title: PBMC_S4

city: Bethesda

first: Xiuli

last: Xu

state: MD

address: Building 10-CRC, Room 5-5140

department: VMB,

institute: NHLBI, NIH

description: standard labeling and hybridization procedure

hyb_protocol: Twenty µg of biotin-labeled RNA was fragmented to ~200 bp size by incubating in fragmentation buffer containing 200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 500 mM magnesium acetate for 35 minutes at 94ºC prior to hybridization. Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer, and hybridized to Affymetrix HG-U133 plus 2.0 chips for 16 hours, washed, and stained on an Affymetrix fluidics station.

scan_protocol: Arrays were scanned using an Affymetrix genechip scanner 3000.

data_processing: Affymetrix GCOS version 1.4 was used to calculate the signal intensity and the percent present calls on the hybridized Affymetrix chip. The signal intensity values obtained for probe sets in the microarrays were transformed using an adaptive variance-stabilizing, quantile-normalizing transformation termed “S10” (Munson, P.J., GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html.).

source_name: peripheral blood

label_protocol: The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA). Briefly, 2 µg of total RNA from PBMC (n=10, 5 controls and 5 SCD), whole blood (PAX) (n=10, 5 controls and 5 SCD) and Globin depleted (PAX-GR) (n=10, 5 controls and 5 SCD) samples was converted to double-stranded cDNA with a T7-(dT) 24 primer. The cDNA was in vitro transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using affymetrix IVT labeling kit.

extract_protocol: Peripheral blood mononuclear cell RNA isolation: Total RNA was extracted from peripheral blood mononuclear cells using RNeasy Mini Kit (Qiagen).  Isolation of RNA from whole blood specimens: Blood Specimen (2.5ml) collected in PAXgene™ tubes from each subject was incubated at room temperature for 4h for RNA stabilization and then stored at − 80 °C. RNA was extracted from whole blood using the PAXgene™ Blood RNA System Kit following the manufacturer's guidelines. Briefly, samples were removed from -80°C and incubated at room temperature for 2 hours to ensure complete lysis. Following lysis, the tubes were centrifuged for 10 min at 5,000 × g the supernatant was discarded and 500 μL of RNase-free water added to the pellet. The tube was vortexed thoroughly to re-suspend the pellet, centrifuged for 10 min at 5000 × g and the entire supernatant was discarded. The pellet was re-suspended in 360 μL of buffer BR1 by vortexing and further purification of RNA was done following the manufacturer's protocol with on-column DNase digestion.  Depletion of Globin Transcripts: Globin mRNA was depleted from a portion of each total RNA sample isolated from PAXgene tubes using the GLOBINclear™-Human kit (Ambion, Austin, TX). In brief 4 µg of total RNA from human whole blood was mixed with a biotinylated Capture Oligo Mix in hybridization buffer. The mixture was incubated for 15 minutes to allow the biotinylated oligonucleotides to hybridize with the globin mRNA species. Streptavidin magnetic Beads were then added, to capture the globin mRNA and the magnetic beads were then pulled to the side of the tube with a magnet and the RNA, depleted of the globin mRNA, was transferred to a fresh tube. The RNA was further purified using a rapid magnetic bead-based purification method.

treatment_protocol: Peripheral blood mononuclear cell isolation: Peripheral blood from sickle-cell patients, and healthy African-American volunteers, was collected into Vacutainer cell preparation tube (CPT) with sodium citrate and Ficoll (Becton Dickinson, Franklin Lakes, NJ). Purified peripheral blood mononuclear cell (PBMC) suspensions were resuspended in buffer RLT (700-1000 µL per 107 cells) and passed through Qiashredder columns (Qiagen, Valencia, CA) then stored at –70° C.

value: peripheral blood

tag: subject

value: sickle-cell patient

tag: rna prep

value: PBMC

tag: molecule

value: RNA extracted from PBMC


title: Pax_S6

status: Public on Jun 20 2009

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: PAXgene

value: total RNA


title: PBMC_C4

value: Control


title: PBMC_C5


title: Pax_S3


title: PBMC_C2


title: PBMC_S2


title: Pax_S1


title: Pax_C5


title: Brain: deiminated-MA-Brent-1_e1_le2

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: RNA species eluted from deiminated MA-Brent-1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

organism: Mus musculus

source_name: brain

label_protocol: standard Affymetrix protocol

extract_protocol: none supplied


title: Pax_C3


title: Pax_C1


title: PBMC_S6


title: Pax_C2


title: PBMC_S1


title: PBMC_C3


title: PBMC_C1


title: Pax_S4


title: PBMC_S3


title: Globin_S6

value: PAXgene Globin reduced

value: Globin-depleted RNA


title: Pax_S2


title: Pax_C4


title: Globin_S3


title: Globin_S2


title: Globin_S4


title: Globin_S1


title: B6.C3H-Bbaa4 joint uninfected

status: Public on Jun 22 2009

city: Salt Lake City

first: Janis

last: Weis

state: UT

address: 15 North Medical Drive East

department: Pathology

institute: University of Utah

description: gene expression from uninfected ISCLrear ankle joint tissue

hyb_protocol: Hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was carried out according to Affymetrix directions.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 laser confocal slide scanner

data_processing:
Data were processed using the affy and gcRobust Multiarray Average packages in R
Statistical analysis were performed using significance analysis of microarrays

source_name: uninfected tissue

label_protocol: cDNA was generated from RNA and was labeled with the One-Cycle Target labeling kit (Affymetrix)

growth_protocol: Generation_of_ISCL: ISCL were generated by repeated backcrossing between C3H and C57BL/6 parental mice, using the speed congenic approach and based on QTL linkage analysis for Lyme arthritis severity

extract_protocol: Joint tissue was homogenized in presence of cold acid guanidine and RNA was recovered following cesium chloride centrifugation. RNA was applied to Rneasy kit (Qiagen).

treatment_protocol: Infection_protocol: Mice were infected with 2000 B. burgdorferi of the N40 strain by intradermal injection in the back and controls received BSK medium.  Mice were sacrificed at 1 wk, joint tissue collected and skin removed.

tag: infection

value: no

value: ankle joint

tag: genotype

value: B6.C3H-Bbaa4, ISCL

tag: age

value: 6-7 weeks


title: Globin_C4


title: Globin_C5


title: Patient 17-D0

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: Patients with MDS, chronic myelomonocytic leukemia (CMMoL), and high risk AML were treated with sequential administration of methylation inhibitor drugs (5AC and entinostat).

hyb_protocol: Hybridization cocktails containing 10 ug of fragmented cRNA was prepared using GeneChip Expression 3'-Amplification Reagents Hybridization Control Kit in a 200 ul final volume according to the manufacturers instructions

scan_protocol: Affymetrix standard scanning protocol

data_processing: Cel files were imported in GeneSpring GX and normalized by GC-RMA. Pairs of specimens passing quality control for hybridization and RNA integrity were analyzed by paired T test

source_name: Day 0

label_protocol: mRNA was subjected to two rounds of linear amplification and biotin labelling in second round was with the Ambion MessageAmp II kit with bio-C and bio-U as stated by manufacturer

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit with on-column DNAse treatment to remove genomic DNA

treatment_protocol: Enrolled patients were treated with sequential administration of 5AC and entinostat.  The study was approved by the Institutional Review Boards (IRB) for each institution, and all patients signed informed consent according to Health and Human Services guidelines.  Specific IRB approved informed consent was obtained for the laboratory research use of patient specimens.  5AC was administered subcutaneously for 10 consecutive days in doses of 30, 40, or 50 mg/m2/day.  Entinostat (2, 4, 6, or 8 mg/m2) was administered orally on days 3 and 10 of the 5AC treatment schedule in the course of a 28-29 day treatment cycle.

tag: diagnosis

value: MDS

tag: cell type

tag: dose

value: 50 mg/m2/day 5-azacytidine

value: 8 mg/m2/day entinostat


title: Patient 13-D15

source_name: Day 15

value: 6 mg/m2/day entinostat


title: Globin_C2

value: peripheral blood


title: Patient 12-D0


title: Patient 12-D15


title: Globin_C3


title: Patient 24-D15

value: CMMoL

value: 30 mg/m2/day 5-azacytidine

value: 2 mg/m2/day entinostat


title: Patient 06-D15

value: 40 mg/m2/day 5-azacytidine


title: Patient 24-D0


title: Globin_C1


title: Patient 05-D15


title: Patient 08-D15

value: 4 mg/m2/day entinostat


title: Patient 04-D15


title: Patient 03-D15

value: AML-TLD


title: Patient 06-D0


title: Patient 13-D0


title: Patient 05-D0


title: Patient 09-D0


title: Patient 09-D15


title: Patient 08-D0


title: Patient 17-D15


title: Patient 04-D0


title: Patient 02-D15


title: Patient 03-D0


title: Patient 01-D15


title: Patient 02-D0


title: Estradiol, rep 2

status: Public on Jun 18 2009

city: Valencia

first: Carlos

last: Hermenegildo

address: Avda. Blasco Ibanez 15

country: Spain

institute: University of Valencia

description: Gene expression data from estradiol-treated HUVEC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station EukGene_ws_2v5.

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

data_processing: Files obtained from GCOS (.cel) were used to analyze significant changes in expression profiles of different experimental groups using the dCHIP Analysis Software and the SpotFire Decision Site software. Data were normalized using the Invariant Set Method and modeled using the PM/MM model

source_name: HUVEC treated with 1 nM for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

growth_protocol: Primary HUVEC were isolated and grown in human endothelial cell-specific Medium EBM-2 supplemented with EGM-2 (Lonza), in an incubator at 37 ºC with 5% CO2

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

treatment_protocol: Cells were exposed to 1 nmol/L 17β-estradiol or its vehicle (0.1% ethanol) for 24 hours. Meduem was discarded, cells washed with PBS and then collected in Trizol.

value: Endothelial cell

tag: agent

value: estradiol

value: 1 nM

tag: time


title: human_CD36_2

status: Public on Jun 19 2009

type: genomic

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

data_processing: Affymetrix MAS5 algorithm.

molecule: genomic DNA

source_name: CD36+ cell

growth_protocol: Growth protocol as described in Cui et al., 2009

extract_protocol: Extract protocol as described in Cui et al., 2009

treatment_protocol: Treatment protocol as described in Cui et al., 2009


title: human_CD133_2

source_name: CD133+ cell


title: Control, rep 2

description: Gene expression data from control HUVEC

source_name: HUVEC control

value: ethanol


title: PBMCs_LG_before exercise_17

status: Public on Jun 17 2009

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

hyb_protocol: 10 µg of  fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix U133+2 arrays.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.4 software (Affymetrix, Inc.) using default values (Scaling Target Signal Intensity=500; Normalization, All probe sets; Parameters, all set at default values). The microarray data was analyzed using ArrayAssist® version 5.2.2 (STRATAGENE® ) using GC-RMA.

source_name: Late girls PBMCs before exercise

label_protocol: 4 μg total RNA was used as a template for double‑stranded cDNA synthesis. Single-stranded then double-stranded cDNA was synthesized from the poly A spike-in controls, and mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA), and a T-7-oligo(dT) primer (Integrated DNA Technologies Inc.,Coralville,IA) that contains a T7 RNA polymerase promoter site added to it’s 3' end. A portion of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit.

extract_protocol: PBMCs were isolated using OptiPrep® Density Gradient Medium (SIGMA).  Total RNA was extracted using TRIzol®  reagent and purified using the RNeasy Midi columns method (Qiagen, Valencia, CA).

tag: PBMCs, healthy female, age 17

tag: before-exercise


title: PBMCs_LG_before exercise_19


title: human_CD133_1


title: PBMCs_LG_after exercise_17

source_name: Late girls PBMCs after 30 min bout of exercise

tag: after-exercise


title: Brain: non-deiminated REFP2 bound RNA-sample 1 (U1)

description: RNA species eluted from  non-deiminated MA-Brent-1

tag: Non-deiminated REFP2 bound RNA-sample 1 (U1)


title: PBMCs_LG_before exercise_18

tag: PBMCs, healthy female, age 15


title: human_CD36_1


title: PBMCs_LG_after exercise_20


title: PBMCs_LG_before exercise_15


title: Estradiol, rep 3


title: PBMCs_LG_before exercise_20


title: PBMCs_LG_after exercise_15


title: PBMCs_LG_after exercise_16


title: Control, rep 3

description: Gene expression data from control HUVEC


title: PBMCs_LG_after exercise_18


title: Patient 01-D0


title: PBMCs_LG_after exercise_14


title: PBMCs_LG_before exercise_14


title: Control, rep 1

description: Gene expression data from control HUVEC


title: PBMCs_LG_before exercise_12


title: PBMCs_LG_after exercise_19


title: PBMCs_EG_after exercise_09

source_name: Early girls PBMCs after 30 min bout of exercise

tag: PBMCs, healthy female, age 9


title: PBMCs_LG_before exercise_13


title: PBMCs_EG_before exercise_09

source_name: Early girls PBMCs before exercise


title: PBMCs_LG_after exercise_13


title: PBMCs_EG_after exercise_10

tag: PBMCs, healthy female, age 10


title: PBMCs_LG_before exercise_16


title: PBMCs_EG_before exercise_10


title: PBMCs_LG_after exercise_12


title: PBMCs_LG_before exercise_11

tag: PBMCs, healthy female, age 16


title: PBMCs_EG_after exercise_03


title: PBMCs_EG_after exercise_04

tag: PBMCs, healthy female, age 8


title: PBMCs_EG_after exercise_06


title: PBMCs_EG_after exercise_05


title: PBMCs_EG_after exercise_07


title: PBMCs_EG_after exercise_02


title: PBMCs_EG_before exercise_04


title: PBMCs_EG_before exercise_02


title: PBMCs_EG_after exercise_08


title: PBMCs_EG_before exercise_06


title: PBMCs_LG_after exercise_11


title: PBMCs_EG_after exercise_01

tag: PBMCs, healthy female, age 11


title: PBMCs_EG_before exercise_05


title: PBMCs_EG_before exercise_07


title: PBMCs_EG_before exercise_01


title: PBMCs_EG_before exercise_03


title: 7WT_3

status: Public on Jun 16 2009

city: Cincinnati

first: Susan

last: Waltz

state: OH

address: 3125 Eden Ave ML0521

institute: University of Cincinnati

description: RNA from 5 week, 6 week, 7 week-old wild-type (RonTK+/+) and Ron tyrosine kinase domain deleted (RonTK-/-) virgin mouse whole mammary glands

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.034 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45?C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Stain: R-Phycoerythrin Streptavidin (Molecular Probes). Antibody: Anti-Streptavidin antibody (goat) biotinylated (Vector Laboratories)

scan_protocol: The probe arrays are scanned using the Affymetrix GeneChip Scanner 3000. Scanning: Scanning software: Genechip Operating Software 1v4 (Affymetrix)

data_processing:
Normalization:  Each array is normalized the same. Global scaling is used adjusting the average intensity or signal value of each probe array to the same Target Intensity value (TGT). Our facility uses a TGT value of 1500. The internal control genes are used to check the quality of the RNA and the assay quality by comparing the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin. Good 3' to 5' ratios are between1-3. Prokaryotic Spike controls are used to determine whether the hybridization of target RNA to the array occurred properly.
Changes in gene expression were then analyzed using Gene Spring GX software (Agilent technologies).  45,000 probe sets were first filtered on expression using a minimum raw intensity value greater than or equal to 120.  The resulting 32,181 probe sets were then normalized to the median intensity value of all wild-types.

source_name: virgin female mouse mammary glands

label_protocol: Next, 400-500ng of total RNA per sample was used in the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies, Madison, WI) to generate cRNA following the manufacturer’s instructions.  Biotin-X-X-NHS (Epicentre Biotechnologies, Madison, WI) was used to label the aminoallyl-aRNA with biotin.  The biotin-labeled cRNA target was then chemically fragmented, and a hybridization cocktail was prepared and hybridized to the Affymetrix Mouse Genechip 430 2.0 array.

extract_protocol:
RNA was harvested from whole mammary glands of 5, 6, and 7 week-old RonTK+/+ and RonTK-/- virgin female mice using TriZol (Invitrogen, Carlsbad, CA) according to the manufacturers instructions with one modification.  To remove fat from the TriZol preparation, centrifugation at 12,000g for 10 minutes at 4?C was preformed prior to the addition of chloroform.  RNA samples were submitted to the Cincinnati Children’s Hospital Medical Center Affymetrix Core, Cincinnati, Ohio.
Quality control steps: The Agilent Bioanalyzer 2100 (Hewlett Packard, Palo Alto, CA) using the RNA 6000 Nano Assay was applied to the RNA for quality assessment.

tag: strain

value: (RonTK+/+)

value: 7 week-old


title: 5WT_3

tag: age

value: 5 week-old


title: PBMCs_EG_before exercise_08


title: 7WT_2


title: 6WT_2

value: 6 week-old


title: 5WT_1


title: 7KO_3

value: (RonTK-/-)


title: 6WT_3


title: 7KO_2


title: 6KO_2


title: 5KO_2


title: 7WT_1


title: 6KO_3


title: 6WT_1


title: 7KO_1


title: 5WT_2


title: 6KO_1


title: median nectary, stage 14-15 rep1

status: Public on Jun 15 2009

city: Duluth

first: Clay

middle: J

last: Carter

state: MN

address: 1035 Kirby Dr

department: Biology

institute: University of Minnesota Duluth

description: Gene expression data from pooled Stage 14-15 median nectaries

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: GeneChips were scanned using a GeneChip 3000 scanner at the University of Minnesota Microarray Facility

data_processing: The probe level signals were quantile-normalized and summarized using RMA algorithm by using the Expressionist® (Genedata, Basel, Switzerland) Refiner module.  Gene expression values were further linear scaled up to a media of 100 in the Expressionist® (Genedata, Basel, Switzerland) Analyst module.

organism: Arabidopsis thaliana

source_name: pooled median nectaries from stage 14-15 flowers

label_protocol: RNA was processed using the MessageAmp™ II-Biotin Enhanced Kit (Ambion, Austin, TX) for a single round of RNA amplification as described by the manufacturer. Briefly, 250-500 ng of total RNA (500 ng from lateral nectaries; 250 ng from median nectaries due to extremely small size) was used in a reverse transcription reaction to generate first-strand cDNA. Following second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotin-labeled, amplified RNA (aRNA). aRNA size distribution was evaluated by conventional denaturing agarose gel analysis according to manufacturer’s instructions (Ambion, Austin, TX). An aRNA fragmentation reaction, employing metal-induced hydrolysis, was used to fragment aRNA as described by the manufacturer (Ambion, Austin, TX).

growth_protocol: Plants were grown in individual pots on a peat-based growth medium with vermiculite and perlite (Pro-Mix BX; Premier Horticulture, Rivière-du-Loup, Quebec, Canada). All plant growth was performed in Percival AR66LX environmental chambers with settings of: 16 hr day/8hr night cycle, photosynthetic photon flux of 150 µmol m-2 s-1, 50% humidity and temperature of 21°C.  All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 30-35 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4-8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at +4°C prior to RNA extraction. Up to two nectaries were collected per flower, with approximately 250-300 nectaries being processed as a single RNA sample.

extract_protocol: RNA was extracted from floral nectariferous tissue by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Denaturing agarose gel electrophoresis (Applied Biosystems, 2008) and UV spectrophotometry were used to assess RNA quality for all samples.

tag: ecotype

tag: tissue

value: median nectaries

tag: developmental stage

value: stage 14-15


title: Estradiol, rep 1

tag: cell type

tag: agent

tag: dose


title: lateral nectary, stage 11-12 rep3

description: Gene expression data from pooled Stage 11-12 lateral nectaries

source_name: pooled lateral nectaries from stage 11-12 flowers

value: lateral nectaries

value: stage 11-12


title: lateral nectary, stage 11-12 rep2


title: 5KO_3


title: 5KO_1


title: median nectary, stage 14-15 rep2


title: lateral nectary, stage 11-12 rep1


title: Human Cesarean delivered term placental villus tree technical replicate 2

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: gene expression data

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: GCOS MAS5 statisical method

source_name: placental villus tree

label_protocol: standard Affymetrix protocols

growth_protocol: Mouse was natually mated and placenta collected on day 17.5 post conception. Human placentas were from term Cesarean deliveries and had normal health pathology.

extract_protocol: Trizol extraction as per manufacture protocol followed by Rneasy spin column

treatment_protocol: Samples were microdissected to enrich for vascular tissue

tag: Normal healthy term placenta


title: lateral nectary, stage 14-15 rep3

description: Gene expression data from pooled Stage 14-15 lateral nectaries

source_name: pooled lateral nectaries from stage 14-15 flowers


title: lateral nectary, stage 14-15 rep1


title: Mouse E17.5 placental labyrinth technical replicate 2

description: gene expression data

source_name: placental labyrinth


title: lateral nectary, stage 14-15 rep2


title: OE/ZL3

city: Niigata

first: Masayuki

last: Nashimoto

address: Higashijima 265-1

country: Japan

institute: Niigata University of Pharmacy and Applied Life Sciences

description: 293 with tRNase ZL

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

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

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

source_name: 293 cells with tRNase ZL

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit（Affymetrix) and TaKaRa cDNA Synthesis Kit （TaKaRa Bio） from 3ug total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit(Affymetrix)

growth_protocol: The 293 cells were cultured in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (MP Biomedicals) and 1% penicillin-streptomycin (Invitrogen) at 37 °C in 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted with ISOGEN according to the manufacturer's instructions.

treatment_protocol: The 293 cells were transfected with the tRNase ZL plasmid using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s protocol.

tag: human embryonic kidney 293 cell


title: Human Cesarean delivered term placental villus tree technical replicate 1

description: gene expression data


title: mock3

description: 293 without tRNase ZL

source_name: 293 cells without tRNase ZL


title: T51783

status: Public on Jun 13 2009

city: Bucharest

first: Liviu

last: Badea

address: 8-10 Averescu Blvd.

department: Research

country: Romania

institute: ICI

description: Gene expression data from surgical samples

hyb_protocol: The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin.

scan_protocol: Scanning was performed with an Affymetrix Microarray Scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4 was used for low-level scanning data processing. The data was subsequently normalized using the RMA algorithm using the Bioconductor 1.9 package (http://www.bioconductor.org/) running under R version 1.9.1.

source_name: pancreas

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was extracted from the frozen tissue samples in two steps: RNA isolation using the TriReagent (Sigma) protocol, followed by RNA clean-up performed as described in the RNeasy (Qiagen) protocol. Briefly, tissues were homogenized in TriReagent (1 mL of TriReagent per 50-100mg of tissue). Then, RNA was precipitated from the aqueous phase with addition of isopropanol at half the volume of the original TriReagent volume and centrifugated at 12000 × g for 10 min. RNA was cleaned using an RNeasy column according to the manufacturer’s instructions (RNeasy Mini Kit, Qiagen) and eluted in 100 µL of RNase-free water. RNA sample quantitation was performed by means of spectrophotometry (Genequant, Pharmacia), while RNA quality (integrity) control was done with microfluidics technology (2100 Bioanalyser, Agilent Technologies).

treatment_protocol: Pairs of normal and tumor tissue samples were obtained at the time of surgery from resected pancreas of 36 pancreatic cancer patients. The tissue samples were snap-frozen in liquid nitrogen immediately upon surgical removal and maintained at −85°C. For histological evaluation, sections were stained with haematoxylin and eosin. The resected cancer specimens were not microdissected.

tag: patient

tag: sample

value: tumor


title: T51091


title: T51292


title: T51628


title: T51176


title: T51315


title: T51721


title: T51722


title: T51572


title: T51308


title: T51681


title: T40892


title: T51677


title: T51294


title: T40899


title: T51084


title: T40977


title: T40843


title: T40975


title: T40875


title: T40645


title: T40836


title: T40726


title: T40656


title: T40730


title: T30617


title: T40741


title: T30364


title: T40728


title: T41027


title: T30582


title: T30308


title: T30162_rep


title: T30057


title: N51722

value: normal


title: T30277


title: T40728_rep


title: T30162


title: T41027_rep


title: T30068


title: N51721


title: N51572


title: N51783


title: N51677


title: N51628


title: N51681


title: N51294


title: AtT20 cells overexpressing NSBP1SE protein rep3

first: Mark

last: Rochman

address: 6000 Rockville Pike 37/3122

department: NCI

institute: NIH

description: NSBP1SE OE

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using manufacturer-suggested script.

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

data_processing: Data was processed using BrB tools program

source_name: mouse pituitary gland cells

label_protocol: Biotinylated antisense cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA using One-cycle target labeling protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: AtT20 pituitary gland cells were grown in DMEM with 10%FCS at 37C

extract_protocol: RNA was isolated by TRIZOL following by RNeasy  clean up and DNAse treatment on the columns

treatment_protocol: Stable overexpressed clones were generated by retroviral infection. siRNA was transfected by Dharmafect 4 transfection reagent. siRNA treatment  was performed for 5 days with the split after 2 days and retransfection of siRNA.

tag: clone type

value: AtT20 clone types overexpressing NSBP1SE protein rep3


title: AtT20 cells infected with empty vector rep2

description: empty vector

value: AtT20 clone types infected with empty vector rep2


title: AtT20 cells overexpressing NSBP1SE protein rep2

description: NSBP1SE OE

value: AtT20 clone types overexpressing NSBP1SE protein rep2


title: AtT20 cells overexpressing NSBP1SE protein rep1

description: NSBP1SE OE

value: AtT20 clone types overexpressing NSBP1SE protein rep1


title: AtT20 cells overexpressing NSBP1WT protein rep2

description: NSBP1 OE

value: AtT20 clone types overexpressing NSBP1WT protein rep2


title: N51176


title: N51091


title: N51292


title: AtT20 cells infected with empty vector rep3

description: empty vector

value: AtT20 clone types infected with empty vector rep3


title: AtT20 cells overexpressing NSBP1WT protein rep1

description: NSBP1 OE

value: AtT20 clone types overexpressing NSBP1WT protein rep1


title: AtT20 cells overexpressing NSBP1WT protein rep3

description: NSBP1 OE

value: AtT20 clone types overexpressing NSBP1WT protein rep3


title: AtT20 cells infected with empty vector rep1

description: empty vector

value: AtT20 clone types infected with empty vector rep1


title: N40975


title: AtT20 cells treated with control siRNA rep 3

description: control siRNA

value: AtT20 clone types treated with control siRNA rep 3


title: AtT20 cells treated with control siRNA rep 1

description: control siRNA

value: AtT20 clone types treated with control siRNA rep 1


title: Mouse E17.5 placental labyrinth technical replicate 1

description: gene expression data


title: AtT20 cells treated with control siRNA rep 2

description: control siRNA

value: AtT20 clone types treated with control siRNA rep 2


title: N51084


title: N51315


title: N40899


title: AtT20 cells treated with NSBP1 siRNA rep 3

description: siRNA NSBP1

value: AtT20 clone types treated with NSBP1 siRNA rep 3


title: N40892


title: AtT20 cells treated with NSBP1 siRNA rep 2

description: siRNA NSBP1

value: AtT20 clone types treated with NSBP1 siRNA rep 2


title: N40875


title: N40977


title: AtT20 cells treated with NSBP1 siRNA rep 1

description: siRNA NSBP1

value: AtT20 clone types treated with NSBP1 siRNA rep 1


title: N40741


title: N40843


title: N40836


title: N40730


title: N40726


title: N30617


title: N30057


title: N30582


title: N30364


title: N30277


title: N40645


title: N30308


title: N30068


title: N40656


title: N40728


title: N30162


title: N40728_rep


title: N41027_rep


title: N41027


title: Arabidopsis thaliana_apex_SD_20-day_se-1 p35S::MIR156_replicate 2

status: Public on Jun 12 2009

city: Tuebingen

first: Jiawei

last: Wang

address: Spemannstr 37-39

country: Germany

institute: Max Planck Institute for Developmental Biology

description: Transcriptome comparison of Col-0, se-1, ago1-27 and se-1 35S::MIR156 in Arabidopsis thaliana.

hyb_protocol: 16 hours at 45 degree at 60 rpm.

scan_protocol: According to Affymetrix workstation (GCOS).

source_name: Arabidopsis thaliana se-1 p35S::MIR156 vegetative apex

label_protocol: According to "MessageAmp II-Biotin Enhancer, Single Round aRNA Amplification Kit" from Ambion.

growth_protocol: Plants were grown in short day for 20 days.

extract_protocol: Total RNAs are extracted with Qiagen RNase plant mini kit.

tag: genotype

value: vegetative apex

value: 20 days

tag: growth condition

value: short day


title: Arabidopsis thaliana_apex_SD_20-day_se-1_replicate 2

data_processing: According to Affymetrix workstation (GCOS).

source_name: Arabidopsis thaliana se-1 vegetative apex


title: Primary breast cancer, sample 73

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50-60

department: Medical Oncology

country: Netherlands

institute: Erasmus Medical Centre

description:
EMC204_73
2419.CEL

scan_protocol: standard Affymetrix protocol on Affymetrix scanner 3000

data_processing: MAS5 parameters from affy R package, available at www.bioconductor.org using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 600.

source_name: Snap frozen primary breast tumor

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

tag: Site of relapse

value: local

tag: Survival time (months)


title: Arabidopsis thaliana_apex_SD_20-day_ago1-27_replicate 2

source_name: Arabidopsis thaliana ago1-27 vegetative apex


title: Primary breast cancer, sample 95

description:
EMC204_95
2450.CEL


title: Arabidopsis thaliana_apex_SD_20-day_Col-0_replicate 1

source_name: Arabidopsis thaliana Col-0 vegetative apex


title: N30162_rep

value: normal


title: Primary breast cancer, sample 9

description:
EMC204_9
1143.CEL


title: Arabidopsis thaliana_apex_SD_20-day_Col-0_replicate 2


title: Primary breast cancer, sample 153

description:
EMC204_153
2882.CEL


title: Arabidopsis thaliana_apex_SD_20-day_se-1 p35S::MIR156_replicate 1


title: Arabidopsis thaliana_apex_SD_20-day_ago1-27_replicate 1


title: Primary breast cancer, sample 57

description:
EMC204_57
1984.CEL


title: Primary breast cancer, sample 150

description:
EMC204_150
1159.CEL


title: Primary breast cancer, sample 101

description:
EMC204_101
2463.CEL


title: Primary breast cancer, sample 81

description:
EMC204_81
2429.CEL


title: Arabidopsis thaliana_apex_SD_20-day_se-1_replicate 1


title: Primary breast cancer, sample 78

description:
EMC204_78
2425.CEL


title: N51308


title: Lung-sarcoidosis-rep2

status: Public on Jun 11 2009

city: columbus

first: Elliott

middle: David

last: Crouser

address: 473 West 12th Ave.

institute: The Ohio State University

description: frozen sarcoidosis lung tissue

hyb_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

data_processing: The data were analyzed with Robust Multichip Average (RMA) procedure using quantile normalization .

source_name: Frozen sarcoidosis lung tissue

tag: disease state

value: sarcoidosis

tag: biopsy type

value: surgical

value: lung


title: Lung-normal-rep6

description: frozen normal lung tissue

scan_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

source_name: Frozen disease-free lung tissue


title: Lung-sarcoidosis-rep5

description: frozen sarcoidosis lung tissue

label_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).


title: Lung-normal-rep5

description: frozen normal lung tissue

extract_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).


title: Lung-sarcoidosis-rep4

description: frozen sarcoidosis lung tissue


title: Lung-sarcoidosis-rep3

description: frozen sarcoidosis lung tissue


title: Lung-normal-rep3

description: frozen normal lung tissue


title: Lung-normal-rep2

description: frozen normal lung tissue


title: Lung-sarcoidosis-rep1

description: frozen sarcoidosis lung tissue

value: transbronchial


title: Lung-normal-rep4

description: frozen normal lung tissue


title: Lung-normal-rep1

description: frozen normal lung tissue


title: Lung-sarcoidosis-rep6

description: frozen sarcoidosis lung tissue


title: Setleis Syndrome patient 3

city: San Juan

first: Carmen

middle: Lydia

last: Cadilla

state: PR

address: University of Puerto Rico Medical Sciences Campus, Area of Medical Center

department: Biochemistry

country: Puerto Rico

institute: University of Puerto Rico School of Medicine

description: 1:1 Pool of RNAs from two siblings, female and male, affected with Setleis Syndrome

hyb_protocol: Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility

scan_protocol: GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.

data_processing: A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.

source_name: skin fibroblasts, passages #3 and 5

label_protocol: Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.

growth_protocol: Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.

extract_protocol: Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.

tag: gender

value: mixed

value: Homozygous for the Q119X mutation in the TWIST2 gene

tag: ethnicity

value: Puerto Rican


title: Normal Puerto Rican control 2

description: unaffected sister of Setleis patient in Samples Setleis_05 and _06.

source_name: skin fibroblasts, passage #1

value: female

value: Wild type for TWIST2


title: Setleis Syndrome patient 4

description: Setleis Syndrome Patient described in Al-Gazali and Al-Talabani (1996) Clin Dysmorphol 5(3):249-53.

source_name: skin fibroblasts, passage #3

value: Homozygous for the Q65X mutation in the TWIST2 gene


title: Setleis Syndrome patient 2

description: Sister of Setleis_01 and _02


title: Liv27Post

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: no additional information

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: RMAExpress

source_name: Liver Biopsy

label_protocol: Ambion MessageAmp Biotin II Enhanced

extract_protocol: Liver Biopsy Tissue was frozen in RNALater. RNA was extracted using Trizol and purified on RNeasy Columns

tag: Donor type = Deceased Donor

tag: Biopsy Type = Post Reperfusion

tag: HCV -


title: Normal Puerto Rican control 1


title: Liv27Pre

description: no additional information

tag: Biopsy Type = Cold Preservation


title: Normal Puerto Rican control 3

description: 1:1 Pool of two control cell lines, one is GM00037, the other is from a normal donor

source_name: skin fibroblasts, passages #2 and 4


title: Liv42Pre

description: no additional information

tag: Donor type = Living Donor


title: Liv25Pre

description: no additional information

tag: HCV +


title: Liv31Post

description: no additional information


title: LivPAPre

description: no additional information


title: Liv30Post

description: no additional information


title: Normal Caucasian control 4

description: Pool of RNAs from cells in passages 14 and 15 of Coriell cell line GM03377

source_name: skin fibroblasts, passages #14 and 15

value: Caucasian


title: Liv47Don

description: no additional information

tag: Biopsy Type = No Manipulation (Donor)


title: Liv50Don

description: no additional information


title: Liv48Pre

description: no additional information


title: LivPADon

description: no additional information


title: Liv46Post

description: no additional information


title: Setleis Syndrome patient 1

description: Sister of Setleis_01 and _02

source_name: skin fibroblasts, passage #4


title: Liv49Post

description: no additional information


title: Liv26Post

description: no additional information


title: Liv30Pre

description: no additional information


title: Liv27Don

description: no additional information


title: Liv30Don

description: no additional information


title: Liv29Don

description: no additional information


title: Liv33Don

description: no additional information


title: Liv32Post

description: no additional information


title: Liv31Pre

description: no additional information


title: Liv48Post

description: no additional information


title: Liv49Don

description: no additional information


title: Liv46Don

description: no additional information


title: Liv42Post

description: no additional information


title: Liv50Pre

description: no additional information


title: Liv47Post

description: no additional information


title: Liv47Pre

description: no additional information


title: Liv48Don

description: no additional information


title: Liv50Post

description: no additional information


title: Liv25Post

description: no additional information


title: Liv29Pre

description: no additional information


title: Liv49Pre

description: no additional information


title: Liv31Don

description: no additional information


title: Liv33Pre

description: no additional information


title: Liv33Post

description: no additional information


title: Liv26Don

description: no additional information


title: Liv32Don

description: no additional information


title: Liv24Post

description: no additional information


title: Liv42Don

description: no additional information


title: Liv26Pre

description: no additional information


title: Liv32Pre

description: no additional information


title: Liv29Post

description: no additional information


title: Liv46Pre

description: no additional information


title: Liv21Don

description: no additional information


title: Liv25Don

description: no additional information


title: Liv21Post

description: no additional information


title: Liv23Pre

description: no additional information


title: Liv20Pre

description: no additional information


title: LivVCUPost(RC)

description: no additional information


title: Liv19Post

description: no additional information


title: Liv19 Don

description: no additional information


title: Liv23Don

description: no additional information


title: LivVCUPre(RC)

description: no additional information


title: Liv20Don

description: no additional information


title: Liv24Pre

description: no additional information


title: Liv23Post

description: no additional information


title: Liv20Post

description: no additional information


title: LivPAPost

description: no additional information


title: Liv24Don

description: no additional information


title: Liv21Pre

description: no additional information


title: Liv19Pre

description: no additional information


title: LivVCUDon(RC)

description: no additional information


title: G1ME_Vector_Control_18hour_repB

status: Public on Jun 10 2009

city: Philadelphia

first: Charles

last: Bailey

state: PA

address: Oncology/4 Wood, 1 Children's Center

institute: Children's Hospital of Philadelphia

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 18 hours following transduction.  Replicate B.

hyb_protocol: Manufacturer's (Affymetrix) protocol

scan_protocol: Manufacturer's (Affymetrix) protocol

data_processing: Expression data was extracted from the resulting CEL files using GenePattern's implementation of the GCRMA algorithm with quantile normalization, and MAS5 algorithm for present/absent calls.

label: Phycoerythrin

source_name: G1ME cell line transduced with MIGR1 vector control

label_protocol: Manufacturer's (Affymetrix) protocol

extract_protocol: Total RNA was extracted using Trizol and the Qiagen RNeasy kit.

treatment_protocol: Cells transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 18 hours following transduction.

tag: cell line


title: G1ME_GATA1_42hour_repB

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate B.

source_name: G1ME cell line transduced with GATA1-expressing construct

treatment_protocol: Cells transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 42 hours following transduction.


title: G1ME_GATA1_42hour_repA

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate A.


title: G1ME_Vector_Control_42hour_repC

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate C.

treatment_protocol: Cells transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 42 hours following transduction.


title: G1ME_Vector_Control_42hour_repB

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate B.


title: Pancreatic Sample 37-Tumor

city: Rochester

first: Liewei

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression of -PancreaticSample37-Tumor

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as normalization method.

label_protocol: Lableing was performed according to Affymetrix Gene Chip technical manual

extract_protocol: RNA extraction was performed as Affymetrix GeneChip expression technical manual (Affymetrix, Inc., Santa Clara, CA). Briefly, total RNA samples were extracted, followed by measurement of the A2260/a280 ratio with at least 1.8 for pure RNA. Quality of the RNA was checked by an Agilent 2100 Bioanalyzer.  The Bioanalyzer gel profile exhibited a 28S band that is 2 times more intense than 18S ribosomal RNA. The quality of RNA was assessed by agarose gel electrophoresis.

tag: tissue

value: Tumor Tissue in Pancreatic Cancer Sample

tag: sex

value: Female

tag: age


title: G1ME_Vector_Control_18hour_repA

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 18 hours following transduction.


title: G1ME_GATA1_42hour_repC

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate C.


title: G1ME_GATA1_18hour_repA

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 18 hours following transduction.  Replicate A.

treatment_protocol: Cells transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 18 hours following transduction.


title: Pancreatic Sample 38-Normal

description: Gene expression of -PancreaticSample38-Normal

value: Normal Tissue in Pancreatic Cancer Sample

value: Male


title: Pancreatic Sample 38-Tumor

description: Gene expression of -PancreaticSample38-Tumor


title: G1ME_GATA1_18hour_repB

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 18 hours following transduction.  Replicate B.


title: G1ME_GATA1_18hour_repC

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1. GFP-positive cells isolated by FACS 18 hours following transduction.  Replicate C.


title: Pancreatic Sample 36-Normal

description: Gene expression of -PancreaticSample36-Normal


title: G1ME_Vector_Control_18hour_repC

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 18 hours following transduction.  Replicate C.


title: G1ME_Vector_Control_42hour_repA

description: G1ME Gata1-negative murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP control vector. GFP-positive cells isolated by FACS 42 hours following transduction.  Replicate A.


title: Pancreatic Sample 36-Tumor

description: Gene expression of -PancreaticSample36-Tumor


title: Pancreatic Sample 35-Normal

description: Gene expression of -PancreaticSample35-Normal


title: Pancreatic Sample 27-Tumor

description: Gene expression of -PancreaticSample27-Tumor


title: Pancreatic Sample 34-Tumor

description: Gene expression of -PancreaticSample34-Tumor


title: Pancreatic Sample 31-Tumor

description: Gene expression of -PancreaticSample31-Tumor


title: Pancreatic Sample 33-Normal

description: Gene expression of -PancreaticSample33-Normal


title: Pancreatic Sample 33-Tumor

description: Gene expression of -PancreaticSample33-Tumor


title: Pancreatic Sample 32-Tumor

description: Gene expression of -PancreaticSample32-Tumor


title: Pancreatic Sample 31-Normal

description: Gene expression of -PancreaticSample31-Normal


title: Pancreatic Sample -Tumor

description: Gene expression of -PancreaticSample-Tumor

source_name: PancreaticSample-Tumor


title: Pancreatic Sample 30-Normal

description: Gene expression of -PancreaticSample30-Normal


title: Pancreatic Sample 26-Tumor

description: Gene expression of -PancreaticSample26-Tumor


title: Pancreatic Sample 35-Tumor

description: Gene expression of -PancreaticSample35-Tumor


title: Pancreatic Sample 28-Tumor

description: Gene expression of -PancreaticSample28-Tumor


title: Pancreatic Sample 19-Tumor

description: Gene expression of -PancreaticSample19-Tumor


title: Pancreatic Sample 30-Tumor

description: Gene expression of -PancreaticSample30-Tumor


title: Pancreatic Sample 24-Normal

description: Gene expression of -PancreaticSample24-Normal


title: Pancreatic Sample 22-Tumor

description: Gene expression of -PancreaticSample22-Tumor


title: Pancreatic Sample 23-Tumor

description: Gene expression of -PancreaticSample23-Tumor


title: Pancreatic Sample 25-Tumor

description: Gene expression of -PancreaticSample25-Tumor


title: Pancreatic Sample 21-Tumor

description: Gene expression of -PancreaticSample21-Tumor


title: Pancreatic Sample 24-Tumor

description: Gene expression of -PancreaticSample24-Tumor


title: Pancreatic Sample 4-Tumor

description: Gene expression of -PancreaticSample4-Tumor


title: Pancreatic Sample 17-Tumor

description: Gene expression of -PancreaticSample17-Tumor


title: Pancreatic Sample 20-Tumor

description: Gene expression of -PancreaticSample20-Tumor


title: Pancreatic Sample 4-Normal

description: Gene expression of -PancreaticSample4-Normal


title: Pancreatic Sample 25-Normal

description: Gene expression of -PancreaticSample25-Normal


title: Pancreatic Sample 29-Tumor

description: Gene expression of -PancreaticSample29-Tumor


title: Pancreatic Sample 14-Tumor

description: Gene expression of -PancreaticSample14-Tumor


title: Pancreatic Sample 5-Tumor

description: Gene expression of -PancreaticSample5-Tumor


title: Pancreatic Sample 14-Normal

description: Gene expression of -PancreaticSample14-Normal


title: Pancreatic Sample 15-Tumor

description: Gene expression of -PancreaticSample15-Tumor


title: Pancreatic Sample 54-Normal

description: Gene expression of -PancreaticSample54-Normal


title: Pancreatic Sample 15-Normal

description: Gene expression of -PancreaticSample15-Normal


title: Pancreatic Sample 12-Tumor

description: Gene expression of -PancreaticSample12-Tumor


title: Pancreatic Sample 54-Tumor

description: Gene expression of -PancreaticSample54-Tumor


title: Pancreatic Sample 13-Tumor

description: Gene expression of -PancreaticSample13-Tumor


title: Pancreatic Sample 11-Normal

description: Gene expression of -PancreaticSample11-Normal


title: treatment, rep 2

city: Ithaca

first: Georg

last: Jander

address: 1 Tower Rd

institute: Boyce Thompson Institute for Plant Research

hyb_protocol: Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.

data_processing: Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the Affymetrix GeneChip® Operating Software (GCOS) system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).

source_name: 3-week-old Arabidopsis leaves, aphid saliva treated, harvested after 24 hrs

growth_protocol: Plants: Seeds of wild-type Arabidopsis (Arabidopsis thaliana) land race Columbia-0 (Col-0) were obtained from the Arabidopsis Biological Resource Center. Seeds were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix (Landry, Chapple & Last, 1995) with Osmocoat fertilizer (Scotts). Plants were grown in Conviron growth chambers in 20x40 cm nursery flats at a photosynthetic photon flux density of 200 mmol/m2s and a 16h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Unless stated differently, plants were grown for 3 weeks and used in experiments before flowering. Aphids: All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea var. Wisconsin Golden Acre; Seedway) with a 16h day (150 mmol/m2s at 24°C) and an 8h night (19°C) at 50% relative humidity.

extract_protocol: RNA was extracted using the Qiagen Plant RNeasy kit (Qiagen, Valencia, CA, USA). RNA quality and quantity was assessed with an Agilent BioAnalyser 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Fifty aphids were allowed to feed from 50 μL artificial diet containing sucrose and amino acids (Kim & Jander, 2007) between two layers of Parafilm (Alcan Packaging). After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates.

tag: ecotype

value: leaves

tag: treatment

value: aphid saliva treated


title: control, rep 3

scan_protocol: Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.

source_name: 3-week-old Arabidopsis leaves, control, harvested after 24 hrs

value: control


title: Pancreatic Sample 9-Tumor

description: Gene expression of -PancreaticSample9-Tumor


title: Pancreatic Sample 53-Tumor

description: Gene expression of -PancreaticSample53-Tumor


title: Pancreatic Sample 16-Tumor

description: Gene expression of -PancreaticSample16-Tumor


title: Pancreatic Sample 7-Tumor

description: Gene expression of -PancreaticSample7-Tumor


title: Pancreatic Sample 53-Normal

description: Gene expression of -PancreaticSample53-Normal


title: Pancreatic Sample 1-Tumor

description: Gene expression of -PancreaticSample1-Tumor


title: Pancreatic Sample 16-Normal

description: Gene expression of -PancreaticSample16-Normal


title: control, rep 1

label_protocol: Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.


title: Pancreatic Sample 11-Tumor

description: Gene expression of -PancreaticSample11-Tumor


title: treatment, rep 3


title: treatment, rep 1


title: Pancreatic Sample 6-Tumor

description: Gene expression of -PancreaticSample6-Tumor


title: control, rep 2


title: N1_2012, MDS, DS

status: Public on Jun 09 2009

city: Pleasanton

first: Wei-Min

last: Liu

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

description: Microarray classification of myelodysplastic syndrome identifies patients with high risk of AML transformation

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278.

source_name: Cardiff

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: not applicable

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols

treatment_protocol: Samples are from untreated patients.

tag: disease state

value: MDS


title: N1_2014, MDS, DS


title: N1_2020, MDS, DS

source_name: Berlin


title: N1_2017, MDS, DS

source_name: Munich


title: N1_2004, MDS, DS


title: N1_2031, non-leukemia, DS

value: none-of-the-targets


title: N1_2018, MDS, DS


title: N1_2023, MDS, DS


title: N1_2009, MDS, DS


title: N1_2008, MDS, DS


title: N1_2007, MDS, DS

source_name: Salamanca


title: N1_2003, MDS, DS


title: N1_1999, MDS, DS


title: N1_2075, non-leukemia, DS


title: N1_1998, MDS, DS


title: N1_1996, MDS, DS


title: N1_1994, MDS, DS


title: N1_1997, MDS, DS


title: N1_1978, MDS, DS


title: N1_1991, MDS, DS


title: N1_1995, MDS, DS


title: N1_1986, MDS, DS


title: N1_1977, MDS, DS


title: N1_1969, MDS, DS


title: N1_1980, MDS, DS


title: N1_1987, MDS, DS


title: N1_1956, MDS, DS


title: N1_1958, MDS, DS


title: N1_1973, MDS, DS


title: N1_1962, MDS, DS


title: N1_1959, MDS, DS


title: N1_1981, MDS, DS


title: N1_1952, MDS, DS


title: N1_1957, MDS, DS


title: N1_1953, MDS, DS


title: N1_1966, MDS, DS


title: N1_1950, MDS, DS


title: N1_1968, MDS, DS


title: N1_1951, MDS, DS


title: N1_1943, MDS, DS


title: N1_1934, MDS, DS


title: N1_1942, MDS, DS


title: N1_1933, MDS, DS


title: N1_1932, MDS, DS


title: N1_1935, MDS, DS


title: N1_1930, MDS, DS


title: N1_1924, MDS, DS


title: N1_1919, MDS, DS


title: N1_1910, MDS, DS


title: N1_1927, MDS, DS


title: N1_1912, MDS, DS


title: N1_1926, MDS, DS


title: N1_1921, MDS, DS


title: N1_1941, MDS, DS


title: N1_1915, MDS, DS


title: N1_1923, MDS, DS


title: N1_1909, MDS, DS


title: N1_1908, MDS, DS


title: N1_1903, MDS, DS


title: N1_1890, MDS, DS


title: N1_1928, MDS, DS


title: N1_1892, MDS, DS


title: N1_1895, MDS, DS


title: N1_1916, MDS, DS


title: N1_1899, MDS, DS


title: N1_1879, MDS, DS


title: N1_1882, MDS, DS


title: N1_1893, MDS, DS


title: N1_1905, MDS, DS


title: N1_1864, MDS, DS


title: N1_1869, MDS, DS


title: N1_1853, MDS, DS


title: N1_1850, MDS, DS


title: N1_1858, MDS, DS


title: N1_1865, MDS, DS


title: N1_1833, MDS, DS


title: N1_1837, MDS, DS


title: N1_1860, MDS, DS


title: N1_1875, MDS, DS


title: N1_1839, MDS, DS


title: N1_1843, MDS, DS


title: N1_1870, MDS, DS


title: N1_1840, MDS, DS


title: N1_1827, MDS, DS


title: N1_1830, MDS, DS


title: N1_1831, MDS, DS


title: N1_1862, MDS, DS


title: N1_1829, MDS, DS


title: N1_1851, MDS, DS


title: N1_1846, MDS, DS


title: N1_1823, MDS, DS


title: N1_1838, MDS, DS


title: N1_1210, AML, DS

value: AML


title: N1_1162, AML, DS


title: N1_1821, MDS, DS


title: N1_1048, AML, DS


title: N1_1261, AML, DS


title: N1_2022, MDS, DQN3


title: N1_1030, AML, DS


title: N1_1985, MDS, DQN3


title: N1_2019, MDS, DQN3


title: N1_2055, non-leukemia, DQN3


title: N1_1982, MDS, DQN3


title: N1_1271, AML, DS


title: N1_2016, MDS, DQN3


title: N1_2001, MDS, DQN3


title: N1_1974, MDS, DQN3


title: N1_1961, MDS, DQN3


title: N1_2005, MDS, DQN3


title: N1_1967, MDS, DQN3


title: N1_1992, MDS, DQN3


title: N1_2058, non-leukemia, DQN3


title: N1_1979, MDS, DQN3


title: N1_2011, MDS, DQN3


title: N1_1984, MDS, DQN3


title: N1_0944, AML, DS


title: N1_1963, MDS, DQN3


title: N1_1955, MDS, DQN3


title: N1_1972, MDS, DQN3


title: N1_1971, MDS, DQN3


title: N1_1954, MDS, DQN3


title: N1_2000, MDS, DQN3


title: N1_1947, MDS, DQN3


title: N1_1944, MDS, DQN3


title: N1_1946, MDS, DQN3


title: N1_1939, MDS, DQN3


title: N1_1945, MDS, DQN3


title: N1_1936, MDS, DQN3


title: N1_1907, MDS, DQN3


title: N1_1902, MDS, DQN3


title: N1_1937, MDS, DQN3


title: N1_1970, MDS, DQN3


title: N1_1949, MDS, DQN3


title: N1_1931, MDS, DQN3


title: N1_1906, MDS, DQN3


title: N1_1917, MDS, DQN3


title: N1_1920, MDS, DQN3


title: N1_1901, MDS, DQN3


title: N1_1929, MDS, DQN3


title: N1_1896, MDS, DQN3


title: N1_1887, MDS, DQN3


title: N1_1900, MDS, DQN3


title: N1_1885, MDS, DQN3


title: N1_1914, MDS, DQN3


title: N1_1898, MDS, DQN3


title: N1_1922, MDS, DQN3


title: N1_1889, MDS, DQN3


title: N1_1884, MDS, DQN3


title: N1_1883, MDS, DQN3


title: N1_1891, MDS, DQN3


title: N1_1878, MDS, DQN3


title: N1_1854, MDS, DQN3


title: N1_1857, MDS, DQN3


title: N1_1874, MDS, DQN3


title: N1_1848, MDS, DQN3


title: N1_1877, MDS, DQN3


title: N1_1849, MDS, DQN3


title: N1_1868, MDS, DQN3


title: N1_1841, MDS, DQN3


title: N1_1925, MDS, DQN3


title: N1_1847, MDS, DQN3


title: N1_1842, MDS, DQN3


title: N1_1855, MDS, DQN3


title: N1_1845, MDS, DQN3


title: N1_1828, MDS, DQN3


title: N1_1867, MDS, DQN3


title: N1_1822, MDS, DQN3


title: N1_1819, MDS, DQN3


title: N1_1836, MDS, DQN3


title: N1_1818, MDS, DQN3


title: N1_1844, MDS, DQN3


title: N1_1817, MDS, DQN3


title: N1_1820, MDS, DQN3


title: N1_1826, MDS, DQN3


title: N1_1824, MDS, DQN3


title: N1_1264, AML, DQN3


title: cortex, biological rep2

first: Ji-Young

last: Lee

address: Tower Rd.

institute: Boyce Thompson Institute

description: Gene expression data from cortex cells of Arabidopsis seedling roots

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

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

source_name: Arabidopsis roots of 6 day old seedlings

label_protocol: Biotinylated cRNA was prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seedlings were grown vertically for 6 days at 22 degree under 16 hours of day and 8 hours of night.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH)

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh in two rows. About 1cm long root tips were harvested and placed in the protoplast solution as described in Birnbaum et al. (2005) Nat. Methods. GFP expressing protoplasts  were isolated from Fluorescence Activated Cell Sorter to collect total RNA.

value: cortex

tag: genotype

value: wild type columbia

value: 6 day old seedlings


title: cortex, biological rep3

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: differentiating xylem, biological rep2

description: Gene expression data from differentiating xylem cells of Arabidopsis seedling roots

value: xylem


title: N1_1208, AML, DQN3


title: differentiating xylem, biological rep3


title: N1_1064, AML, DQN3


title: N1_1165, AML, DQN3


title: phloem sieve cells and companion cells, biological rep1

description: Gene expression data from phloem sieve cells and companion cells of Arabidopsis seedling roots

value: phloem


title: N1_1148, AML, DQN3


title: N1_1122, AML, DQN3


title: N1_1053, AML, DQN3


title: phloem sieve cells and companion cells, biological rep2


title: differentiating xylem, biological rep1


title: cortex, biological rep1


title: m.Gas:  castration, 2.5 mg testosterone pellet implantation; biological rep2

status: Public on Jun 08 2009

city: St. Louis

first: Harvey

last: Armbrecht

state: MO

address: #1 Jefferson Barracks Drive

department: Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology

institute: St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine

description: Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, 2.5 mg testosterone pellet implantation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package.  The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects).  The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.

treatment_protocol: Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N = 12/group, total 36 mice).  Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone).  Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery.  After 14-days, blood was sampled from the carotid artery of anesthetized  animals, and the non-fasted animals were sacrificed by decapitation.  The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.

value: gastrocnemius muscle (m.Gas) in young adult CD-1 mice

tag: castration surgery

value: castration

tag: testosterone supplementation

value: 2.5 mg testosterone pellet implantation


title: m.Gas:  castration, placebo pellet implantation; biological rep2

description: Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, placebo pellet implantation

value: placebo pellet implantation


title: m.Gas:  castration, 2.5 mg testosterone pellet implantation; biological rep3


title: m.Gas:  sham surgery, placebo pellet implantation; biological rep2

description: Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; sham surgery, placebo pellet implantation

value: sham


title: m.Gas:  sham surgery, placebo pellet implantation; biological rep1


title: Day11.5_Placenta_RbE2f4NULL_183-6

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 18 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430A_2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Bioconductor Affy (1.20.0) and gcRMA (2.14.1) packages

label: Biotin

source_name: Embryonic Day 11.5 Placenta; Rb -/- knock-out

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

growth_protocol: Mice were maintained in the MIT animal facility and samples were dissected 11 or 13 days after vaginal plug detection.

extract_protocol: Trizol according to the manufacturer's protocol

treatment_protocol: Treatment conditions were the same for all samples

tag: Mixed (C57BL/6 x 129/Sv) background E2F4+/- and Rb+/- mice used in breeding.


title: m.Gas:  castration, placebo pellet implantation; biological rep1


title: m.Gas:  sham surgery, placebo pellet implantation; biological rep3


title: m.Gas:  castration, 2.5 mg testosterone pellet implantation; biological rep1


title: Day13.5_Placenta_WT_4

source_name: Embryonic Day 13.5 Placenta; wild-type


title: m.Gas:  castration, placebo pellet implantation; biological rep3


title: Day13.5_Placenta_RbNULL_3

source_name: Embryonic Day 13.5 Placenta; Rb -/- knock-out


title: N1_0917, AML, DQN3


title: Day13.5_Placenta_WT_5


title: Day11.5_Placenta_RbE2f4NULL_183-10


title: Day13.5_Placenta_RbNULL_2


title: Day11.5_Placenta_RbE2f4NULL_169-4


title: Day11.5_Placenta_WT_172-6

source_name: Embryonic Day 11.5 Placenta; wild-type


title: Day11.5_Placenta_WT_183-1


title: Day11.5_Placenta_WT_150-8


title: TRAF6KOmouseTcell_d10_rep3

status: Public on Jun 05 2009

first: Li-San

address: 1424 Blockley Hall, 423 Guardian Drive

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

hyb_protocol: Hybridization was performed by the University of Pennsylvania Microarray Core Facility. The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C to the microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

scan_protocol: Gene chips were scanned using the Affymetrix GCS3000 high resolution scanner.

data_processing: GCRMA was used to compute expression levels for each probeset.

source_name: Donor Traf6-deficient OTI CD8+ T cells sorted from blood and spleen 10 days following infection

label_protocol: Labeling was perfomed by the University of Pennsylvania Microarray Core Facility.  All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly,  sscDNA was purified and yields determined after amplification using NuGEN Ovation System kit protocol, starting with 200ng total RNA.   5ug of amplified RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: OTI-cells (<5000) from OTI-WT and OTI-TRAF-6-deficient mice were adoptively transferred into congenic recipient mice and infected with attenuated (ActA-deficient) Listeria monocytogenes expressing Ova. Splenocytes and blood were harvested (at d6 and d10 post-infection) from individual mice, red cells lysed, and donor cells were sorted (FACS Vantage, BD bioscience) on the CD45.2 donor marker directly into Trizol LS (Invitrogen).

extract_protocol: RNA was extracted by the University of Pennsylvania Microarray Core Facility according to the protocol outlined for use with Trizol LS (Invitrogen).

treatment_protocol: There was no additional treatment of the cells.

value: blood and spleen

tag: cell type

value: T lymphocyte (sorted cells)

value: TRAF6 knockout

tag: timepoint

value: 10 days after infection


title: TRAF6KOmouseTcell_d10_rep5


title: med macs-LN-2

city: Sydney

first: Tri

middle: Giang

last: Phan

state: NSW

address: 384 Victoria St, Darlinghurst

department: Immunology and Inflammation

country: Australia

institute: Garvan Institute

description: non-immunized

hyb_protocol: 3.75 ug of total fragmented cDNA was hybridized for 16 h at 45C

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

source_name: med macs from sort 2

label_protocol: FL-Ovation cDNA Biotin Module V2

extract_protocol: RNAEasy Micro kit,Ovation RNA Amplification System V2

treatment_protocol: LNs were digested with an protease cocktail and isolated cells passed enriched by density gradient separation before fluorescence-activated cell sorting

tag: strain

tag: gender

value: female

value: 6-12 weeks

value: lymph node


title: TRAF6KOmouseTcell_d10_rep4


title: TRAF6KOmouseTcell_d10_rep1


title: WTmouseTcell_d10_rep5

source_name: Donor WT OTI CD8+ T cells sorted from blood and spleen 10 days following infection

value: Wildtype


title: WTmouseTcell_d10_rep2


title: med macs-LN-1

description: non-immunized

source_name: med macs from sort 1


title: WTmouseTcell_d10_rep4


title: SCS macs-LN-3

description: non-immunized

source_name: SCS macs from sort 3


title: TRAF6KOmouseTcell_d6_rep2

source_name: Donor Traf6-deficient OTI CD8+ T cells sorted from blood and spleen 6 days following infection

value: 6 days after infection


title: med macs-LN-3

description: non-immunized

source_name: med macs from sort 3


title: SCS macs-LN-2

description: non-immunized

source_name: SCS macs from sort 2


title: WTmouseTcell_d6_rep2

source_name: Donor WT OTI CD8+ T cells sorted from blood and spleen 6 days following infection


title: WTmouseTcell_d10_rep3


title: TRAF6KOmouseTcell_d10_rep2


title: WTmouseTcell_d6_rep1


title: WTmouseTcell_d10_rep1


title: SCS macs-LN-1

description: non-immunized

source_name: SCS macs from sort 1


title: TRAF6KOmouseTcell_d6_rep3


title: TRAF6KOmouseTcell_d6_rep1


title: WTmouseTcell_d6_rep3


title: centrocyte, tonsil#7

status: Public on Jun 04 2009

city: RENNES

first: Thierry

last: FEST

address: 2 avenue du Pr. Léon Bernard

country: France

institute: Unité INSERM

description: centrocyte, tonsil#7

hyb_protocol: Following fragmentation, 12 µg of cARN were hybridized for 16h at 45°C and 60rpm on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the GeneChip Scanner Affymetrix 3000

data_processing: The normalized hybridization intensity for each probe set was calculated using GC-RMA method, background noise was decreased by eliminating probe set with a CV<0.8. Both analyses were done with ArrayAssist software package (Agilent Technologies).

source_name: Inflamed non tumoral human tonsil#7

label_protocol: Biotinylated cARN were prepared according to the small sample Affymetrix protocol using 100ng total RNA

extract_protocol:
The CD10posCD44lowCXCR4pos and CXCR4neg B cell subpopulations were separated by FACS sorting using anti-CXCR4 PE (BD Biosciences, San Jose, CA), anti-CD10 ECD (Beckman Coulter, Villepinte, France), anti-CD44 PC7 and anti-CD19 Pacific Blue (eBioscience, San Diego, CA) mAbs. Sorts were performed on a FACSAriaTM cell sorter (BD Biosciences)
Total RNA from each purified population was extracted using an RNeasy kit (Qiagen), and RNA integrity assessed using a bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell suspension

value: Flow sorted cells

value: centrocyte, tonsil


title: centrocyte, tonsil#11

description: centrocyte, tonsil#11

source_name: Inflamed non tumoral human tonsil#11


title: centrocyte, tonsil#8

description: centrocyte, tonsil#8

source_name: Inflamed non tumoral human tonsil#8


title: centroblast, tonsil#6

description: centroblast, tonsil#6

source_name: Inflamed non tumoral human tonsil#6

value: centroblast, tonsil


title: Smooth muscle cells  uninfected control, 48 hours,  biological rep 3

city: Quito

first: Jaime

middle: Alfredo

last: Costales

address: 12 de Octubre y Patria

department: Biological Sciences

country: Ecuador

institute: Pontificia Universidad Catolica del Ecuador

description: Gene expression data from untreated human vascular smooth muscle cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw data was uploaded into the Rosetta Resolver  System  for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.

source_name: Vascular smooth muscle control 48 hours

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: Human foreskin fibroblasts (HFF) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.  Human vascular smooth muscle cells (VSMC) were grown in Ham’s F12K medium with 2  mM L-glutamine, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 10 mM TES, 0.05 mg/ml ascorbic acid, 0.001 mg/ml insulin, 0.01 mg/ml transferrin, 10ng/ml sodium selenite, 0.03 mg/ml endothelial cell growth supplement (ECGS) and 10% FBS.  Human cardiac microvascular endothelial cells (HMVEC) were maintained in endothelial cell basal medium-2 and endothelial cell growth supplements (Cambrex Bio Science) including 5% FBS. All cells were allowed to grow for 48 hours at 37 C in a CO2 incubator until they reached 80% confluency. To achieve 80% confluence 48 hrs post-plating VSMC were seeded at a density of 2 x 105 cells/ 10 cm dish.  For Transwell experiments, the lower wells of 10 cm Transwell plates (Corning Inc; 3μm pore size) were seeded at a density of 2 x 105 cells/dish (HFF) or 4 x 105 cells/dish (HMVEC) with half the amount, respectively, plated in the upper chamber.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen). RNA integrity was monitored with a Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA)

treatment_protocol: VSMC or HFF/HMVEC in the lower chamber of Transwell were infected for 2 hours with 1 x 10^8/ml trypomastigotes at 37˚C in a CO2 incubator in the appropriate growth medium for each cell type supplemented with 2% FBS.  Extracellular parasites were aspirated, and infected monolayers rinsed 5 times with PBS before incubation in complete growth medium (10% FBS for VSMC and HFF and 5% FBS for HMVECs) for the indicated times.

tag: Human vascular smooth muscle cell (VSMC)


title: centroblast, tonsil#8

description: centroblast, tonsil#8


title: centrocyte, tonsil#6

description: centrocyte, tonsil#6


title: Smooth muscle cells  infected with T. cruzi for 48 hours, biological rep 1

description: Gene expression data from human vascular smooth muscle cells infected with T. cruzi for 48 hours

source_name: Vascular smooth muscle cells infected with T. cruzi for 48 hours


title: Endothelial cells on control transwell top, biological rep 1

description: Gene expression data from human microvascular endothelial cells bathed with medium from untreated cells

source_name: Endothelial cells bathed with media from  control cells  (transwell top)

tag: Human microvascular endothelial cells (HMVEC)


title: Endothelial cells on infected transwell top, biological rep 1

description: Gene expression data from human microvascular endothelial cells bathed with medium from T. cruzi infected cells

source_name: Endothelial cells bathed with media from  cells infected  with T. cruzi (transwell top)


title: Endothelial cells infected with T. cruzil, biological rep 2

description: Gene expression data from human microvascular endothelial cells infected with T. cruzi

source_name: Endothelial cells infected with T. cruzi (transwell bottom)


title: centroblast, tonsil#7

description: centroblast, tonsil#7


title: Smooth muscle cells  infected with T. cruzi for 48 hours, biological rep 2


title: Smooth muscle cells  uninfected control, 48 hours,  biological rep 1


title: Endothelial cells infected with T. cruzil, biological rep 1


title: Smooth muscle cells  uninfected control, 24 hours,  biological rep 2

source_name: Vascular smooth muscle control 24 hours


title: Endothelial cells on infected transwell top, biological rep 2


title: Smooth muscle cells  infected with T. cruzi for 24 hours, biological rep 1

description: Gene expression data from human vascular smooth muscle cells infected with T. cruzi for 24 hours

source_name: Vascular smooth muscle cells infected with T. cruzi for 24 hours


title: Smooth muscle cells  uninfected control, 48 hours,  biological rep 2


title: Smooth muscle cells  infected with T. cruzi for 48 hours, biological rep 3


title: Fibroblasts on control transwell top, biological rep 2

description: Gene expression data from  human fibroblast bathed with medium from untreated cells

source_name: Fibroblasts bathed with media from  control cells  (transwell top)

tag: Human foreskin fibroblasts (HFF) BJ


title: Endothelial cells on control transwell top, biological rep 2


title: Smooth muscle cells  infected with T. cruzi for 24 hours, biological rep 2


title: Smooth muscle cells  uninfected control, 24 hours,  biological rep 1


title: Fibroblasts on control transwell top, biological rep 1


title: Endothelial cells uninfected control, biological rep 2

description: Gene expression data from untreated human microvascular endothelial cells

source_name: Endothelial cells control (transwell bottom)


title: Fibroblasts on infected transwell top, biological rep 1

description: Gene expression data from  human fibroblast bathed with medium from T. cruzi infected cells

source_name: Fibroblasts bathed with media from  cells infected  with T. cruzi (transwell top)


title: Fibroblasts on infected transwell top, biological rep 2


title: Endothelial cells uninfected control, biological rep 1


title: centroblast, tonsil#11

description: centroblast, tonsil#11


title: Fibroblasts uninfected control, biological rep 2

description: Gene expression data from untreated human fibroblast

source_name: Fibroblast control (transwell bottom)


title: Fibroblasts uninfected control, biological rep 1


title: RH41, Alveolar, rhabdomyosarcoma cell line

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description:
RH41 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 expression profiles.

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 MAS5.0 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. 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.

growth_protocol: RH41 cells were cultured in RPMI (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: Cell line from a rhabdomyosarcoma tumor


title: RD,Embryonal,rhabdomyosarcoma cell line

description:
RD 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 expression profiles.

source_name: RD

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


title: RH30,Alveolar,rhabdomyosarcoma cell line

description: RH30 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 expression profiles.

data_processing: Expression data (.cel files) were normalized with the MAS5.0 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. 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.

growth_protocol: RH30 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: CW9019,Alveolar,rhabdomyosarcoma cell line

description:
CW9019 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 expression profiles.

growth_protocol: CW9019 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: Fibroblasts infected with T. cruzi, biological rep 2

description: Gene expression data from human fibroblast infected with T. cruzi

source_name: Fibroblasts infected with T. cruzi (transwell bottom)


title: TE617T, rhabdomyosarcoma cell line

description:
TE617T 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 expression profiles.

growth_protocol: TE617T cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: liver, txnrd1 cond/+ albCre0, 82

status: Public on Jun 03 2009

city: Bozeman

first: Ed

last: Schmidt

state: MT

department: M&I Dept

institute: Montana State University

description: Gene expression in liver, Txnrd1 wildtype and knockout

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA was hybridized for 16 h at 45oC on Affymetrix Mouse 430 2.0 arrays.  Washes and staining were done in Affymetrix Fludics Station 400.

scan_protocol: Affymetrix 7G scanner.

data_processing: The data were imported into Genespring using RMA preprocessing for analysis.

source_name: Mus musculus adult liver

label_protocol: One cycle biotinylated cRNA generated from 1 µg total RNA with Ambion Message Amp-II Biotin Enhanced system.

growth_protocol: Experimental livers come from mice with a conditional-null allele of txnrd1 disrupted by albCre.

extract_protocol: Total liver RNA sedimented through CsCl cushions.

treatment_protocol: Young male mice, singly housed 10d, 14:10h light cycle, 2:30 pm harvest.

tag: tissue

value: liver

tag: age

value: adult

tag: genetic modification

value: txnrd1 cond/+ albCre0


title: RH18,Alveolar,rhabdomyosarcoma cell line

description:
RH18 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 expression profiles.

growth_protocol: RH18 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: liver, txnrd1 cond/- albCre1, 81

value: txnrd1 cond/- albCre1


title: liver, txnrd1 cond/- albCre1, 72


title: RH4,Alveolar,rhabdomyosarcoma cell line

description: RH4 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 expression profiles.

growth_protocol: RH4 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: liver, txnrd1 cond/- albCre1, 73


title: liver, txnrd1 cond/+ albCre0, 71


title: RMS-YM,Embryonal,rhabdomyosarcoma cell line

description:
RMS-YM 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 expression profiles.

source_name: RMS-YM

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


title: liver, txnrd1 cond/+ albCre0, 80


title: liver, txnrd1 cond/+ albCre0, 70


title: Fibroblasts infected with T. cruzi, biological rep 1


title: Hs729T,Pleomorphic,rhabdomyosarcoma cell line

description:
Hs729T 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 expression profiles.

growth_protocol: Hs729T cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: RUCH-2,Embryonal,rhabdomyosarcoma cell line

description: RMS 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 expression profiles.

growth_protocol: RUCH-2 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: RUCH3,Embryonal,rhabdomyosarcoma cell line

description:
RUCH3 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 expression profiles.

growth_protocol: RUCH3 cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.


title: liver, txnrd1 cond/- albCre1, 69


title: RMS,Alveolar,rhabdomyosarcoma cell line

description:
RMS 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 expression profiles.

source_name: RMS

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


title: SCMC-RMZ,Alveolar,rhabdomyosarcoma cell line

source_name: SCMC-RMZ

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