last: Spinola

state: IN

address: 545 Barnhill Dr.

department: Infectious Diseases

country: USA

institute: Indiana University School of Medicine

description: Gene expression from dendritic cells from human subject with resolver phenotype uninfected.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

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 set to 1000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Monocyte derived Dendritic Cells from healthy human subjects

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.

growth_protocol: Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time.  CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN).  After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.

extract_protocol: RNeasy® Mini Kit, according to the manufacturer's instructions.

treatment_protocol: Untreated Dendritic cells (Control)

tag: Dendritic Cells uninfected (control) from resolver, id 200


title: RR200_infected_DC

description: Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi.

growth_protocol: Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time.  CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN).  After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry.  DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.

treatment_protocol: Dendritic Cells incubated with H.ducreyi

tag: Dendritic Cells infected with H. ducreyi from resolver, id 200


title: PP243_unifected_Skin biopsy

source_name: Skin biopsy from healthy human subjects

extract_protocol: Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy.  Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions.  Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads.  The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.

tag: PBS treated skin (control) from pustule former, id 243


title: PP243_infected_DC

description: Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi.

tag: Dendritic Cells infected with H. ducreyi from pustule former, id 243


title: RR216_unifected_Skin_biopsy

description: Gene expression data from biopsy of PBS treated skin of subject with resolver phenotype. (control)

source_name: Skin biopsy from healthy human subject

tag: PBS treated skin (control) from resolver, id 216


title: RR200_unifected_Skin_biopsy

tag: PBS treated skin (control) from resolver, id 200


title: HOXB4 const_w/o TMX, 1hour, biological rep1

status: Public on Sep 11 2007

city: Hannover

first: Bernhard

last: Schiedlmeier

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description: HOXB4const-LSK+ cells_ 1 hour after TMX withdrawal

hyb_protocol: All hybridizations were carried out using 15 µg labeled cRNA in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (EukGE-WS2v4) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 (Affymetrix, Inc., Santa Clara, CA) for gene expression profiling as set forth by the manufacturer’s recommendations.

data_processing: Scanned images (DAT files) were converted into CEL files using GCOS software (Affymetrix, Santa Clara, CA). log2 expression estimates were calculated by RMAExpress using the RMA algorithm.

organism: Mus musculus

label_protocol: cRNA was synthesized according to the CodeLink Expression Bioarray System (Amersham, Biosciences, Pittsburgh, PA, USA) small-sample target-labeling protocol. Briefly, 0.7 to 1 µg of total RNA per sample was used to prepare a biotin-labeled cRNA target by linear amplification. cDNA synthesis was done using an oligo-dT primer that contains a T7 polymerase recognition sequence. This was followed by in vitro transcription to generate cRNA, followed by recovery of the biotin-labeled product in accordance with protocols recommended by CodeLink system manual target preparation.

growth_protocol: HOXB4ER- and HOXB4const- transduced Lin-Sca1+ cells were expanded for 14 days in cytokine-supplemented (mSCF, huFL, huIL-11, mIL-3), serum-free medium  in the presence of 10 nM 4-hydroxytamoxifen (TMX).

extract_protocol: Trizol extraction of total RNA  and further RNeasy Kit purification was performed according to the manufacturer's instructions. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies).

treatment_protocol: After 14 days of expansion, HOXB4ER+ and HOXB4const LSK  (GFP+ , lineage negative, Sca1+, ckit+) cells, respectively, were FACS sorted and further cultivated for 12 hours in cytokine supplemented serum-free medium in the presence of 10 nM TMX. Finally, both cell populations,  HOXB4-ER+LSK  and HOXB4const LSK,  were split into two fractions and further incubated either with or without TMX. After 1 and 4 hours of TMX-withdrawal, the cells were lysed in Trizol (Invitrogen) and RNA purified using the RNeasy Kit (Qiagen).

tag: C57BL/6, female, age 12 weeks, bone marrow cells,retrovirally transduced and cultivated in vitro


title: RR216_infected_skin_biopsy

description: Gene expression data from biopsy of infected skin of subject with resolver phenotype.

treatment_protocol: skin innoculated with H.ducreyi

tag: H. ducreyi infected skin from resolver, id 216


title: RR203_infected_skin_biopsy

tag: H. ducreyi infected skin from resolver, id 203


title: HOXB4ERT_w/o TMX, 4hours, biological rep2

description: HOXB4ERT-LSK+ cells_ 4 hours after TMX withdrawal


title: HOXB4ERT_+10nM TMX, 1hour, biological rep2

description: HOXB4ERT-LSK+ cells_ 1 hour plus TMX (continous exposure)


title: HOXB4ERT_w/o TMX, 1hour, biological rep1

description: HOXB4ERT-LSK+ cells_ 1 hour after TMX withdrawal


title: HOXB4 const_+10nM TMX, 1hour, biological rep2

description: HOXB4const-LSK+ cells_ 1 hour plus TMX (continous exposure)


title: HOXB4ERT_w/o TMX, 1hour, biological rep2

source_name: HOXB4ERT-LSK+ cells_ 1 hour after TMX withdrawal


title: HOXB4ERT_+10nM TMX, 1hour, biological rep1

source_name: HOXB4ERT-LSK+ cells_ 1 hour plus TMX (continous exposure)


title: RR200_infected_skin_biopsy

tag: H. ducreyi infected skin from resolver, id 200


title: TS-10

city: Atlanta

first: Todd

middle: A

last: Schlenke

state: GA

address: 1510 Clifton Road NE

department: Department of Biology

institute: Emory University

description: Labeling, hybridization, and scanning protcols were carried out at the Weill Medical College Microarray Core Facility of Cornell University.

hyb_protocol: Each fragmented cRNA sample was hybridized to the Affymetrix Drosophila Genome microarray for 16 hours at 60 rpm at 45°C.  The microarray was washed and stained on the Affymetrix Fluidics Station 450 according to manufacture’s protocol.  After washing out the nonhybridized material the array was incubated with phycoerythrin-streptavidin (SAPE, Molecular Probes, Eugene, OR).  The signal intensity was amplified by second staining with biotin-labeled antistreptavidin antibody followed by SAPE staining.

scan_protocol: Fluorescent images were read using Affymetrix GeneChip Scanner 3000.  The microarrays were processed on the fluidics station under the control of the GeneChip Operating software (GCOS) and read according to the standard Affymetrix protocol.  The signal, which represents the intensity of each gene, was extracted from the image.  The target intensity value from each chip was scaled to 500.  All RNA samples passed the quality control and ratio of 3’ to 5’ less than three.

data_processing: The GeneTraffic (Stratagene) software package was used for microarray data processing.  Probe intensities were normalized using Robust Multi-Chip Analysis, using the three control replicates from each time point as the designated baseline.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 21 to 24 hours post-infection, replicate 1.

label_protocol: RNA processing and hybridization protocols are available at www.affymetrix.com (Santa Clara, CA) and in the Genechip Expression Analysis Technical Manual.  Two micrograms of total RNA were converted into double-stranded cDNA by using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit with the T7-(dT)24-primer [sequence 5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3’].  The cDNA was purified as per protocol by using the GeneChip Sample Cleanup Modules.  Purified cDNA was then used for in vitro transcription using the GeneChip Expression 3’-Amplification Reagents for IVT Labeling.  Biotin-labeled cRNA was purified by GeneChip Sample Cleanup Modules and then randomly chemically fragmented to approximately 35 - 200 bp pieces.

extract_protocol: RNA was extracted using the standard Trizol method (Gibco), and was purified using RNeasy spin columns (Qiagen).

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina heterotoma (strain Lh14).  Fly larvae were collected 21 to 24 hours post-infection for tissue homogenization and RNA extraction.


title: TS-12

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 21 to 24 hours post-infection, replicate 3.


title: TS-5

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 21 to 24 hours post-infection, replicate 2.

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina boulardi (strain Lb17).  Fly larvae were collected 21 to 24 hours post-infection for tissue homogenization and RNA extraction.


title: TS-109

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 9 to 12 hours post-infection timepoint, replicate 3.

tag: 40 second-instar (72 hours old at 22 degrees C) uninfected Drosophila melanogaster larvae (strain Oregon R) were collected for tissue homogenization and RNA extraction in the same manner as the infected larvae collected 9 to 12 hours post-infection.


title: TS-11

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 21 to 24 hours post-infection, replicate 2.


title: TS-16

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 21 to 24 hours post-infection timepoint, replicate 1.

tag: 40 second-instar (72 hours old at 22 degrees C) uninfected Drosophila melanogaster larvae (strain Oregon R) were collected for tissue homogenization and RNA extraction in the same manner as the infected larvae collected 21 to 24 hours post-infection.


title: TS-18

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 21 to 24 hours post-infection timepoint, replicate 3.


title: RR203_unifected_Skin_biopsy

tag: PBS treated skin (control) from resolver, id 203


title: HOXB4 const_w/o TMX, 1hour, biological rep2

source_name: HOXB4const-LSK+ cells_ 1 hour after TMX withdrawal


title: HOXB4 const_+10nM TMX, 1hour, biological rep1

source_name: HOXB4const-LSK+ cells_ 1 hour plus TMX (continous exposure)


title: HOXB4ERT_w/o TMX, 4 hours, biological rep1

source_name: HOXB4ERT-LSK+ cells_ 4 hours after TMX withdrawal


title: TS-4

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 21 to 24 hours post-infection, replicate 1.


title: PP164_unifected_Skin biopsy

tag: PBS treated skin (control) from pustule former, id 164


title: TS-6

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 21 to 24 hours post-infection, replicate 3.


title: TS-17

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 21 to 24 hours post-infection timepoint, replicate 2.


title: MNR 2-3 KO 4

city: Baltimore

first: Narsa

middle: Reddy

last: Machireddy

state: MD

address: 615, N Wolfe St

department: Environmental Health Sciences

institute: Bloomberg School of Public Health

description: Mouse Lung Type II cell gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: Type II cells from Nrf2-/- mouse.

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: Type II cells were isolated by instilling and incubating lung with Dispase II for 45 munutes.lungs were teased and cells were incubated on IgG coated plates for an hour to remove lung macrophases. The non adherent cells were further incubated on petridishes for two hours for fibroblast adherence.  The non adherent cells were cultured on fibronectin/collagen coated plates in the presense of keratinocyte growth factor for five days.

extract_protocol: Trizol extraction of total RNA was performed followed by RNA clean up using Qiagen Rneasy kit according to the manufacturers' instructions.

treatment_protocol: no treatment

tag: ICR10 mouse strain (Nrf2-/-)  gender- female, age- 2 months, n = 1, # of tissue = 1, tissue

value: Lung, Cell:Type II.


title: MNR 3-3 KO Treated 4

description: Mouse Lung Type II cell gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

source_name: Type II cells from Nrf2-/- mouse supplemented with GSH.

value: Lung, Cell:Type II, Supplementation:GSH.


title: MNR 1-3 WT 5

description: Mouse Lung Type II cell gene expression

source_name: Type II cells from Nrf2+/+ mouse.

tag: ICR10 mouse strain (WT,)  gender- female, age- 2 months, n = 1, # of tissue = 1, tissue


title: TS-103

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 9 to 12 hours post-infection, replicate 3.

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina boulardi (strain Lb17).  Fly larvae were collected 9 to 12 hours post-infection for tissue homogenization and RNA extraction.


title: TS-108

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 9 to 12 hours post-infection timepoint, replicate 2.


title: TS-102

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 9 to 12 hours post-infection, replicate 2.


title: TS-14

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 2 to 5 hours post-infection timepoint, replicate 2.

tag: 40 second-instar (72 hours old at 22 degrees C) uninfected Drosophila melanogaster larvae (strain Oregon R) were collected for tissue homogenization and RNA extraction in the same manner as the infected larvae collected 2 to 5 hours post-infection.


title: TS-105

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 9 to 12 hours post-infection, replicate 2.

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina heterotoma (strain Lh14).  Fly larvae were collected 9 to 12 hours post-infection for tissue homogenization and RNA extraction.


title: TS-106

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 9 to 12 hours post-infection, replicate 3.


title: TS-104

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 9 to 12 hours post-infection, replicate 1.


title: TS-107

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 9 to 12 hours post-infection timepoint, replicate 1.


title: TS-101

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 9 to 12 hours post-infection, replicate 1.


title: TS-1

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 2 to 5 hours post-infection, replicate 1.

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina boulardi (strain Lb17).  Fly larvae were collected 2 to 5 hours post-infection for tissue homogenization and RNA extraction.


title: TS-13

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 2 to 5 hours post-infection timepoint, replicate 1.


title: TS-9

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 2 to 5 hours post-infection, replicate 3.

tag: 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina heterotoma (strain Lh14).  Fly larvae were collected 2 to 5 hours post-infection for tissue homogenization and RNA extraction.


title: TS-3

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 2 to 5 hours post-infection, replicate 3.


title: TS-15

source_name: Control Drosophila melanogaster larvae not infected by wasps, comparable to 2 to 5 hours post-infection timepoint, replicate 3.


title: TS-2

source_name: Drosophila melanogaster larvae infected by Leptopilina boulardi, 2 to 5 hours post-infection, replicate 2.


title: TS-8

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 2 to 5 hours post-infection, replicate 2.


title: TS-7

source_name: Drosophila melanogaster larvae infected by Leptopilina heterotoma, 2 to 5 hours post-infection, replicate 1.


title: Exosomal RNA, biological rep3

status: Public on Sep 05 2007

city: Gothenburg

first: Hadi

last: Valadi

address: Guldhedsgatan 10A

department: Dept. of Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

description: Gene expression data from exosomes derived from mast cell line MC/9

hyb_protocol: Hybridisation cocktail was prepared with the biotinylated and fragmented cRNA, control oligonucleotide B2, herring sperm DNA, acetylated BSA, 4-morpholinepropanesulfonic acid (MES), Tween 20, and bacterial cRNA controls respectively. The hybridisation cocktail was heated to 99°C for 5 min and to 45°C for 5 min, and was briefly centrifuged before hybridization. The prewet GeneChipTM probe array cartridge was filled with the hybridisation cocktail and incubated on rotation, 60 rpm at 45°C for 16–18 h. The cartridge was then subjected to an automated washing procedure, using the GeneChipTM Fluidics Station 400 and with a non stringent wash buffer, containing saline, sodium, phosphate, EDTA (SSPE), Tween 20 and antifoam according to the Affymetrix manual. A final wash with the stringent buffer, containing MES-sodium salt and Tween 20 was performed. The probe array was then stained with a solution of acetylated BSA, streptavidin and R-phycoerythrin in stain buffer, containing sodium-MES and Tween 20 and antifoam, followed by non stringent wash buffer. A second stain was performed with a solution of acetylated BSA, normal goat IgG and biotinylated goat antistreptavidin antibody in stain buffer. A third staining step with streptavidin R-phycoerythrin was performed as described above, before a final one with non-stringent wash buffer at 30°C.

scan_protocol: The probe arrays were scanned with the Gene Array Scanner (Affymetrix, Inc. www.affymetrix.com).

data_processing: The software GenChip Operating System 1.2 (GCOS; Affymtrix Inc.) were used for data processing.

source_name: Exosomes derived from murine mast cell line MC/9

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

growth_protocol: MC/9 cells were maintained in Dulbecco's modified Eagle's medium supplemented with 0, 05 mM 2-mercaptoethanol, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 10% FBS and 10% T-Cell Culture Supplement with conA (Rat T-stim) at 37 °C, 5% CO2 in a humidified incubator.

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

treatment_protocol: Exosomes were prepared from the supernatant of MC/9 cells. The cells were harvested, centrifuged at 500 g for 10 min to eliminate cells and at 23 000 g for 20 min, followed by filtration through 0.22 µm filter to remove cell debris. Exosomes were pelleted by ultra-centrifugation at 145 000 g for 70 min.

tag: Mast cell line MC/9 (ATCC)


title: Mast cells RNA, biological rep4

description: Gene expression data from mast cell line MC/9

source_name: Murine mast cell line MC/9


title: Exosomal RNA, biological rep4


title: Ler_rep1

status: Public on Sep 10 2007

city: Philadelphia

first: Doris

last: Wagner

state: PA

department: Biology

institute: University of Pennsylvania

description: 10 day old Ler seedlings grown at 22 degrees Celsius in 16 hrs cool white light (120 µmol/m2sec)

data_processing: MAS 5.0 algorithm implemented in Bioconductor using the Affy package

organism: Arabidopsis thaliana

source_name: 10 day old wild type Landsberg erecta seedlings

tag: Age

value: 10 day old seedlings

tag: Genotype

value: Landsberg erecta, wild type


title: Mast cells RNA, biological rep1


title: Exosomal RNA, biological rep2


title: Mast cells RNA, biological rep3


title: brm-101_rep2

description: 10 day old brm-101 seedlings grown at 22 degrees Celsius in 16 hrs cool white light (120 µmol/m2sec)

source_name: 10 day old brm-101 seedlings


title: Mast cells RNA, biological rep2


title: syd-2_rep1

description: 10 day old syd-2 seedlings grown at 22 degrees Celsius in 16 hrs cool white light (120 µmol/m2sec)

source_name: 10 day old syd-2 seedlings


title: brm-101_rep1

value: 10 days after germination


title: Ler_rep2


title: syd-2_rep2


title: Exosomal RNA, biological rep1


title: MCF7_EtOH_24h_rep3

status: Public on Sep 01 2007

city: Montreal

first: David

last: Laperriere

state: QC

address: 2950, chemin de Polytechnique

department: IRIC - Institut de recherche en immunologie et en cancerologie

country: Canada

institute: Université de Montréal

description: MCF7 treated with vehicule for 24h

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R/Bioconductor RMA

source_name: MCF7 breast cancer cells

label_protocol: standard Affymetrix protocol

growth_protocol: MCF-7 breast carcinoma cells were maintained in {alpha}-minimal Eagle’s medium ({alpha}-MEM) (Wisent, St-Bruno, QC, Canada) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, Oakville, On, Canada). Three days before experiments, cells were switched to phenol red-free Dulbecco’s modified Eagle’s medium (DMEM) (Wisent) containing 10% charcoal-treated FBS, 1% sodium pyruvate (Wisent), 1% penicillin/streptomycin (Wisent) and 1% L-glutamine (Wisent). Cells were seeded in 10 cm plates at a density such that near-confluency is obtained at the end of the treatment. The day before hormonal stimulation, the medium was changed to phenol red-free DMEM supplemented with 0,5% charcoal-treated FBS.

extract_protocol: After completion of hormonal treatments, medium was completely removed and cells were collected in 1 ml of TRI-Reagent (Sigma). Total RNA was extracted as recommended by the manufacturer and further purified with RNeasy MinElute Cleanup Kit (QIAgen, Mississauga, On, Canada).

treatment_protocol: Pre-treatments with cycloheximide (10 microg/ml, Sigma) or vehicle DMSO (0.1%) were initiated 1 h before hormonal treatment with 17{beta}-estradiol (E2, 25 nM, Sigma) or vehicle (0.1% ethanol) for 24h.

tag: MCF7 DMSO+EtOH


title: MCF7_E2_24h_rep2

description: MCF7 treated with E2 for 24h

tag: MCF7 DMSO+E2


title: MCF7_E2_24h_rep1

description: MCF7 treated with E2 for 24h


title: MCF7_EtOH_24h_rep2

description: MCF7 treated with vehicule for 24h


title: MCF7_E2_24h_rep4

description: MCF7 treated with E2 for 24h


title: MCF7_E2_24h_rep3

description: MCF7 treated with E2 for 24h


title: MCF7_EtOH_24h_rep4

description: MCF7 treated with vehicule for 24h


title: MCF7_CHX_E2_24h_rep4

description: MCF7 pre-treated for 1h with cycloheximide, treated with E2 for 24h

tag: MCF7 CHX+E2


title: MCF7_CHX_EtOH_24h_rep2

description: MCF7 pre-treated for 1h with cycloheximide, treated with vehicule for 24h

tag: MCF7 CHX+EtOH


title: MCF7_CHX_EtOH_24h_rep4


title: MCF7_CHX_EtOH_24h_rep3


title: MCF7_CHX_E2_24h_rep3


title: MCF7_CHX_E2_24h_rep1


title: MCF7_CHX_E2_24h_rep2


title: MCF7_EtOH_24h_rep1

description: MCF7 treated with vehicule for 24h


title: MCF7_CHX_EtOH_24h_rep1


title: expression at 0hr, bio rep3

city: Houston

first: Wei

last: Li

state: TX

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

description: Gene expression data from LNCaP cell line treated with steroid hormone DHT

hyb_protocol: A35fluidics protocol EukGE-WS2v4_450 using Affymetrix fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner (GCS) 3000

data_processing: creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036

source_name: The RNA samples from DHT 0hr treated LNCaP cells

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNAs that fall outside of an acceptable range will not be carried forward in the analysis. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.

extract_protocol: Total RNA was first isolated using an RNeasy kit (Qiagen Catalog number 74104) according to the manufacturer’s instructions.

tag: LNCaP prostate cancer epithelial cell line


title: expression at 0hr, bio rep2


title: expression at 16hr, bio rep3

source_name: The RNA samples from DHT 16hr treated LNCaP cells


title: expression at 4hr, bio rep2

source_name: The RNA samples from DHT 4hr treated LNCaP cells


title: expression at 4hr, bio rep3


title: expression at 16hr, bio rep2


title: expression at 16hr, bio rep1


title: expression at 0hr, bio rep1


title: expression at 4hr, bio rep1


title: B16-D5-Arm_Day5_95080

city: Blacksburg

first: kommidi

last: Chaitanya

state: VA

address: Virginia Tech

institute: VBI

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was carried out by using the GeneArray scanner (Hewlett-Packard).

data_processing: The data were analyzed using the R Bioconductor package using the gcRma algorithm

organism: Macaca mulatta

source_name: Blood from Rhesus Macaques infected intravenously with a LCMV-Armstrong strain .Sampling is done on the 5th day.

label_protocol: Staining with R-phycoerythrin-streptavidin (Molecular Probes) was followed by antibody amplification with a biotinylated streptavidin antibody (Vector Laboratories).

growth_protocol: adults infected with LCMV-Armstrong.the LCMV-Arm-infected monkeys did not experience viremia, i.e. viral nucleic acid were detected in tissues but virus loads were not high enough to be detected in the circulation

extract_protocol: PBMC were isolated from blood using density centrifugation. RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen Rneasy kit to clean the RNA

treatment_protocol: Rhesus macaques infected intravenously with a dose of LCMV-Armstrong

tag: healthy adult Rhesus Macaque 5 to 9 years of age infected with LCMV-Armstrong


title: B16-D5-Arm_Day3_97080

source_name: Blood from Rhesus Macaques infected intravenously with a LCMV-Armstrong strain .Sampling is done on the 3rd day.

extract_protocol: PBMC were isolated from blood using density centrifugation. RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen Rneasy kit to clean the RNArocessing


title: B14-D7b-Arm_Day7_ 95078

description: B14-D7b-Arm_Day7_ 95078

source_name: Blood from Rhesus Macaques infected intravenously with a LCMV-Armstrong strain .Sampling is done on the 7th day.


title: B13-D3a-Arm_Day3_95078


title: B8-D6a-WE_Day6

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done onon the 6th day (post-viremic)

growth_protocol: Infected adults in there post verimic stage

treatment_protocol: Rhesus macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)

tag: healthy adult Rhesus Macaque 5 to 9 years of age infected with LCMV-WE


title: B1-D1a-WE-Day1

description: B1-D1a-WE _Day1

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE) . .Sampling is done on the 1st day (pre-viremic)

growth_protocol: Infected adults in there pre verimic stage


title: HEK293 Transcriptome maps (duplicate 2)

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
Data accompanying the paper: Domain-Wide Regulation of Gene Expression in the Human Genome, Gierman HJ et al. (submitted).
HEK293 cells were grown under standard conditions and harvested at 70% confluency. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate transcriptome maps.

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to  manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.

source_name: HEK293 cells

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: HEK293 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

tag: Fetus derived cell line from female human embryonic kidney.


title: B6-D4a-WE_Day4

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done on the 4th day (post-viremic)


title: HEK293 Transcriptome maps (duplicate 1)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.


title: B14-D7b-Arm_Day3_95078


title: beforeinf_day7_mk2

source_name: Blood from a pre-infected Rhesus Macaque taken before infection

growth_protocol: Uninfected adults

treatment_protocol: Untreated healthy adults

tag: healthy adult Rhesus Macaque 5 to 9 years of age


title: B6-D4a-Pre-inf._Day0

extract_protocol: PBMC were isolated from blood using density centrifugation. RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen Rneasy kit to clean the RNA.


title: B2-D1b-WE_Day1

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done on the 1st day (pre-viremic)


title: B9-D6b-WE_Day_6

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE) .Sampling is done on the 6th day (post-viremic)


title: B5-D3a-Pre-inf._Day_0


title: beforeinf_day5


title: B3-D2a-Pre-inf._Day0


title: B9-D6b-Pre-inf._Day0


title: B10-D7a-WE-Day_7

description: B10-D7a-WE _Day_7

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done on the 7th day (post-viremic)


title: B5-D3a-WE_Day3

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done on the 3rd day (pre-viremic)


title: B2-D1b-Pre-inf._Day0


title: B13-D3a-Pre-inf.-Day0

description: B13-D3a-Pre-inf. _Day0


title: B3-D2a-WE_Day2

source_name: Blood from Rhesus Macaques infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV-WE)  .Sampling is done on the 2nd day (pre-viremic)


title: B1-D1a-Pre-inf.-Day0

description: B1-D1a-Pre-inf. _Day0


title: B10-D7a-Pre-inf._Day0

source_name: Blood from pre-infected Rhesus Macaque taken before infection


title: B8-D6a-Pre-inf._Day0


title: III-C

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

description: Zone III of growth plate

hyb_protocol: see LRGC specifications

scan_protocol: see LRGC specifications

data_processing:
Microarray data was pre-processed using the GC (guanine and cytosine) Robust Multi-chip Averaging (RMA) algorithm in Genespring GX*.
Expression values were further filtered by retaining only those probe sets with expression values of at least 50 in at least 25% of all conditions, thus generating a list of 22 497 probe sets.
Subsequent zone comparisons from the microdissected tibiae data set (MD) were filtered using a 1.5-fold change threshold that produced lists of 6185, 8134 and 7220 probe sets for the zone I vs. II, II vs. III and zone I vs. III, respectively.
The same data set was also normalized in parallel using RMA using RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley (Bolstad et al., 2003).
Background adjustment and quantile normalization parameters were selected for data processing.

label: ONE COLOUR: SAPE

source_name: Manually microdissected embryonic tibiae; zone III of growth plate

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

growth_protocol: No growth

extract_protocol: Qiazol lipid tissue extraction kit

treatment_protocol: No treatment

tag: Tibiae derived from four litters of CD1 mice (Charles River) staged at embryonic day E15.5 were isolated and manually separated into three segments corresponding to early, middle and

tag: late chondrocyte differentiation (Figure 3.1 A, left panel); each litter represented one independent experiment.  Starting at either extremity, the region corresponding to approximately the first

tag: third of the bone was segmented and designated zone I, which contains both proliferating and resting cells.  Zone II includes segments corresponding to the central region, starting from each

tag: end of the bone and contains mostly prehypertrophic and early hypertrophic chondrocytes.  The final zone, zone III, constitutes both the most mature hypertrophic chondrocytes and

tag: the mineralized portion of the tibiae.


title: I-C

description: Zone I of growth plate

source_name: Manually microdissected embryonic tibiae; zone I of growth plate


title: I-B

description: Zone I of growth plate


title: III-D

description: Zone III of growth plate


title: I-D

description: Zone I of growth plate


title: III-B

description: Zone III of growth plate


title: SW1463

status: Public on Aug 31 2007

city: South San Francisco

first: Guy

last: Cavet

state: CA

address: 1 DNA Way MS93

institute: Genentech, Inc.

description: Baseline gene expression for cancer cell line grown in vitro

hyb_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings (see Clin Cancer Res 2005;11(24) December 15, 2005).  The mean value of replicates was used.

source_name: SW1463 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES

growth_protocol: B128RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES

tag: No treatment.  See ATCC/DSMZ for cell line details.


title: SW620

scan_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005

source_name: SW620 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: II-B

description: Zone II of growth plate

source_name: Manually microdissected embryonic tibiae; zone II of growth plate


title: II-C

description: Zone II of growth plate


title: SW948

source_name: SW948 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES

label_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005


title: II-D

description: Zone II of growth plate


title: SW1990

source_name: SW1990 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES

extract_protocol: Affymetrix standard protocols.  See Clin Cancer Res 2005;11(24) December 15, 2005


title: SW480

source_name: SW480 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: II-A

description: Zone II of growth plate


title: T84

source_name: T84 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SU86.86

source_name: SU86.86 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SW403

source_name: SW403 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SW837

source_name: SW837 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: I-A

description: Zone I of the growth plate

hyb_protocol: LRGC specifications

scan_protocol: LRGC specifications

source_name: Manually microdissected embryonic tibiae; zone I of the growth plate

growth_protocol: NO GROWTH PROTOCOL

treatment_protocol: NO TREATMENT


title: III-A

description: Zone III of growth plate


title: SK-MES-1

source_name: SK-MES-1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SKMEL28

source_name: SKMEL28 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SK23

source_name: SK23 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SW1573

source_name: SW1573 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SW1116

source_name: SW1116 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SK_CO

source_name: SK_CO_1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: SW1417

source_name: SW1417 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: RPMI7951

source_name: RPMI7951 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: RKO_AS45

source_name: RKO_AS45 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: PL45

source_name: PL45 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc02.03

source_name: Panc02.03 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc1

source_name: Panc1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc05.04

source_name: Panc05.04 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: MeWo

source_name: MeWo cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc04.03

source_name: Panc04.03 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: MIAPaCa2

source_name: MIAPaCa2 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: PATU8902

source_name: PATU8902 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: PATU8988T

source_name: PATU8988T cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: PSN1

source_name: PSN1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: MALME3M

source_name: MALME3M cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc0327

source_name: Panc0327 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc1005

source_name: Panc1005 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: LS180

source_name: LS180 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: KM12

source_name: KM12 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: RKO

source_name: RKO cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Hs695T

source_name: Hs695T cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HS766T

source_name: HS766T cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Panc08.13

source_name: Panc08.13 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HuPT3

source_name: HuPT3 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Hs294T

source_name: Hs294T cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: LS1034

source_name: LS1034 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: MDST8

source_name: MDST8 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HPAFII

source_name: HPAFII cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: LoVo

source_name: LoVo cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: MDA435

description: Baseline gene expression for cancer cell line grown in vitro; not used in sensitivity analysis

source_name: MDA435 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: LXFL529

source_name: LXFL_529 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HPAC

source_name: HPAC cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: LOXIMVI

source_name: LOXIMVI cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HT55

source_name: HT55 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HLF-a

source_name: HLF-a cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Hop62

source_name: Hop_62 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HOP18

source_name: HOP_18 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Hop92

source_name: Hop_92 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HCT8

source_name: HCT8 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H647

source_name: H647 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HCT116

source_name: HCT116 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H650

source_name: H650 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H2009

source_name: H2009 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H2126

source_name: H2126 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H522

source_name: H522 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H838

source_name: H838 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H226

source_name: H226 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HCT15

source_name: HCT15 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H661

source_name: H661 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H441

source_name: H441 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1838

source_name: H1838 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1975

source_name: H1975 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H292

source_name: H292 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H358

source_name: H358 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H596

source_name: H596 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H460

source_name: H460 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H2405

source_name: H2405 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H520

source_name: H520 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H2122

source_name: H2122 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1793

source_name: H1793 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H322T

source_name: H322T cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H23

source_name: H23 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: HCT29

source_name: HCT29 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H2030

source_name: H2030 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1703

source_name: H1703 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1781

source_name: H1781 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1650

source_name: H1650 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1568

source_name: H1568 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1299

source_name: H1299 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a- & g-tocopherol agT-Br-1

city: Boulder

first: Sang-Kyu

last: Park

state: CO

department: IBG

institute: University of Colorado at Boulder

description: We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples.

hyb_protocol: Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix MOE 430 2.0 arrays (Affymetrix, Santa Clara, CA). The Affymetrix MOE 430 2.0 array has 45,037 probe sets. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.

scan_protocol: After staining, the gene chips were read at a resolution of 3 μm using a Hewlett Packard GeneArray Scanner (Affymetrix, Santa Clara, CA). The averaged images collected from two scanned images were used for the analysis.

data_processing: The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize an overall variability in hybridization intensities by a global scaling method.

molecule: polyA RNA

source_name: Old neocortex

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Br: brain(neocortex)
1: sample number

growth_protocol: Male B6C3F1 mice were purchased from Harlan Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidified water ad libitum.

extract_protocol: Total RNA was extracted from frozen tissue using the TRIZOL reagent (Life Technologies, Grand Island, NY) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Then, double-stranded cDNA was synthesized from 1ug of mRNA using the SuperScript Choice System (Life Technologies, Grand Island, NY) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, La Jolla, CA), purified with phenol-chloroform-isoamyl alcohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen, Valencia, CA). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.

treatment_protocol: The α- and γ-tocopherol-supplemented group was fed with a diet containing 500mg/kg of α- and γ-tocopherol each since the middle age (15 months).

tag: strain

value: B6/C3H F1 hybrid

tag: gender

value: male

tag: age


title: H1155

source_name: H1155 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1666

source_name: H1666 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: H1435

source_name: H1435 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a- & g-tocopherol agT-Br-2

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Br: brain(neocortex)
2: sample number


title: Mouse old brain w/ a- & g-tocopherol agT-Br-4

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Br: brain(neocortex)
4: sample number


title: H1651

source_name: H1651 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: COLO320HSR

source_name: COLO320HSR cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: G361

source_name: G361 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a-tocopherol aT-Br-5

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Br: brain(neocortex)
5: sample number

treatment_protocol: The α-tocopherol-supplemented group received a diet supplemented with 1000mg/kg of α-tocopherol since the middle age (15 months).


title: Mouse old brain w/ a- & g-tocopherol agT-Br-5

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Br: brain(neocortex)
5: sample number


title: Mouse old brain w/ a-tocopherol aT-Br-1

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Br: brain(neocortex)
1: sample number


title: COLO829

source_name: COLO829 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Colo741

source_name: Colo741 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a-tocopherol aT-Br-2

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Br: brain(neocortex)
2: sample number


title: EKVX

source_name: EKVX cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: COLO320DM

source_name: COLO320DM cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a- & g-tocopherol agT-Br-3

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Br: brain(neocortex)
3: sample number


title: Mouse old brain w/ a-tocopherol aT-Br-4

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Br: brain(neocortex)
4: sample number


title: DLD1

source_name: DLD-1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: CX1

source_name: CX1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Mouse old brain w/ a-tocopherol aT-Br-3

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Br: brain(neocortex)
3: sample number


title: COLO206

source_name: COLO206 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: COLO678

source_name: COLO678 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: COLO205

source_name: COLO205 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: C32

source_name: C32 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: CL40

source_name: CL40 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: CFPAC1

source_name: CFPAC1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: COLO201

source_name: COLO201 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Capan1

source_name: Capan1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Calu-1

source_name: Calu-1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: CL34

source_name: CL34 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: CL11

source_name: CL11 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Capan2

source_name: Capan2 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: C170

source_name: C170 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: D2 2months-3

first: vikas

last: misra

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

description: DBA Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: D2 2m-3 Lung

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

tag: DBA/2J mouse strain (Jackson Lab)  gender- male, age- 2 months, n = 1, # of tissue = 1 tissue

value: Lung


title: CACO2

source_name: CACO2 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: D2 2months-2

description: DBA Lung gene expression

source_name: D2 2m-2 Lung


title: A549

source_name: A549 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: BxPC3

source_name: BxPC3 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: ASPC1

source_name: ASPC1 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: D2 18months-3

description: DBA Lung gene expression

source_name: D2 18m-3 Lung

tag: DBA/2J mouse strain (NIA)  gender- male, age- 18 months, n = 1, # of tissue = 1 tissue


title: D2 18months-2

description: DBA Lung gene expression

source_name: D2 18m-2 Lung


title: D2 18months-1

description: DBA Lung gene expression

source_name: D2 18m-1 Lung


title: B6 18months-2

description: DBA/2J carotid body gene expression

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J x 3 sets DBA/2J comparison (1.5 fold cutoff, Mann-Whitney test < 0.05, 6 out of 9 comparisons)

source_name: B6 18m-2 Lung

tag: C57BL/6J mouse strain (NIA)  gender- male, age- 18 months, n = 1, # of tissue = 1 tissue


title: D2 2months-1

description: DBA Lung gene expression

source_name: D2 2m-1 Lung


title: A2058

source_name: A2058 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: A375

source_name: A375 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: 928MEL

source_name: 928MEL cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: A427

source_name: A427 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: 527MEL

source_name: 527MEL cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: B6 18months-1

description: B6 Lung gene expression

source_name: B6 18m-1 Lung


title: B6 26months-3

description: B6 Lung gene expression

source_name: B6 26m-3 Lung

tag: C57BL/6J mouse strain (NIA)  gender- male, age- 26 months, n = 1, # of tissue = 1 tissue


title: 888

source_name: 888 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: B6 2months-3

description: B6 Lung gene expression

source_name: B6 2m-3 Lung

tag: C57BL/6J mouse strain (Jackson Lab)  gender- male, age- 2 months, n = 1, # of tissue = 1 tissue


title: B6 2months-2

description: B6 Lung gene expression

source_name: B6 2m-2 Lung


title: B6 26months-2

description: B6 Lung gene expression

source_name: B6 26m-2 Lung


title: 624

source_name: 624 cell line, RPMI1640, 10%FBS, 2mM L-glutamine, 10mM HEPES


title: Donor 2 - LTD4 stimulated

status: Public on Aug 30 2007

city: Bethesda

first: Grzegorz

last: Woszczek

address: 9000 Rockville Pike

department: Critical Care Medicine Department

institute: NIH

description: Elutriated monocytes from donor 2 treated with LTD4 for 30 min.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized (in the presence of DMSO) for 16 hr at 45C on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetric Scanner 3000 6G model

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: Human elutriated monocytes

label_protocol: Affymetix GeneChip Expression 3' amplification reagents for IVT labeling (P/N 900449) was used to prepare Biotinylated cRNA

growth_protocol: Monocytes cultured in RPMI1640, 10% heat inactivated fetal bovine serum, 2 mM L-glutamine overnight before stimulation

extract_protocol: Qiagen RNeasy mini kit with Dnase treatment (P/N 74104)

treatment_protocol: Monocytes were stimulated with LTD4 (100nM) or with vehicle (EtOH) control for 30 min. and total RNA was extracted.

tag: Monocytes stimulated with LTD4 (100nM) for 30 min.


title: Donor 3 - control

description: Elutriated monocytes from donor 3 treated with vehicle control for 30 min.

tag: Monocytes exposed to vehicle control (EtOH)


title: Donor 4 - control

description: Elutriated monocytes from donor 4 treated with vehicle control for 30 min.


title: Donor 1 - LTD4 stimulated

description: Elutriated monocytes from donor 1 treated with LTD4 for 30 min.


title: Donor 4 - LTD4 stimulated

description: Elutriated monocytes from donor 4 treated with LTD4 for 30 min.


title: B6 2months-1

description: B6 Lung gene expression

source_name: B6 2m-1 Lung


title: Donor 3 - LTD4 stimulated

description: Elutriated monocytes from donor 3 treated with LTD4 for 30 min.


title: Donor 2 - control

description: Elutriated monocytes from donor 2 treated with vehicle control for 30 min.


title: B6 18months-3

description: DBA/2J carotid body gene expression

source_name: B6 18m-3 Lung


title: IU/Hahn_Drosophila_H8_128B

city: Bloomington

first: Matthew

middle: W.

last: Hahn

institute: Indiana University

description: Sample 2 from this line

hyb_protocol: Hybridizations to the Affymetrix Drosophila 2.0 GeneChip microarray took place in the Microarray Core Facility at UC Davis.

data_processing: Standard Affymetrix data processing

source_name: D. melanogaster embryo 8 hours

label_protocol: An IVT Reaction mix was added to the samples to synthesis Biotin-Labeled cRNA, and they were allowed to incubate at 370C overnight (~16 hours).  The newly Biotin-labeled cRNA was cleaned up and quantified using a spectrophotometer.  Sample purity was between 1.96 and 1.7 (A260/A280).  Fragmented samples were then stored at –200C until hybridizations.

extract_protocol:
Two RNA samples per line per time point (5 and 8 hours) were extracted using manufacturer's TRIzol reagent protocol (Invitrogen, Carlsbad, CA).  The concentrations of these samples were tested using a spectrophotometer and Na2HPO4 spec solution. The 36 samples (9 lines x 2 time points x 2 samples) of extracted RNA were labeled using the one-cycle cDNA Synthesis protocol from Affymetrix.  cDNA was made from the extracted RNA by first making a T7-Oligo(dT) Primer Master Mix and letting it incubate with the samples for 10 min at 700C and cooling for 2min at 40C.  A First-Strand Master Mix was added and the samples were incubated for 2 min at 420C.  After 200U/μL SuperScript II was added the samples were incubated for an additional hour at 420C and then cooled at 40C for 2min.  A Second-Strand Master Mix was added to the samples and then they were incubated at 160C for 2 hours and then cooled for 2min at 40C.  The samples were incubated for another
 5min at 160C after T4 DNA Polymerase was added, the samples were cooled at 40C for 2min and 0.5M EDTA was added.  The now double stranded cDNA was cleaned up using spin columns and 100% Ethanol.

tag: 30-50 embryos from line 128


title: IU/Hahn_Drosophila_H8_134B

description: Sample 2 from this line

scan_protocol: Hybridizations to the Affymetrix Drosophila 2.0 GeneChip microarray took place in the Microarray Core Facility at UC Davis.

tag: 30-50 embryos from line 134


title: Donor 1 - control

description: Elutriated monocytes from donor 1 treated with vehicle control for 30 min.


title: IU/Hahn_Drosophila_H8_128A

description: Sample 1 from this line


title: Placenta Adra2bKO 2

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

description: The whole procedure was carried out according to the Affymetrix standard protocol (Eukaryotic Sample and Array Processing).

hyb_protocol: 10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

scan_protocol: The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

source_name: placenta (E 10.5)

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

extract_protocol: Total RNA (5 µg) from Placenta (E10.5) was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: No additional treatment was applied.

tag: The placenta (E 10.5) of a congenic adra2B-/- mouse embryo (maternal genotype Adra2b+/-) was rapidly dissected and flash frozen.


title: IU/Hahn_Drosophila_H8_89B

description: Sample 2 from this line

tag: 30-50 embryos from line 89


title: IU/Hahn_Drosophila_H8_145B

description: Sample 2 from this line

tag: 30-50 embryos from line 145


title: Placenta Adra2bWT 1

tag: The placenta (E 10.5) of a congenic adra2B+/+ mouse embryo (maternal genotype Adra2b+/-) was rapidly dissected and flash frozen.


title: Placenta Adra2bKO 3


title: Placenta Adra2bWT 2

description: The whole procedure was carried out according to the Affymetrix standard protocol.

data_processing: The whole procedure was carried out according to the Affymetrix standard protocol (Eukaryotic Sample and Array Processing).


title: IU/Hahn_Drosophila_H8_145A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_H8_89A

description: Sample 1 from this line


title: Placenta Adra2bWT 3


title: Placenta Adra2bKO 1

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).).


title: IU/Hahn_Drosophila_H8_134A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_H8_83B

description: Sample 2 from this line

tag: 30-50 embryos from line 83


title: IU/Hahn_Drosophila_H8_58B

description: Sample 2 from this line

tag: 30-50 embryos from line 58


title: IU/Hahn_Drosophila_H8_83A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_H8_75B

description: Sample 2 from this line

tag: 30-50 embryos from line 75


title: IU/Hahn_Drosophila_H8_75A

description: Sample 1 from this line


title: Mouse embryonic stem cell derived cardiomyocytes 1

first: Nicolas

last: Christoforou

address: 733 North Broadway

department: ICE/ OBGYN

institute: Johns Hopkins Medical Institutions

description:
Cell culture and cell differentiation
Mouse embryonic stem cells (mESCs) were maintained undifferentiated by culturing on a feeder layer of mitomycin C pretreated primary mouse embryonic fibroblasts (PMEFs, Specialty Media, cat.# PMEF-H) at 37oC, 90% humidity and 5% CO2. The cell line used was the mESC D3 (passage #12-18). The basic culture medium was comprised of DMEM (Invitrogen, cat.# 11965-092), heat inactivated (56oC for 30 minutes) fetal bovine serum (Hyclone, cat#. S11550, 15%), Glutamax (Invitrogen, cat.# 35050-065, 1%), non-essential amino acids (Invitrogen, cat.# 11140-050, 1%), sodium pyruvate (Invitrogen, cat.# 11360-070, 1%), ?-mercaptoethanol (Sigma, cat.# M7522, 0.1mM), gentamicin (Cambrex, cat.# 17-518, 25?g/ml) and ESGRO leukemia inhibitory factor (Chemicon, cat.# ESG1106, 1000units/ml). Prior to initiation of differentiation The PMEF feeder layer was subtracted and the mESCs were maintained on a 0.01% gelatin pretreated plate for 24-48 hours. Differentiation through embryoid body (EB) formation was initiated by dissociating the mESCs using trypsin (Invitrogen, cat#. 25300-054, 0.05%) and resuspending them in basic culture medium (without the leukemia inhibitory factor) at a final concentration of 5x104 cells/ml. The hanging droplet (HD) technique was used for EB formation. HDs were plated on the lid of H2O containing tissue culture dishes at a volume of 20?L/droplet (approximately 1000 cells/ droplet). Two days post initiation of differentiation the EBs were transferred in suspension on poly-HEMA (Sigma, cat#. P3932) treated tissue culture dishes. The plates were pretreated with poly-HEMA in order to avoid any cell attachment on the plastic. Basic culture medium was supplemented with ascorbic acid(Takahashi et al., 2003) (Sigma, cat#. A4403, 0.1mg/ml) and it was exchanged with fresh medium every 2 days during differentiation.
Transfection of mouse embryonic stem cells
	The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells.
	In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above.
FACS Analysis
	For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted.
FACS sorting
	The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in mESC culture medium at a concentration of 5x105 cells/ml and cultured in suspension for 48 hours. The cells were then transferred on tissue culture plates for another 48 hours. For RNA isolation the cells were spun down and washed in PBS before the RNA isolation procedure.
	To assay their proliferation capacity, GFP+ CPCs were FACS sorted on day 5 of differentiation. Cells were reaggregated in suspension (5x105 cells/ ml) in the presence of mouse recombinant Igf1 (Chemicon, Cat.# GF121, 100ng/ml) for 14 days. Cell aggregates were fixed and stained for the colocalization of the antigens: Nkx2-5 and Ki67 or Pcna. The same ICC reagents were used as described above.
GeneChip microarray hybridization
	Total RNA for the microarray expression analysis was isolated from FACS sorted cells (GFP+ and GFP-) on days 5, 6, 7, and 8 of differentiation as described above. Two separate differentiation batches were prepared for the sake of data reproducibility. Total RNA was also isolated from terminally differentiated mESC derived genetically selected cardiomyocytes 3 weeks post initiation of differentiation. The GeneChip� two cycle target labeling kit (Affymetrix, cat.# 900494) was used to convert 100ng of total RNA to biotinylated labeled cRNA. This was then hybridized to the Affymetrix murine MOE430 2.0 genome GeneChip� array (Affymetrix, cat.# 900496). Fluorescence was detected using the Affymetrix GS3000 GeneArray scanner and image analysis for each chip was done through the GeneChip� operating system software from Affymetrix (GCOS1.3) using the standard default settings.
Microarray data analysis
To estimate the gene expression signals, data analysis was conducted on the chips� CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical technique RMA (Robust Multiarray Analysis) (Irizarry et al., 2003) with the bioconductor package Affy. The data normalization procedure utilized the quantile normalization method (Bolstad et al., 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.
The Spotfire DecisionSite software package was used for the identification of uniquely upregulated or downregulated (at least 1.5 times increase or decrease in the expression value) probe sets in the CPC population when compared to the rest of the cells in the differentiating EBs. Probe sets that were considered unique for the CPC population were found to be commonly upregulated or downregulated during all four days of analysis. Probe sets that exhibited an increasing or decreasing pattern of expression with at least 1.5 times increase or decrease in the expression values of day 5 CPCs and day 8 CPCs were also reported. Probe sets of the CPC population that exhibited upregulation or downregulation by at least 1.5 times when compared to the mESC derived cardiomyocytes were also reported. The final analysis included probe sets that exhibited a different temporal pattern of expression in the CPC population when compared to the rest of the cells along the four days of differentiation. Specifically in order to identify these probe sets gene expression curve over time was modeled flexibly on a natural cubic spline basis.  A q-value for each gene was computed to estimate the false discovery rate (FDR) incurred when calling the gene significant.   Differentially expressed genes were obtained by setting a cut-off to the calculated q-values (Storey et al., 2005).  The probe level data analysis was implemented with the bioconductor package, Affy under R environment and the time course analysis was performed with the software package EDGE. Finally, only probe sets with gene ontology information associated with them were reported. The Ingenuity Pathways Analysis software package was used to identify canonical pathways that are active in the CPC population (www.ingenuity.com).

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

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

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

label: Biotin

source_name: Mouse embryonic stem cells

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

growth_protocol: See description

extract_protocol: Qiagen mini shredder, Qiagen Rneasy kit.

treatment_protocol: See description

tag: Mouse embryonic stem cells. Line D3. Differentiated through embryoid body formation (hanging droplet technique). Selected with G418. Transgene

value: aMHC promoter Neomycin phosphotransferase


title: Mouse embryonic stem cell derived cardiomyocytes 2


title: IU/Hahn_Drosophila_H8_23A

description: Sample 1 from this line

tag: 30-50 embryos from line 23


title: Day 6 GFP Positive Batch 2

tag: Mouse embryonic stem cells. Line D3. Differentiated through embryoid body formation (hanging droplet technique). Dissociated on noted day of differentiation and FACS sorted for the Green fluorescent protein. Transgene

value: Nkx2-5 enhancer, Hsp68 minimal promoter, GFP.


title: Day 7 GFP Positive Batch 2


title: Day 7 GFP Negative Batch 2


title: IU/Hahn_Drosophila_H8_58A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_H8_17B

description: Sample 2 from this line

tag: 30-50 embryos from line 17


title: Day 5 GFP Negative Batch 2


title: IU/Hahn_Drosophila_H8_23B

description: Sample 2 from this line


title: Day 8 GFP Positive Batch 2


title: Day 8 GFP Negative Batch 2


title: IU/Hahn_Drosophila_145A

description: Sample 1 from this line

source_name: D. melanogaster embryo 5 hours


title: Day 7 GFP Negative Batch 1


title: IU/Hahn_Drosophila_H8_17A

description: Sample 1 from this line


title: Day 5 GFP Positive Batch 2


title: IU/Hahn_Drosophila_134A

description: Sample 1 from this line


title: Day 8 GFP Negative Batch 1


title: IU/Hahn_Drosophila_134B

description: Sample 2 from this line


title: Day 6 GFP Negative Batch 2


title: IU/Hahn_Drosophila_128B

description: Sample 2 from this line

extract_protocol: Two RNA samples per line per time point (5 and 8 hours) were extracted using manufacturer's TRIzol reagent protocol (Invitrogen, Carlsbad, CA).  The concentrations of these samples were tested using a spectrophotometer and Na2HPO4 spec solution. The 36 samples (9 lines x 2 time points x 2 samples) of extracted RNA were labeled using the one-cycle cDNA Synthesis protocol from Affymetrix.  cDNA was made from the extracted RNA by first making a T7-Oligo(dT) Primer Master Mix and letting it incubate with the samples for 10 min at 700C and cooling for 2min at 40C.  A First-Strand Master Mix was added and the samples were incubated for 2 min at 420C.  After 200U/μL SuperScript II was added the samples were incubated for an additional hour at 420C and then cooled at 40C for 2min.  A Second-Strand Master Mix was added to the samples and then they were incubated at 160C for 2 hours and then cooled for 2min at 40C.  The samples were incubated for another 5min at 160C after T4 DNA Polymerase was added, the samples were cooled at 40C for 2min and 0.5M EDTA was added.  The now double stranded cDNA was cleaned up using spin columns and 100% Ethanol.


title: Day 7 GFP Positive Batch 1


title: IU/Hahn_Drosophila_128A

description: Sample 1 from this line


title: Day 6 GFP Negative Batch 1


title: IU/Hahn_Drosophila_145B

description: Sample 2 from this line


title: IU/Hahn_Drosophila_83B

description: Sample 2 from this line


title: Day 5 GFP Positive Batch 1

description:
Cell culture and cell differentiation
Mouse embryonic stem cells (mESCs) were maintained undifferentiated by culturing on a feeder layer of mitomycin C pretreated primary mouse embryonic fibroblasts (PMEFs, Specialty Media, cat.# PMEF-H) at 37oC, 90% humidity and 5% CO2. The cell line used was the mESC D3 (passage #12-18). The basic culture medium was comprised of DMEM (Invitrogen, cat.# 11965-092), heat inactivated (56oC for 30 minutes) fetal bovine serum (Hyclone, cat#. S11550, 15%), Glutamax (Invitrogen, cat.# 35050-065, 1%), non-essential amino acids (Invitrogen, cat.# 11140-050, 1%), sodium pyruvate (Invitrogen, cat.# 11360-070, 1%), ?-mercaptoethanol (Sigma, cat.# M7522, 0.1mM), gentamicin (Cambrex, cat.# 17-518, 25?g/ml) and ESGRO leukemia inhibitory factor (Chemicon, cat.# ESG1106, 1000units/ml). Prior to initiation of differentiation The PMEF feeder layer was subtracted and the mESCs were maintained on a 0.01% gelatin pretreated plate for 24-48 hours. Differentiation through embryoid body (EB) formation was initiated by dissociating the mESCs using trypsin (Invitrogen, cat#. 25300-054, 0.05%) and resuspending them in basic culture medium (without the leukemia inhibitory factor) at a final concentration of 5x104 cells/ml. The hanging droplet (HD) technique was used for EB formation. HDs were plated on the lid of H2O containing tissue culture dishes at a volume of 20?L/droplet (approximately 1000 cells/ droplet). Two days post initiation of differentiation the EBs were transferred in suspension on poly-HEMA (Sigma, cat#. P3932) treated tissue culture dishes. The plates were pretreated with poly-HEMA in order to avoid any cell attachment on the plastic. Basic culture medium was supplemented with ascorbic acid(Takahashi et al., 2003) (Sigma, cat#. A4403, 0.1mg/ml) and it was exchanged with fresh medium every 2 days during differentiation.
Transfection of mouse embryonic stem cells
	The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells.
	In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above.
FACS Analysis
	For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted.
FACS sorting
	The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in mESC culture medium at a concentration of 5x105 cells/ml and cultured in suspension for 48 hours. The cells were then transferred on tissue culture plates for another 48 hours. For RNA isolation the cells were spun down and washed in PBS before the RNA isolation procedure.
	To assay their proliferation capacity, GFP+ CPCs were FACS sorted on day 5 of differentiation. Cells were reaggregated in suspension (5x105 cells/ ml) in the presence of mouse recombinant Igf1 (Chemicon, Cat.# GF121, 100ng/ml) for 14 days. Cell aggregates were fixed and stained for the colocalization of the antigens: Nkx2-5 and Ki67 or Pcna. The same ICC reagents were used as described above.
GeneChip microarray hybridization
	Total RNA for the microarray expression analysis was isolated from FACS sorted cells (GFP+ and GFP-) on days 5, 6, 7, and 8 of differentiation as described above. Two separate differentiation batches were prepared for the sake of data reproducibility. Total RNA was also isolated from terminally differentiated mESC derived genetically selected cardiomyocytes 3 weeks post initiation of differentiation. The GeneChip® two cycle target labeling kit (Affymetrix, cat.# 900494) was used to convert 100ng of total RNA to biotinylated labeled cRNA. This was then hybridized to the Affymetrix murine MOE430 2.0 genome GeneChip® array (Affymetrix, cat.# 900496). Fluorescence was detected using the Affymetrix GS3000 GeneArray scanner and image analysis for each chip was done through the GeneChip® operating system software from Affymetrix (GCOS1.3) using the standard default settings.
Microarray data analysis
To estimate the gene expression signals, data analysis was conducted on the chips’ CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical technique RMA (Robust Multiarray Analysis) (Irizarry et al., 2003) with the bioconductor package Affy. The data normalization procedure utilized the quantile normalization method (Bolstad et al., 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.
The Spotfire DecisionSite software package was used for the identification of uniquely upregulated or downregulated (at least 1.5 times increase or decrease in the expression value) probe sets in the CPC population when compared to the rest of the cells in the differentiating EBs. Probe sets that were considered unique for the CPC population were found to be commonly upregulated or downregulated during all four days of analysis. Probe sets that exhibited an increasing or decreasing pattern of expression with at least 1.5 times increase or decrease in the expression values of day 5 CPCs and day 8 CPCs were also reported. Probe sets of the CPC population that exhibited upregulation or downregulation by at least 1.5 times when compared to the mESC derived cardiomyocytes were also reported. The final analysis included probe sets that exhibited a different temporal pattern of expression in the CPC population when compared to the rest of the cells along the four days of differentiation. Specifically in order to identify these probe sets gene expression curve over time was modeled flexibly

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

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

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


title: Day 6 GFP Positive Batch 1


title: IU/Hahn_Drosophila_89B

description: Sample 2 from this line


title: IU/Hahn_Drosophila_89A

description: Sample 1 from this line


title: HCT116 Control treatment group

status: Public on Aug 28 2007

middle: S

last: Shames

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

description: Control treatment group

hyb_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

source_name: Colorectal carcinoma

growth_protocol: See publication for details.

extract_protocol: Trizol

treatment_protocol: Control treatment group. DMSO qod for 6 days.

tag: See publication for details


title: IU/Hahn_Drosophila_17B

description: Sample 2 from this line


title: MCF7 Control treatment group

description: MCF7 Control treatment group

scan_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

source_name: Ductal Breast Carcinoma Cell Line


title: Day 8 GFP Positive Batch 1


title: IU/Hahn_Drosophila_83A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_75B

description: Sample 2 from this line


title: HCT116 High dose treatment group

description: High dose treatment group

data_processing: please see the Southwestern Medical Center Microarray Core Facility website for details

treatment_protocol: High dose treatment. 5-aza-2-deoxycytidine qod for 6 days.


title: H526 Control treatment group

description: H526 Control treatment group

source_name: SCLC cell line

label_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

treatment_protocol: Control treatment group (DMSO). DMSO qod for 6 days.

tag: See publication for details.


title: IU/Hahn_Drosophila_75A

description: Sample 1 from this line


title: MCF7 High dose treatment group

description: High dose treatment group

treatment_protocol: High dose treatment group. 5-aza-2-deoxycytidine qod for 6 days.


title: IU/Hahn_Drosophila_v2.0

description: Sample 1 from this line


title: IU/Hahn_Drosophila_23B

description: Sample 2 from this line


title: IU/Hahn_Drosophila_58A

description: Sample 1 from this line


title: IU/Hahn_Drosophila_58B

description: Sample 2 from this line


description: H1819 Lose dose treatment group (100 nM). DMSO qod for 6 days.

data_processing: Raw signal data without normalization

source_name: NSCLC cell line

label_protocol: Affymetrix


title: HBEC2 Control group treatment

description: HBEC2 Control group treatment. DMSO qod for 6 days.

source_name: Immortalized human bronchial epithelial cells


description: H1819 High dose treatment group (1000 nM). DMSO qod for 6 days.


title: H526 High dose treatment group (1000 nM)

description: H526 Control treatment group

treatment_protocol: High dose treatment group. 1000 nM 5-aza-2'-deoxycytidine qod for 6 days.


title: IU/Hahn_Drosophila_23A

description: Sample 1 from this line


title: H157 Control group treatment.

description: H157 Control group treatment


title: H1819 Control group treatment

description: H1819 Control treatment group. DMSO qod for 6 days.


title: H157 High dose treatment group

description: H157 High dose treatment group (1000 nM).

treatment_protocol: High dose treatment group (1000 nM). 5-aza-2'-deoxycytidine qod for 6 days.


title: SHEP-21N, t=8 hrs

status: Public on Aug 24 2007

description: SHEP-21N cells were grown under standard conditions in presence of tetracycline (no MYCN expression) for two weeks. Tetracyclin was washed away and cells were harvested, at 70% confluency, at different time points after tetracycline removal. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix).

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SHEP-21N cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using LiCl/ureum and purified with RNeasy (Qiagen) according to manufacturer's protocol.

treatment_protocol: Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0, tetracyclin was removed to induce MYCN

tag: Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector


title: SHEP-21N, t=120 hrs

treatment_protocol: Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0 , tetracyclin was removed to induce NMYC


title: H157 Low dose treatment group (100 nM)

description: H157 Low dose treatment group (100 nM).

treatment_protocol: Low dose treatment group (100 nM). 5-aza-2'-deoxycytidine qod for 6 days.


title: IMR32-DKK1 c66, t=24 hrs

description: IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

source_name: IMR32-DKK1 c66

growth_protocol: IMR32-DKK1 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

treatment_protocol: To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml


title: SHEP-21N, t=24 hrs


title: SHEP-21N, t=0


title: IMR32-DKK1 c66, t=0

tag: Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector


title: IMR32-DKK1 c66, t=288 hrs


title: IMR32-DKK1 c63, t=72 hrs

source_name: IMR32-DKK1 c63


title: SKNAS-NmycER, t=24 hrs

description: SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

source_name: SKNAS-NmycER cells

growth_protocol: SKNAS-NmycER cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

treatment_protocol: To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.

tag: Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector