title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 1

status: Public on Jul 04 2008

type: RNA

city: College Station

first: Phillip

middle: D.

last: Beremand

state: TX

department: Biology

country: USA

institute: Texas A&M University

data_processing: GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software. Data were then subjected to LOWESS normalization, and each time-point was reported as the normalized ratio of Cy5 to Cy3 intensity.

molecule: total RNA

organism: Gallus gallus

source_name: Chick pinealocytes; 18 hours after beginning of subjective day with 6-hour vehicle administration

tag: Strain

tag: Gender

value: Male

tag: Developmental Age

tag: Tissue of origin

value: Pineal gland


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 3


title: Pineal Culture CT6 NE vs. Vehicle Replicate 5

source_name: Chick pinealocytes; 6 hours after beginning of subjective day with 6-hour NE administration

source_name: Chick pinealocytes; 6 hours after beginning of subjective day with 6-hour vehicle administration


title: Pineal Culture CT6 NE vs. Vehicle Replicate 7


title: Pineal Culture CT6 NE vs. Vehicle Replicate 4


title: Pineal Culture CT6 NE vs. Vehicle Replicate 6


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 2


title: Pineal Culture CT6 NE vs. Vehicle Replicate 2


title: soshin WT-3

status: Public on Jul 11 2008

city: Tokyo

first: Tomomi

last: Soshin

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: the University of Tokyo

description: All required informations are described in other fields.

hyb_protocol: After 20 μg of biotin-labeled cRNA was fragmented, hybridization solution was prepared using a GeneChip Eukaryotic Hybridization Control Kit (Affymetrix) and was hybridized to the Affymetrix Mouse Genome MOE430B Array for 45 ℃ for 16 hrs in GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: For microarray imaging data analysis, the proprietary software (GeneChip Microarray Suite, v. 5.0, Affymetrix) was used.  In brief, total array normalization was performed comparing the data between hr<Hos>/hr<Hos> and +/hr<Hos>, and normalized data were expressed as a fold change (log 10 ratio).

data_processing: Normalization was performed in accordance with mouse maintenance genes on the Mouse Set 430A (Affymetrix).

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: WT-3 hair follicle, postnatal day 14

label_protocol: cDNA was prepared from 1 μg of aRNA using the SuperScript Double Strand cDNA Synthesis Kit (Invitrogen).  T7-(dT)24 primer (primer sequence: 5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(T)24-3’), was used for first strand cDNA synthesis (Amersham Biosciences, Tokyo, Japan).  Then, biotinylated cRNA was synthesized employing the GeneChip Expression Reagents for IVT Labeling Kit (Affymetrix, USA).

extract_protocol:
Fresh skin samples were embedded in Tissue-Tek O.C.T. Compound (SAKURA Finetechnical Co., Ltd. Tokyo, Japan) and kept at -80 ℃ until used.  Tissues were sectioned using a cryostat at 8-μm thickness and placed on Membrane Slides (Leica Microsystems Inc., Tokyo, Japan).  The sections were fixed in methanol for 30 sec, rinsed in water, stained with HistoGeneTM Staining Solution (Takara Shuzo, Ohtsu, Japan) for 30 sec, and dehydrated by sequential exposure to 75 %, 95 %, and 100 % ethanol, and xylene.
Sections were air-dried and used for LCM of hair follicles with an Application Solutions Laser Micrdissection System (Leica Microsystems Inc., Tokyo, Japan) Fifty to seventy hair follicles per sample were collected in Buffer RLT (QIAGEN) and preserved at -80 ℃ until RNA extraction.  RNA was extracted with an RNeasy Micro Kit (QIAGEN).  The quality of RNA in samples was checked by Agilent 2100 Bioanalyzer (Agilent Technologies).

value: N1 offspring (+/Hr<Hos>) between +/Hr<Hos> and Hr<Hos>/Hr<Hos>

tag: Tissue

value: Hair follicles of dorsal skin, non-treatment


title: Pineal Culture CT18 NE vs. Vehicle Replicate 4

source_name: Chick pinealocytes; 18 hours after beginning of subjective day with 6-hour NE administration


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 6

data_processing: GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software. Data were then subjected to LOWESS and dye-swap normalizations, and each time-point was reported as the normalized ratio of Cy3 to Cy5 intensity.


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 7


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 3


title: Pineal Culture CT6 NE vs. Vehicle Replicate 1


title: Pineal Culture CT6 NE vs. Vehicle Replicate 3


title: Pineal Culture CT18 NE vs. Vehicle Replicate 7


title: soshin WT-4

source_name: WT-4 hair follicle, postnatal day 14


title: soshin HR-3

hyb_protocol: After 20 microgram of biotin-labeled cRNA was fragmented, hybridization solution was prepared using a GeneChip Eukaryotic Hybridization Control Kit (Affymetrix) and was hybridized to the Affymetrix Mouse Genome MOE430B Array for 45 ℃ for 16 hrs in GeneChip Hybridization Oven 640 (Affymetrix).

source_name: HR-2 hair follicle, postnatal day 14


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 2


title: soshin HR-2

value: N1 offspring (Hr<Hos>/Hr<Hos>) between +/Hr<Hos> and Hr<Hos>/Hr<Hos>


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 5


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 4


title: Pineal Culture CT6 NE vs. Vehicle (Dye-Swap) Replicate 1


title: Pineal Culture CT18 NE vs. Vehicle Replicate 6


title: Pineal Culture CT18 NE vs. Vehicle Replicate 3


title: Pineal Culture CT18 NE vs. Vehicle Replicate 8


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 6


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 5


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 8


title: Pineal Culture CT18 NE vs. Vehicle Replicate 2


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 7


title: Pineal Culture CT18 NE vs. Vehicle Replicate 1


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 2


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 4


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 3


title: Pineal Culture CT18 NE vs. Vehicle (Dye-Swap) Replicate 1


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 7

source_name: Chick pinealocytes; 6 hours after beginning of subjective day with 6-hour light pulse

source_name: Chick pinealocytes; 6 hours after beginning of subjective day with no light pulse


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 5


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 7


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 8


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 4


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 8


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 6


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 3


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 1


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 8

source_name: Chick pinealocytes; 18 hours after beginning of subjective day with 6-hour light pulse

source_name: Chick pinealocytes; 18 hours after beginning of subjective day with no light pulse


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 6


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 5


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 4


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 5


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 2


title: Pineal Culture CT6 Light Pulse vs. Control Replicate 2


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 1


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 4


title: Pineal Culture CT6 Light Pulse vs. Control (Dye-Swap) Replicate 3


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 6


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 8


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 2


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 7


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 6


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 3


title: Pineal Culture CT6 Control vs. Control Replicate 5


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 2


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 1


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 7


title: Pineal Culture CT6 Control vs. Control Replicate 4


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 1


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 5


title: Pineal Culture CT6 Control vs. Control Replicate 7


title: Pineal Culture CT18 Light Pulse vs. Control Replicate 3


title: Pineal Culture CT18 Light Pulse vs. Control (Dye-Swap) Replicate 4


title: Pineal Culture CT6 Control vs. Control Replicate 8


title: Pineal Culture CT18 Control vs. Control Replicate 3


title: Pineal Culture CT18 Control vs. Control Replicate 2


title: Pineal Culture CT6 Control vs. Control Replicate 3


title: Pineal Culture CT18 Control vs. Control Replicate 4


title: Pineal Culture CT18 NE vs. Vehicle Replicate 5


title: Pineal Culture CT18 Control vs. Control Replicate 7


title: Pineal Culture CT18 Control vs. Control Replicate 5


title: Pineal Culture CT6 Control vs. Control Replicate 1


title: Pineal Culture CT6 Control vs. Control Replicate 2


title: Pineal Culture CT18 Control vs. Control Replicate 8


title: Pineal Culture CT18 Control vs. Control Replicate 6


title: Pineal Culture CT18 Control vs. Control Replicate 1


title: Pineal Culture DD CT6 Replicate 8

description: Pineal Culture DD CT6 Replicate 8

source_name: Chick pinealocytes; 6 hours after beginning of subjective day

source_name: Chick pinealocytes; 18 hours after beginning of subjective day


title: Pineal Culture DD CT6 Replicate 7

description: Pineal Culture DD CT6 Replicate 7


title: Pineal Culture DD CT6 Replicate 6

description: Pineal Culture DD CT6 Replicate 6


title: Pineal Culture DD CT6 Replicate 5

description: Pineal Culture DD CT6 Replicate 5


title: Pineal Culture DD CT6 Replicate 4

description: Pineal Culture DD CT6 Replicate 4


title: Pineal Culture DD CT22 Replicate 5

description: Pineal Culture DD CT22 Replicate 5

source_name: Chick pinealocytes; 22 hours after beginning of subjective day


title: Pineal Culture DD CT22 Replicate 8

description: Pineal Culture DD CT22 Replicate 8


title: Pineal Culture DD CT22 Replicate 4

description: Pineal Culture DD CT22 Replicate 4


title: Pineal Culture DD CT22 Replicate 6

description: Pineal Culture DD CT22 Replicate 6


title: Pineal Culture DD CT6 Replicate 3

description: Pineal Culture DD CT6 Replicate 3


title: Pineal Culture DD CT22 Replicate 7

description: Pineal Culture DD CT22 Replicate 7


title: Pineal Culture DD CT22 Replicate 3

description: Pineal Culture DD CT22 Replicate 3


title: Pineal Culture DD CT6 Replicate 1

description: Pineal Culture DD CT6 Replicate 1


title: Pineal Culture DD CT6 Replicate 2

description: Pineal Culture DD CT6 Replicate 2


title: Pineal Culture DD CT22 Replicate 2

description: Pineal Culture DD CT22 Replicate 2


title: Pineal Culture DD CT22 Replicate 1

description: Pineal Culture DD CT22 Replicate 1


title: Pineal Culture DD CT2 Replicate 7

description: Pineal Culture DD CT2 Replicate 7

source_name: Chick pinealocytes; 2 hours after beginning of subjective day


title: Pineal Culture DD CT2 Replicate 3

description: Pineal Culture DD CT2 Replicate 3


title: Pineal Culture DD CT18 Replicate 4

description: Pineal Culture DD CT18 Replicate 4


title: Pineal Culture DD CT2 Replicate 8

description: Pineal Culture DD CT2 Replicate 8


title: Pineal Culture DD CT18 Replicate 8

description: Pineal Culture DD CT18 Replicate 8


title: Pineal Culture DD CT2 Replicate 2

description: Pineal Culture DD CT2 Replicate 2


title: Pineal Culture DD CT18 Replicate 5

description: Pineal Culture DD CT18 Replicate 5


title: Pineal Culture DD CT18 Replicate 6

description: Pineal Culture DD CT18 Replicate 6


title: Pineal Culture CT6 Control vs. Control Replicate 6


title: Pineal Culture DD CT2 Replicate 6

description: Pineal Culture DD CT2 Replicate 6


title: Pineal Culture DD CT18 Replicate 2

description: Pineal Culture DD CT18 Replicate 2


title: Pineal Culture DD CT2 Replicate 5

description: Pineal Culture DD CT2 Replicate 5


title: Pineal Culture DD CT14 Replicate 8

description: Pineal Culture DD CT14 Replicate 8

source_name: Chick pinealocytes; 14 hours after beginning of subjective day


title: Pineal Culture DD CT18 Replicate 3

description: Pineal Culture DD CT18 Replicate 3


title: Pineal Culture DD CT2 Replicate 4

description: Pineal Culture DD CT2 Replicate 4


title: Pineal Culture DD CT2 Replicate 1

description: Pineal Culture DD CT2 Replicate 1


title: Pineal Culture DD CT18 Replicate 7

description: Pineal Culture DD CT18 Replicate 7


title: Pineal Culture DD CT18 Replicate 1

description: Pineal Culture DD CT18 Replicate 1


title: Pineal Culture DD CT14 Replicate 5

description: Pineal Culture DD CT14 Replicate 5


title: Pineal Culture DD CT14 Replicate 7

description: Pineal Culture DD CT14 Replicate 7


title: Pineal Culture DD CT14 Replicate 6

description: Pineal Culture DD CT14 Replicate 6


title: Pineal Culture DD CT14 Replicate 4

description: Pineal Culture DD CT14 Replicate 4


title: Pineal Culture DD CT14 Replicate 2

description: Pineal Culture DD CT14 Replicate 2


title: Pineal Culture DD CT10 Replicate 8

description: Pineal Culture DD CT10 Replicate 8

source_name: Chick pinealocytes; 10 hours after beginning of subjective day


title: Pineal Culture DD CT10 Replicate 7

description: Pineal Culture DD CT10 Replicate 7


title: Pineal Culture DD CT10 Replicate 2

description: Pineal Culture DD CT10 Replicate 2


title: Pineal Culture DD CT14 Replicate 1

description: Pineal Culture DD CT14 Replicate 1


title: Pineal Culture DD CT14 Replicate 3

description: Pineal Culture DD CT14 Replicate 3


title: Pineal Culture DD CT10 Replicate 3

description: Pineal Culture DD CT10 Replicate 3


title: Pineal Culture LD ZT6 Replicate 8

description: Pineal Culture LD ZT6 Replicate 8

source_name: Chick pinealocytes; 18 hours after lights on


title: Pineal Culture LD ZT22 Replicate 7

description: Pineal Culture LD ZT22 Replicate 7

source_name: Chick pinealocytes; 22 hours after lights on


title: Pineal Culture LD ZT22 Replicate 5

description: Pineal Culture LD ZT22 Replicate 5


title: Pineal Culture LD ZT22 Replicate 8

description: Pineal Culture LD ZT22 Replicate 8


title: Pineal Culture LD ZT22 Replicate 2

description: Pineal Culture LD ZT22 Replicate 2


title: Pineal Culture DD CT10 Replicate 6

description: Pineal Culture DD CT10 Replicate 6


title: Pineal Culture DD CT10 Replicate 4

description: Pineal Culture DD CT10 Replicate 4


title: Pineal Culture DD CT10 Replicate 5

description: Pineal Culture DD CT10 Replicate 5


title: Pineal Culture LD ZT6 Replicate 4

description: Pineal Culture LD ZT6 Replicate 4

source_name: Chick pinealocytes; 6 hours after lights on


title: Pineal Culture DD CT10 Replicate 1

description: Pineal Culture DD CT10 Replicate 1


title: Pineal Culture LD ZT6 Replicate 9

description: Pineal Culture LD ZT6 Replicate 9


title: Pineal Culture LD ZT6 Replicate 5

description: Pineal Culture LD ZT6 Replicate 5


title: Pineal Culture LD ZT6 Replicate 3

description: Pineal Culture LD ZT6 Replicate 3


title: Pineal Culture LD ZT2 Replicate 6

description: Pineal Culture LD ZT2 Replicate 6

source_name: Chick pinealocytes; 2 hours after lights on


title: Pineal Culture LD ZT22 Replicate 9

description: Pineal Culture LD ZT22 Replicate 9


title: Pineal Culture LD ZT22 Replicate 6

description: Pineal Culture LD ZT22 Replicate 6


title: Pineal Culture LD ZT6 Replicate 1

description: Pineal Culture LD ZT6 Replicate 1


title: Pineal Culture LD ZT6 Replicate 2

description: Pineal Culture LD ZT6 Replicate 2


title: Pineal Culture LD ZT22 Replicate 3

description: Pineal Culture LD ZT22 Replicate 3


title: Pineal Culture LD ZT6 Replicate 7

description: Pineal Culture LD ZT6 Replicate 7


title: Pineal Culture LD ZT18 Replicate 6

description: Pineal Culture LD ZT18 Replicate 6


title: Pineal Culture LD ZT22 Replicate 1

description: Pineal Culture LD ZT22 Replicate 1


title: Pineal Culture LD ZT18 Replicate 9

description: Pineal Culture LD ZT18 Replicate 9


title: Pineal Culture LD ZT6 Replicate 6

description: Pineal Culture LD ZT6 Replicate 6


title: Pineal Culture LD ZT2 Replicate 1

description: Pineal Culture LD ZT2 Replicate 1


title: Pineal Culture LD ZT2 Replicate 9

description: Pineal Culture LD ZT2 Replicate 9


title: Pineal Culture LD ZT22 Replicate 4

description: Pineal Culture LD ZT22 Replicate 4


title: Pineal Culture LD ZT2 Replicate 7

description: Pineal Culture LD ZT2 Replicate 7


title: Pineal Culture LD ZT2 Replicate 8

description: Pineal Culture LD ZT2 Replicate 8


title: Pineal Culture LD ZT2 Replicate 4

description: Pineal Culture LD ZT2 Replicate 4


title: Pineal Culture LD ZT2 Replicate 3

description: Pineal Culture LD ZT2 Replicate 3


title: Pineal Culture LD ZT2 Replicate 5

description: Pineal Culture LD ZT2 Replicate 5


title: Pineal Culture LD ZT18 Replicate 7

description: Pineal Culture LD ZT18 Replicate 7


title: Pineal Culture LD ZT10 Replicate 9

description: Pineal Culture LD ZT10 Replicate 9

source_name: Chick pinealocytes; 10 hours after lights on


title: Pineal Culture LD ZT18 Replicate 5

description: Pineal Culture LD ZT18 Replicate 5


title: Pineal Culture LD ZT18 Replicate 8

description: Pineal Culture LD ZT18 Replicate 8


title: Pineal Culture LD ZT14 Replicate 4

description: Pineal Culture LD ZT14 Replicate 4

source_name: Chick pinealocytes; 14 hours after lights on


title: Pineal Culture LD ZT10 Replicate 2

description: Pineal Culture LD ZT10 Replicate 2


title: Pineal Culture LD ZT18 Replicate 4

description: Pineal Culture LD ZT18 Replicate 4


title: Pineal Culture LD ZT2 Replicate 2

description: Pineal Culture LD ZT2 Replicate 2


title: Pineal Culture LD ZT10 Replicate 4

description: Pineal Culture LD ZT10 Replicate 4


title: Pineal Culture LD ZT10 Replicate 6

description: Pineal Culture LD ZT10 Replicate 6


title: Pineal Culture LD ZT10 Replicate 5

description: Pineal Culture LD ZT10 Replicate 5


title: Pineal Culture LD ZT18 Replicate 3

description: Pineal Culture LD ZT18 Replicate 3


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 8

source_name: Chick pinealocytes; 6 hours after beginning of subjective day with 6-hour vehicle administration


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 5


title: Pineal Culture LD ZT14 Replicate 8

description: Pineal Culture LD ZT14 Replicate 8


title: Pineal Culture LD ZT18 Replicate 2

description: Pineal Culture LD ZT18 Replicate 2


title: Pineal Culture LD ZT14 Replicate 5

description: Pineal Culture LD ZT14 Replicate 5


title: Pineal Culture LD ZT18 Replicate 1

description: Pineal Culture LD ZT18 Replicate 1

source_name: hick pinealocytes; 18 hours after lights on


title: Pineal Culture LD ZT14 Replicate 9

description: Pineal Culture LD ZT14 Replicate 9


title: Pineal Culture LD ZT14 Replicate 3

description: Pineal Culture LD ZT14 Replicate 3


title: Pineal Culture LD ZT14 Replicate 1

description: Pineal Culture LD ZT14 Replicate 1


title: Pineal Culture LD ZT14 Replicate 2

description: Pineal Culture LD ZT14 Replicate 2


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 3


title: Pineal Culture LD ZT14 Replicate 6

description: Pineal Culture LD ZT14 Replicate 6


title: Pineal Culture LD ZT10 Replicate 7

description: Pineal Culture LD ZT10 Replicate 7


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 8

source_name: Chick pinealocytes; 18 hours after beginning of subjective day with 6-hour vehicle administration


title: Pineal Culture LD ZT10 Replicate 8

description: Pineal Culture LD ZT10 Replicate 8


title: Pineal Culture LD ZT14 Replicate 7

description: Pineal Culture LD ZT14 Replicate 7


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 7


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 2


title: Pineal Culture LD ZT10 Replicate 1

description: Pineal Culture LD ZT10 Replicate 1

data_processing: GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software.  Data were then subjected to LOWESS normalization, and each time-point was reported as the normalized ratio of Cy5 to Cy3 intensity.

label: Cy 3


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 6


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 6


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 4


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 4


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 7


title: Pineal Culture CT18 Vehicle vs. Vehicle Replicate 5


title: Pineal Culture CT6 Vehicle vs. Vehicle Replicate 1


title: Tumour, AML (SP_540)

status: Public on Jun 01 2008

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent

data_processing: Global median normalized value of the log2ratio.

molecule: genomic DNA

source_name: Tumour, AML

extract_protocol: gDNA was purified from tails and hematopoietic tissues in order to genotype and analyze and identify retroviral insertion sites, respectively. The tissues were digested in 700 ml lysis buffer (10 mM Tris-Cl, pH 7,5; 10 mM EDTA; 10 mM NaCl; 0,5% sarcosyl; 100 mg/ml proteinase K; RNase A) at 55°C o.n. on an end-over-end rotator. Susequently, 250 ml saturated NaCl was added and samples were centrifuged at 14.000 rpm, 4°C for 10 min. Supernatants were recovered and extracted twice with phenol-chloroform and once with chloroform. Finally, DNA was pelleted (0,1 M Na-acetat, pH 5,2; 70% EtOH), washed in 70% EtOH, air dried, and resuspended in H2O.

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(BRM2/BRM2), Tissue:spleen

source_name: tail

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(BRM2/BRM2), Tissue:tail


title: Tumour, T-ALL (SP_380)

hyb_protocol: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

source_name: Tumour, T-ALL

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(+/+), Tissue:spleen

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(+/+), Tissue:tail


title: Tumour, AML (SP_377)

label_protocol: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(+/BRM2), Tissue:spleen

value: F1 pups of 129S6/svEvTac and C57B6/j Cebpa(+/BRM2), Tissue:tail


title: Tumour,mix T-ALL and AML (SP_590)

source_name: Tumour,mix T-ALL and AML


title: Tumour, AML (SP_534)


title: Tumour, B-ALL (SP_193)

source_name: Tumour, B-ALL


title: 2000051359_Kidney Macs cy5vsBrain Macs cy3

status: Public on Feb 16 2008

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: Pairwise comparison of Kidney Macrophage RNA vs Brain Macrophage RNA

hyb_protocol: Followed protocol described in: PMID: 15998744

data_processing: Imagene5.0, Lowess Normalisation (R)

source_name: Kidney Macs

label_protocol: Indirect aRNA Ambion

extract_protocol: RNAAmplification Ambion

tag: RNA extract of Isolation of EGFP positive kidney macrophages

source_name: Brain Macs

tag: RNA extract of Isolation of EGFP positive brain macrophages


title: 2000051352_Brain Macs_cy5vsLung Macs_cy3

description: Pairwise comparison of Brain Macrophage RNA vs Lung Macrophage RNA (dye swap)

scan_protocol: Followed protocol described in: PMID: 15998744

source_name: Lung Macs

tag: RNA extract of Isolation of EGFP positive lung macrophages


title: 2000051360_Kidney Macs cy5vsBrain Macs cy3


title: 2000051358_Brain Macs cy5vsKidney Macs cy3

description: Pairwise comparison of Kidney Macrophage RNA vs Brain Macrophage RNA(dye swap)


title: Tumour, T-ALL (SP_400)


title: Tumour, B-ALL (SP_197)


title: 2000051357_Lung Macs cy5vsKidney Macs cy3

description: Pairwise comparison of Kidney Macrophage RNA vs Lung Macrophage RNA


title: deacclimation treatment rep2

status: Public on Feb 02 2008

city: Riverside

first: Livia

last: Tommasini

state: CA

address: 2150 Batchelor Hall

department: Botany and Plant Science

institute: University of California, Riverside

description: deacclimation treatemnt

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

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

data_processing: MAS files from the GCOS software were used for determining the ‘present’ gene list. Probe set intensity values above the level set by the gcRMA normalization processor were imported into GeneSpring GX 7.3 software (Silicon Genetics, CA, USA), which was used for the rest of the analysis.

organism: Hordeum vulgare

source_name: crown

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

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

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

treatment_protocol: Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºC•h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.

tag: deacclimation treatment


title: Tumour, AML (SP_341)


title: Tumour, AML (SP_379)


title: 2000051353_Lung Macs_cy5vsBrain Macs_cy3

description: Pairwise comparison of Brain Macrophage RNA vs Lung Macrophage RNA


title: freeze treatment rep1

description: freeze treatment

tag: freeze treatment


title: deacclimation treatment rep3

description: deacclimation treatemnt


title: 2000051354_Lung Macs cy5vsBrain Macs cy3


title: Pineal Culture LD ZT10 Replicate 3

description: Pineal Culture LD ZT10 Replicate 3

source_name: Chick pinealocytes; 18 hours after lights on


title: cold treatment rep2

description: cold treatment

tag: cold treatment


title: 2000051356_Lung Macs cy5vsKidney Macs cy3


title: 2000051355_Kidney Macs cy5vsLung Macs cy3

description: Pairwise comparison of Kidney Macrophage RNA vs Lung Macrophage RNA (dye swap)


title: cold treatment rep3

description: cold treatment


title: cold treatment rep1

description: cold treatment


title: 7% SWC rep2

description: drought treatment

label: Biotin

source_name: Crown

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

treatment_protocol: Drought treatment began seven days after sowing and lasted for 21 days. Soil Water Content (SWC) was calculated relative to the field capacity of the soil by weighing at regular intervals. Control (91 % SWC) and stressed samples were collected at soil water contents of approximately 68%, 38%, 20%, 11% and 9% SWC.

tag: drought treatment


title: freeze treatment rep2

description: freeze treatment


title: deacclimation treatment rep1

description: deacclimation treatemnt

tag: deacclimation treatemnt


title: freeze treatment rep3

description: freeze treatment


title: low temperature control rep3

description: low temperature control

tag: low temperature control


title: 19% SWC rep2

description: drought treatment


title: low temperature control rep2

description: low temperature control


title: 38% SWC rep3

description: drought treatment


title: 19% SWC rep1

description: drought treatment


title: 7% SWC rep3

description: drought treatment


title: 38% SWC rep1

description: drought treatment


title: low temperature control rep1

description: low temperature control


title: 68% SWC rep2

description: drought control

tag: drought control


title: 7% SWC rep1

description: drought treatment


title: Large White control (dh06a_sc_sg_6h_070706_180_52_LWcontrol56)

status: Public on Jan 07 2008

city: Bordeaux

first: Dominique

last: Hazard

address: Institut Francois Magendie 146 rue Léo Saignat

department: Animal Genetic

country: France

institute: INRA

hyb_protocol: Microarrays were hybridized with 33P-labeled complex probes during 24 hours at 68°C in 2 ml of hybridization solution (5X SSC, 5X Denhardt\u2019s, 05%SDS, 100µg/ml salmon testes DNA). After washes, arrays were exposed for 6 hours to radioisotopic-sensitive imaging plates.

scan_protocol: scanned using BAS-5000 Fuji, images were quantified using AGScan.

data_processing: Before statistical analysis, data were log transformed and centred by median. A filter procedure eliminated non informative genes on the basis of being well measured (expression level > mean + 2 standard deviation of background signal) in 100% of the samples.

organism: Sus scrofa

source_name: Adrenal gland

label_protocol: 33P-labeled complex probes were synthetized and labelled from 5 ~g of total RNA with Supersript II RNAse H- reverse transcriptase (Invitrogen).

extract_protocol: Total RNA was isolated from adrenal tissue with TRIzol reagent (Invitrogen Life Technologies), followed by column purification (RNeasy MinElute kit, Qiagen). DNA was digested using an RNase-free DNase set (Qiagen) during RNA purification. Total RNA was quantified by spectrophotometer (NanoDrop~) and its integrity was assessed on an Agilent 2100 Bioanalyser (RNA 6000 Nano LabChip, Agilent Technologies).

tag: Microarray type

value: Probe

tag: Genotype

value: Large White

tag: Treatment

value: Control


title: 68% SWC rep1

description: drought control

tag: drought 68% SWC


title: 19% SWC rep3

description: drought treatment


title: 38% SWC rep2

description: drought treatment


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_16_MSacth48)

value: Meishan

value: ACTH


title: Meishan control (dh06a_sc_sg_6h_070706_180_14_MScontrol28)


title: drought control rep1

description: drought control

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

scan_protocol: The arrays were scanned on a Hewlett-Packard GeneArray scanner. cRNA preparation and hybridization were performed at University of California, Irvine Microarray Facility.

data_processing:
Signal row data was first processed in MicroArray Suite (MAS) 5.0 software (Affymetrix).
MAS files from the GCOS software were used for determining the ‘present’ gene list.
Probe set intensity values above the level set by the gcRMA normalization processor were imported into GeneSpring GX 7.3 software (Silicon Genetics, CA, USA), which was used for the rest of the analysis.


title: Meishan control (dh06a_sc_sg_6h_070706_180_23_MScontrol46)


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_20_MSacth52)


title: Large White control (dh06a_sc_sg_6h_070706_180_21_LWcontrol47)


title: drought control rep2

description: drought control


title: 68% SWC rep3

description: drought treatment

tag: 68% SWC


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_51_MSacth54)


title: Large White control (dh06a_sc_sg_6h_070706_180_17_LWcontrol45)


title: Meishan control (dh06a_sc_sg_6h_070706_180_10_MScontrol26)


title: drought control rep3

description: drought control


title: Large White control (dh06a_sc_sg_6h_070706_180_09_LWcontrol25)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_19_LWacth49)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_07_LWacth20)


title: Large White control (dh06a_sc_sg_6h_070706_180_05_LWcontrol16)


title: Vector (dh06a_oligo_on_020606_180_52)

type: other

hyb_protocol: Microarrays were hybridized with a 33P-labeled oligonucleotide sequence (T7) over-night at 42°C in 2 ml of hybridization solution (5X SSC, 5X Denhardt\u2019s, 05%SDS, 100µg/ml salmon testes DNA). After washes, arrays were exposed over-night to radioisotopic-sensitive imaging plates.

molecule: other

source_name: Vector

label_protocol: 33P-labeled oligonucleotide sequence common to all PCR products were used to control the quality of spotting and quantity of target DNA accessible in each spot (Phosphorylation 5').

value: Vector


title: Meishan control (dh06a_sc_sg_6h_070706_180_18_MScontrol44)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_15_LWacth24)


title: Vector (dh06a_oligo_on_020606_180_51)


title: Large White control (dh06a_sc_sg_6h_070706_180_13_LWcontrol27)


title: Vector (dh06a_oligo_on_020606_180_23)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_11_LWacth22)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_03_LWacth18)


title: Meishan control (dh06a_sc_sg_6h_070706_180_06_MScontrol17)


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_04_MSacth19)


title: Vector (dh06a_oligo_on_020606_180_19)


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_08_MSacth21)


title: Vector (dh06a_oligo_on_020606_180_24)


title: Vector (dh06a_oligo_on_020606_180_15)


title: Meishan control (dh06a_sc_sg_6h_070706_180_02_MScontrol15)


title: Vector (dh06a_oligo_on_020606_180_09)


title: Vector (dh06a_oligo_on_020606_180_16)


title: Vector (dh06a_oligo_on_020606_180_14)


title: Vector (dh06a_oligo_on_020606_180_05)


title: Vector (dh06a_oligo_on_020606_180_18)


title: Vector (dh06a_oligo_on_020606_180_10)


title: Vector (dh06a_oligo_on_020606_180_11)


title: Vector (dh06a_oligo_on_020606_180_20)


title: Vector (dh06a_oligo_on_020606_180_21)


title: Vector (dh06a_oligo_on_020606_180_07)


title: Vector (dh06a_oligo_on_020606_180_06)


title: Vector (dh06a_oligo_on_020606_180_02)


title: Vector (dh06a_oligo_on_020606_180_17)


title: Vector (dh06a_oligo_on_020606_180_12)


title: Vector (dh06a_oligo_on_020606_180_03)


title: Vector (dh06a_oligo_on_020606_180_08)


title: Brain Fish11

status: Public on Jan 01 2008

city: Exeter

first: Eduarda

middle: M

last: Santos

state: Devon

address: Prince of Wales Road

department: School of Biosciences

country: United Kingdom

institute: University of Exeter

description: Brain Fish11

hyb_protocol: The reference and sample, labeled with Cy5 and Cy3, respectively, were combined and denatured for 3 minutes at 95oC. An equal volume of hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) was added to each sample, and the mixture was added to the arrayed slides. The slides were hybridized in a humidified airtight box for 36 hours at 42oC.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Array Express fluorescent scanner and image intensity data were extracted and analyzed with Imagene V5 analysis software.

data_processing: Pre-processed in R using the LimmaGUI package with background subtraction, followed by a pin based-Lowess within array normalization and a scaled between chip normalization.  For each experimental group, data were filtered on ‘flags’ and on intensity of the raw data, and each spot was required to have flag=1 and above 0.01 in at least 40% of the conditions to be considered for further analysis

organism: Danio rerio

source_name: Brain Fish11

label_protocol: 5ug of aaRNA were labelled with Cy3 using FluoroLink  Cy3 monofunctional dye 5-pack (Amersham), according to the instructions provided within the Amino Allyl MessageAmp aRNA amplification kit (Ambion, USA).

growth_protocol: Brains extracted from adult breeding zebrafish kept in 15L breeding tanks ( 10 L of water were displaced daily), under a 12 light/dark cycle, and fed twice daily with commercial flake food and live Artemia.

extract_protocol: RNA was extracted using the TRI reagent method (Sigma, UK) followed by a LiCl precipitation. A RNA amplification step was carried out using the Amino Allyl MessageAmp aRNA amplification kit (Ambion, USA).

tag: Brain Tissue

source_name: Pool of Danio rerio brain RNA

label_protocol: 5ug of aaRNA Pool was labeled with Cy5 using FluoroLink Cy5 monofunctional dye 5-pack (Amersham), according to the instructions provided within the Amino Allyl MessageAmp aRNA amplification kit (Ambion, USA).

tag: Pool of 5ug of aRNA from each brain extract included in this experiment


title: Meishan ACTH (dh06a_sc_sg_6h_070706_180_12_MSacth23)


title: Vector (dh06a_oligo_on_020606_180_04)


title: Vector (dh06a_oligo_on_020606_180_13)


title: Large White ACTH (dh06a_sc_sg_6h_070706_180_24_LWacth53)


title: Brain Fish12

description: Brain Fish12

source_name: Brain Fish12


title: Brain Fish10

description: Brain Fish10

source_name: Brain Fish10


title: Brain Fish6

description: Brain Fish6

source_name: Brain Fish6


title: Brain Fish4

description: Brain Fish4

source_name: Brain Fish4


title: Brain Fish5

description: Brain Fish5

source_name: Brain Fish5


title: Brain Fish8

description: Brain Fish8

source_name: Brain Fish8


title: Gene profiling in hearts of 2d heat acclimated rats

status: Public on Dec 31 2007

city: Jerusalem

first: Michal

last: Horowitz

country: Israel

institute: The hebrew University

description: left ventricle of  heart excised from rats subjected to heat acclimation (34oC) for 2d.

hyb_protocol: The membranes were prehybridized for 1 h at 68oC in a hybridization solution (Clontech) containing 0.1 mg/ml sheared salmon testes DNA (Sigma) to block nonspecific binding. Synthesized radio labeled cDNA probe was applied to each membrane and hybridized overnight at 68oC. Cot-1 DNA (Clontech) (1 _g/ml) was added to block nonspecific binding.

scan_protocol: For analysis, the membranes were exposed for 15 and 24 h to a phosphor screen and detected using a Bio-imaging Analyzer BAS2000 (Fuji Photo Film Co. Ltd Japan.

data_processing: We used Atlas Image 2.01 software (Clontech) to grid the phosphor image, to record the pixel density of each spot, and to perform background subtraction. The background-subtracted data were then further analyzed.

organism: Rattus norvegicus

source_name: heart

label_protocol: Standard Clontech protocol was used

extract_protocol: Total RNA was prepared from individual tissue samples using Tri-Reagent isolation protocol. Three pools (6 animals) were prepared for each experimental group.

tag: Sabra strain, males, 3 mo old, heart


title: Brain Fish9

description: Brain Fish9

source_name: Brain Fish9


title: Nocodazol treatment_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 (HM-1/R1) ratio of the result file after normalisation

source_name: HM-1 ES cell line, Nocodazol treatment

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: HM-1 ES cell line derived from HPRT-deficient inbred mouse strain (129/Ola x 129/Ola), Nocodazol treated

source_name: R1 ES cell line, Nocodazol treatment

tag: R1 ES cells from (129X1/Svj x 129/Sv-CP) F1 3.5 day blastocyst, Nocodazol treated


title: Brain Fish3

description: Brain Fish3

source_name: Brain Fish3


title: Brain Fish1

description: Brain Fish1

source_name: Brain Fish1


title: Nocodazol treatment_rep1


title: Gene profiling in heat stressed rat's heart

description: left ventricle of  hearts excised from heat stressed (41oC, 2 h followed by 1h recovery at 24oC) nonacclimated rats.


title: Brain Fish2

description: Brain Fish2

source_name: Brain Fish2


title: Gene profiling in hearts of heat stressed rats, acclimated for 1mo

description: left ventricle of  heart excised from rats subjected to heat stress at 41oC (2h followed by 1h recovery at  24oC,  following heat acclimation (34oC, 1mo).


title: Gene profiling in hearts of rats, reacclimated for 2d.

description: left ventricle of  hearts excised from rats subjected to reacclimation (at 34oC, 2d) following heat acclimation (34oC, 1mo and  deacclimation at 24oC for 1 mo).


title: Gene profiling in hearts of 1mo heat acclimated rats

description: left ventricle of  heart excised from rats subjected to heat acclimation (34oC) for 1mo.


title: Gene profiling in hearts of rats, deacclimated for 1mo

description: left ventricle of  heart excised from rats subjected to deacclimation (at 24oC, 1mo) following heat acclimation (34oC, 1mo).


title: Nocodazol treatment_rep3


title: Gene profiling in untreated heart

description: left ventricle of rat's heart


title: without Nocodazol treatment_rep1

source_name: HM-1 ES cell line

tag: 1.	HM-1 ES cell line derived from HPRT-deficient inbred mouse strain (129/Ola x 129/Ola)

source_name: R1 ES cell line

tag: R1 ES cells from (129X1/Svj x 129/Sv-CP) F1 3.5 day blastocyst


title: Nocodazol treatment_rep4


title: without Nocodazol treatment_rep2


title: without Nocodazol treatment_rep3


title: without Nocodazol treatment_rep4

tag: HM-1 ES cell line derived from HPRT-deficient inbred mouse strain (129/Ola x 129/Ola)


title: Gene profiling in hearts of heat stressed rats, acclimated for 2d

description: left ventricle of  heart excised from rats subjected to heat stress at 41oC (2h followed by 1h recovery at  24oC,  following heat acclimation (34oC, 2d).


title: Day7D_Cy3_BT474

description: protocols according to manufacturer (Enzo Life Scienceswww.agilent.com)

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Median Signal intensity minus median Background intensity; excluding negative values

organism: Homo sapiens

source_name: breast cancer cell line

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: According to Snijders et al. Nat Genet 2001

tag: BT474 breast cancer cell line


title: Day7B_Cy3_XY

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Pooled DNA from the blood of 18 normal individuals


title: Day3C_Cy5_BT474

source_name: breast cancer Cell line

tag: BT474 breast cancer Cell line


title: Day8D_Cy5_BT474


title: Day4B_Cy5_XY


title: Day3C_Cy3_BT474


title: Day6A_Cy3_XY

description: protocols according to manufacturer (Enzo Life Sciences)

source_name: Blood

label_protocol: Sample_label_protocol_ch1 = DNA labeling protocol according to Enzo Life Sciences

tag: Gender

value: male; Blood of healthy persons


title: Day6A_Cy5_BT474


title: Day7A_Cy5_XY


title: Day5A_Cy5_mnmCRC2

source_name: normal colon mucosa

extract_protocol:
DNA isolation protocol available via www.vumc.nl/microarrays.
Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

tag: normal colon mucosa obtained from the same patient as CRC2 (colorectal cancer)


title: Day7C_Cy5_XY


title: Gene profiling in hearts of heat stressed rats, reacclimated for 2d.

description: left ventricle of  hearts excised from heat stressed rats (41oC, 2 h followed by 1 h recovery at 24oC)  subjected to reacclimation protocol ( 34oC, 2d after: heat acclimation (34oC, 1mo and  deacclimation at 24oC for 1 mo).


title: Day7D_Cy5_XY


title: Day7C_Cy3_BT474

tag: BY474 breast cancer cell line


title: Day4D_Cy5_XY


title: Day5A_Cy3_CRC2

source_name: colon

tag: colorectal cancer


title: Day3A_Cy5_XY


title: Day8D_Cy3_XY


title: Day3B_Cy3_XY


title: Day1A_Cy5_XY


title: Expression analysis of human neuroblastoma (Codelink)

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

institute: Hiroshima University

description: Three commercially available single-color oligonucleotide microarray platforms for profiling gene expression - CodeLinkTM Human Whole Genome Bioarray (~55,000 transcripts, GE Healthcare, Tokyo, Japan), Affymetrix GeneChipTM Human Genome U133 Plus 2.0 array (~47,000 transcripts, Affymetrix, Santa Clara, CA), and Agilent Whole Human Genome Oligo Microarray (~41,000 transcripts, Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing are provided in the following source: CodeLinkTM User Protocols.

scan_protocol: The CodeLink microarray was scanned using an Agilent™ DNA Microarray Scanner and processed using CodeLink™ System Software for Analysis.

data_processing: Data processing Data were processed using functional ‘ON/OFF’ state of a gene

source_name: human neuroblastoma tissue

label_protocol: 2 μg of total RNA was used for first strand synthesis and 10 μg of cRNA was used for hybridization using the CodeLinkTM Expression Assay Reagent Kit. Conversion of double stranded cDNA into biotin-labeled cRNA was accomplished using the First and Second Strand cDNA Synthesis Kit and In Vitro Transcription (IVT) Kit  (BE Healthcare) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from tissue specimen using RNA isolation kit according to the manufacturer’s instructions (Stratagene, Agilent techonology, Santa Clara , CA) and the quality of the RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: At surgery, right adrenal tumor and lymph node metastasis were resected. Then, small peccieces of primary tumor was picked up and frozen immediately until use.

tag: human neuroblastoma tissue RNA

tag: Patient characteristics

value: Female, 13 months old, stage III unfavorable type neuroblastoma having developed in the adrenal gland.


title: Day3D_Cy5_CRC1

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51


title: Day3B_Cy5_BT474


title: Day3A_Cy3_GC

source_name: stomach

extract_protocol:
DNA isolation protocol available via www.vumc.nl/microarrays
Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

tag: gastric cancer


title: Day2C_Cy5_XY


title: Day1A_Cy3_BT474


title: Colon mucosa, control diet, Rat 53

status: Public on Dec 01 2007

city: Wageningen

first: Wendy

last: Rodenburg

address: Bornsesteeg 45

department: Food Bioactives Group

institute: RIKILT-Institute of food safety

description: Rat Colon Mucosa

hyb_protocol: Equal volumes of Cy5 target samples and Cy3 reference sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and 10x control targets (Agilent Technologies) and hybridized to a Whole Rat Genome ologo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies). After hybridization the arrays were washed with an SSPE wash procedure (Agilent Technologies) according to manufacturers protocol. "

scan_protocol: Arrays were scanned using the Scanarray Express HT (Perkin Elmer, Wellesley, MA) at a laserpower of 90% and a photomultiplier tube voltage of 55% for Cy5 and 60% for Cy3."

data_processing: The signals were extracted using ArrayVision (version 7.0, Imaging Research, Ontario, Canada). The intensity of each spot was measured as median density. Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average intensity, over all arrays, of either Cy5 or Cy3 lower than 1.5-fold above average background were cleaned up. Then, the Cy5 intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106). "

source_name: Colon mucosa, control diet, Rat 53

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy5-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O."

extract_protocol: Total RNA was isolated from the colon homogenates using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer’s instructions. Total RNA was purified using Rneasy columns (Qiagen, Chatsworth, CA).

treatment_protocol: Colon scrapings were homogenized in liquid N2 using a mortar and pestle cooled with liquid N2.(Fisher Emergo, Landsmeer, The Netherlands)."

tag: Wistar, Gender

value: Male, Age:10 weeks, Tissue:Colon Mucosa.

source_name: Reference RNA

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy3-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O."


title: Colon mucosa, control diet, Rat 57

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 57


title: Colon mucosa, FOS diet, Rat 54

description: Rat Colon Mucosa

hyb_protocol: Equal volumes of Cy5 target samples and Cy3 reference sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and 10x control targets (Agilent Technologies) and hybridized to a Whole Rat Genome ologo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies). After hybridization the arrays were washed with an SSPE wash procedure (Agilent Technologies) according to manufacturers protocol.

scan_protocol: Arrays were scanned using the Scanarray Express HT (Perkin Elmer, Wellesley, MA) at a laserpower of 90% and a photomultiplier tube voltage of 55% for Cy5 and 60% for Cy3.

data_processing: The signals were extracted using ArrayVision (version 7.0, Imaging Research, Ontario, Canada). The intensity of each spot was measured as median density. Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average intensity, over all arrays, of either Cy5 or Cy3 lower than 1.5-fold above average background were cleaned up. Then, the Cy5 intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

source_name: Colon mucosa, FOS diet, Rat 54

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy5-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.

treatment_protocol: Colon scrapings were homogenized in liquid N2 using a mortar and pestle cooled with liquid N2.(Fisher Emergo, Landsmeer, The Netherlands).

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy3-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.


title: Colon mucosa, FOS diet, Rat 58

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 58


title: Starved vs. Fed 2

status: Public on Nov 02 2007

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

description: Starved vs. Fed 2

hyb_protocol: The hybridizations were carried out for 3 hours at 60°C followed by another 13 hours at 55°C.  Arrays were washed twice in 2XSSC, 01% SDS, followed by twice in 0.1XSSC, 0.1% SDS at room temperature.  Following 2 more washes in 0.1XSSC, the slides were rinsed in water and dried by centrifugation.

scan_protocol: ScanArray Lite® microarray scanner was used to scan arrays and ScanArray Express® software (PerkinElmer, Wellesley, MA) was used to process array images, align spots, integrate robot-spotting files with the microarray images and quantify spots as we previously described.

data_processing: Pre-processing and normalization of data were accomplished using the R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) through the GenePix AutoProcessor (GPAP) website (http://darwin.biochem.okstate.edu/gpap).  Data were pre-processed by: 1) Removing data points where signal intensities in both channels were less than a baseline threshold value of 200, 2) Calculating and subtracting local background fluorescence values from all feature intensities, 3) Log2-transforming the background subtracted Cy3/Cy5 ratios, 4) Averaging the technical replicates within and across the replicates, and 5) Defining spots that are larger or smaller than 2 standard deviations from the mean as outliers and eliminating them from calculation of the final average Log2 ratios within and across array replicates.  All hybridizations were also subjected to manual review to ensure flagging and exclusion of all unacceptable spots.  Following pre-processing, the expression results were normalized using global LOWESS normalization.  For each spot, t-statistic, P-value (probability), and fold change were calculated.  Spots with one and half-fold change or more were considered differentially expressed using p value < 0.05.  Four experiments were conducted.

organism: Oncorhynchus mykiss

source_name: Fed fish

label_protocol: A salmonid microarray containing cDNAs representing 16,006 genes selected from Atlantic salmon and RBT expressed sequence tag databases was used to profile changes in gene expression.  Microarray chips were obtained from Drs.  Ben Koop and William Davidson at the University of Victoria through the Genomic Research on Atlantic Salmon Project (GRASP).  A compete list of the genes on the array is available at http://web.uvic.ca/cbr/grasp/.  Gene expression levels were determined by comparing the amount of mRNA transcript present in the experimental sample (starved fish) compared to a control sample (fed fish).  RNAs isolated from each experimental fish were run on separate microarrays in independent experiments, with no pooling.  A total of 8 fish were used in this experiment (1 fish X 4 replicate X 2 genetic group).  Fluorophors (Cy3 and Cy5) were randomly assigned to RNA from each of the starved and fed fish to limit the dye effect.  cDNA labeling and microarray hybridization procedures were essentially as we previously described.  Briefly, 0.4 μg of mRNA from each trout tissue was used as a template in reverse transcription reactions incorporating amino-allyl dUTP into the cDNA using oligo-d (T) primer and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA ).  The synthesized cDNAs from each starved and fed fish were differentially labeled using N-hydroxysuccinate-derived Cy3 or Cy5 dyes (GE Healthcare, Piscataway, NJ).  Labeled cDNAs were purified using a PCR purification kit (Roche, Indianapolis, IN) to remove unincorporated dyes.  The Cy3 and Cy5 labeled cDNAs were then combined and concentrated down to 20 μl using a Vacufuge vacuum concentrator (Eppendorf, Westbury, NY) followed by addition of 130 µl of Slidehyb 3 solution (Ambion, Inc.  Austin, TX).  Microarray hybridizations were performed on a Tecan HS400 automated microarray hybridization station (Tecan US, Durham, NC).  The slides were placed on the machine at 60°C for 2 minutes followed by pre-hybridization at 55°C for 30 minutes with pre-hybridization solution (5XSSC, 1% SDS, 1% BSA) under medium agitation.  After a brief washing at 60°C for 1 minute, differentially labeled cDNAs in hybridization buffer (~145 µl) were injected into the hybridization chamber.

growth_protocol: The fish used in this study were from the NCCCWA strain. Prior to the study the fish were reared under standard laboratory practices, and were fed to apparent satiation daily. For both treatments six fish were each reared in a separate 10 liter tank for a total of 12 tanks.  The fish were acclimated to the individual rearing units for 2 weeks prior to beginning the study and all fish were feeding well at the initiation of the treatments.  Water temperature was maintained at 140C, and dissolved oxygen concentration was maintained close to saturation.  Initial weight of the fish in the two treatments was not different (P>0.37) at 193.0 ±15.7g.

extract_protocol: Total RNA was isolated from each fish (6 fish/group) using the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instruction.  Concentrations of isolated RNA were determined by measuring absorbance at 260 nm.  The integrity of RNA was determined by agarose gel electrophoresis.  Poly (A) mRNA was purified using Oligotex mRNA Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

treatment_protocol: We evaluated changes in hepatic global gene expression in response to 3-week starvation in rainbow trout.  After three weeks the feed deprived fish  weighed significantly less than the fed fish, 279.7 ±19.8g versus 172.0 ±10.6g.  For the final weighing, fish were anesthetized one at a time with 0.1mg/L MS-222.  Following the weight sample, a piece of liver and a section of white muscle from the epaxial musculature were rapidly removed and transferred to 1.0ml test-tubes, flash frozen in liquid nitrogen and then held at -800C until sample preparation.  All animal handling and sampling procedures were reviewed and approved by the NCCCWA Institutional Animal Care and Use Committee.

tag: Liver from fed fish

source_name: Starved fish

tag: Liver from starved fish


title: Colon mucosa, control diet, Rat 49

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 49


title: Colon mucosa, control diet, Rat 45

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 45


title: T .rubrum PH11B rep1

status: Public on Nov 21 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

description: Signals were normalized using a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.

hyb_protocol: Labeled cDNA was purified using QIAquick columns and mixed with 2μl polyA; 5× Denharts; 3× SSC; yeast tRNA 24 μg; 25 mM HEPES, pH 7.0; 0.25% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization.

data_processing: Genes were considered to be differentially expressed if (i) average expression changed by at least 2-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

organism: Trichophyton rubrum

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime? DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy? Plant Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions. Poly(A)+ mRNA was isolated with Oligotex mRNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: T.rubrum treated with PH11B

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime? DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy3-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

tag: T.rubrum treated with DMSO


title: Fed vs. Starved 2

department: Division of Animal and Nutritional Sciences

description: Fed vs. Starved 2


title: T .rubrum PH11B rep3


title: Colon mucosa, FOS diet, Rat 46

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 46


title: Fed vs. Starved 1

description: Fed vs. Starved 1


title: Colon mucosa, FOS diet, Rat 42

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 42


title: Colon mucosa, FOS diet, Rat 14

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 14


title: Colon mucosa, control diet, Rat 19

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 19


title: Starved vs. Fed 1

description: Starved vs. Fed 1

tag: Liver form starved fish


title: CHP, t=120 min, biological replicate 3

status: Public on Oct 24 2007

city: Blacksburg

first: Vladimir

last: Shulaev

state: VA

address: Virginia Bioinformatics Inst., Virginia Tech, Washington st.

institute: Virginia Bioinformatics Institute

description: Culture treated with CHP 0.19 mM, collected at t=120 min (after adding CHP), biological replicate 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 640.

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

data_processing: The data were normalized with RMA.

organism: Saccharomyces cerevisiae

source_name: yeast, CHP, t=120 min, replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast cultures were grown in controlled batch conditions, in 1 L fermentors at 30C, pH 6.0, 500 rpm, and dO2> 80%.

extract_protocol: RNA was extracted with a procedure modified from the hot phenol protocol, as described (Martins, A. et al (2007) Yeast 24, 181-188)

treatment_protocol: In mid-exponential phase (OD600 ~ 1.5), three replicate cultures were treated with 0.19 mM CHP, while three untreated cultures were used as controls.

tag: Strain BY4743

tag: Mid-exponental phase


title: CHP, t=40 min, biological replicate 3

description: Culture treated with CHP 0.19 mM, collected at t=40 min (after adding CHP), biological replicate 3

source_name: yeast, CHP, t=40 min, replicate 3


title: CHP, t=70 min, biological replicate 3

description: Culture treated with CHP 0.19 mM, collected at t=70 min (after adding CHP), biological replicate 3

source_name: yeast, CHP, t=70 min, replicate 3


title: Colon mucosa, control diet, Rat 25

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 25


title: Colon mucosa, FOS diet, Rat 08

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 08


title: Colon mucosa, FOS diet, Rat 32

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 32

source_name: Reference RNA


title: T .rubrum PH11B rep2

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime® DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy® Plant Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions. Poly(A)+ mRNA was isolated with Oligotex mRNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime® DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy3-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.


title: Colon mucosa, control diet, Rat 13

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 13


title: CHP, t=120 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=120 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=120 min, replicate 1


title: Colon mucosa, Control diet, Rat 01

description: Rat Colon Mucosa

source_name: Colon mucosa, Control diet, Rat 01


title: CHP, t=70 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=70 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=70 min, replicate 1


title: CHP, t=120 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=120 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=120 min, replicate 2


title: Colon mucosa, control diet, Rat 31

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 31


title: Colon mucosa, FOS diet, Rat 26

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 26


title: Colon mucosa, FOS diet, Rat 02

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 02

extract_protocol: Total RNA was isolated from the colon homogenates using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer’s instructions. Total RNA was purified using Rneasy columns (Qiagen, Chatsworth, CA). "


title: CHP, t=40 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=40 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=40 min, replicate 1


title: Colon mucosa, FOS diet, Rat 50

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 50


title: Colon mucosa, FOS diet, Rat 20

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, Rat 20


title: Colon mucosa, control diet, Rat 07

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 07


title: CHP, t=40 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=40 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=40 min, replicate 2


title: Colon mucosa, control diet, Rat 41

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 41


title: Control, t=40 min, biological replicate 3

description: Control (untreated culture), collected at t=40 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=40 min, replicate 3


title: Control, t=120 min, biological replicate 3

description: Control (untreated culture), collected at t=120 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=120 min, replicate 3


title: Control, t=70 min, biological replicate 3

description: Control (untreated culture), collected at t=70 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=70 min, replicate 3


title: Control, t=120 min, biological replicate 2

description: Control (untreated culture), collected at t=120 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=120 min, replicate 2


title: Control, t=120 min, biological replicate 1

description: Control (untreated culture), collected at t=120 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=120 min, replicate 1


title: Control, t=40 min, biological replicate 2

description: Control (untreated culture), collected at t=40 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=40 min, replicate 2


title: Control, t=70 min, biological replicate 1

description: Control (untreated culture), collected at t=70 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=70 min, replicate 1


title: Control, t=40 min, biological replicate 1

description: Control (untreated culture), collected at t=40 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=40 min, replicate 1


title: Control, t=70 min, biological replicate 2

description: Control (untreated culture), collected at t=70 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=70 min, replicate 2


title: CHP, t=70 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=70 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=70 min, replicate 2


title: Colon mucosa, control diet, Rat 37

description: Rat Colon Mucosa

source_name: Colon mucosa, control diet, Rat 37

source_name: Reference RNA


title: wheat_shoot_salt_24h_swap

status: Public on Oct 02 2007

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

description: RNA extraction and microarray hybridization were carried out as described (Kawaura et al. 2006).

hyb_protocol: Microarray was hybridized for 17 h at 60 ºC with a mixture of cy3 and cy5 labeled cRNA in 510 ul of hybridization buffer. After hybridization, the microarray was washed for 5 min at room temperature with 6XSSC containing 0.005% Triton X-120, followed by 5 min at 4 ºC with 0.1XSSC contain 0.005% Triton X-120.

scan_protocol: The microarray was scanned using the DNA microarray scanner (Agilent Technologies).  Signal intensities were detected from the obtained digital images using the Feature Extraction software (Agilent Technologies).

data_processing: Log10 ratio of processed signal intensity, defined as treatment/control

organism: Triticum aestivum

source_name: wheat shoot treated with NaCl for 24h

label_protocol: Total RNA was labeled using the Agilent Low Input Fluorescent Linear Amplification kit (Agilent Technologies) according ot the manufacturer's instructions.

growth_protocol: Plants were grown in sterilized vermiculite in growth chamber for two weeks under 16h light condition at constant 22 ºC.

extract_protocol: Total RNA was extracted with the RNeasy Plant mini kit (QIAGEN) according to the manufacturer's protocol.

treatment_protocol: Two-week-plants were treated with 150mM NaCl solution for 24h.

tag: Cultivar

value: Chinese Spring

tag: Tissue

value: Shoot

tag: Stage

value: Two weeks after germination

source_name: wheat shoot control

treatment_protocol: Two-week-plants with no-treatment


title: wheat_soot_salt_6h_swap

source_name: wheat shoot treated with NaCl for 6h

treatment_protocol: Two-week-plants were treated with 150mM NaCl solution for 6h.

value: Root


title: wheat_shoot_salt_6h


title: wheat_shoot_salt_24h


title: wheat_root_salt_1h_swap

source_name: wheat root treated with NaCl for 1h

treatment_protocol: Two-week-plants were treated with 150mM NaCl solution for 1h.

source_name: wheat root control


title: wheat_soot_salt_1h_swap


title: wheat_root_salt_1h


title: wheat_root_salt_6h_swap

source_name: wheat root treated with NaCl for 6h


title: wheat_root_salt_6h


title: wheat_root_salt_24h

source_name: wheat root treated with NaCl for 24h


title: wheat_root_salt_24h_swap


title: wheat_shoot_salt_6h

hyb_protocol: Microarray was hybridized for 17 h at 60 ºC with a mixture of cy3 and cy5 labeled cRNA (0.75 ug each) in 510 ul of hybridization buffer. After hybridization, the microarray was washed for 5 min at room temperature with 6XSSC containing 0.005% Triton X-120, followed by 5 min at 4 ºC with 0.1XSSC contain 0.005% Triton X-120.


title: wheat_shoot_salt_24h_swap


title: wheat_shoot_salt_1h

source_name: wheat shoot treated with NaCl for 1h


title: wheat_shoot_salt_1h


title: wheat_root_salt_24h_swap


title: wheat_shoot_salt_24h


title: MLN_SC infected pig, 21 dpi, rep2

status: Public on Sep 30 2007

city: Ames

first: Christopher

middle: K

last: Tuggle

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description: Gene expression data from the mesenteric lymph nodes of Salmonella Choleraesuis infected pig, 21 dhpi post-infection

hyb_protocol: Following fragmentation, 6.5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Porcine Genome Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: mesenteric lymph nodes, 21d post infected pig

label_protocol: Biotinylated cRNA were prepared by the GeneChip® One-Cycle target labeling kit according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Total RNA was isolated from ~200 mg of porcine MLN tissues by using the RNeasy Midi kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) based on the manufacture’s protocol

treatment_protocol: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA, and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed twice on rectal swabs before the experiments. At seven weeks of age, the pigs were randomly allocated to the non-infected group which has 3 pigs and the infected group which contains 12 pigs. Three non-infected control pigs were necropsied 3 days prior to experimental infection. On day 0, pigs in the infected groups were intranasally challenged with 1 x 109 CFU of S. Choleraesuis ?3246. Three infected pigs were necropsied at each time point of 8 hpi, 24 hpi, 48 hpi and 21 dpi, respectively

tag: Age

value: 7 weeks old pigs were used for this experiment


title: wheat_shoot_salt_6h_swap


title: MLN_SC infected pig, 24 hpi, rep2

description: Gene expression data from the mesenteric lymph nodes of Salmonella Choleraesuis infected pig, 24 hpi post-infection

source_name: mesenteric lymph nodes, 24h post infected pig


title: MLN_SC infected pig, 48 hpi, rep1

description: Gene expression data from the mesenteric lymph nodes of Salmonella Choleraesuis infected pig, 48 hpi post-infection

source_name: mesenteric lymph nodes, 48h post infected pig


title: wheat_root_salt_1h


title: wheat_root_salt_6h_swap


title: MLN_SC non_infected pig, rep3

description: Gene expression data from the mesenteric lymph nodes of non-infected pig

source_name: mesenteric lymph nodes, non-infected pig


title: MLN_SC infected pig, 21 dpi, rep3


title: MLN_SC infected pig, 8 hpi, rep2

description: Gene expression data from the mesenteric lymph nodes of Salmonella Choleraesuis infected pig, 8 hpi post-infection

source_name: mesenteric lymph nodes, 8h post infected pig


title: wheat_root_salt_1h_swap


title: MLN_SC infected pig, 8 hpi, rep1


title: MLN_SC infected pig, 21 dpi, rep1


title: MLN_SC non_infected pig, rep2


title: MLN_SC infected pig, 24 hpi, rep1


title: MLN_SC infected pig, 24 hpi, rep3


title: MLN_SC infected pig, 48 hpi, rep2


title: MLN_SC infected pig, 48 hpi, rep3


title: wheat_root_salt_24h


title: wheat_root_salt_6h

data_processing: Log ratio of processed signal intensity, defined as CH2 divided by CH1

treatment_protocol: Two-week-plants were treated with 150mM NaCl solution.


title: MLN_SC infected pig, 8 hpi, rep3


title: MLN_SC non_infected pig, rep1


title: 6.5hr_vehicle_control_biological_rep_2

status: Public on Sep 01 2007

city: San Diego

first: Sara

last: Dozier

address: 10420 Wateridge Circle

institute: Kalypsys, Inc.

hyb_protocol: As described in Affymetrix Eukaryotic Sample and Array Processing v. 701024 Rev. 3

data_processing: GeneSpring software was used to normalize data.  Mean expression value was arbitratily set to 1.  gcRMA was used to normalize data.

growth_protocol: A172 human glioblastoma cells were cultured in DMEM containing 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin incubated at 37C with 10% CO2.  2e6 cells/ well of a 6-well tissue culture dish were incubated for 18 hours prior to stimulation and treatment with compound.

extract_protocol: After incubation with compound and stimulation media, cells were lysed in 350ul buffer RLT, homogenized over QiaShredder columns, and total RNA was purified using the RNeasy kit with on-column DNase digestion (Qiagen).  RNA quality and concentration was determined using the Bioanalyzer RNA6000 assay (Agilent).  5µg of the RNA was analyzed on U133A 2.0 Gene chips (Affymetrix).

treatment_protocol: Compound was added at 10uM with a final concentration of 0.1% DMSO.  Cells were stimulated with a cytokine cocktail containing hIFN-γ (4,000 U/ml), hTNF-α (40 ng/ml), hIL-1β (4ng/ml).

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM DMSO vehicle control (0.1%) for 6.5 hours.


title: 6.5hr_vehicle_control_biological_rep_1

scan_protocol: As described in Affymetrix Eukaryotic Sample and Array Processing v. 701024 Rev. 3


title: 18hr_nostressin_biological_rep_1

label_protocol: As described in Affymetrix Eukaryotic Sample and Array Processing v. 701024 Rev. 3

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM nostressin for 18 hours.


title: 18hr_nostressin_biological_rep_2


title: 18hr_erstressin_unstimulated_biological_rep_1

tag: A172 human glioblastoma cells in culture treated with 10uM erstressin for 18 hours. (no cytokine stimulaion)


title: 18hr_erstressin_biological_rep_1

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM erstressin for 18 hours.


title: 6.5hr_nostressin_biological_rep_1

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM nostressin for 6.5 hours.


title: 30min_erstressin_biological_rep_2

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM erstressin for 30 minutes.


title: 30min_nostressin_biological_rep_1

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM nostressin for 30 minutes.


title: 6.5hr_erstressin_biological_rep_2

tag: A172 human glioblastoma cells in culture, simultaneously stimulated with cytokine and treated with 10uM erstressin for 6.5 hours.


title: 6.5hr_nostressin_biological_rep_2


title: 18hr_erstressin_biological_rep_2


title: 18hr_erstressin_unstimulated_biological_rep_2


title: 30min_erstressin_biological_rep_1


title: 6.5hr_erstressin_biological_rep_1


title: YDp2

status: Public on Aug 15 2007

city: Montreal

first: Daniela

last: Cernea

state: Quebec

address: 3775 University Street, Room 332

department: Computer Science

country: Canada

institute: McGill

hyb_protocol: Seven hundred fifty nanograms of labelled aRNA was hybridized onto Agilent Whole  Mouse Genome Oligo Microarray Kit (G4122A; 44K) using the Agilent In situ Hybridization  Plus Kit Large for 17 hrs at 65°C (Agilent Technologies). Microarrays were washed according to  the manufacturer’s protocol (Agilent microarray processing protocol)

scan_protocol: Microarray slides were scanned using a Microarray Scanner (Model G2565BA, Agilent  Technologies) at 10 µm resolution according to the manufacturer’s protocol (manual ID #G4140-  90030).

data_processing: Data from dyeswap hybridizations were condensed as part of the data processing strategy.  Raw feature intensities were background corrected using the RMA background correction algorithm. The resulting expression estimates were converted to log2-ratios. Within array normalization was performed using 2D loess correction and intensity dependent loess correction of log-ratios. The resulting data set was scale-normalized using Linear Models for Microarray Analysis (LIMMA) package from BioConductor (version 1.8) and R (version 2.3.0).

label: Cy3 or Cy5

source_name: YD mammary tumor. Strain YD, Gender: female, Age:..., Tissue: breast tumor

label_protocol: Ten micrograms of the resulting aRNA was labelled with Cy3 and Cy5 dyes (CyTMPost-labelling Reactive Dye Pack; Amersham Biosciences, UK)

growth_protocol: Mammary tumours and lung tissue were harvested from mice that were tumour-bearing for 6 weeks.

extract_protocol: Total RNA was isolated from 10 individual flash frozen mammary tumour samples  derived from our MMTV/neundl-NYPD, -YB, -YC, -YD, -YE and the parental MMTV/neu  NDL2-5 strains using the RNeasy Midi Kit (QIAGEN, Valencia, CA). RNA quantity and quality  was determined using a spectrophotometer (Nanodrop), the BioAnalyzer 2100 and the RNA 6000  Pico Assay Kit (Agilent Technologies, Palo Alto, CA). Two RNA pools, containing equal  amount of total RNA from five individual tumours, were generated from each strain and  functioned as a biological repeat. Five hundred nanograms of total RNA from each pool was  subjected to one round of T7 linear amplification using the Amino Allyl MessageAmpTM aRNA  Kit (Ambion, Austin, Texas)

treatment_protocol: Tumours were flash frozen in liquid nitrogen and stored in liqiud nitrogen until further use.

source_name: Universal Mouse Reference RNA (Stratagene).

tag: Reference


title: NYPDp1

source_name: NYPD mammary tumor. Strain NYPD, Gender: female, Age:..., Tissue: breast tumor


title: YEp2

source_name: YE mammary tumor. Strain YE, Gender: female, Age:..., Tissue: breast tumor


title: YDp1


title: YEp1


title: Sample # 1682-1

status: Public on Aug 01 2007

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Standard affymetrix protocol

data_processing: RMA normalized

label: Streptavidin-phycoerythrin

source_name: Bladder tumor biopsy

tag: T2-4 bladder tumor

tag: Survival (months)


title: NYPDp2


title: YBp2

source_name: YB mammary tumor. Strain YB, Gender: female, Age:..., Tissue: breast tumor


title: Sample # 1663-1

description: Standard affymetrix protocol


title: YCp2

source_name: YC mammary tumor. Strain YC, Gender: female, Age:..., Tissue: breast tumor


title: NDL25p2

source_name: NDL25 mammary tumor. Strain NDL25, Gender: female, Age:..., Tissue: breast tumor


title: YBp1


title: YCp1


title: NDL25p1

source_name: NDL25 mammary tumor. Strain NDL25, Gender:female, Age:..., Tissue: breast tumor


title: Sample # 1485-1

description: Standard affymetrix protocol


title: Sample # 1530-1

description: Standard affymetrix protocol


title: 30min_nostressin_biological_rep_2


title: M61_Catheter_rep2_150716

city: Urbana

first: Lois

last: Hoyer

state: IL

address: 2001 S Lincoln Ave

department: Pathobiology

institute: University of Illinois

description:
To determine an appropriate normalization method for the data, MA-plots, as described in Dudoit et al. (2002), were used to initially analyze the fluorescence (R [cy5], G [cy3]) data.  These are plots of the intensity log-ratio M = log2R/G vs. the mean log intensity A =  log2(R/G).  A global normalization model of log2 transformed fluorescence data was used (Wolfinger et al., 2001).  The residuals from this model, which are regarded as a crude indicator of relative expression level and are referred to as ‘normalized expression levels’, were then subjected to individual gene-specific models.  The normalization and gene models were fit using the MIXED procedure of SAS (SAS Institute Inc, 2000).  SAS code for this analysis was based on code available in the Introductory Manual for Mixed Model Analysis of Microarray Data (MANMADA, 2002).
To assess the magnitude and significance of the effects of the strains, surface, time, and their interactions on the normalized expression level of each gene, least square means using the LSMEANS option of SAS (SAS Institute Inc, 2000) were calculated as described in the MANMADA (2002).  The LSMEANS statement calculates the mean value for each target category, adjusted for the other terms in the model.  For each pairwise comparison, the difference between the two normalized expression levels and their standard errors are calculated along with the results of t-tests for the statistical significance of the difference between the means in each pair (Littell et al., 1996).  The resulting p-values are Bonferroni adjusted using the ‘bon’ option with LSMEANS of SAS (SAS Institute, Inc.)

hyb_protocol: The samples of cDNA coupled with fluorescent dyes were resuspended in a solution containing 50% formamide, 10X SSC, and 0.2% sodium dodecyl sulfate. The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before the samples were applied to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and then analyzed as described below.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Foster City, Calif.), and data were quantified by using GenePix Pro version 4.0.

data_processing: VALUE as presented here is the log of the ratio of medians and was calculated in the GenePix Pro version 4.0. Further description of data processing is detailed in the Description section above.

organism: Candida albicans

source_name: Strain_M61 Surface_Catheter 6 hour Biofilm

label_protocol: The methods for labeling probes and hybridization to microarrays were adapted from protocols developed by The Institute for Genomic Research (TIGR, http://pga.tigr.org/protocols.html).  cDNA was synthesized using Superscript II RT (Invitrogen Life Technologies; 100 units of reverse transcriptase) in reaction mixtures containing 0.5 mM (total) deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates [4:1]).  After cDNA synthesis overnight at 42°C, the RNA was hydrolyzed with 1 N NaOH and 0.5 M EDTA. The reaction was neutralized with 1 N HCl.  The cDNA was purified using the Qiagen QIAquick PCR purification kit and modified protocol (TIGR).  The cDNA was recovered and dried in a Speed-Vac (ThermoLabs). The cDNA was coupled with fluorescent dyes by resuspension in 0.05 M sodium bicarbonate buffer, pH 9.0, and incubation with either Cy3 or Cy5 dye (Amersham Biosciences) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a Speed-Vac.

extract_protocol: Total RNA was obtained from cells using a hot phenol extraction method (Collart and Oliviero, 1993).  Total RNA was further purified using RNeasy kit (Qiagen) according to the manufacturer’s suggested protocol (Mackenzie et al., 1997).

tag: C. albicans strains SC5314 (Gillum et al., 1984), GDH2346 and M61 were used in this work.  Strain GDH2346 was from a patient with denture stomatitis and provided by Julia Douglas, University of Glasgow, UK.  Strain M61 was obtained from an intravascular line culture at the University Hospitals of Cleveland (Kuhn et al., 2002).  The strains were cultured according to methods reported in Chandra et al. (2001) and Kuhn et al. (2002).  Model biofilms of strains GDH2346 and SC5314 were grown on denture acrylic (Chandra et al., 2001) and model biofilms of strains M61 and SC5314 were formed on silicone elastomer catheter material (Kuhn et al., 2002) as described previously.  Samples were grown for 6, 12, and 48 hours.  Additionally, planktonic cultures of each strain were grown and collected for each surface and time combination.  Samples were flash-frozen in liquid nitrogen and stored at -80ºC until used.

source_name: Strain_M61 Surface_Catheter 48 hour Planktonic


title: Sample # 1385-1

description: Standard affymetrix protocol

source_name: Bladder tumor sample


title: M61_Catheter_rep2_150715


title: Sample # 1154-1

description: Standard affymetrix protocol


title: Sample # 1167-1

description: Standard affymetrix protocol


title: M61_Catheter_rep2_150718

source_name: Strain_M61 Surface_Catheter 12 hour Planktonic

source_name: Strain_M61 Surface_Catheter 12 hour Biofilm


title: Sample # 1271-1

description: Standard affymetrix protocol


title: M61_Catheter_rep2_150707

source_name: Strain_M61 Surface_Catheter 48 hour Biofilm


title: Sample # 1124-1

description: Standard affymetrix protocol


title: Sample # 1178-1

description: Standard affymetrix protocol


title: Sample # 1113-8

description: Standard affymetrix protocol


title: M61_Catheter_rep2_150710


title: Sample # 1321-1

description: Standard affymetrix protocol


title: Sample # 1285-1

description: Standard affymetrix protocol


title: M61_Catheter_rep2_150709


title: M61_Catheter_rep2_150714

source_name: Strain_M61 Surface_Catheter 6 hour Planktonic