title: Cercariae differentially expressed gene compare to adult worm

description:
Adult worm were obtained by perfusion of the hepatic portal system of infected rabbits (7 weeks post-infection), and cercariae were released from infected snails and concentrated by centrifugation.Adult worm and cercariae were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from adult worm RNA and cercariae RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.
!Sample_description = The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = adult worm
Keywords = cercariae
Keywords = differentially expressed gene


title: C57L/J C57_J_152-3

status: Public on Mar 09 2009

type: RNA

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

country: USA

institute: Johns Hopkins University School of Medicine

description: Hematopoietic stem/progenitor cells

hyb_protocol: The samples were applied to MouseWG-6 v1.1 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity. (See manuscript)

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader. (See manuscript)

data_processing: quantile normalization

label: biotin

molecule: polyA RNA

organism: Mus musculus

label_protocol: IVT (see manuscript)

extract_protocol: Trizol LS

tag: Hematopoietic stem/progenitor cells


title: BALB/cByJ BALB-cByJ_32-3

description: Hematopoietic stem/progenitor cells


title: C57BL/6J C57BL-6J_80-81

description: Hematopoietic stem/progenitor cells


title: C57BL/6J C57BL-6J_94-5

description: Hematopoietic stem/progenitor cells


title: BALB/cByJ BALB-cByJ_30-1

description: Hematopoietic stem/progenitor cells


title: C58/J C58_J_148-9

description: Hematopoietic stem/progenitor cells


title: C57L/J C57_J_154-5

description: Hematopoietic stem/progenitor cells


title: C57BL/6J C57BL-6J_108-9

description: Hematopoietic stem/progenitor cells


title: C3H/HeJ C3H-J_90-1

description: Hematopoietic stem/progenitor cells


title: DBA/2J DBA2-J_104-5

description: Hematopoietic stem/progenitor cells


title: BTBR_T+_tf/J B6BRT_tf_J_22-3

description: Hematopoietic stem/progenitor cells


title: Egg differentially expressed gene compare to adult worm

status: Public on Mar 10 2009

city: shanghai

first: yuan

last: chunxiu

country: China

institute: shanghai research institute of domestic animal parasitolgy

description:
Egg were recovered from infected liver of rabbits (7 weeks post-infection), and adult worm were obtained by perfusion of the hepatic portal system of infected rabbits. Egg and adult worm were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O.The cDNA from Egg RNA and adult worm RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from adult worm were labeled with Cy3-dUTP and those from egg with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = egg
Keywords = adult worm
Keywords = differentially expressed gene

molecule: total RNA

organism: Schistosoma japonicum

source_name: Egg

source_name: Adult worm


title: BTBR_T+_tf/J B6BRT_tf_J_24-5

description: Hematopoietic stem/progenitor cells


title: A/J A-J_92-3

description: Hematopoietic stem/progenitor cells


title: 129X1/SvJ 129X1-SvJ_42-3

description: Hematopoietic stem/progenitor cells


title: A/J A-J_82-83

description: Hematopoietic stem/progenitor cells


title: 129X1/SvJ 129X1-SvJ_40-1

description: Hematopoietic stem/progenitor cells


title: AKR/J AKR-J_106-7

description: Hematopoietic stem/progenitor cells


title: 129S1/SvImJ 129S1_SvImJ_38-9

description: Hematopoietic stem/progenitor cells


title: AKR/J AKR-J_96-7

description: Hematopoietic stem/progenitor cells


title: 129X1/SvJ 129X1-SvJ_44-5

description: Hematopoietic stem/progenitor cells


title: 129S1/SvImJ 129S1_SvImJ_142-3

description: Hematopoietic stem/progenitor cells


title: A/J A-J_68-9

description: Hematopoietic stem/progenitor cells


title: Muscle Transgenic 5 GF007041

city: West Vancouver

first: Dionne

last: Sakhrani

state: BC

address: 4160 Marine Drive

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 70).  Fluorescence intensity data were extracted from TIF images using QuantArray version 3.0 software (Perkin Elmer).

data_processing: Data transformation (setting background corrected values <0.01 to 0.01 and Lowess normalization) and analysis were performed in GeneSpring GX 7.3.1 software (Agilent Technologies).  Spots with intensity less than the empty spot mean plus 2.5 times their standard deviation were excluded from the analysis.

organism: Oncorhynchus kisutch

source_name: Muscle Wild pool

label_protocol: Reverse transcriptase of 10ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Wild RNA pool

source_name: Muscle Transgenic individual 5

tag: Transgenic RNA individual 5


title: KK/HlJ KK_H1J_46-7

description: Hematopoietic stem/progenitor cells


title: sa2-fosf-4-40min

status: Public on Mar 26 2009

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

description: sa2-fosf-4-40min 0027-2311.cel

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Expression Console version 1.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Staphylococcus aureus

source_name: fosformycin 4ug 40min

label_protocol: Standard Affymetrix procedures

growth_protocol: Staphylococcus aureus, strain ATTC 29213 was used in the experiments. Overnight culture was set in a small volume of cation-adjusted Mueller–Hinton broth medium (Sigma-Aldrich) and grown in Erlenmeyer flask on gyratory shaker (200 rpm) at 37°C. The overnight culture was diluted 100-fold in 300 ml of medium and grown under same conditions in 1-L Erlenmeyer flasks until OD600 (measured by Beckman DU640 spectrophotometer) reached 0.3, which corresponded to the early exponential stage of the growth curve.

extract_protocol: RNA was isolated from an aliquot of 7ml of the culture using enzyme cell wall lysis (30) followed by RNeasy Mini Kit (Qiagen) purification.

treatment_protocol: Bacterial cultures were treated with 0, 1 and 4 µg/ml, respectively, of fosfomycin. Bacterial cells were harvested at the start of the experiment (t0) and at 3 time points (10, 20 and 40 minutes) after treatment. The experiment was repeated at least three times.

tag: strain


title: Muscle Transgenic 4 GF007035

source_name: Muscle Transgenic individual 4

tag: Transgenic RNA individual 4


title: Muscle Transgenic 3 GF007027

source_name: Muscle Transgenic individual 3

tag: Transgenic RNA individual 3


title: Muscle Transgenic 1 GF007021

source_name: Muscle Transgenic individual 1

tag: Transgenic RNA individual 1


title: Muscle Transgenic 2 GF007023

source_name: Muscle Transgenic individual 2

tag: Transgenic RNA individual 2


title: Muscle Domestic 5 GF007040

source_name: Muscle Domestic individual 5

tag: Domestic RNA individual 5


title: Muscle Domestic 4 GF007039

source_name: Muscle Domestic individual 4

tag: Domestic RNA individual 4


title: Muscle Domestic 3 GF007038

source_name: Muscle Domestic individual 3

tag: Domestic RNA individual 3


title: Patient 24R2_Gain70

status: Public on Mar 25 2009

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: For more details, please see Gillet J-P, J. Pathol. in submission

hyb_protocol: Hybridization, quantification and data analysis were performed as described by de Longueville et al. Toxicol Sci 2003; 75:378-392 and Biochem Pharmacol 2002; 64:137-149. and provided in the DualChip microarray protocol of direct labelling.(http://www.eppendorf.com/int/index.php?l=l&action=support&sitemap=4.1&catalognode=27780).

scan_protocol: Briefly, after hybridization, the detection was performed using a Cy3-conjugated anti-biotin IgG antibody (Jackson Immuno Research Laboratories, USA). The arrays were scanned with the ScanArray 4000 XL laser confocal scanner (Applied Biosystems, USA) at a resolution of 10 µm. To maximize the dynamic range of microarrays, the same arrays were scanned using different photomultiplier settings (PMT). The use of different intensities (termed gains) allows the quantification of genes that are expressed at both high and low copy numbers.

data_processing: After image acquisition, the scanned 16-bit image was used to quantify the signal intensities with ImaGene 5.5 software (BioDiscovery, USA) and the file was imported into the DualChip software provided by Eppendorf (Hamburg, Germany).  The signal intensities were normalized by housekeeping genes and internal standards.

organism: Homo sapiens

source_name: Lymph node

label_protocol: After performing a total RNA concentration curve, a concentration of 25 µg was chosen for preparation of labeled cDNA, for more details please see de Longueville F et al. Biochem Pharmacol 2002;64:137– 49.

growth_protocol: Cell lines were seeded in RPMI 1640 (Invitrogen, UK) supplemented with 10% FCS (GibcoBRL, USA).

extract_protocol: Total RNA was extracted by the Trizol method (GibcoBRL, USA) from 6 frozen 50 µm sections of each biopsy.

tag: Follicular lymphoma


title: Muscle Domestic 2 GF007033

source_name: Muscle Domestic individual 2

tag: Domestic RNA individual 2


title: Muscle Domestic 1 GF007022

source_name: Muscle Domestic individual 1

tag: Domestic RNA individual 1


title: Muscle Wild 4 GF007036

source_name: Muscle Wild individual 4

tag: Wild RNA individual 4


title: Muscle Wild 3 GF007032

source_name: Muscle Wild individual 3

tag: Wild RNA individual 3


title: Muscle Wild 2 GF007028

source_name: Muscle Wild individual 2

tag: Wild RNA individual 2


title: C57BL/6J Liver 135500_SOM01KY1

type: genomic

description: C57BL/6J 135500_SOM01KY1

data_processing: normalization: qspline

molecule: genomic DNA

extract_protocol: Phenol chloroform. DNA from one animal.

tag: sex

value: male

tag: tissue

value: liver

extract_protocol: Phenol chloroform

value: pooled from spleen, kidney, and tail


title: Liver Transgenic 5 GG002042

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 68).  Fluorescence intensity data were extracted from TIF images using QuantArray version 3.0 software (Perkin Elmer).

source_name: Liver Wild pool

label_protocol: Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

tag: Wild RNA pool

source_name: Liver Transgenic individual 5

tag: Transgenic RNA individual 5


title: AKR/J 136278_SOM01KY7

description: AKR/J 136278_SOM01KY7

source_name: AKR/J

extract_protocol: Phenol chloroform. DNA pooled from 2-6 animals.

value: kidney


title: Liver Transgenic 4 GG002016

source_name: Liver Transgenic individual 4

tag: Transgenic RNA individual 4


title: Liver Transgenic 3 GG002009

source_name: Liver Transgenic individual 3

tag: Transgenic RNA individual 3


title: BTBR_T+_tf/J 136276_SOM01KYD

description: BTBR_T+_tf/J 136276_SOM01KYD


title: Liver Transgenic 2 GG002006

source_name: Liver Transgenic individual 2


title: SM/J 136277_SOM01KYE

description: SM/J 136277_SOM01KYE

source_name: SM/J


title: LG/J 135559_SOM01GFH

description: LG/J 135559_SOM01GFH

source_name: LG/J


title: Liver Transgenic 1 GG002004

source_name: Liver Transgenic individual 1

tag: Transgenic RNA individual 1


title: C58/J 135559_SOM01KYF

description: C58/J 135559_SOM01KYF


title: Liver Domestic 4 GG002017

source_name: Liver Domestic individual 4


title: Liver Domestic 5 GG002018

source_name: Liver Domestic individual 5


title: KK/HlJ 120839_SOM01KXY

description: KK/HlJ 120839_SOM01KXY

source_name: KK/HlJ


title: Liver Domestic 3 GG002010

source_name: Liver Domestic individual 3


title: C3H/HeJ 19338102_SOM02W9J

description: C3H/HeJ 19338102_SOM02W9J


title: Liver Domestic 1 GG002003

source_name: Liver Domestic individual 1


title: NOD/LtJ 135560_SOM01GF4

description: NOD/LtJ 135560_SOM01GF4

source_name: NOD/LtJ


title: SWR/J 136273_SOM01GFN

description: SWR/J 136273_SOM01GFN

source_name: SWR/J


title: Liver Domestic 2 GG002005

source_name: Liver Domestic individual 2


title: Liver Wild 4 GG002013

source_name: Liver Wild pool

source_name: Liver Wild individual 4


title: 129S1/SvImJ 135560_SOM01KY9

description: 129S1/SvImJ 135560_SOM01KY9


title: PL/J 135502_SOM01GFM

description: PL/J 135502_SOM01GFM

source_name: PL/J


title: FVB/NJ 119969_SOM01GFJ

description: FVB/NJ 119969_SOM01GFJ

source_name: FVB/NJ


title: Muscle Wild 1 GF007026

source_name: Muscle Wild pool

source_name: Muscle Wild individual 1

tag: Wild RNA individual 1


title: Carbon-limited chemostat of Penicillium chrysogenum DS54465 (hdfA delta strain) in absence of PAA -2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

data_processing: Acquisition and quantification of array images were performed using Affymetrix GeneChip Operating Software (GCOS version 1.2). Before comparison, all arrays were globally scaled to a target value of 100 using the average signal from all gene features.

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

organism: Penicillium chrysogenum

source_name: Chemostat culture

growth_protocol:
Aerobic glucose-limited chemostat cultivation was performed at 25ºC in 3-litre turbine-stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermentor was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 h of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device. The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH Chemicals Ltd, Poole, UK) was discontinuously added at timed intervals. The offgas was cooled by a condensor at 4ºC after drying with a Perma Pure dryer (type MD-110-48P-4, Perma Pure, Toms River, USA) oxygen and carbon dioxide concentrations were determined with a NGA 2000 analyser (Rosemount Analytical, Orville, USA). Off-gas flow rates were determined from an average of 10 measurements using a SAGA digital flow meter (Ion Science, Cambridge, UK). Specific rates of carbon dioxide and oxygen consumption were calculated.
The mineral medium was prepared as described [37] and contained per litre of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O.

extract_protocol: 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminium foil, quenched in liquid nitrogen and stored at -80ºC until further use. For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

treatment_protocol: liquid nitrogen quenching

tag: The hdfAdelta (amdS) DS54465 was generated from the high penicillin producer strain DS17690 (Harris DM, Diderich JA, van der Krogt ZA, Luttik MA, van Gulik WM, van Dijken JP, Pronk JT

value: Enzymic analysis of NADPH metabolism in Penicillium chrysogenum:presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab Eng 2006, 8:91-101.).


title: Liver Wild 1 GG002007

source_name: Liver Wild individual 1


title: DBA/2J 135558_SOM01GFK

description: DBA/2J 135558_SOM01GFK


title: Liver Wild 2 GG002008

source_name: Liver Wild individual 2


title: Liver Wild 3 GG002011

source_name: Liver Wild individual 3


title: C57L/J 120840_SOM01KYC

description: C57L/J 120840_SOM01KYC


title: Liver Wild 5 GG002043

source_name: Liver Wild individual 5

tag: Wild RNA individual 5


title: BALB/cByJ 120840_SOM01GFD

description: BALB/cByJ 120840_SOM01GFD

source_name: BALB/cByJ


title: SJL/J 135558_SOM01KY8

description: SJL/J 135558_SOM01KY8

source_name: SJL/J


title: NZB/BlNJ 135500_SOM01GFP

description: NZB/BlNJ 135500_SOM01GFP

source_name: NZB/BlNJ


title: A/J 119920_SOM01GFF

description: A/J 119920_SOM01GFF

source_name: A/J


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 KO 33

status: Public on Mar 08 2009

city: Seattle

first: Xia

last: Yang

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: Liver gene expression profiling of three cytosolic malic enzyme (Me1 or Mod1) knockout mice and 5 littermate control mice.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Liver

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Liver WT Control Pool (n=5)

tag: Mouse Liver Mod1 KO 33


title: Carbon-limited chemostat of Penicillium chrysogenum DS54465 (hdfA delta strain) in absence of PAA -1

scan_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 WT 15

tag: Mouse Liver Mod1 WT 15


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 WT 26

tag: Mouse Liver Mod1 WT 26


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 WT 14

tag: Mouse Liver Mod1 WT 14


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 WT 21

tag: Mouse Liver Mod1 WT 21


title: Carbon-limited chemostat of Penicillium chrysogenum DS54465 (hdfA delta strain) in presence of PAA -1

label_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol:
Aerobic glucose-limited chemostat cultivation was performed at 25ºC in 3-litre turbine-stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermentor was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 h of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device. The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH Chemicals Ltd, Poole, UK) was discontinuously added at timed intervals. The offgas was cooled by a condensor at 4ºC after drying with a Perma Pure dryer (type MD-110-48P-4, Perma Pure, Toms River, USA) oxygen and carbon dioxide concentrations were determined with a NGA 2000 analyser (Rosemount Analytical, Orville, USA). Off-gas flow rates were determined from an average of 10 measurements using a SAGA digital flow meter (Ion Science, Cambridge, UK). Specific rates of carbon dioxide and oxygen consumption were calculated.
The mineral medium was prepared as described [37] and contained per litre of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O.  Production of penicillin-G was induced by adding 0.58 g•L-1 phenylacetic acid (PAA) to the medium.


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 WT 22

tag: Mouse Liver Mod1 WT 22


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -7

description: Liver gene expression profiling of 8 lipoprotein lipase (Lpl) heterozygous knockout mice and 8 littermate control mice.


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 KO 27

tag: Mouse Liver Mod1 KO 27


title: Liver WT Control Pool (n=5) vs. Mouse Liver Mod1 KO 31

tag: Mouse Liver Mod1 KO 31


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -5


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -6


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -2


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -1


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -4


title: Carbon-limited chemostat of Penicillium chrysogenum DS54465 (hdfA delta strain) in presence of PAA -2


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -9

tag: Liver, Male wt, Chow Diet  -9


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -8


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male Lipoprotein lipase KO (-/+), Chow Diet  -3


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -7

tag: Liver, Male wt, Chow Diet  -7


title: Lactb-M10RW

city: Los Angeles

first: Josh

last: Deignan

state: CA

address: 675 Charles E Young Dr South, MRL 3220

department: Cardiology

institute: UCLA

hyb_protocol: 800 ng of labeled cRNA product is hybridized to prepared whole genome arrays and allowed to incubate overnight ( 16 –20 hrs) at 55 degrees C.  Arrays are washed then stained with Cy3 labeled streptavadin. Excess stain is removed by washing and the arrays are dried and scanned on an Illumina BeadScan con-focal laser scanner.

scan_protocol: Scanning was performed using Illumina BeadScan con-focal laser scanner.

data_processing: Data were scaled and normalized using the rank invariant method in the Beadstudio software v. 1.5.1.3. (Illumina Inc.)

source_name: Strain: FVB wildtype gender:male, age: 23 weeks, tissue: liver

label_protocol: RNA samples queued for whole genome analysis using Illumina gene expression chips are first quanted using the ribogreen RNA quantitation kit. Samples are normalized to 11 ng per ul. 100 ng of normalized total RNA is used as a template for the synthesis of cDNA using Ambion cDNA synthesis kit AMIL1791. Newly synthesized  cDNA becomes the template for the amplification and biotinylation of cRNA . Labeled cRNA is quanted (ribogreen) and normalized to 77 ng per ul.

growth_protocol: These mice were fed a 4% fat chow diet until 11 weeks of age.

extract_protocol: Liver tissues were homogenized and total RNA extracted using Trizol reagent (Invitrogen, CA) according to the manufacturer’s instructions.  RNA samples were isolated from liver tissues using a Qiagen RNeasy Kit and quality-checked with an Agilent 2100 Bioanalyzer (Foster City, CA).

treatment_protocol: Mice were fed a 6% fat chow diet from 11 weeks of age until sacrifice at 23 weeks of age.

tag: Liver, 6% fat diet, 12 weeks


title: Lactb-M13RC


title: Lactb-M11LC


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -6

tag: Liver, Male wt, Chow Diet  -6


title: Lactb-M5LC


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -4

tag: Liver, Male wt, Chow Diet  -4


title: Lactb-M10BC


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -5

tag: Liver, Male wt, Chow Diet  -5


title: Lactb-M12RC


title: Lactb-M12BC

source_name: Strain: Lactb transgenic, gender:male, age: 23 weeks, tissue: liver


title: Lactb-M11RC


title: Lactb-M13BC


title: Lactb-M12RW


title: Lactb-M5RC


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -2

tag: Liver, Male wt, Chow Diet  -2


title: Lactb-M12LC


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -1

tag: Liver, Male wt, Chow Diet  -1


title: Lactb-M9RC


title: Lactb-M9LC


title: Lactb-M2RC


title: Lactb-M1RC


title: Gyk-7LCRW

source_name: Strain: Gyk wildtype gender:female, age: 23 weeks, tissue: liver


title: Gyk-1LWRC


title: Gpx-M1BC

source_name: Strain: B6/DBA wildtype gender:male, age: 23 weeks, tissue: liver


title: Gyk-2RC

source_name: Strain: Gyk heterozygous gender:female, age: 23 weeks, tissue: liver


title: Gyk-7RC


title: Gpx-M7RC

source_name: Strain: Gpx3 transgenic, gender:male, age: 23 weeks, tissue: liver


title: Gyk-2BC


title: Gyk-2RW


title: Gpx-M4LC


title: Gas63.2-M8RC

source_name: Strain: Gas7 wildtype gender:male, age: 23 weeks, tissue: liver


title: Gyk-1LCRW


title: Gpx-M1LC


title: Gpx-M1RC


title: Gpx-M4RC


title: Gyk-1BC


title: Gyk-1RC


title: Gpx-M4BC


title: Gas63.2-M8LC


title: Gpx-M1RW


title: Gas63.2-M7RW


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar (-/-) KO Chow Diet  -4

description: Liver gene expression profiling of 3 complement component 3a receptor 1 (C3ar1) knockout mice and 4 littermate control mice.

tag: Liver, WT Chow Diet Control pool (n=6)

tag: Liver, C3ar (-/-) KO Chow Diet  -4


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar (-/-) KO Chow Diet  -3

tag: Liver, C3ar (-/-) KO Chow Diet  -3


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar (-/-) KO Chow Diet  -2

tag: Liver, C3ar (-/-) KO Chow Diet  -2


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar1 WT Chow Diet-2

tag: Liver, C3ar1 WT Chow Diet-2


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar1 WT Chow Diet-4

tag: Liver, C3ar1 WT Chow Diet-4


title: Gas63.2-M1RC


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar1 WT Chow Diet-3

tag: Liver, C3ar1 WT Chow Diet-3


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -5

description: Liver gene expression profiling of 6 transforming growth factor receptor beta 2 (Tgfbr2) heterozygous knockout mice and 4 littermate control mice.

tag: Liver, Tgfbr-/+ males Chow Diet  -5


title: Gas63.2-M4LC


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -6

tag: Liver, Tgfbr-/+ males Chow Diet  -6


title: Gas63.2-M6LC

source_name: Strain: Gas7 transgenic, gender:male, age: 23 weeks, tissue: liver


title: Gas63.2-M7BC


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -1

tag: Liver, Tgfbr-/+ males Chow Diet  -1


title: Gas63.2-M5RW


title: Gas63.2-M3BC


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, WT Chow Diet  -3

tag: Liver, WT Chow Diet  -3


title: Gas63.2-M3LC

tag: Liver, 6% fat diet, 12 weeks


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -4

tag: Liver, Tgfbr-/+ males Chow Diet  -4


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, WT Chow Diet  -4

tag: Liver, WT Chow Diet  -4


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, WT Chow Diet  -1

tag: Liver, WT Chow Diet  -1


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, ZFP90 tg, male  -2

description: Liver gene expression profiling of 3 Zinc finger binding protein (Zfp90) transgenic mice and 4 littermate control mice.

tag: Liver, ZFP90 tg, male  -2


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, WT Chow Diet  -2

tag: Liver, WT Chow Diet  -2


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -2

tag: Liver, WT Chow Diet Control pool (n=6)

tag: Liver, Tgfbr-/+ males Chow Diet  -2


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, C3ar1 WT Chow Diet-1

tag: Liver, C3ar1 WT Chow Diet-1


title: Gas63.2-M3RC


title: Gas63.2-M2LW


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, ZFP90 tg, male  -1

tag: Liver, ZFP90 tg, male  -1


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, WT, male  -4

tag: Liver, WT, male  -4


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, WT, male  -3

tag: Liver, WT, male  -3


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, ZFP90 tg, female  -1

tag: Liver, ZFP90 tg, female  -1


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, WT, male  -2

tag: Liver, WT, male  -2


title: Gas63.2-M2RW


title: Liver, WT Control Pool, males&females (n=4) vs. Liver, WT, female  -3

tag: Liver, WT, female  -3


title: Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet  -3

tag: Liver, Tgfbr-/+ males Chow Diet  -3


title: Gas63.2-M1LC


title: GBM xenograft tumor, line 46, generation 1, microarray hybridization batch 1

status: Public on Mar 07 2009

city: San Francisco

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

description: Gene expression data from GBM subcutaneous xenograft tumor tissue

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: CEL files were read into R/Bioconductor using the Affy/affyPLM package, and RMA (robust multi-array average) intensity in log2 scale was generated for each probe set (gene). The 11 perfect match (PM) intensities per probe set were (i) background corrected; (ii) quantile-normalized (to make the distribution of intensities the same for all arrays); and (iii) summarized for each probe set using a robust fit of linear models as described.

source_name: GBM xenograft tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted from GBMX tumors and non-neoplastic control brain using the mirVana RNA isolation system (Ambion), further purified using RNeasy columns (Qiagen), and RNA integrity assessed using a bioanalyzer (Aglient).

tag: tissue type

value: Glioblastoma multiforme (GBM) xenograft tumor tissue

tag: tumor grade

value: Grade-IV tumor


title: GBM xenograft tumor, line 56, generation 2, microarray hybridization batch 1


title: GBM xenograft tumor, line 46, generation 9, microarray hybridization batch 1


title: GBM xenograft tumor, line 58, generation 3, microarray hybridization batch 1


title: GBM xenograft tumor, line 43, generation 2, microarray hybridization batch 1


title: GBM xenograft tumor, line 59, generation 2, microarray hybridization batch 1


title: GBM xenograft tumor, line 40, generation 2, microarray hybridization batch 1


title: GBM xenograft tumor, line 40, generation 2, microarray hybridization batch 2


title: GBM xenograft tumor, line 44, generation 5, microarray hybridization batch 1


title: GBM xenograft tumor, line 34, generation 5, microarray hybridization batch 1


title: GBM xenograft tumor, line 36, generation 6, microarray hybridization batch 1


title: GBM xenograft tumor, line 40, generation 1, microarray hybridization batch 1


title: GBM xenograft tumor, line 22, generation 3, microarray hybridization batch 1


title: GBM xenograft tumor, line 28, generation 3, microarray hybridization batch 1


title: GBM xenograft tumor, line 15, generation 15, microarray hybridization batch 2


title: GBM xenograft tumor, line 28, generation 1, microarray hybridization batch 1


title: GBM xenograft tumor, line 38, generation 5, microarray hybridization batch 1


title: GBM xenograft tumor, line 39, generation 4, microarray hybridization batch 1


title: GBM xenograft tumor, line 16, generation 4, microarray hybridization batch 1


title: 5T (Hind240)

status: Public on Mar 24 2009

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

scan_protocol: Standard Affymetrix protocol

data_processing: Genotyping was performed using Affymetrix Genotyping Tools Version 2.0.  dChip was used to normalize probe-level signal intensities to a baseline array with median intensity using invariant set normalization and obtain SNP-level signal intensities using a model-based (PM/MM) method,

source_name: endometrial cancer

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

extract_protocol: biotin

treatment_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.

tag: gender

value: F

tag: histologic type

value: endometrioid

tag: metastatic phenotype

value: FIGO I/II and no recurrence


title: GBM xenograft tumor, line 22, generation 3, microarray hybridization batch 2


title: GBM xenograft tumor, line 10, generation 9, microarray hybridization batch 2


title: GBM xenograft tumor, line 15, generation 1, microarray hybridization batch 2


title: GBM xenograft tumor, line 14, generation 4, microarray hybridization batch 1


title: GBM xenograft tumor, line 15, generation 15, microarray hybridization batch 1


title: GBM xenograft tumor, line 15, generation 1, microarray hybridization batch 1


title: GBM xenograft tumor, line 12, generation 3, microarray hybridization batch 1


title: GBM xenograft tumor, line 10, generation 9, microarray hybridization batch 1


title: GBM xenograft tumor, line 8, generation 2, microarray hybridization batch 1


title: GBM xenograft tumor, line 8, generation 1, microarray hybridization batch 1


title: GBM xenograft tumor, line 5, generation 10, microarray hybridization batch 1


title: GBM xenograft tumor, line 6, generation 8, microarray hybridization batch 1


title: GBM xenograft tumor, line 46, generation 9

description: SNP array data from GBM subcutaneous xenograft tumor tissue

data_processing: SNP array data was pre-processed as follows: PM probe intensities of the 21 GBMX tumors were quantile normalized with those of 90 normal tissue controls (Hapmap trios, Affymetrix). The total hybridization intensities, PMA+PMB (in logarithm base two), were median-summarized over the 5-7 probe quartets for each SNP, followed by a fragment length adjustment using cubic splines. We then calculated the log2 copy number (CN) ratio for each SNP by subtracting the mean SNP log2 intensity of all 90 Hapmap reference samples from the per-SNP intensity within each GBMX tumor to remove SNPspecific effects. CN was segmented along each chromosome into regions of equal copy number changes with a circular binary segmentation algorithm implemented in the DNAcopy package of R/Bioconductor, using the NCBI Build 36.1 annotation from Affymetrix (dated July 12, 2007). Neighboring genomic segments were merged if their estimated copy numbers did not differ by more than one standard deviation. Frequencies of CN gain or loss were calculated using segment mean thresholds of +/- 0.3. For analyses of GBM clinical specimens segment mean thresholds of +/- 0.3 were used on data generated 5 from SNP arrays, and thresholds of +/- 0.1 were used on data generated from BAC arrays, and Agilent 244K oligonucleotide arrays.

extract_protocol: We extracted genomic DNA using the Wizard DNA Purification Kit (Promega), further purified it with a phenol/chloroform extraction and quantitated it using a fluorometer. Phenol/chloroform extraction of the resulting DNA increased measurement precision significantly in some experiments, presumably by removing proteins that interfered with DNA labeling and hybridization.

source_name: normal tissue controls, Hapmap trios, Affymetrix

extract_protocol: Affymetrix HapMap


title: GBM xenograft tumor, line 10, generation 1, microarray hybridization batch 1


title: GBM xenograft tumor, line 44, generation 5

value: normal tissue controls, Hapmap trios, Affymetrix


title: GBM xenograft tumor, line 43, generation 2


title: GBM xenograft tumor, line 56, generation 2


title: Mix breed, hemangiosarcoma: DD1

city: Denver

first: Beth

last: Tamburini

state: CO

address: 1400 Jackson Street, K503

department: Immunology

institute: University of Colorado Denver

description: Gene expression data from dogs with hemangiosarcoma of different breeds

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

label: Biotin

organism: Canis lupus familiaris

source_name: primary hemangiosarcoma tumor cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cryopreserved cultured cells from the earliest available passages were used

extract_protocol: RNA was prepared using the RNEasy Mini Kit and QIAshredder columns (QIAGEN, Valencia, CA)

tag: tumor type and origin

value: hemangiosarcoma, spleen

tag: breed

value: Golden Mix


title: GBM xenograft tumor, line 3, generation 1, microarray hybridization batch 1


title: Gliosis non-neoplastic control tissue, ID number SF7178, microarray hybridization batch 2

description: Gene expression data from gliosis brain tissue

source_name: Gliotic brain tissue

value: Gliotic brain tissue

value: Non-tumor brain


title: Gliosis non-neoplastic control tissue, ID number SF6700, microarray hybridization batch 2


title: Gliosis non-neoplastic control tissue, ID number SF4916, microarray hybridization batch 2


title: Gliosis non-neoplastic control tissue, ID number SF6637, microarray hybridization batch 2


title: GBM xenograft tumor, line 40, generation 2


title: GBM xenograft tumor, line 39, generation 4


title: 13852153 - MIPS J4JC-3 vs Col J4JC-3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: In Arabidopsis thaliana, how does MIPS knock out influence gene expression? In AtMIPS mutants how does photoperiod influence gene expression.

hyb_protocol: Col J4JC-3 Cy5 / MIPS J4JC-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Col J4JC-3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - JC : short days	 Media=compost	 hygrometry=60% day / 55% night	 Temperature=20 day / 18 night	 Light=8 hours

treatment_protocol: Name:Short days - environmental treatment - light,light:time 4day . Light : 8 hours.

tag: dev.stage (boyes et al. plant cell 2001)

tag: cultivar

value: Columbia

tag: genotype

value: wild type

source_name: MIPS J4JC-3

extract_protocol: MIPS J4JC-3:11.7ug.

value: mips ko


title: 13852154 - Col J4JC-3 vs MIPS J4JC-3

hyb_protocol: MIPS J4JC-3 Cy5 / Col J4JC-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GBM xenograft tumor, line 38, generation 5


title: GBM xenograft tumor, line 36, generation 6


title: 13852092 - MIPS J4JL-3 vs Col J4JL-3

hyb_protocol: Col J4JL-3 Cy5 / MIPS J4JL-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col J4JL-3

growth_protocol: leaf - JL : long days	 Media=compost	 hygrometry=60% day / 55% night	 Temperature=20 day / 18 night	 Light=16 hours

extract_protocol: Col J4JL-3:8.1ug.

treatment_protocol: Name:Long days - environmental treatment - light,light:time 4day . Light : 16 hours.

source_name: MIPS J4JL-3

extract_protocol: MIPS J4JL-3:32.7ug.


title: 13852091 - Col J4JL-3 vs MIPS J4JL-3

hyb_protocol: MIPS J4JL-3 Cy5 / Col J4JL-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MFE 280 (Hind240)

source_name: endometrial cancer cell line

tag: cell line

value: MFE


title: Golden Retriever, hemangiosarcoma: Tucker

value: Golden Retriever


title: Rottweiler, hemangiosarcoma: Joey

value: Joey


title: GBM xenograft tumor, line 34, generation 5


title: 13852090 - MIPS J4JL-3 vs MIPS J4JC-3

hyb_protocol: MIPS J4JC-3 Cy5 / MIPS J4JL-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Golden Retriever, hemangiosarcoma: Journey


title: Golden Retriever, hemangiosarcoma: Frog


title: 13689496 - MIPS J4JL-2 vs MIPS J4JC-2

hyb_protocol: MIPS J4JC-2 Cy5 / MIPS J4JL-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

source_name: MIPS J4JC-2

growth_protocol: leaf - Media : compost	 hygrometry : 60% day / 55% night	 Temperature : 20 day / 18 night	 Light : 8 hours

extract_protocol: MIPS J4JC-2:5ug.

value: mutant mips 1-1

source_name: MIPS J4JL-2

extract_protocol: MIPS J4JL-2:5ug.


title: 13689495 - MIPS J4JC-2 vs MIPS J4JL-2

hyb_protocol: MIPS J4JL-2 Cy5 / MIPS J4JC-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689494 - MIPS J4JC-2 vs Col J4JC-2

hyb_protocol: Col J4JC-2 Cy5 / MIPS J4JC-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col J4JC-2

extract_protocol: Col J4JC-2:5ug.


title: Dalmation, hemangiosarcoma: Dal4

value: Dalmation


title: 13689492 - MIPS J4JL-2 vs Col J4JL-2

hyb_protocol: Col J4JL-2 Cy5 / MIPS J4JL-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col J4JL-2

extract_protocol: Col J4JL-2:5ug.


title: GBM xenograft tumor, line 28, generation 3

value: Glioblastoma multiforme (GBM) xenograft tumor tissue

value: Grade-IV tumor


title: 13852074 - MIPS J4JC-3 vs MIPS J4JL-3

hyb_protocol: MIPS J4JL-3 Cy5 / MIPS J4JC-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Golden Retriever, hemangiosarcoma: ChadG8


title: GBM xenograft tumor, line 26, generation 7


title: GBM xenograft tumor, line 22, generation 3


title: 13689491 - Col J4JL-2 vs MIPS J4JL-2

hyb_protocol: MIPS J4JL-2 Cy5 / Col J4JL-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GBM xenograft tumor, line 16, generation 4


title: Golden Retriever, hemangiosarcoma: ChadG6


title: MCF7_NPAS2_Rep1-1

city: New Haven

first: Aaron

middle: Ezra

last: Hoffman

state: CT

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

description: All Arrays were processed at Mogene, LC; an Agilent-certified service provider

hyb_protocol: SureHyb Hybridization Chamber according to Agilent's Instructions

scan_protocol: Agilent’s Microarray Scanner with SureScan Technology

data_processing: A whole-chip error model was used for array data analysis and to call a bound gene (target gene). The neighborhood error model takes into account neighboring probes and calls a region as bound, not just a single probe. Genes associated with significant regions are therefore considered target genes.

source_name: Input

label_protocol: Agilent Genomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309)

extract_protocol: GENECLEAN Turbo kit

tag: antibody

value: rabbit IgG

tag: target

value: control

tag: replicate

value: rep 1, part 1

source_name: NPAS2 targets

extract_protocol: The ChIP assay was performed using the ChIP Assay Kit ((Millipore, Billerica, MA) according to the manufacturer’s protocol. Briefly, cells were grown in 100 mm cell culture plates to 80% confluence. Cross-linking of protein and DNA was performed using cell culture medium containing 1% formaldehyde at room temperature for 10 minutes. Sonication was performed using an Omni Ruptor 250 Ultrasonic Homogenizer (omni International, Marietta, GA) to generate input material. This input sample was then incubated with primary antibody (anti-NPAS2) and negative control (Rabbit IgG) for immunoprecipitation (IP). Agarose beads were added to the reactions to bind protein-conjugated antibody. The antibody-protein-DNA complex was then eluted from the agarose beads with freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) and the cross-linking was reversed by adding 5M NaCl for 4 hours at 65ºC followed by proteinase K digestion at 45ºC for one hour.  The final DNA, representing NPAS2 target sequences, was purified using the GENECLEAN Turbo kit (Qbiogene, Carlsbad, CA) according to the manufacturer’s instructions. Ligation-mediated PCR (LM-PCR) (Agilent Technologies, Foster City, CA) was used to amplify DNA according to the manufacturer’s protocol.

value: NPAS2 targets, ChIP-enriched


title: Portugese Water Dog, hemangiosarcoma: ChadP9

value: hemangiosarcoma, spleen

value: Portugese Water Dog


title: S. griseus IFO13350 vs adpA deficient mutant grown on SMM medium 3rd

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

description: To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.

hyb_protocol: Microarray hybridization was carried out at 42°C for 18 h with mixing by using 120 μl per slide of SlideHyb#1 hybridization solution (Ambion) in a GeneTac HybStation (Genomic Solution). The posthybridization washing consisted of three cycles of 20-second incubations with each of the following solutions: 2× SSC plus 0.1% SDS (medium stringency) at 42°C, 0.1× SSC plus 0.05% SDS (high stringency) at 25°C, and 0.1× SSC (low stringency) at 25°C. After being washed, the slides were dried by centrifugation for 5 min at 350 × g at room temperature.

scan_protocol: The slides scanned with with a 428 array scanner (Affymetrix). The spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).

data_processing:
Expression ratios were normalized using the Limma loess method by ArrayPipe 2.0. Average normalized expression ratios (S. griseus IFO13350/ΔadpA mutant) were calculated for each gene and tested for significance (p < 0.05). Ratio of S. griseus IFO13350 compared with ΔadpA were further screened for difference from ΔadpA mutant, which was defined as having an expression ratio of either >2.0 or <0.5.

In the Sample data tables, Control represents the adpA deficient mutant, and Experiment represents wild type. The VALUE column represents log2 (mutant/wild type) ratios.

organism: Streptomyces griseus subsp. griseus NBRC 13350

source_name: wild type

label_protocol: Cy3 labeled cDNA were prepared by indirect labeling.

growth_protocol: SMM medium

extract_protocol: Total RNA was isolated by RNAqueous mini kit (Ambion) and carried out DNaseI treatment to remove contaminated genomic DNA.

tag: strain

source_name: adpA deficient mutant

label_protocol: Cy5 labeled cDNA were prepared by indirect labeling.

value: delta-adpA


title: GBM xenograft tumor, line 15, generation 15

source_name: GBM xenograft tumor tissue

value: normal tissue controls, Hapmap trios, Affymetrix


title: Golden Retriever, hemangiosarcoma: ChadG4


title: Wt_+/- bile_17-17

city: Lebanon

first: Francisca

middle: A

last: Cerda-Maira

state: NH

address: 16 Cavendish Court

department: Microbiology and Immunology

institute: Dartmouth College

hyb_protocol: 25% formamide 42 degrees O/N

scan_protocol: Scanned at 550 and 650 nm at 70-90% laser power using a GMS418 Scanner. Image saved as tif and imported into Scanalyze (Michael Eisen ver. 2.50, Stanford University)

data_processing: Data uploaded into Gene Traffic software (Stratagene ver. 3.2-12). Intensities normalized using global intensity method. Spot flagged if less than 2X background. Ratios represent Cy5/Cy3 (channel 2/channel1)

organism: Vibrio cholerae

source_name: Vibrio cholerae

label_protocol: Reverse transcription using aadUTP followed by coupling to Alexa555

growth_protocol: Bacteria was grown in AKI media in virulence genes inducing conditions (standing and shaking) in the abscence of bile

extract_protocol: Trizol extraction and RNAesy purification column from Qiagen

treatment_protocol: Bacteria was grown in the abscence of bile for 4 hours

tag: Wt Vibrio cholerae

label_protocol: Reverse transcription using aadUTP followed by coupling to Alexa647

growth_protocol: Channel Growth Protocol Bacteria was grown in AKI media in virulence genes inducing conditions (standing and shaking) in the presence of 0.4% bile

treatment_protocol: Bacteria was grown in the presence of 0.4% bile for 4 hours


title: MCF7_NPAS2_Rep1-2

value: rep 1, part 2


title: Wt_+/- bile_17-15


title: GBM xenograft tumor, line 14, generation 4

hyb_protocol: Affymetrix protocol

source_name: normal tissue controls, Hapmap trios, Affymetrix


title: Wt_+/- bile_17-16


title: HT29siRNAc.E

city: Tel Aviv

first: Eyal

last: Sagiv

address: 6th Weizmann st

department: The Integrated Cancer Prevention Center

country: Israel

institute: Tel Aviv Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The algorithm, implanted in Affymetrix Suite Version 5.0 (MAS5) generates signal value (which designates a relative measure of the abundance of the transcript), a detection p-value (which indicates the reliability of the transcript’s detection call) and detection call (present, absent or marginal). For interarray comparisons, the data from each array was scaled using MAS5. The bioinformatics analysis was carried out using GeneSpring® version7 software (Silicon Genetics, Redwood City, CA, USA). Normalization procedure: Values below 0.01 were set to 0.01.  Each measurement was divided by the 50.0th percentile of all measurements in that sample (per chip normalization). Each gene was divided by the median of its measurements in all samples (per gene normalization). Genes were filtered out if appearing present in only none or 1 of the 8 samples.

source_name: HT29 derived clone with 2 vectorS expressing CD24 directed shRNA

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted from cells as described before and quality was assessed on Agilent 2100 Bioanalyzer device (Agilent Technologies, Palo Alto, CA) from the indicated cell lines and clones. If MAB treatment is indicated, cells were exposed for 1:40 SWA11 MAB for 72h. RNA was labeled and hybridized as described before (8), only this time, using the human (HG-U133A) Genechip® (Affymetrix Inc., Santa Clara, CA).

tag: tissue

value: colon


title: GBM xenograft tumor, line 12, generation 3

tag: tissue type


title: MCF7_NPAS2_Rep2-2

value: rep 2, part 2


title: HT29 siRNAc.G


title: Wt_+/- bile_17-14

treatment_protocol: Bacteria was grown in the abscence of bile for 2 hours

treatment_protocol: Bacteria was grown in the presence of 0.4% bile for 2 hours


title: MCF7_NPAS2_Rep2-1

value: rep 2, part 1


title: S. griseus IFO13350 vs adpA deficient mutant grown on SMM medium 1st

value: wild type


title: Deep-sowing 10d treatment UCZ, biological rep2

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from maize mesocotyl

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

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

data_processing: The data were analyzed with GCOS software (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.

organism: Zea mays

source_name: Mesocotyl, UCZ

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

extract_protocol: The total RNA was extracted by the TRIzol method (Invitrogen, USA). Mesocotyls were ground in liquid nitrogen, and 50-100 mg of frozen tissue was transferred into a tube with 1 ml TRIzol. Next, RNA was isolated, dried and dissolved in 50 µl DEPC-H2O. RNA quality and concentration were determined by 1.0% agarose gel electrophoresis and spectrophotometry.

value: Maize inbred line 3681-4

tag: age

value: 10d after sowing


title: HT29siRNAc.833

source_name: HT29 derived clone with vector expressing CD24 directed shRNA


title: 13689493 - Col J4JC-2 vs MIPS J4JC-2

hyb_protocol: MIPS J4JC-2 Cy5 / Col J4JC-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: mutant mips 1-1


title: S. griseus IFO13350 vs adpA deficient mutant grown on SMM medium 2nd


title: GBM xenograft tumor, line 10, generation 9

value: Glioblastoma multiforme (GBM) xenograft tumor tissue

tag: tumor grade

value: Grade-IV tumor


title: Deep-sowing 10d treatment GA3, biological rep2

source_name: Mesocotyl, GA3


title: GFP

source_name: HT29 derived clone with vector expressing GFP directed shRNA


title: Wt_+/- bile_17-13


title: GBM xenograft tumor, line 8, generation 2


title: Wt_+/- bile_17-12


title: Deep-sowing 10d treatment Control, biological rep2

source_name: Mesocotyl, control


title: Wt_+/- bile_16-39

growth_protocol: Channel Growth Protocol Bacteria was grown in AKI media in virulence genes inducing conditions (standing and shaking) in the presence of 0.02% bile

treatment_protocol: Bacteria was grown in the presence of 0.02% bile for 2 hours


title: Colo357 AB

source_name: Colo357 cells treated with anti-CD24 mAb

value: pancreas


title: Wt_+/- bile_16-38

treatment_protocol: Channel Treatment Protocol Bacteria was grown in the presence of 0.02% bile for 2 hours


title: HT29 AB

source_name: HT29 cells treated with anti-CD24 mAb


title: Colo357

source_name: Pancreatic cancer cell line Colo357


title: Wt_+/- bile_16-37


title: GBM xenograft tumor, line 5, generation 10


title: GBM xenograft tumor, line 6, generation 8


title: Deep-sowing 10d treatment Control, biological rep1


title: GBM xenograft tumor, line 3, generation 11


title: Deep-sowing 10d treatment UCZ, biological rep1


title: HT29

source_name: Colorectal cancer cell line HT29


title: SW 1573

status: Public on Mar 06 2009

city: Charlestown

first: Patricia

last: Greninger

department: Center for Molecular Therapeutics

institute: Massachusetts General Hospital Cancer Center

description: Gene expression data

hyb_protocol: Labelled RNA was processed using a protocol from Affymetrix's GeneChip Expression Analysis Technical Manual under Eukaryotic Sample and Array Processing

scan_protocol: Scanning was performed with an Affymetrix GeneChip 3000 Scanner

data_processing: Data was processed with GCOS ver 1.4

label_protocol: Biotinylation of RNA with Perkin Elmer PN Biotin-11-UTP, and Biotin-11-CTP)

extract_protocol: Qiagen RNA easy kit

tag: k-ras dependence

value: independent


title: SW 1116

description: Gene expression data

source_name: Intestine

value: Intestine

value: dependent


title: SW 900

description: Gene expression data

value: not tested


title: T84

description: Gene expression data


title: SNG-M

description: Gene expression data

source_name: Uterus

value: SNG-M

value: Uterus


title: SUIT-2

description: Gene expression data

source_name: Pancreas

value: Pancreas


title: Deep-sowing 10d treatment GA3, biological rep1


title: TCO-1

description: Gene expression data

source_name: Thyroid

value: Thyroid


title: SW837

description: Gene expression data


title: SK-LU-1

description: Gene expression data


title: SW 1463

description: Gene expression data


title: PA-TU-8988T

description: Gene expression data


title: Panc 08.13

description: Gene expression data


title: NOMO-1/ADM

description: Gene expression data

source_name: Blood

value: Blood


title: NCI-H460

description: Gene expression data


title: NCI-H358

description: Gene expression data


title: NCI-H727

description: Gene expression data

source_name: Lung

value: Lung


title: NCI-H441

description: Gene expression data


title: NCI-H2122

description: Gene expression data


title: NCI-H1792

description: Gene expression data


title: LU99A

description: Gene expression data


title: LU65

description: Gene expression data


title: LS174T

description: Gene expression data


title: NCI-H23

description: Gene expression data


title: RCM-1

description: Gene expression data


title: NCI-H1573

description: Gene expression data


title: NCI-H1155

description: Gene expression data


title: KYSE-410

description: Gene expression data

source_name: Esophagus

value: Esophagus


title: KP-1N

description: Gene expression data


title: NCI-H2009

description: Gene expression data


title: NCI-H1734

description: Gene expression data


title: HUP-T4

description: Gene expression data


title: HPAF-II

description: Gene expression data

value: HPAF-II


title: HuCCT1

description: Gene expression data

source_name: Liver

value: Liver


title: KP-4

description: Gene expression data


title: GP5d

description: Gene expression data


title: Calu-1

description: Gene expression data


title: A-427

description: Gene expression data


title: AGS

description: Gene expression data

source_name: Stomach

value: AGS

value: Stomach


title: HCT 116

description: Gene expression data

value: HCT 116


title: HEC-1

description: Gene expression data


title: BG02 EB-derived cells rep1 expression

city: Stanford

first: Rami

last: Rauch

address: 300 Pasteaur Dr

institute: Stanford U

hyb_protocol: Samples were hybridized using manufacturer instructions

scan_protocol: Samples were scanned using manufacturer instructions

data_processing: Array intensities were rank-invariant normalized a

source_name: RNA:  BG02 embryoid body (EB)-derived cells generated by growing H9 hESCs in suspension and plating the embryoid bodies

label_protocol: Samples were amplified and labeled using standard procedures from the Illumina TotalPrep RNA Kit (Ambion)

extract_protocol: RNA was prepared with Trizol (Invitrogen)

tag: cell type


title: Human adult liver rep1 expression

source_name: RNA from normal adult human liver, obtained through Asterand plc.

value: normal adult human liver


title: Human adult liver rep3 expression


title: BG02 hESC rep2 expression

source_name: RNA from CXCR4 FACS sorted BG02 human embryonic stem cells


title: Human adult liver rep2 expression


title: H9 hESC rep1 expression

source_name: RNA from CXCR4 FACS sorted H9 human embryonic stem cells


title: BG02 EB-derived cells rep2 expression

value: BG02 embryoid body (EB)-derived cells generated by growing H9 hESCs in suspension and plating the embryoid bodies


title: BG02 hESC rep1 expression

value: CXCR4 FACS sorted BG02 human embryonic stem cells


title: H9 hESC rep2 expression

value: CXCR4 FACS sorted H9 human embryonic stem cells


title: H9 EB-derived cells rep2 expression

source_name: RNA:  H9 embryoid body (EB)-derived cells generated by growing H9 hESCs in suspension and plating the embryoid bodies


title: H9 EB-derived cells rep1 expression

value: H9 embryoid body (EB)-derived cells generated by growing H9 hESCs in suspension and plating the embryoid bodies


title: H9 endoderm rep1 expression

source_name: RNA:  H9 endoderm cells generated from H9 hESCs using activin A and FACS sorted with CXCR4


title: SmUA159-pH5.5-rep1

city: Halifax

first: Yung-Hua

last: Li

state: NS

address: 5981 University Ave. Rm5215

department: Applied Oral Sciences

institute: Dalhousie University

hyb_protocol: The labeled cDNA probes were hybridized to the S. mutans UA159 microarray slides obtained from PFGRC (http://pfgrc.tigr.org). Array hybridization was conducted using a protocol from the PFGRC with minor modification.

scan_protocol: After hybridization, washes and dried, the array slides were scanned by ScanArray 5000XL Reader (Perkin Elmer, Boston, MA).

data_processing: After the array slides were scanned, the resulting images were loaded into TIGR Spotfinder software (http://www.tigr.org/software/) and overlaid. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, and the intensity values of each spot were determined. Signal intensities of individual channels from an array slide were averaged and normalized using an array data analysis software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis.

label: AlexaFluor 647

organism: Streptococcus mutans

label_protocol: The purified RNAs were used to generate cDNA probes by an indirect labeling method based on the protocol from TIGR. The cDNAs were coupled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen).

growth_protocol: Streptococcus mutans UA159 was grown in a TYG broth (3% tryptone, 0.3% yeast extract and 20 mM glucose) up to a density of 0.6 at OD600.

extract_protocol: Total RNAs were extracted from S. mutans UA159 cells by a FastPrep method using 1 ml of cool Trizol (Invitrogen). The RNAs were treated with RNase-free DNase 1 and purified by Qiagen RNeasy mini columns

treatment_protocol: The cells were grown at either pH 5.5 or pH 7.5 for additional 2 hours.

label: AlexaFluor 555


title: SmUA159-pH5.5-rep3


title: SmUA159-pH5.5-rep2


title: 439T (expression)

hyb_protocol: Per manufacturer's instructions

scan_protocol: Agilent Microarray Scanner Bundle

data_processing: Signal intensities were determined using J-express, filtered to remove genes with low signal intensity, batch corrected, and mean-centered across the tumor set.

source_name: endometrial cancer

label_protocol: Per manufacturer's instructions

extract_protocol: RNA was isolated from tissue or cell pellets using Rneasy kit (Qiagen).

tag: gender

value: F

tag: histologic type

value: endometrioid

tag: metastatic phenotype

value: FIGO III/IV or recurrence

source_name: Stratagene Universal RNA


title: H9 endoderm rep2 expression

value: H9 endoderm cells generated from H9 hESCs using activin A and FACS sorted with CXCR4


title: HCT-116 rep1 expression

source_name: RNA from HCT116 human cells

value: HCT116 human cells


title: TA-control-R11

city: Philadelphia

first: Thomas

middle: S

last: Postler

state: PA

address: 421 Curie Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)

hyb_protocol: As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.

scan_protocol: As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.

data_processing: Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.

organism: Rattus norvegicus

source_name: tibialis anterior, dissected, fresh

label_protocol: 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.

extract_protocol: RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.

treatment_protocol: Untreated control

tag: Strain

value: Sprague-Dawley

tag: Age category

value: adult


title: TA-control-R7


title: TA-control-R9


title: TA-control-R8


title: The CH10T1/2 cell line transfected with the wild type PTHR1

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

institute: Hospital for Sick Children

description: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310)  or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39).  Cells were grown overnight in serum free media and treated with either 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.  RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1.  RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.  This data is from control cells expressing the wild type PTHR1.

data_processing: Expression console software (Affymetrix)

growth_protocol: Cells were grown overnight in serum free media and treated with either 10-7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.

extract_protocol: RNA was extracted using Trisol as per the manufacturer's instructions. RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer

treatment_protocol: Cells were grown overnight in serum free media.  RNA was isolated from the cells at the same time as cells subjected to one hour of PTHrP treatment

tag: cell line

value: CH10T1/2 fibroblast cell line

tag: agent

value: tranfected with the wild type PTHR1


title: TA-hyperthyroid-R3

treatment_protocol: 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks


title: The CH10T1/2 cell line transfected with the wild type PTHR1 treated with PTHrP

description: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310)  or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39).  Cells were grown overnight in serum free media and treated with either 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.  RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1.  RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.  This data is from cells expressing the wild type PTHR1 treated with PTHrP.

treatment_protocol: Cells were grown overnight in serum free media. Cells were then treated treated with 10− 7 M PTHrP for one hour. RNA was then isolated from the cells.

value: tranfected with wild type PTHR1 treated with PTHrP


title: EOM-control-R9

source_name: extraocular muscles, dissected, fresh


title: TA-hyperthyroid-R5