title: Single cell profile of E12.5 peripheral cell A6

first: jeffrey

last: trimarchi

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Single cells were harvested from a dissociated CD1 mouse retina at embryonic day 12.5 (E12.5). The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.

source_name: E12.5 single developing ciliary body cell A6

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: The isolated single cells were lysed, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle.

tag: developmental stage

value: embryonic day 12.5 (E12.5)

value: retina

value: ciliary body


title: As4.1 cells, interleukin treatment_2

status: Public on May 01 2009

type: RNA

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

country: USA

institute: University of Iowa

description: Gene expression data from As4.1 cells.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

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.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: As4.1 cells, treated with interleukin

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

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

treatment_protocol: Interleukin treatment

tag: As4.1 cells are a renin-expressing cell line.


title: PPARα KO Wyeth+Heat Shock treated 23

city: Research Triangle Park

first: beena

last: vallanat

address: 109 Tw Alexanser Dr

institute: EPA

description: Studies utilized wild-type and PPARα-null male mice 9–12 weeks of age on a mixed SV129/C57BL/6 background. Control and treated mice were provided with NIH-07 rodent chow (Zeigler Brothers, Gardeners, PA) and deionized, filtered water ad libitum.  Lighting was on a 12-hr light/dark cycle.  Mice were sacrificed 4 hrs, 24 hrs and 3 days after the heat stress.

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

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000

data_processing: The data were analyzed with Rosetta Resolve 7.0  using Affymetrix default profile builder analysis settings.

source_name: PPARα KO Wyeth+Heat Shock treated 23

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

extract_protocol: Liver RNA was isolated using a modified guanidium isothiocyanate method (TRIzol®; Invitrogen) and was further purified using silica membrane spin columns (RNeasy®; Qiagen, Valencia, CA).  RNA integrity was assessed by the RNA 6000 LabChip® kit using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

treatment_protocol: Lighting was on a 12-hr light/dark cycle.  Mice (n = 5-6 per group) were fed a control diet or a diet containing the PPARα agonist WY-14,643 (ChemSyn Science, Lenexa, KS) (WY) in the diet (500 ppm) for 1 week followed by a 40-min heat stress at 42°C or held at room temperature in wire rack cages.  Mice were sacrificed 4 hrs, 24 hrs and 3 days after the heat stress.    Heat in the exposure chamber was generated by a combination of the building reheat system, an in-line air heater and two small surface heaters.  The in-line heater (Riley Equipment Company, Inc., Houston, TX) was set to approximately 300 °F.  The heated air traveled through a 2 foot by 2 inch inlet tube constructed on PVC, stainless steel and Teflon into the bottom of the H1000 inhalation chamber.  A small diverter was placed in the bottom of the H1000 inhalation chamber to prevent a chimney effect in the chamber and increasing the efficiency of the heat distribution.  The stainless steel animal cage unit was placed in the center of the H1000 inhalation chamber and a feces/urine catch pan was placed in the top-most position of the chamber.  A small (1500 watt) heater was placed on either side of the H1000 inhalation chamber approximately 4 inches from the surface.  These heaters heated the stainless steel sides and heated the surface enough to allow the internal temperature of the chamber to reach approximately 43°C.  The temperature was monitored in three locations of the H1000 inhalation chamber:  front door above the animal cage unit, back door below the animal cage unit and in the center approximately two inches using probes (Rotronic Hygrometer Series 1200, Rotronic Instrument Corp., Huntington, NY).

tag: tissue

value: whole liver

tag: genotype

value: PPARα-null

tag: age

value: 9–12 weeks

tag: gender

value: male

tag: background

value: mixed SV129/C57BL/6 background


title: PPARα KO Wyeth 20

source_name: PPARα KO Wyeth 20


title: PPARα KO Wyeth 21

source_name: PPARα KO Wyeth 21


title: As4.1 cells, Vehicle treatment_2

description: Gene expression data from As4.1 cells.

source_name: As4.1 cells, control

treatment_protocol: Vehicle treatment


title: Single cell profile of P0 peripheral cell E8

city: Boston

state: MA

description: Single cells were harvested from a dissociated CD1 mouse retina at postnatal day 0 (P0). The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

source_name: P0 single ciliary body cell E8

tag: strain

value: postnatal day 0 (P0)

tag: cell type


title: As4.1 cells, hydrogen peroxide treatment_1

description: Gene expression data from As4.1 cells.

source_name: As4.1 cells, treated with hydrogen peroxide

treatment_protocol: Hydrogen peroxide treatment


title: PPARα KO Control 14

source_name: PPARα KO Control 14


title: PPARα KO Wyeth 19

source_name: PPARα KO Wyeth 19


title: PPARα KO Heat Shock treated 16

source_name: PPARα KO Heat Shock treated 16


title: PPARα WT Wyeth treated 9

source_name: PPARα WT Wyeth treated 9

value: wild-type


title: PPARα KO Wyeth+Heat Shock treated 24

source_name: PPARα KO Wyeth+Heat Shock treated 24


title: PPARα WT Heat shock treated 6

source_name: PPARα WT Heat shock treated 6


title: PPARα WT Wyeth treated 7

source_name: PPARα WT Wyeth treated 7


title: PPARα WT Wyeth+ Heat Shock treated 12

source_name: PPARα WT Wyeth+ Heat Shock treated 12


title: PPARα KO Control 15

source_name: PPARα KO Control 15


title: PPARα KO Heat Shock treated 18

source_name: PPARα KO Heat Shock treated 18


title: PPARα WT Wyeth+ Heat Shock treated 10

source_name: PPARα WT Wyeth+ Heat Shock treated 10


title: PPARα WT Control 1

source_name: PPARα WT Control 1


title: PPARα WT Control 3

source_name: PPARα WT Control 3


title: PPARα WT Wyeth treated 8

source_name: PPARα WT Wyeth treated 8


title: PPARα WT Heat shock treated 4

source_name: PPARα WT Heat shock treated 4


title: PPARα WT Heat shock treated 5

source_name: PPARα WT Heat shock treated 5


title: PPARα WT Wyeth+ Heat Shock treated 11

source_name: PPARα WT Wyeth+ Heat Shock treated 11


title: PPARα WT Control 2

source_name: PPARα WT Control 2


title: Keratinocytes_scrambledsiRNA_rep2

status: Public on May 03 2009

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

description: Primary human keratinocytes were grown in vitro and treated with either a scrambled control siRNA, a pair of siRNA oligomers against Erk1 and Erk2, or an independent pair of siRNA oligomers against Erk1 and Erk2.  RNA was harvested four days later.  Three biological replicates were performed for each of the three groups. See PA Dumesic et al. 2009 Journal of Cell Biology for experimental details.

hyb_protocol: Performed by Stanford PAN Facility

scan_protocol: Performed by Stanford PAN Facility

data_processing: RMA preprocessing normalization by GeneSpring 7.3.

label: Biotin

organism: Homo sapiens

source_name: Primary human keratinocytes treated with scrambled control siRNA

label_protocol: Performed by Stanford PAN Facility

growth_protocol: Keratinocyte SFM

extract_protocol: QIAGEN RNeasy

value: Primary human foreskin keratinocytes


title: BC11-23

type: mixed

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeRNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 14:07:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from the hybridized species with >65% of pixels >1 standard deviations above background in both channels.

organism: Saccharomyces bayanus x Saccharomyces cerevisiae

source_name: BC11-23 RNA

growth_protocol: Growth Temperature : 23C

extract_protocol:
Extracted molecule : RNA
Extraction method : acid phenol extraction

treatment_protocol: Growth Condition : midlog

tag: species

value: S. bayanus/S. cerevisiae hybrid

tag: strain name

molecule: genomic DNA

source_name: BC3 DNA

extract_protocol:
Extracted molecule : DNA
reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf


title: CC5-30

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 13:19:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

organism: Saccharomyces cerevisiae

source_name: CC5-30 RNA

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeRNA.pdf

growth_protocol: Growth Temperature : 30C

value: S. cerevisiae

source_name: CC8 DNA

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf


title: BC11-30

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 15:29:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: BC11-30 RNA


title: U937_control_72hours_rep2

first: Kimberly

last: Stegmaier

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

description: Gene expression data from U937 at 72 hours, replicate 2

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U95Av2 arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: The data were analyzed with Microarray Suite version 4.0 (MAS 4.0) using Affymetrix's default analysis settings.  The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.

source_name: U937 cells with conditional expression of an AML-ETO construct under the control of the tetracycline promoter

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.

extract_protocol: RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.

treatment_protocol: An AML1-ETO-inducible dataset was obtained from U937 cells conditionally expressing an AML-ETO construct under the control of the tetracycline promoter using the protocol previoulsy described (Pabst T, Mueller BU, Harakawa N, et al. AML1-ETO downregulates the granulocytic differentiation factor C/EBPalpha in t(8;21) myeloid leukemia. Nat Med. 2001;7:444-451.). These cells were profiled on Affymetrix U95Av2 oligonucleotide microarrays and preprocessed as above. Samples were collected at 0, 12, 24, 48, and 72 hours after induction. Control samples at 0, 12, 24, 48, and 72 hours were also collected (two samples at each time point).

tag: class

value: Control

tag: exposure time

tag: sample scale factor

tag: cell line


title: BB9-30C

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 13:10:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

organism: Saccharomyces bayanus

source_name: BB9-30C RNA

value: S. bayanus

source_name: BB11 DNA


title: CKO Wild Type TP4

city: Baltimore

first: Thomas

middle: W

last: Kensler

state: MD

address: 615 N Wolfe St SPH Rm E7541

institute: Johns Hopkins School of Medicine

description: genetic control wild-type mice treated with CDDO-Im gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

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

data_processing: The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed.  The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.

source_name: genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue

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

growth_protocol: no growth protocol

extract_protocol: Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS  and sacrificed 6 h later

value: genetic control for cko mice, alb-cre:Keap1(flox/+)

value: 9 weeks

value: Liver


title: CC5-23

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 12:54:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: CC5-23 RNA


title: U937_control_48hours_rep2

description: Gene expression data from U937 at 48 hours, replicate 2


title: BB9-23c

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-17 Scan Time : 15:37:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: BB9-23c RNA


title: U937_control_24hours_rep2

description: Gene expression data from U937 at 24 hours, replicate 2


title: U937_control_72hours_rep1

description: Gene expression data from U937 at 72 hours, replicate 1


title: U937_control_48hours_rep1

description: Gene expression data from U937 at 48 hours, replicate 1


title: U937_control_24hours_rep1

description: Gene expression data from U937 at 24 hours, replicate 1


title: U937_AML1-ETO_induced_72hours_rep2

description: Gene expression data from U937 at 72 hours, AML1-ETO induced, replicate 2

value: AML1-ETO Induced


title: U937_AML1-ETO_induced_48hours_rep2

description: Gene expression data from U937 at 48 hours, AML1-ETO induced, replicate 2


title: U937_AML1-ETO_induced_24hours_rep2

description: Gene expression data from U937 at 24 hours, AML1-ETO induced, replicate 2


title: U937_AML1-ETO_induced_12hours_rep2

description: Gene expression data from U937 at 12 hours, AML1-ETO induced, replicate 2


title: Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep3

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 3

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings.  The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.

source_name: Kasumi-1 AML cell line

treatment_protocol: The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.

tag: construct

tag: transfect method

value: Amaxa nucleofection


title: U937_control_0hours_rep1

description: Gene expression data from U937 at 0 hours, replicate 1


title: U937_AML1-ETO_induced_72hours_rep1

description: Gene expression data from U937 at 72 hours, AML1-ETO induced, replicate 1


title: Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 1


title: U937_control_0hours_rep2

description: Gene expression data from U937 at 0 hours, replicate 2


title: Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 1

value: Biorad siLentFect


title: Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep3

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 3


title: U937_AML1-ETO_induced_12hours_rep1

description: Gene expression data from U937 at 12 hours, AML1-ETO induced, replicate 1


title: Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep2

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 2


title: U937_AML1-ETO_induced_24hours_rep1

description: Gene expression data from U937 at 24 hours, AML1-ETO induced, replicate 1


title: Kasumi-1_luciferase_construct_Amaxa_nucleofection_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Amaxa nucleofection transfection, replicate 1

value: luciferase


title: Kasumi-1_luciferase_construct_Amaxa_nucleofection_transfection_rep2

description: Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Amaxa nucleofection transfection, replicate 2


title: Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep3

description: Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 3


title: rpb1-1-YPAD_37deg_B

type: genomic

first: Hiten

last: Madhani

department: Biochemistry and Biophysics

description: No further information

hyb_protocol: arrays were blocked with a SDS/BSA solution and each probe was hybridized 1:1 using Agilent hybridization buffer; hybes were allowed to proceed at 65 degrees for at least 12 hours

scan_protocol: Scanned with a GenePix 4000B at 5 or 10 uM, depending on the size of print tips used to print array

data_processing: Median background subtracted first, then each print block normalized using a loess algorithm

label_protocol: DNA was linear amplified by first T-tailing with TdT, then adapting a T7 promoter (using complementary A tails), followed by IVT using a mix of aaUTP:UTP to generate aminoallyl-RNA probe that could be labeled with either Cy3 or Cy5 dye

growth_protocol: Cells were grown in rich (YPA) media supplemented with 2% dextrose to log phase (OD=0.7-0.9)

extract_protocol: culture was crosslinked with 1% formaldehyde for 15 minutes at growth temperature and quenched with 0.125M glycine for 5 minutes at room temperature.  Spheroplasts were prepared by digestion with Zymolyase 100T, followed by chromatin digestion with MNase in a buffer containing NP-40 for permeabilization

tag: formaldehyde-crosslinked chromatin digested with MNase to >90% mononucleosomal-sized DNA

source_name: reference DNA obtained from strain isogenic for features being probed

growth_protocol: Culture containing reference DNA isogenic to mononucleosome DNA source was grown in rich media to log phase (OD=1.0) prior to harvesting for purification of genomic DNA

extract_protocol: pure genomic DNA was purified using a Qiagen 100T column as specified by the manufacturer

tag: purified genomic DNA digested with MNase to ~200bp


title: Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep2

description: Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 2


title: U937_AML1-ETO_induced_48hours_rep1

description: Gene expression data from U937 at 48 hours, AML1-ETO induced, replicate 1


title: Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep2

description: Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 2


title: rpb1-1-YPAD_37deg_A

description: No further information

tag: reference DNA obtained from strain isogenic for features being probed


title: Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 1


title: Kasumi-1_no_construct_Amaxa_nucleofection_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, no construct, Amaxa nucleofection transfection, replicate 1


title: Kasumi-1_no_construct_no_transfection_rep3

description: Gene expression data from Kasumi-1 at 96 hours, no construct, no transfection, replicate 3


title: swr1-YPAD-culture_C

description: No further information

source_name: swr1delta, Reb1:dT7 inserted into PRM1

tag: swr1delta, Reb1:dT7 inserted into PRM1


title: rpb1-1-YPAD_25deg_A

description: No further information


title: rpb1-1-YPAD_25deg_B

description: No further information


title: swr1-YPAD-culture_B

description: No further information


title: swr1-YPAD-culture_A

description: No further information


title: htz1-YPAD-culture_D

description: No further information

source_name: htz1delta, Reb1:dT7 inserted into PRM1

tag: htz1delta, Reb1:dT7 inserted into PRM1


title: Kasumi-1_no_construct_no_transfection_rep1

description: Gene expression data from Kasumi-1 at 96 hours, no construct, no transfection, replicate 1


title: swr1-YPAD-culture_D

description: No further information


title: htz1-YPAD-culture_B

description: No further information


title: Control_for_degrons-degron_ON-culture_B

description: No further information

source_name: pGAL1::UBR1, Reb1:dT7 inserted into PRM1

growth_protocol: Cells that were growing in synthetic complete media lacking methionine and cysteine at 30 degrees were spiked with 2% galactose for 30 minutes and collected by centrifugation at room temperature, then added to rich (YPA) media supplemented with 2% galactose and prewarmed at 37 degrees.  After 5 hours of growth at 37 degrees, cells were collected.


title: htz1-YPAD-culture_C

description: No further information


title: Control_for_degrons-degron_ON-culture_C

description: No further information

tag: pGAL1::UBR1, Reb1:dT7 inserted into PRM1


title: Control_for_htz1_swr1-YPAD-culture_B

description: No further information

source_name: Reb1:dT7 inserted into PRM1

tag: Reb1:dT7 inserted into PRM1


title: Control_for_degrons-degron_OFF-culture_A

description: No further information

growth_protocol: Culture was grown to log phase (OD=0.7-0.9) in synthetic complete media lacking methionine and cysteine and supplemented with 2% raffinose and 0.1% dextrose at 30 degrees prior to collecting cells


title: htz1-YPAD-culture_A

description: No further information


title: Control_for_degrons-degron_OFF-culture_D

description: No further information


title: Control_for_degrons-degron_OFF-culture_B

description: No further information


title: Control_for_degrons-degron_OFF-culture_C

description: No further information


title: Control_for_htz1_swr1-YPAD-culture_A

description: No further information


title: Control_for_htz1_swr1-YPAD-culture_C

description: No further information


title: Abf1_Reb1_degron-degron_ON-culture_C

description: No further information

source_name: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::REB1,  pMET3::UB14::abf1(M1R), Reb1:dT7 inserted into PRM1


title: Control_for_htz1_swr1-YPAD-culture_D

description: No further information


title: Control_for_degrons-degron_ON-culture_D

description: No further information


title: Abf1_Reb1_degron-degron_ON-culture_B

description: No further information

tag: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::REB1,  pMET3::UB14::abf1(M1R), Reb1:dT7 inserted into PRM1


title: Abf1_Reb1_degron-degron_ON-culture_A

description: No further information


title: Abf1_Reb1_degron-degron_OFF-culture_D

description: No further information


title: Abf1_Reb1_degron-degron_OFF-culture_C

description: No further information


title: Abf1_Reb1_degron-degron_OFF-culture_A

description: No further information


title: Reb1_degron-degron_ON-culture_D

description: No further information

source_name: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::REB1, Reb1:dT7 inserted into PRM1


title: Reb1_degron-degron_ON-culture_A

description: No further information

tag: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::REB1, Reb1:dT7 inserted into PRM1


title: Reb1_degron-degron_OFF-culture_D

description: No further information


title: Reb1_degron-degron_OFF-culture_B

description: No further information


title: Sm N6B1

city: Hamilton

first: HONG

last: GUO

state: Ontario

address: 1280Main St. West

department: BIOLOGY

country: Canada

institute: MCMASTER UNIVERSITY

hyb_protocol: Two differentially labeled genomic DNA samples were included for each hybridization; the reference strain Rm1021 and another strain depending on the experiment. Thus, each hybridization reaction contained a 10 μl (equivalent 2μg DNA) of Alexa 555 and Alexa-647 labeled genomic DNA samples mixed in the hybridization solution (Pronto! Long Oligo/cDNA, 3x SSC, 0.1% SDS, 0.1 mg of sonicated Salmon Sperm DNA/ml) in a final volume of 70μl.

scan_protocol: Scanned on a ScanArrayExpress microarray scanner (Perkin-Elmer TM, Boston, MA, USA).

data_processing: Spot quantification, signal normalization, and data visualization were performed with the ScanArray Express 3.0 software (Perkin-Elmer TM Instruments)

organism: Sinorhizobium meliloti

source_name: Sm N6B1

label_protocol: Microarrays were hybridized using Pronto!™ Universal Hybridization Kits (Corning Incorporated, Life Sciences, Acton, USA Cat# 40026), following the protocol provided.

growth_protocol: To obtain genomic DNA for microarray analysis, cells of individual strains were inoculated into 5ml LBmc broth (LB supplemented with 2.5 mM MgSO4 and 2.5 mM CaCl2). The cells were incubated at 30oC with a constant agitation at 120rpm and harvested when the population density reached an OD600 reading between 0.8-1.0.

extract_protocol: Genomic DNA was extracted by using the Wizard Genomic DNA purification kit (Promega, Madison, WI, USA # A1120) according to the protocols provided.

tag: strain

tag: type

value: Bacterium-natural strain

value: Bacterium-sequenced strain


title: PPARα KO Control 13

description: Studies utilized wild-type and PPARα-null male mice 9–12 weeks of age on a mixed SV129/C57BL/6 background. Control and treated mice were provided with NIH-07 rodent chow (Zeigler Brothers, Gardeners, PA) and deionized, filtered water ad libitum.  Lighting was on a 12-hr light/dark cycle.  Mice were sacrificed 4 hrs, 24 hrs and 3 days after the heat stress.

source_name: PPARα KO Control 13

tag: tissue

value: whole liver

tag: genotype

value: PPARα-null

tag: age

value: 9–12 weeks

tag: gender

value: male

tag: background

value: mixed SV129/C57BL/6 background


title: Sm M286

source_name: Sm M286


title: Sm M248

source_name: Sm M248


title: Abf1_Reb1_degron-degron_OFF-culture_B

description: No further information


title: Sm 102F85


title: Reb1_degron-degron_OFF-culture_C

description: No further information


title: Sm M99

source_name: Sm M99


title: Sm M95

source_name: Sm M95


title: Abf1-degron-degron_ON-culture_C

description: No further information

source_name: pGAL1::UBR1, pMET3::UB14::abf1(M1R), Reb1:dT7 inserted into PRM1


title: Reb1_degron-degron_OFF-culture_A

description: No further information


title: Abf1-degron-degron_ON-culture_D

description: No further information

tag: pGAL1::UBR1, pMET3::UB14::abf1(M1R), Reb1:dT7 inserted into PRM1


title: Sm CC1023

source_name: Sm CC1023


title: Sm 74B12


title: Reb1_degron-degron_ON-culture_B

description: No further information

tag: formaldehyde-crosslinked chromatin digested with MNase to >90% mononucleosomal-sized DNA


title: Reb1_degron-degron_ON-culture_C

description: No further information

tag: purified genomic DNA digested with MNase to ~200bp


title: Sm ATCC9930

source_name: strain: ATCC9930


title: Abf1-degron-degron_ON-culture_A

description: No further information

tag: reference DNA obtained from strain isogenic for features being probed


title: Abf1-degron-degron_OFF-culture_D

description: No further information


title: Abf1-degron-degron_OFF-culture_C

description: No further information


title: PPARα KO Heat Shock treated 17

source_name: PPARα KO Heat Shock treated 17


title: Control1021/F910

source_name: Sm F909

value: Bacterium-deletion strain


title: Sm V7

source_name: Sm V7


title: Control1021/F909


title: WT_no_PRM1_insert-YPAD-culture_A

description: No further information

source_name: Wild-type strain

extract_protocol: culture was crosslinked with 1% formaldehyde for 15 minutes at growth temperature and quenched with 0.125M glycine for 5 minutes at room temperature.  Spheroplasts were prepared by digestion with Zymolyase 100T and digested with MNase in a buffer containing NP-40 for permeabilization

tag: Wild-type strain

source_name: reference DNA obtained from strain isogenic for features being probed


title: Sth1-degron-degron_OFF-culture_A

description: No further information

source_name: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::STH1, Reb1:dT7 inserted into PRM1


title: Abf1-degron-degron_OFF-culture_A

description: No further information


title: Abf1-degron-degron_OFF-culture_B

description: No further information


title: Control Sm 1021 replicate2


title: Sth1-degron-degron_OFF-culture_D

description: No further information

tag: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::STH1, Reb1:dT7 inserted into PRM1


title: Control Sm 1021 replicate1


title: Sth1-degron-degron_OFF-culture_C

description: No further information


title: Sth1_degron-degron_ON-culture_B

description: No further information


title: Sth1_degron-degron_ON-culture_A

description: No further information


title: Sth1_degron-degron_ON-culture_C

description: No further information


title: Sth1_degron-degron_ON-culture_D

description: No further information


title: Sth1-degron-degron_OFF-culture_B

description: No further information


title: Mus_Liver_3000_2

status: Public on Apr 30 2009

city: Reno

first: Monica

middle: M

last: Baze

state: NV

address: Dept. of Biology/ 314

department: Biology

institute: University of Nevada, Reno

description: no additional information

hyb_protocol: Hybridization of purified and fragmented cRNAs to Affymetrix® GeneChip® Mouse Genome 430 2.0 Array was performed using standard Affymetrix® protocols.

scan_protocol: A Hewlett-Packard GeneArray® Scanner was used to scan the microarrays,

data_processing: Eight of the nine arrays were used for data analysis; one array was excluded as several Affymetrix quality control metrics indicated data quality that was not reliable. Affymetrix® microarray data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters settings. The Bioconductor 'affy' package from R [http://cran.r-project.org/] was used for data analysis. Probe values were normalized via quantile normalization, and a median polish was applied to compute one expression measure from all probe values. Resulting RMA expression values were log2-transformed; presence calls and detection p-values were calculated with the 'mas5calls' function using default parameters.

organism: Mus musculus domesticus

source_name: liver of mice housed at simulated 3000 m for 32 days

label_protocol: Biotinylated cRNA were synthesized from 5 microg. total RNA following standard Affymetrix® protocols

growth_protocol: Mice were housed in one of three hypoxic treatments: 1400 m (Reno ambient air), 3000 m and 4500 m .

extract_protocol: Total RNA was extracted from liver tissue using Qiagen® RNeasy Mini Kit according to manufacturer’s directions.

treatment_protocol: At the end of the hypoxic treatment period, mice were sacrificed via cervical dislocation and livers were immediately removed and preserved in RNALater (Ambion, Inc.) for later RNA extraction.

value: liver

value: 16 weeks

tag: stress

value: hypoxic environment of 3000 m


title: Mus_Liver_4500_3

description: no additional information

source_name: liver of mice housed in simulated 4500 m for 32 days

value: hypoxic environment of 4500 m


title: WT_no_PRM1_insert-YPAD-culture_B

description: No further information


title: Mus_Liver_3000_1

description: no additional information


title: Mus_Liver_4500_2

description: no additional information


title: Mus_Liver_1400_3

description: no additional information

source_name: liver of mice housed at 1400m for 32 days

value: control (ambient Reno air, 1400 m)


title: Abf1-degron-degron_ON-culture_B

description: No further information


title: TSA3_24HR

city: London

first: veronica

last: ulici

address: 1151 Richmond Street

department: Physiology and Pharmacology

institute: University of Western Ontario

description: DMSO is the vehicle for the pharmacological inhibitors LY294002, TSA(trichostatin A), UO126, SB202190 and represents the experimental control.

hyb_protocol: LRGC specifications

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

data_processing: MAS 5.0 Algorythm : "The procedure is to construct a plot of each chip's probes against the corresponding probes on the baseline chip; eliminate the highest 1% of probes (and for symmetry the lowest 1%), and fit a regression line to the middle 98% of probes (ie. estimate slope and intercept: two parameters). Transform the values in each probe, by subtracting the intercept, and dividing by the slope, so that the regression line becomes the identity ( y = x ) line." http://discover.nci.nih.gov/microarrayAnalysis/Affymetrix.Preprocessing.jsp

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

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

growth_protocol: Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-glycerophosphate, 0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted. Chondrocytes were resuspended in media containing 2: 3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml). Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight.

extract_protocol: Qiagen RNeasy extraction

treatment_protocol: Primary monolayer chondrocytes were treated with 100 M TSA reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.

value: cartilage

tag: developmental stage

value: embryonic 15.5 days


title: Mus_Liver_1400_2

description: no additional information


title: TSA1_24HR


title: SB202190_3_24HR

description: DMSO is the vehicle for the pharmacological inhibitors LY294002, TSA, UO126, SB202190 and represents the experimental control.

source_name: SB202190-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

treatment_protocol: Primary monolayer chondrocytes were treated with 10 µM SB90 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.


title: SB202190_1_24HR


title: Mus_Liver_1400_1

description: no additional information


title: Mus_Liver_4500_1

description: no additional information


title: Control_for_degrons-degron_ON-culture_A

description: No further information

source_name: pGAL1::UBR1, Reb1:dT7 inserted into PRM1


title: LY3_24HR

source_name: LY294002-treated embryonic primary chondrocyte cultures, incubated for 24hrs.

treatment_protocol: Primary monolayer chondrocytes were treated with 10 µM LY reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.


title: UO126_2_24HR

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

treatment_protocol: Primary monolayer chondrocytes were treated with 10 uM UO126 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.


title: LY1_24HR

treatment_protocol: Primary monolayer chondrocytes were treated with 10 µM LY reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: DMSO2_24HR

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

treatment_protocol: Primary monolayer chondrocytes were treated with the DMSO control (vehicle) and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.


title: TSA2_24HR


title: Bmi1 wildtype MEF

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Center for Genomic Regulation

description: Expression study was performed in conjunction with genome-wide localization of ubiquitylated H2A.

hyb_protocol: 10 ug of cRNA was used for hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640. The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.

scan_protocol: the arrays were scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.

data_processing: MAS5 algorithm was used for data generation.

source_name: Bmi1 wildtype mouse embryonic fibroblast cells

label_protocol: 7 ug of total RNA was used to synthesize cDNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).

growth_protocol: TBX2 immortalized cells were cultured in DMEM supplemented with 10% FBS.  Cells were split 1:5 every three days using 0.01% Trypsin-EDTA for the duration of culturing.

extract_protocol: Qiagen RNeasy Kit by manufacturers protocol for extraction from animal cells.

value: Male

tag: reference

value: Jacobs, J.J. et al. Nat.Genetics. 2000

tag: antibody


title: Bmi1 knockout MEF

source_name: Bmi1 knockout mouse embryonic fibroblast cells

tag: strain


title: UO126_3_24HR


title: UO126_1_24HR

treatment_protocol: Primary monolayer chondrocytes were treated with 10 uM UO126 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.


title: DMSO3_24HR

growth_protocol: Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in a-mem media (Invitrogen) containing 0.2% bovine serum albumin (BSA), 1 mm ß-glycerophosphate, 0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°c in a humidified 5% co2 incubator overnight. The following morning media was removed and the bones placed in 4 ml of 0.25% trypsin-edta (invitrogen) for 15 min at 37oc. Trypsin was subsequently replaced with 1 mg/ml collagenase p (roche) in dmem / 10% fetal bovine serum (invitrogen), and cells were incubated at 37°c with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted. Chondrocytes were resuspended in media containing 2: 3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml). Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight.

treatment_protocol: Primary monolayer chondrocytes were treated with the DMSO control (vehicle) and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM ß-glycerophosphate (Sigma) and incubated for 24 hrs.


title: SB202190_2_24HR


title: LY2_24HR


title: DMSO1_24HR

treatment_protocol: Primary monolayer chondrocytes were treated with DMSO control (vehicle) diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for 24 hrs.


title: Parental PA2

city: Lausanne

first: Mauro

last: Delorenzi

address: 155 Boveresses

country: Switzerland

institute: ISREC

description: PA, SCCVII cells maintained in culture under standard conditions (37C, 5%C02) NIR, SCCVII cell line derived from tumors formed by PA SCCVII cells injected in non-irradiated stroma. The tumors are poorly invasive and metastatic, and the derived NIR liens are also poorly invasive and metastatic. IR, SCCVII cell line derived from tumors formed by PA SCCVII cells injected in pre-irradiated stroma. These tumors are highly hypoxic, invasive and metastatic, and the derived IR lines retain invasive and metastatic capacities even when cultured and expanded under normoxic conditions in vitro.

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: RMA

source_name: SCCVII (Tumor cell lines derived from a spontaneously arisen oral squamous cell carcinoma in CH3 mice)

label_protocol: Standard Affymetrix procedure

extract_protocol: Qiagen RNeasy Mini Kit

tag: PA2, parental SCCVII, sample 2


title: TC252_knockdown

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Gene expression data from Ewing's sarcoma cell line Ewing's sarcoma cell line transfected with a specific siRNA against the EWS-FLI1 fusion.

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 1.5µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: All ESFT cell lines were propagated on fibronectincoated  plastics in RPMI 1640+10% fetal calf serum at 37°C.

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with LipofectAMINE Plus reagent (Invitrogen, Groningen, The Netherlands) and subjected to puromycin selection (1μg/mL) the next day. On day 4 after transfection, puromycin selected cells were processed for RNA and protein extraction. SiRNAs against the fusion regions of type 1 (EF30) in TC252, WE68, SK-N-MC, STA-ET-1, and type 2 (EF22) EWS-FLI1 in STA-ET-7.2 were expressed as small hairpin (sh) RNAs from pSUPER-based retroviral expression constructs. For negative control, pSTNeg (Ambion, Applied Biosystems, Brunn am Gebirge, Austria) encoding a scrambled shRNA with no significant similarity to human sequences was used.

tag: EWS-FLI1 fusion type 1


title: SK-N-MC_knockdown

source_name: Ewing's sarcoma cell line transfected with a specific siRNA against the EWS-FLI1 fusion.


title: Parental PA3

tag: PA3, parental SCCVII, sample 3


title: Parental PA1

tag: PA1, parental SCCVII, sample 1


title: STA-ET-7.2_knockdown

tag: EWS-FLI1 fusion type 2


title: STA-ET-1_knockdown


title: WE68_knockdown


title: Non-irradiated NIR3

tag: NIR3, SCCVII cell line derived from tumors grown in non-irradiated stroma, sample 3


title: STA-ET-1_control

description: Gene expression data from Ewing's sarcoma cell line transfected with pSTNeg (Ambion, Applied Biosystems, Brunn am Gebirge, Austria) encoding a scrambled shRNA with no significant similarity to human sequences.


title: Non-irradiated NIR2

tag: NIR2, SCCVII cell line derived from tumors grown in non-irradiated stroma, sample 2


title: STA-ET-7.2_control

source_name: Ewing's sarcoma cell line transfected with pSTNeg (Ambion, Applied Biosystems, Brunn am Gebirge, Austria) encoding a scrambled shRNA with no significant similarity to human sequences.


title: Irradiated IR2

tag: IR2, SCCVII cell line derived from tumors grown in pre-irradiated stroma, sample 2


title: MDS.U36

status: Public on Aug 01 2009

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U36

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0

source_name: MDS primary specimens

label_protocol: Affymetrix standard protocol

extract_protocol: As per PUREGENE DNA extracting kit

tag: disease

value: Myelodysplastic syndromes (MDS)

tag: who classification


title: Irradiated IR3

tag: IR3, SCCVII cell line derived from tumors grown in pre-irradiated stroma, sample 3


title: SK-N-MC_control


title: TC252_control


title: Non-irradiated NIR1

tag: NIR1, SCCVII cell line derived from tumors grown in non-irradiated stroma, sample 1


title: WE68_control


title: Irradiated IR1

tag: IR1, SCCVII cell line derived from tumors grown in pre-irradiated stroma, sample 1


title: SHSY5Y_MSCV-ZNF423

status: Public on Apr 29 2009

city: Amsterdam

first: Sidong

last: Huang

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description:
Analysis was done using public R-routines from the BioConductor packadge Lumi and Limma that have been designed for Illumina expression array analysis. See http://www.bioconductor.org/ and
http://www.bioconductor.org/packages/2.3/bioc/vignettes/lumi/inst/doc/lumi_VST_evaluation.pdf

hyb_protocol: According to Illumina IntelliHyb protocol: Whole-Genome Gene Expression Direct Hybridization (Assay Guide) Chips used: Sentrix(r) HumanWG-6 v3 Expression Beadchip.

scan_protocol: The BeadChip is scanned on the Illumina BeadArray Reader, according to Illumina settings.

data_processing:
The normalization is done using the bioconductor(1) package lumi(2). The data is tranformed using the vst(3) method and normalised with the robust spline normalization scheme. All arrays from the same set of experiment were normalized together.
1 Bioconductor: Open software development for computational biology and bioinformatics R. Gentleman, V. J. Carey, D. M. Bates, B.Bolstad, M.Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and others 2004, Genome Biology, Vol. 5, R80
2 Du, P., Kibbe, W.A. and Lin, S.M., (2008) ’lumi: a pipeline for processing Illumina microarray’, Bioinformatics 24(13):1547-1548
3 Lin, S.M., Du, P., Kibbe, W.A., (2008) ’Model-based Variance-stabilizing Transformation for Illumina Microarray Data’,  Nucleic Acids Res. 36, e11

source_name: SHSY5Y, ZNF423

label_protocol:
RNA amplification+biotin labeling: Illumina(r) TotalPrep(tm) RNA Amplification Kit (Cat# AMIL1791)
Extra: We started the protocol by adding 1ul T7 primer to the 11ul sample (input 350 ng) and incubate this for 10 minutes at 70 degrees Celsius, then let sample come to RT then place on ice.
In the next step (adding the first strand mix) we left out the T7 primer and followed the protocol as described in the manual.

extract_protocol:
Total RNA isolation: TRizol(r) Reagent (Cat# 15596-018)
RNA Purification (including a DNase treatment): ChargeSwitch(r) Total RNA Cell Kit (Cat# CS14010)

treatment_protocol: SH-SY5Y cells were retrovirally infected with MSCV-ZNF423 (Puro).

tag: cell type

value: human neuroblastoma SH-SY5Y cells expressing the murine ecotropic receptor


title: SHSY5Y_MSCV-control

source_name: SHSY5Y, control

treatment_protocol: SH-SY5Y cells were retrovirally infected with MSCV (Puro) vector control.


title: 4117185023_B [18h blinded; PBS exposed]

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

description: Sham 1: PBS exposed

hyb_protocol: Amplified cRNA was then hybridized and labeled on Sentrix Mouse-6 Expression BeadChips (Illumina, Inc., San Diego, CA).

scan_protocol: All microarrays were scanned on a BeadStation 500 (Illumina).

data_processing: Data were background corrected using the RMA method, then  transformed by taking the base-two logarithm, and quantile normalized. Analysis of the microarray output was performed using a one-way ANOVA to identify infection-induced changes.  P values were modeled using a beta-uniform mixture (BUM) model (30), and combined with false discover rate to determine a  cutoff of p values.  The analysis program was written in R (R Foundation for Statistical Computing, Vienna, Austria), utilizing the Illumina library developed by Simon Lin and Pan Du, Northwestern University.

source_name: lung 18h after challenge

label_protocol: Hybridized cRNA was labeled for 10 minutes with Cy3.

extract_protocol: At designated timepoints after the infectious challenge, the mice were anesthetized and sacrificed.  To reduce the gene expression signal of circulating leukocytes in the pulmonary vasculature, the pulmonary vasculature was exsanguinated and the pulmonary arterial system was flushed with PBS.  The lungs were also submitted to repeated BAL to reduce the leukocyte burden of the airspaces.  The lungs were then excised, homogenized, and total RNA was isolated using the RNeasy system (Qiagen, Valencia, CA).  cRNA was synthesized, then amplified, from equal masses of total RNA extracted from the lungs of infected/sham challenged mice using the Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).

value: BALB/c

tag: tissue

value: lung

tag: age

value: 5-8 wk old


title: 1519111027_E [6h training; Pseudomonas infected]

description: Pa4: pseudomonas infected

source_name: lung 6h after challenge

tag: strain


title: 1519111027_C [6h training; no treatment]

description: C6: no treatment


title: 4117185023_D [18h blinded; Aspergillus challenged]

description: Af 1: Aspergillus challenged


title: 4117185023_A [18h blinded; Pseudomonas infected]

description: Pa 1: pseudomonas infected


title: 1519111027_F [6h training; PBS exposed]

description: Sham6: PBS exposed


title: 1519111027_A [6h training; Pneumococcus challenged]

description: Sp4: pneumococcus challneged


title: 1519111027_B [6h training; Aspergillus challenged]

description: Af4: Aspergillus challenged


title: 4117185023_C [18h blinded; Pseudomonas infected]

description: Pa 2: pseudomonas infected


title: 1519111028_D [6h training; no treatment]

description: C4: no treatment


title: 1519111028_F [6h training; no treatment]

description: C5: no treatment


title: 1519111028_E [6h training; PBS exposed]

description: Sham4: PBS exposed


title: 1519111027_D [6h training; PBS exposed]

description: Sham5: PBS exposed


title: 1519111028_B [6h training; Pneumococcus challenged]

description: Sp3: pneumococcus challneged


title: 1519111028_A [6h training; Pseudomonas infected]

description: PA3: pseudomonas infected


title: 1519111028_C [6h training; Aspergillus challenged]

description: Af3: Aspergillus challenged


title: 1519111042_F [6h training; PBS exposed]

description: Sham3: PBS exposed


title: 1519111042_B [6h training; Pseudomonas infected]

description: Pa2: pseudomonas infected


title: 1519111042_E [6h training; no treatment]

description: C3: no treatment


title: 1519111055_F [6h training; no treatment]

description: C2: no treatment


title: 1519111042_C [6h training; Pneumococcus challenged]

description: Sp2: pneumococcus challneged


title: 1519111042_A [6h training; PBS exposed]

description: Sham2: PBS exposed


title: 1519111042_D [6h training; Aspergillus challenged]

description: Af2: Aspergillus challenged


title: 1519111055_E [6h training; Aspergillus challenged]

description: Af1: Aspergillus challenged


title: 1519111055_D [6h training; Pneumococcus challenged]

description: Sp1: pneumococcus challneged


title: 1519111055_C [6h training; Pseudomonas infected]

description: Pa1: pseudomonas infected


title: Albina e-16 Control rep2

city: Riverside

first: Livia

last: Tommasini

address: 2150 Batchelor Hall

department: Botany and Plant Science

institute: University of California, Riverside

description: Albina e-16 Control

hyb_protocol: 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned on a Hewlett-Packard GeneArray scanner.

data_processing: GCOS MAS 5

organism: Hordeum vulgare

label_protocol: The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.

growth_protocol: Wild type and mutants were germinated in peat pots and grown in a controlled-environment chamber for 8 d at 20 C with 12-h photoperiod (300 mmol m22 s21).

extract_protocol: For RNA isolation, two methods were applied: RNA from embryo and endosperm collected during seed development was isolated by Trizol (Gibco BRL Life Technologies, Rockville, MD) and passed through an RNeasy spin column (Qiagen, Hilden, Germany) for further clean up as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). For embryo and endosperm collected after imbibition, PURESCRIPT® RNA isolation kits (Gentra Systems, Inc., Minneapolis, MN) and RNeasy spin column (Qiagen, Hilden, Germany) were used. Quality of RNA was assessed on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: When the first leaf was fully emerged the plants were treated for 6 d at 3 C, 12-h light (150 mmol m22 s21)/1 C, 12-h dark. Control plants were harvested after 8 d at 20 C. All samples were collected in the middle of the light period. This experiment was conducted three times to yield three independent biological replicates. To analyze the involvement of the photooxidative stress, seeds of wild type and mutants were imbibed for 3 h in water containing 0 (control) or 50 mM norfluorazon. The hydrated seeds were grown in a growth-controlled environment chamber as above except that light intensity was 10 mmol m22 s21 for the first 8 d and 200 mmol m22 s21 for the next 6 d. During the growth, treated plants were watered two times with 50 mM norfluorazon.For analysis of Cbf expression, treated samples were collected after 4, 8, and 24 h of cold treatment in the light.

tag: Albina e-16 Control


title: 1519111055_B [6h training; PBS exposed]

description: Sham1: PBS exposed


title: Albina e-16 Control rep3

description: Albina e-16 Control


title: 1519111055_A [6h training; no treatment]

description: C1: no treatment


title: Albina e-16 Hardened rep3

description: Albina e-16 Hardened

tag: Albina e-16 Hardened


title: Albina e-16 Hardened rep1

description: Albina e-16 Hardened


title: 1519111050_F [2h training; PBS exposed]

description: Sham6: PBS exposed

source_name: lung 2h after challenge


title: 1519111050_E [2h training; Pseudomonas infected]

description: Pa4: pseudomonas infected


title: 1519111050_C [2h training; no treatment]

description: C6: no treatment


title: Albina e-16 Hardened rep2

description: Albina e-16 Hardened


title: Albina f-17 Hardened rep2

description: Albina f-17 Hardened

tag: Albina f-17 Hardened


title: 1519111050_B [2h training; Aspergillus challenged]

description: Af4: Aspergillus challenged


title: Albina f-17 Hardened rep1

description: Albina f-17 Hardened


title: Albina e-16 Control rep1

description: Albina e-16 Control


title: Albina f-17 Hardened rep3

description: Albina f-17 Hardened


title: 1519111050_A [2h training; Pneumococcus challenged]

description: Sp4: pneumococcus challneged


title: Albina f-17 Control rep3

description: Albina f-17 Control

tag: Albina f-17 Control


title: 1519111050_D [2h training; PBS exposed]

description: Sham5: PBS exposed


title: Albina f-17 Control rep2

description: Albina f-17 Control


title: 1519111030_E [2h training; PBS exposed]

description: Sham4: PBS exposed


title: 1519111030_F [2h training; no treatment]

description: C5: no treatment


title: 1519111030_C [2h training; Aspergillus challenged]

description: Af3: Aspergillus challenged


title: 1519111030_D [2h training; no treatment]

description: C4: no treatment


title: Xantha s-46 Hardened rep2

description: Xantha s-46 Hardened

tag: Xantha s-46 Hardened


title: Albina f-17 Control rep1

description: Albina f-17 Control


title: Xantha b-12 Hardened rep3

description: Xantha b-12 Hardened

tag: Xantha b-12 Hardened


title: 1519111030_A [2h training; Pseudomonas infected]

description: Pa3: pseudomonas infected


title: 1519111010_D [2h training; Aspergillus challenged]

description: Af2: Aspergillus challenged


title: 1519111030_B [2h training; Pneumococcus challenged]

description: Sp3: pneumococcus challneged


title: Xantha s-46 Hardened rep1

description: Xantha s-46 Hardened


title: 1519111010_E [2h training; no treatment]

description: C3: no treatment


title: Xantha s-46 Control rep2

description: Xantha s-46 Control

tag: Xantha s-46 Control


title: Xantha s-46 Control rep3

description: Xantha s-46 Control


title: Xantha b-12 Hardened rep2

description: Xantha b-12 Hardened


title: 1519111010_B [2h training; Pseudomonas infected]

description: Pa2: pseudomonas infected


title: Xantha s-46 Control rep1

description: Xantha s-46 Control


title: Xantha b-12 Hardened rep1

description: Xantha b-12 Hardened


title: Barley root gene expression 7d Treatment: P.indica, Replication III

city: Giessen

first: Patrick

last: Schaefer

address: Heinrich-Buff-Ring 26-32

country: Germany

institute: Institute of Phytopathology and Applied Zoology

hyb_protocol: Following fragmentation, 1,65 ug of cRNA were hybridized for 17 hr at 65°C on 4 x 44K Barley Agilent Array. Arrays were washed accroding to the protocol (One-Color Microarray-based Gene Expression analysis, version 5.0.1).

scan_protocol: Microarrays were scanned on an Agilent Microarray Scanner.

data_processing: Raw data were generated with the Agilent Microarray Scanner and the feature extraction software FE Version 9.5.3.1 (Agilent, Waldbronn, Germany), The raw data contains 2,600 replicate probes and internal controls. Data analysis was performed by Biconductor/R (http://www.bioconductor.org/). Raw data were read by read.maimage function of R, filtered in order to remove replicate probes and internal controls. Background corrected intensities (gProcessedSignal) lower than 1 were set to 1 (in order to avoid negative values), converted by log2 and normalised by the quantile normalisation (normalizeQuantiles).

source_name: root tissue

label_protocol: Cy3-labeled cRNA were prepared according to the standard Agilent protocol from 500 ng total RNA (One-Color Microarray-based Gene Expression analysis, version 5.0.1).

growth_protocol: Barley plants of the cultivar Golden Promise were germinated for two days  in the dark at RT. After inoculation, plants were grown in a phytochamber in a 16 h / 8 h light-dark cycle. Temperature was 22°C and 18°C, relative humidity 60% during light and dark periods, respectively. Five seedlings were planted per pot in a mixture of Seramis/oil dri (v.v 2:1).

extract_protocol: For RNA isolation, material from 40 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.

treatment_protocol: P. indica was grown on solid complete media, scratched from the media with a spatula and resuspended in water to 500.000 spores per ml. Seedlings were dip-inoculated for two hours and thereafter transferred to a seramis/oil dri mixture (v.v 2:1) (described in Proc Natl Acad Sci USA 103: 18450-18457)

tag: Roots of seedlings 7 days after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1519111010_F [2h training; PBS exposed]

description: Sham3: PBS exposed


title: Xantha s-46 Hardened rep3

description: Xantha s-46 Hardened


title: Barley root gene expression 7d Treatment: P.indica, Replication II


title: 1519111036_E [2h training; Aspergillus challenged]

description: Af1: Aspergillus challenged


title: Barley root gene expression 7d Treatment: P.indica, Replication I

data_processing: Raw data were generated with the Agilent Microarray Scanner and the feature extraction software FE Version 9.5.3.1 (Agilent, Waldbronn, Germany), The raw data contains 2,600 replicate probes and internal controls. Data analysis was performed by Biconductor/R (http://www.bioconductor.org/). Raw data were read by read.maimage function of R, filtered in order to remove replicate probes and internal controls. Background corrected intensities (gProcessedSignal) lower then 1 were set to 1 (in order to avoid negative values), converted by log2 and normalised by the quantile normalisation (normalizeQuantiles).


title: 1519111036_D [2h training; Pneumococcus challenged]

description: Sp1: pneumococcus challneged


title: 1519111010_C [2h training; Pneumococcus challenged]

description: Sp2: pneumococcus challneged


title: Xantha b-12 Cotrol rep3

description: Xantha b-12 Cotrol

tag: Xantha b-12 Cotrol


title: Barley root gene expression 7d Treatment: Mock, Replication III

tag: Roots of seedlings 7 day after mock-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1519111036_C [2h training; Pseudomonas infected]

description: Pa1: pseudomonas infected


title: Xantha b-12 Cotrol rep2

description: Xantha b-12 Cotrol


title: 1519111010_A [2h training; PBS exposed]

description: Sham2: PBS exposed


title: 1519111036_B [2h training; PBS exposed]

description: Sham1: PBS exposed


title: 1519111036_A [2h training; no treatment]

description: C1: no treatment


title: 1519111036_F [2h training; no treatment]

description: C2: no treatment


title: Barley root gene expression 7d Treatment: Mock, Replication II

tag: Roots of seedlings 7 day after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1740174057_F [18h training; PBS exposed]

description: Sham 6: PBS exposed


title: Bonus Hardened rep3

description: Bonus Hardened

tag: Bonus Hardened


title: Xantha b-12 Cotrol rep1

description: Xantha b-12 Cotrol


title: Barley root gene expression 3d Treatment: P.indica, Replication II

tag: Roots of seedlings 3 day after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1740174057_C [18h training; Pseudomonas infected]

description: Pa 4: pseudomonas infected


title: Barley root gene expression 3d Treatment: P.indica, Replication III


title: 1740174057_D [18h training; Pneumococcus challenged]

description: Sp 4: pneumococcus challneged


title: Bonus Hardened rep2

description: Bonus Hardened


title: 1740174057_A [18h training; PBS exposed]

description: Sham 5: PBS exposed


title: Barley root gene expression 7d Treatment: Mock, Replication I


title: 1519111023_F [18h training; PBS exposed]

description: Sham 4: PBS exposed


title: Barley root gene expression 3d Treatment: Mock, Replication III

tag: Roots of seedlings 3 days after mock-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1740174057_B [18h training; Aspergillus challenged]

description: Af 3: Aspergillus challenged

tag: tissue


title: 1519111023_E [18h training; Pneumococcus challenged]

description: Sp 3: pneumococcus challneged

tag: age


title: Bonus Control rep2

description: Bonus Control

tag: Bonus Control


title: 1740174057_E [18h training; Aspergillus challenged]

description: Af 4: Aspergillus challenged

tag: strain


title: Barley root gene expression 3d Treatment: P.indica, Replication I

tag: Roots of seedlings 3 days after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: Bonus Control rep3

description: Bonus Control


title: Bonus Hardened rep1

description: Bonus Hardened


title: 1519111023_D [18h training; Pseudomonas infected]

description: Pa 3: pseudomonas infected


title: Bonus Control rep1

description: Bonus Control


title: 1519111023_A [18h training; PBS exposed]

description: Sham 3: PBS exposed


title: Barley root gene expression 3d Treatment: Mock, Replication I

tag: Roots of seedlings 3 day after mock-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: 1519111023_C [18h training; Aspergillus challenged]

description: Af 2: Aspergillus challenged


title: 1519111021_F [18h training; PBS exposed]

description: Sham 2: PBS exposed


title: 1519111023_B [18h training; Pneumococcus challenged]

description: Sp 2: pneumococcus challneged


city: New Hyde Park

first: Andrea

last: Vambutas

state: NY

address: 430 Lakeville Road

department: Otolaryngology

institute: Long Island Jewish Medical Center

description: control patient #3 PBMC unstimulated

hyb_protocol: Affymetrix protocol to HG-U133A 2.0

scan_protocol: Genesifter

data_processing: Affymetrix

source_name: unstimulated PBMC from control patient

label_protocol: Enzo protocol

extract_protocol: affinity spin column

treatment_protocol: 16 hour culture with no stimulation (baseline control)

tag: unstimulated PBMC from control patient #3, baseline for stimulated conditions


title: Barley root gene expression 3d Treatment: Mock, Replication II


title: 1519111021_E [18h training; Pseudomonas infected]

description: Pa 2: pseudomonas infected


title: Barley root gene expression 1d Treatment: P.indica, Replication III

tag: Roots of seedlings 1 day after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: unstimulated PBMC control #2

description: control patient #2 PBMC unstimulated

source_name: unstimulated PBMC control

tag: unstimulated PBMC from control #2 patient as baseline for stimulated conditions


title: 1519111021_D [18h training; Aspergillus challenged]

description: Af 1: Aspergillus challenged


title: 1519111021_B [18h training; Pseudomonas infected]

description: Pa 1: pseudomonas infected


title: Barley root gene expression 1d Treatment: P.indica, Replication I


title: after 3 days in mannitol medium rep2

description: after 3 days in mannitol medium

growth_protocol: Donor plants were grown in growth chambers with controlled temperature (18-21ºC), relative humidity (70-80%) and photoperiod (16 h light), as described by Cistué et al. (2003).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) from frozen crown samples taken from above soil tissue excluding most fully extended lamina. The protocol is available on the Arabidopsis Information Resource website at http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. RNA was purified using Qiagen RNeasy spin columns with DNase treatment. Quality was assessed by running 25-250 ng on a RNA Lab-On-A-Chip (Caliper Technologies) using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Anthers extracted from the spikes under a stereoscopic microscope were inoculated in a treatment medium containing 0.7 M mannitol, 40 mM CaCl2, and 8 g/l agarose, and kept at 25 C in the dark for 4 days (Cistue´et al. 2003). Samples were collected before and after 4 days in mannitol medium. Three samples from each step were harvested and used for microarray analysis.

tag: after 3 days in mannitol medium


title: 1519111021_A [18h training; PBS exposed]

description: Sham 1: PBS exposed


title: pneumococcal stimulated PBMC from control patient #2

description: control patient #2 PBMC stimulated with pneumococcal antigen

treatment_protocol: 16 hour culture with 100ul 23 valent pneumococcal antigen stimulation

tag: pneumococcal stimulated PBMC from control #2


title: pneumococcal stimulated PBMC from control #3

description: control patient #3 PBMC stimulated with pneumococcal antigen

tag: pneumococcal stimulated PBMC from control patient #3


title: 1519111021_C [18h training; Pneumococcus challenged]

description: Sp 1: pneumococcus challneged


title: before 3 days in mannitol medium rep3

description: before 3 days in mannitol medium

tag: before 3 days in mannitol medium


title: unstimulated PBMC from control #1

description: control patient #1 PBMC unstimulated

source_name: unstimulated PBMC from control

tag: unstimulated PBMC from control #1 for comparison to stimulated conditions


title: after 3 days in mannitol medium rep1

description: after 3 days in mannitol medium


title: before 3 days in mannitol medium rep1

description: before 3 days in mannitol medium


title: before 3 days in mannitol medium rep2

description: before 3 days in mannitol medium


title: 4068846038_F [18h blinded; Aspergillus challenged]

description: Af 5: Aspergillus challenged


title: cochlear stimulated PBMC from control #2

description: control patient #2 PBMC stimulated with autologous cochlear perilymph

source_name: cochlear stimulated PBMC from control

treatment_protocol: 16 hour culture with autologous cochlear fluid stimulation

tag: cochlear stimulated PBMC from control patient#2


title: Barley root gene expression 1d Treatment: P.indica, Replication II


title: Dicktoo-deacclimation-rep3

description: Dicktoo-deacclimation

growth_protocol: Barley cv. Morex plants were grown in steam-sterilized soil in a growth chamber (Model GC-15, EGC Chagrin Falls, OH) with 12 h photopheriod (148 µmol m-2 s-1 average photosynthetic active radiation) at 23ºC, 12 h dark at 20ºC and 70% relative humidity.

treatment_protocol: Plants were grown at 20ºC for seven days and subject to 10 mol ABA treatment

tag: Dicktoo-deacclimation


title: pneumococcal stimulated PBMC of control patient #1

description: control patient #1 PBMC stimulated with pneumococcal antigen

tag: pneumococcal stimulated PBMC from control patient #1


title: Barley root gene expression 1d Treatment: Mock, Replication III

tag: Roots of seedlings 1 day after mock-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.


title: cochlear stimulated PBMC from control #3

description: control patient #3 PBMC stimulated with autologous cochlear perilymph


title: Barley root gene expression 1d Treatment: Mock, Replication I


title: Barley root gene expression 1d Treatment: Mock, Replication II


title: 4068846038_E [18h blinded; Pseudomonas infected]

description: Pa 4: pseudomonas infected

tag: tissue

tag: age


title: Dicktoo-deacclimation-rep2

description: Dicktoo-deacclimation


title: 4068846038_D [18h blinded; Aspergillus challenged]

description: Af 4: Aspergillus challenged

tag: strain


title: 4068846038_C [18h blinded; PBS exposed]

description: Sham 5: PBS exposed


title: Dicktoo-deacclimation-rep1

description: Dicktoo-deacclimation


title: cochlear stimulated PBMC control patient #1

description: control patient PBMC stimulated with autologous cochlear perilymph

tag: cochlear stimulated PBMC from control patient #1


title: PBMC stimulated with pneumococcal antigen, AIED patient #3

description: AIED patient 3 PBMC stimulated with pneumococcal antigen

treatment_protocol: 16 hour culture with 100ul pneumococcal antigen stimulation

tag: PBMC from AIED patient #3 stimulated with pneumococcal antigen


title: Dicktoo-subzero-rep2

description: Dicktoo-subzero

tag: Dicktoo-subzero


title: Dicktoo-subzero-rep3

description: Dicktoo-subzero


title: PBMC from AIED patient #3

description: AIED patient 3 PBMC unstimulated

source_name: PBMC from AIED patient

treatment_protocol: 16 hour culture without stimulation

tag: unstimulated PBMC from AIED patient #3 for comparison to stimulated conditions


title: 4117185006_D [18h blinded; Aspergillus challenged]

description: Af 2: Aspergillus challenged


title: unstimulated PBMC from AIED patient #2

description: AIED patient 2  PBMC stimulated with pneumococcal antigen

source_name: unstimulated PBMC from AIED patient

tag: PBMC from AIED patient#2, for comparison to stimulated conditions


title: 4068846038_B [18h blinded; Pneumococcus challenged]

description: Sp 4: pneumococcus challneged


title: cochlear stimulated PBMC from AIED patient #3

description: AIED patient 3 PBMC stimulated with autologous cochlear perilymph

treatment_protocol: 16 hour culture with autologous cochlear perilypmh fluidstimulation

tag: autologous cochlear perilymph stimulated PBMC from AIED patient #3


title: Dicktoo-subzero-rep1

description: Dicktoo-subzero


title: 4068846038_A [18h blinded; Aspergillus challenged]

description: Af 3: Aspergillus challenged


title: 4117185006_C [18h blinded; PBS exposed]

description: Sham 4: PBS exposed


title: 4117185006_E [18h blinded; Pneumococcus challenged]

description: Sp 2: pneumococcus challneged


title: Dicktoo-chilling-rep1

description: Dicktoo-chilling

tag: Dicktoo-chilling


title: cochlear perilymph stimulated PBMC of AIED patient #2

description: AIED patient 2  PBMC stimulated with autologous perilymph

treatment_protocol: 16 hour culture with stimulation with autologous perilymph

tag: autologous cochlear stimulated PBMC of AIED patient #2


title: 4117185006_B [18h blinded; PBS exposed]

description: Sham 3: PBS exposed


title: pneumococcal stimulated PBMC, AIED patient #2

treatment_protocol: 16 hour culture with stimulation with 1ooul of 23 valent pneumococcal antigen

tag: AIED patient #2 PBMC stimulated with pneumococcal antigen


title: Adult_Prostate_Sca-1Neg_rep4

city: New York

first: Roy

last: Blum

address: 552 First Ave

department: Cancer Institute

institute: New York University

description: We established transcriptional profiles for urogenital sinus epithelium, Sca-1Hi, Sca-1Lo, and for the Sca-1Neg differentiated cells. Three replicates of urogenital sinus epithelium (FPSC) and Sca-1Hi (APSC) samples and four replicates of Sca-1Lo and Sca-1Neg samples were analyzed.

hyb_protocol: Ten micrograms of labeled and fragmented cRNA were hybridized to the mouse genome MOE430 2.0 array (Affymetrix).

scan_protocol: Raw expression data were analyzed using GCOS 1.4 (Affymetrix). Data were normalized to a target intensity of 500 to account for differences in global chip intensity.

data_processing: Utilizing ArrayAssist (Stratagene), raw Affymetrix CEL files were processed by applying the MAS5 algorithm, where detection calls (Present/ Marginal/Absent) were assigned. Then, the pre-selected data set was further analyzed with the more sophisticated hybrid algorithm PLIER for initial normalization.

source_name: Sca-1Neg cells from adult male prostate

label_protocol: Samples with a RNA Integrity Number (RIN) >7.0 were considered suitable for labeling and 20 ng were labeled using the GeneChip two-cycle target labeling kit (Affymetrix).

extract_protocol: Total RNA was isolated from 10,000-50,000 FACS sorted cells using TRIzol Reagent (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: FACS sorted Sca-1Neg-labelled cells of normal prostate

value: adult (6-8 weeks)

tag: gender

value: male


title: Dicktoo control-rep3

description: Dicktoo-control

tag: Dicktoo-control


title: 4117185006_F [18h blinded; Pneumococcus challenged]

description: Sp 3: pneumococcus challneged


title: urogenital_sinus_epithelium_rep2

source_name: Urogenital sinus epithelium cells from 16-day-old mice embryos

value: Urogenital sinus epithelium cells from embryos


title: urogenital_sinus_epithelium_rep3


title: Dicktoo-chilling-rep2

description: Dicktoo-chilling


title: urogenital_sinus_epithelium_rep1


title: pneumococcal stimulated PBMC from AIED patient #1

description: AIED patient 1 stim PBMC with pneumococcal antigen

treatment_protocol: pneumococcal antigen (100ul of 23 valent vaccine) stimulated PBMC of AIED patient 1

tag: PBMC from AIED patient #1 stimulated with pneumococcal antigen


title: Dicktoo-chilling-rep3

description: Dicktoo-chilling


title: cochlear stim PBMC from AIED patient #1

description: AIED patient 1 stim PBMC with autologous perilymph

source_name: cochlear stim PBMC from AIED patient

treatment_protocol: autologous cochlear perilymph fluid stimulated PBMC of AIED patient 1

tag: comparison of PBMC from AIED and control patients


title: 4117185023_F [18h blinded; Pseudomonas infected]

description: Pa 3: pseudomonas infected

tag: tissue


title: Dicktoo-control-rep1

description: Dicktoo-control


title: 4117185006_A [18h blinded; PBS exposed]

description: Sham 2: PBS exposed

tag: age


title: Adult_Prostate_Sca-1Neg_rep3

tag: strain


title: Dicktoo-control-rep2

description: Dicktoo-control


title: ABA-Late-rep3

description: ABA-Late

tag: ABA-Late


title: 4117185023_E [18h blinded; Pneumococcus challenged]

description: Sp 1: pneumococcus challneged


title: Adult_Prostate_Sca-1Neg_rep1


title: siRNA beta3 2  HB00F9O

city: Naples

first: gabriella

last: rodolico

address: Via Costantinopoli 16

country: Italy

institute: Second University of Naples

description: myeloma bone resorbing cell lines silenced for beta3

hyb_protocol: Ten μg of DIG-labeled cRNA was hybridized to the Applied Biosystems Human Genome Survey Microarray. The AB Human microarray contains 33,096 60-mer oligonucleotide probes representing 29,098 individual human genes

scan_protocol: Array hybridization, chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer

data_processing: Only microarrays showing average normalized signal intensity above 5,000 and a median background below 600 were included in the study. Signal intensities were imported into Spotfire and Intergomics software (Spotfire Inc., Cambridge, MA, USA) where inter-array quantile normalization was performed in order to minimise the effect of external variables introduced into the data. Quality filtering of unreliable spots (S/N<3) was performed before normalization

label: Dig-UTP

source_name: Cell Cultures

label_protocol: Digoxigenin-UTP labeled cRNA was generated and linearly amplified from 1 ug of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0. Amount (10–70 μg) and quality of the DIG-labeled cRNA was controlled by the NanoDrop® ND-1000 spectrophotometer

growth_protocol: Myeloma plasma cells, purified from needle marrow aspirates by Ficoll-Hypaque gradient centrifugation and subsequently enriched by using anti-CD138 MoAb conjugated magnetic beads (Miltenyi Biotech, Bologna, Italy).

extract_protocol: Total RNA was extracted by using the RNeasy Micro kit (QIAGEN) and treated with DNase I to eliminate possible genomic DNA contamination.

treatment_protocol: The Myeloma plasma cells were purified from needle marrow and cultured to obtain established cell lines

value: Myeloma plasma

tag: cell line

value: silenced for beta3


title: Adult_Prostate_Sca-1Neg_rep2


title: Neuroblastoma_sample_NB15899

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

description: tumor sample from neuroblastoma (stage III) patient

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

label_protocol: A total of 10 µg RNA from each sample was used to prepare biotinylated target cRNA as previously described (Staege MS, et al. Cancer Res 2004;64:8213-21). A detailed protocol is available at www.affymetrix.com.

extract_protocol: Total RNA was prepared from tumor biopsies by using TRIzol (Invitrogen; Karlsruhe, Germany) followed by purification with RNeasy Mini Kit (Qiagen; Hilden, Germany) according to the manufacturer's instructions and was quantified spectro-photometrically. The quality of the purified RNA was assessed by agarose gel analysis.

tag: tumor type

value: neuroblastoma

tag: stage

value: III


title: ABA-Late-rep2

description: ABA-Late


title: ABA-Late-rep1

description: ABA-Late


title: siRNA alphav 1 HB00E8D

description: myeloma bone resorbing cell lines silenced for alphav

value: silenced for alphav


title: unstimulated PBMC from AIED patient #1

description: AIED patient 1  PBMC

tag: PBMC from AIED patient #1 as baseline for stimulation with either pneumococcal antigen or cochlear perilymph fluid


title: Neuroblastoma_sample_NB15296

description: tumor sample from neuroblastoma (stage I) patient

value: I


title: siRNA beta3  1 HB00E90


title: siRNA alphav 2 HB00E8E


title: Neuroblastoma_sample_NB14530


title: Neuroblastoma_sample_NB15205


title: Adult_Prostate_Sca-1Lo_rep4

source_name: Sca-1Lo cells from adult male prostate

value: FACS sorted Sca-1Lo-labelled cells of normal prostate


title: after 3 days in mannitol medium rep3

description: after 3 days in mannitol medium

tag: after 3 days in mannitol medium


title: Neuroblastoma_sample_NB13586

description: tumor sample from neuroblastoma (stage IV) patient

value: IV


title: ABA-Early-rep3

description: ABA-Early

tag: ABA-Early


title: sample2 HB00E8P

description: myeloma bone resorbing cell lines alphav-beta3 positive

value: alphav-beta3 positive


title: Adult_Prostate_Sca-1Lo_rep3


title: ABA-Early-rep2

description: ABA-Early


title: control2 HB004QH

description: myeloma non bone resorbing cell lines negative for the expression of avb3

value: negative for the expression of avb3


title: Adult_Prostate_Sca-1Lo_rep2


title: sample1 HB00E85


title: Ewing_tumor_sample_2

description: Gene expression data from Ewing tumor sample

source_name: Ewing tumor biopsy

value: Ewing tumor


title: Ewing_tumor_sample_4


title: Adult_Prostate_Sca-1Lo_rep1


title: ABA-Control-rep3

description: ABA-Control

tag: ABA-Control


title: Ewing_tumor_sample_3


title: Adult_Prostate_Sca-1Hi_rep1

source_name: Sca-1Hi cells from adult male prostate

value: FACS sorted Sca-1Hi-labelled cells of normal prostate


title: ABA-Early-rep1

description: ABA-Early


title: Adult_Prostate_Sca-1Hi_rep3


title: ABA-Control-rep2

description: ABA-Control


title: Adult_Prostate_Sca-1Hi_rep2


title: control1 HB00E91


title: Ewing_tumor_sample_1


title: ABA-Control-rep1

description: ABA-Control


title: Ovarian_tumor 14

status: Public on Apr 28 2009

city: Cold Spring Harbor

first: Robert

last: Lucito

address: 1 Bungtown Road

department: Genome Center

institute: Cold Spring Harbor Laboratory

description: genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification

hyb_protocol: In order to find the location of the array on the slide, use the Nimblegen array locator and mark it with a diamond pencil.  Wash the slides in a beaker with diH2O and then immerse the slides in ice-cold ethanol.  Dry the slides using nitrogen.  Next, prepare 35mL of hybridization buffer by adding 340uL of Low TE, 1750uL 100% formamide, 875uL 20X SSC, 35uL 10% SDS and bring volume up to 35mL with diH2O and preheat in 37C water bath for 5 minutes.  After preparing the buffer add 30uL of hybridization buffer to 5uL of labeled sample and add 0.2uL alignment control oligonucleotides.  Denature the sample in thermal cycle set at 95C for 5 minutes linked to 37C for at least 5 but no more than 30 minutes.  During this incubation, prepare the slides by placing them in the hybridization tray and installing coverslips on top of the slides.  Place whatman filters on either side of each slide in the tray and soak with 800uL of 5X SSC.  Finally, remove samples from thermocycler and pipette under coverslip and place in oven set for 42C for 14-16 hours.  After the incubation remove the slides from the oven and quickly dip them in 0.2% SDS with 0.2X SSC to remove the coverslip.  Then place slides in rack and twirl rack for 1 minute in 0.2% SDS with 0.2X SSC, then for 30 seconds in 0.2X SSC and then for 30 seconds in 0.05X SSC.  Dry the slides with nitrogen and place in light resistant slide box and scan at 5um.

scan_protocol: Microarray Images were scanned on GenePix 4000B scanner and data extracted using Nimblescan software (Nimblegen Systems Inc).

data_processing: For each probe, the geometric mean of the ratios (GeoMeanRatio) of McrBc and control treated samples were then calculated for each experiment and its associated dye swap. The GeoMeanRatios of all the samples in a dataset were then normalized using quantile normalization method (Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) Bioinformatics, 19, 185-193)

source_name: ovarian tumor tissue

label_protocol: Take 5ug of DNA template and place in a 0.2mL PCR tube and add 5uL of primer solution and bring volume up to 40uL with diH20, mix gently and quickly spin.  Then place the tubes in thermal cycler at 100 C for 5 minutes, quickly spin and immediately place on ice for 5 minutes.  After this add 6uL of Klenow Buffer, 4uL Cy3-dCTP and 4uL Cy5-dCTP, 2uL klenow fragment, 6uL dNTPs and 2uL diH2O in a total volume of 60uL.   Mix by pipetting, quickly spin and incubate at 37 C for 2 hours in thermal cycler.  After the incubation combine the labeled samples into one Eppendorf tube and add 50uL Human Cot-I DNA, 10uL yeast tRNA and 200uL low TE.  Load this into a Microcon YM-30 filter and spin at 12,600 rcf for 10 minutes.  Discard deep purple flow through and add 450uL low TE and spin again.  Repeat this until flow through is clear and then invert filter into new tube and spin for 2 minutes.  Transfer the sample into a new 0.2mL PCR tube and adjust volume to 10uL with low TE

extract_protocol: DNA was extracted by first homeginizing tumor in lysis buffer and incubating for 60 minutes followed by 3 phenol extractions and precipitiation.

value: ovarian

tag: disease state

value: tumor


title: Ovarian_tumor 13


title: Ovarian_tumor 8


title: Ovarian_tumor 10


title: Ovarian_normal 5

source_name: ovarian normal tissue

value: normal


title: Ovarian_tumor 18


title: Ovarian_normal 4


title: Ovarian_normal 1


title: Ovarian_tumor 16


title: Ovarian_normal 2


title: Ovarian_tumor 11


title: Ovarian_tumor 15


title: Ovarian_normal 6


title: Ovarian_tumor 17


title: Breast_tumor T378

source_name: breast tumor tissue

value: breast


title: Breast_tumor T373


title: Ovarian_normal 3


title: Breast_tumor T451


title: Breast_tumor T298


title: Breast_tumor T341


title: Breast_tumor T300


title: Breast_tumor T275


title: Breast_tumor T371


title: Breast_tumor T355


title: Breast_tumor T267


title: Ovarian_normal 7


title: Breast_tumor T363


title: Breast_tumor T163


title: Ovarian_tumor 12


title: Breast_tumor T091


title: Breast_tumor T165


title: Breast_tumor T139


title: Breast_tumor T167


title: Breast_tumor T053


title: Breast_tumor T065


title: Breast_tumor T067


title: Breast_tumor T140


title: Breast_tumor T264


title: Breast_tumor T031


title: Ovarian_tumor 9


title: Breast_tumor CHTN0198


title: Breast_tumor T015


title: Breast_tumor CHTN0596


title: Breast_tumor T044


title: Breast_tumor T020


title: Breast_normal CHTN0178

source_name: breast normal tissue


title: Breast_tumor T085


title: Breast_normal CHTN0597


title: Breast_tumor T042


title: Breast_normal CHTN0129


title: Breast_normal CHTN0133


title: Breast_tumor T079


title: Cancer BC0194T

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

description: gene expression data from breast tumor

hyb_protocol: Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C on Human U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and GCOS version 2.0 using Affymetrix default analysis settings. The global trimmed mean signal intensity value were set to ensure the scale factors were in the range of 1.000 – 3.000.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNAs

growth_protocol: tissues were collected from the operation theater and immediately stored in liquid nitrogen prior to total RNA isolation.

extract_protocol: total RNAs were extracted using Trizol reagent and purified through Qiagen purification column according to manufacturer's recommendations

tag: histopathological exam

value: infiltrating ductal carcinoma

tag: grade

value: grade 1

tag: age in years

tag: race

value: Chinese


title: Normal BC0194N

description: gene expression data from normal breast tissue

source_name: normal breast tissue


title: Breast_tumor CHTN0131


title: Breast_tumor CHTN0080


title: Breast_tumor CHTN0067


title: Normal BC0192N


title: Cancer BC0190T

description: gene expression data from breast tumor

value: grade 2

value: Malay


title: Cancer BC0191T

description: gene expression data from breast tumor


title: Normal BC0191N


title: Cancer BC0192T

description: gene expression data from breast tumor

value: grade 3


title: Breast_tumor CHTN0177


title: Breast_tumor CHTN0118


title: Normal BC0186N


title: Breast_tumor CHTN0097


title: Normal BC0185N


title: Cancer BC0188T

description: gene expression data from breast tumor

value: infiltrating ductal carcinoma with DCIS


title: Breast_normal CHTN0039


title: Breast_normal CHTN0119


title: Cancer BC0185T

description: gene expression data from breast tumor


title: Breast_normal CHTN0068


title: Breast_normal CHTN0073


title: Breast_normal CHTN0199


title: Normal BC0188N


title: Breast_normal CHTN0098


title: Breast_tumor CHTN0128


title: Normal BC0183N


title: Breast_tumor CHTN0043


title: Normal BC0181N


title: Breast_normal CHTN0044


title: Cancer BC0183T

description: gene expression data from breast tumor


title: Cancer BC0181T

description: gene expression data from breast tumor


title: Normal BC0190N


title: Cancer BC0179T

description: gene expression data from breast tumor


title: Normal BC0180N


title: Normal BC0179N


title: Cancer BC0180T

description: gene expression data from breast tumor


title: Breast_normal CHTN0081


title: Normal BC0174N


title: Cancer BC0186T

description: gene expression data from breast tumor


title: Normal BC0172N


title: Breast_tumor CHTN0072


title: Normal BC0177N


title: Cancer BC0172T

description: gene expression data from breast tumor


title: Cancer BC0174T

description: gene expression data from breast tumor


title: Normal BC0173N


title: Cancer BC0168T

description: gene expression data from breast tumor

value: Indian


title: Normal BC0170N


title: Breast_tumor CHTN0038


title: Cancer BC0173T

description: gene expression data from breast tumor


title: Normal BC0171N


title: Normal BC0168N


title: Normal BC0165N


title: Cancer BC0177T

description: gene expression data from breast tumor


title: Normal BC0163N


title: Cancer BC0165T

description: gene expression data from breast tumor


title: Normal BC0159N


title: Cancer BC0164T

description: gene expression data from breast tumor

value: infiltrating lobular carcinoma


title: Normal BC0164N