title: CL1-5-F4: Adenocarcinoma

status: Public on Aug 30 2007

city: Taipei

first: Li-Jen

last: Su

address: No. 201, Sec. 2, Shih-Pai Road

department: Department of Surgery

country: Taiwan

institute: Taipei Veterans General Hospital

description: Gene expression data from cell line.

hyb_protocol: Protocols and reagents for hybridization, washing and staining followed the Affymetrix’s instructions (http://www.affymetrix.com/support/technical/manuals.affx).

scan_protocol: GeneChips were scanned using the Affemetrix Genechip scanner 6G.

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA preparation and analysis were performed according to the Affymetrix's instructions. The quality of the total RNA for microarray analysis was determined using Spectra Max Plus (Molecular Devices) and had an OD260/OD280 ratio ranging from 1.9 to 2.1.

tag: Adenocarcinoma

tag: sex

value: male


title: upf1.1

status: Public on Aug 31 2007

type: RNA

city: Santa Cruz

first: Manny

last: Ares

state: CA

address: 1125 High St

department: Molecular and Cellular Biology

country: USA

institute: UCSC

description: Mouse N2A cells were transfected with Upf1 siRNA in order to inhibit nonsense-mediated mRNA decay(NMD) pathway.

hyb_protocol: Targets were hybridized to chips in 7% DMSO solution for 16 hrs overnight at 50. Microarrays were washed, processed with anti-biotin antibodies and streptavidin-phycoerythrin according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix procedures

data_processing: Intensity values from the DNA arrays were normalized using a quantile normalization (Bolstad et al., 2003), and probe set summaries were derived using the Robust Multi-chip Analysis (RMA) procedure (Irizarry et al., 2003a; Irizarry et al., 2003b) with two modifications. The first modification was to remove all probes with 17 or more continuous bases that match to any other mouse transcript in order to minimize cross-hybridization issues. The second modification was to use the mode of the probe intensity values of similar GC content probes for the background estimate of a particular probe. For example, if a probe has a GC count of 16, then the mode of the intensity of all the probes with a GC count of 16 was used as a background estimate as opposed to RMA in which the mode of all the probes is used as a background estimate for all the probes.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Neuroblastoma N2A cells

label_protocol: Total RNA was primed with random hexamers and reverse transcribed. After the reaction was completed, RNA was removed from the reaction by alkaline hydrolysis and the cDNA was purified using Qiagen PCR Quick Purification Kit. A typical reaction started with 5-6ug of total RNA usually yielded ~3ug of cDNA. The cDNA was then fragmented using DNAseI in an empirically controlled reaction that yields DNA fragments of 50-200 bases. This fragmented cDNA was then end labeled using terminal deoxynucleotidyl transferase and "DNA-Labeling-Reagent-1a (DLR-1a)", which is a biotinylated dideoxynucleoside triphosphate.

extract_protocol: Total RNA was extracted using Invitrogen Trizol reagent. RNA samples were quantified using NanoDrop ND-1000 Spectrophotometer.


title: NL-20: Immortalized, nontumorigenic human bronchial epithelial cell line (ATCC No.: CRL-2503™ )

description: Gene expression data from cell line.

label: biotin

organism: Homo sapiens

value: female


title: emetine_control.2

description: Mouse N2A cells

tag: Mouse N2A cells


title: N. (Stratagene): Normal lung tissues (Cat. 735020)

description: Gene expression data from commercial human normal lung tissues.

source_name: N. (Stratagene)

tag: Normal lung tissues (Cat. 735020)


title: CL1-0: Adenocarcinoma

description: Gene expression data from cell line.


title: A549: Carcinomatoma (ATCC No.: CCL-185™)

description: Gene expression data from cell line.

tag: Carcinomatoma (ATCC No.


title: N. (Clontech): Normal lung tissues (Cat. 636524)

source_name: N. (Clontech)

tag: Normal lung tissues (Cat. 636524)

value: mixture


title: emetine.2

description: Mouse N2A cells were treated with emetine in order to inhibit nonsense-mediated mRNA decay(NMD) pathway.

tag: Mouse N2A cells treated with 100(g/ml of emetine dihydrochloride hydrate (Fluka) 10 hours


title: Melanoma xenograft, MA1_Lung_B (LeiATCC)

status: Public on Oct 02 2007

city: cambridge

first: steve

last: shen

state: MA

address: 77 mass ave

institute: MIT

description: human melanoma tumors grown  in mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on one U133A human chip and one test chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: raw data (CEL file) were normalized with RMA and further analyzied with GenePatter comparative marker selection module.

source_name: Melanoma metastatic derivatives, lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (701025, Revision 3).

extract_protocol: Rneasy mini kit

tag: Genotype

value: highly metastatic

tag: Age


title: CL1-5: Adenocarcinoma

description: Gene expression data from cell line.


title: H661: Large cell lung cancer (ATCC No.: HTB-183™)

description: Gene expression data from cell line.

tag: Large cell lung cancer (ATCC No.


title: Kidney young rep4

city: College Station

first: Alan

middle: R.

last: Parrish

state: TX

address: 364 Reynolds

department: Systems Biology

institute: Texas A&M Health Science Center

description: Microarray sample labeling, hybridization, and scanning were performed by the Genomics Core Facility of the Center for Environmental and Rural Health at Texas A&M University (College Station, TX, USA)

hyb_protocol: Biotin-labeled cRNA was hybridized to arrays, washed, and detected using Cy5-Steptavidin conjugate according to the CodeLink Expression Bioarray System instructions (080067-00/Rev. AA/2003-10, GE Healthcare/Amersham Biosciences).  The hybridization period was 18hrs.

scan_protocol: Cy5-labeled arrays were scanned on a GenePix Array Scanner set to wavelength: 635nm, PMT voltage: 600V, laser power: 100%, pixel size: 10um, focus position: 0um.  Images files were analyzed using Codelink Expression Analysis software (GE Healthcare/Amersham Biosciences); raw intensity values for each feature were exported to Microsoft Excel spreadsheets.

data_processing: Raw intensity values were imported into GeneSpring 7.1 (Agilent Technologies) and normalized by setting all measurements less than 0.01 to 0.01, normalizing each array to the 50th percentile of all feature measurements taken for that array, and normalizing each feature to the median measurement for that feature across all arrays.

organism: Rattus norvegicus

source_name: kidney, 4 month old

label_protocol: Biotin-labeled cRNA was generated from total RNA by a linear amplification method using the CodeLink Expression Assay Reagent Kit (GE Healthcare/Amersham Biosciences code number 320012) according to the CodeLink Expression Bioarray System instructions (080067-00/Rev. AA/2003-10, GE Healthcare/Amersham Biosciences)

growth_protocol: Male Fischer 344 rats 4 month old were purchased from NIA colony and housed in the College of Medicine Animal Facilities, Texas A&M Health Science Center. The animal room was temperature controlled and on a 12/12 h light/dark cycle. Following anesthesia (ketamine 87 mg/kg and xylazine 13 mg/kg body weight), the abdominal cavity was opened, and the kidneys were removed and snap frozen.

extract_protocol: Total RNA isolated using RNAqueous-4PCR according to manufacturer's protocol (catalog #1914, Ambion Inc.)

tag: Strain

value: Fisher F344; Gender:Male; Age:4 months; Diet:ad libitum; Tissue:kidney


title: Adj. N. mixture: Adjacent normal part of adenocarcinoma

description: Gene expression data from lung cancer patient.

source_name: Adj. N. mixture

tag: Adjacent normal part of adenocarcinoma


title: T. mixture: Tumor part of adenocarcinoma

source_name: T. mixture

tag: Tumor part of adenocarcinoma


title: Kidney young rep3


title: Kidney young rep2


title: H1299: Non-small cell lung cancer (ATCC No.: CRL-5803™)

description: Gene expression data from cell line.

tag: Non-small cell lung cancer (ATCC No.


title: Kidney young rep1


title: Kidney aged AL rep3

source_name: kidney, 24 month old

growth_protocol: Male Fischer 344 rats 24 month old were purchased from NIA colony and housed in the College of Medicine Animal Facilities, Texas A&M Health Science Center. The animal room was temperature controlled and on a 12/12 h light/dark cycle. Following anesthesia (ketamine 87 mg/kg and xylazine 13 mg/kg body weight), the abdominal cavity was opened, and the kidneys were removed and snap frozen.

value: Fisher F344; Gender:Male; Age:24 months; Diet:ad libitum; Tissue:kidney


title: NCYC_0.3mM Cd_30 min

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 30min

hyb_protocol: Hybridization was performed using 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) according to the manufacturer's instructions as described previously (Oh et al.).

scan_protocol: The hybridized slides were scanned with ScanArray 5000 scanner (Axon, Foster City, CA, U.S.A.).

data_processing: Using GenePixTM Pro 4.0 (Axon) software, spot intensity was quantified for each channel and transferred to Microsoft Excel spreadsheet.

organism: Ogataea angusta

source_name: Hansenula reference (30min)

label_protocol: The labeling of target cDNAs was performed using 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described previously (Oh et al.).

extract_protocol:
Isolation of RNA, cDNA synthesis were carried out as described in Oh et al., 2004.
Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.

tag: strain NCYC495

source_name: Hansenula exposure to 0.3mM cadmium for 30min


title: Kidney aged AL rep4


title: NCYC_0.3mM Cd_15 min_repeat

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 15min dye swap

source_name: Hansenula exposure to 0.3mM cadmium for 15min

tag: strain NCYC 495

source_name: Hansenula reference

extract_protocol: Isolation of RNA, cDNA synthesis were carried out as described in Oh et al., 2004.


title: NCYC_0.3mM Cd_60 min_repeat

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 60MIN_DYE SWAP

source_name: Hansenula exposure to 0.3mM cadmium for 60min

extract_protocol: Isolation of RNA, cDNA synthesis were carried out as described in Oh et al., 2004. Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.

tag: strain NCYC495 (leu1-1)

source_name: Hansenula REFERENCE


title: Kidney aged AL rep2


title: Kidney aged AL rep1


title: Kidney aged CR rep3

source_name: kidney, 24 month old caloric-restricted

growth_protocol: Male Fischer 344 rats 24 month caloric-restricted [caloric restriction begins at 10 weeks; 10% restriction until 15 weeks where it is increased to 25% and 40% restriction beginning at 4 months] were purchased from NIA colony and housed in the College of Medicine Animal Facilities, Texas A&M Health Science Center. The animal room was temperature controlled and on a 12/12 h light/dark cycle. Following anesthesia (ketamine 87 mg/kg and xylazine 13 mg/kg body weight), the abdominal cavity was opened, and the kidneys were removed and snap frozen.

value: Fisher F344; Gender:Male; Age:24 months; Diet:Caloric-restricted; Tissue:kidney


title: NCYC_0.3mM Cd_30 min_repeat

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 30min_DYE SWAP


title: CL1-1: Adenocarcinoma

description: Gene expression data from cell line.

tag: Adenocarcinoma


title: NCYC_0.3mM Cd_60 min


title: NCYC_0.3mM Cd_15 min

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 15min


title: Kidney aged CR rep4


title: Kidney aged CR rep1


title: Kidney aged CR rep2


title: Heart WT 42h 48h APF rep4

status: Public on Aug 29 2007

city: MARSEILLE Cedex 9

first: Bruno

last: ZEITOUNI

address: Campus de Luminy Case 907

country: France

institute: CNRS

description: Cy3 and Cy5 labelled aRNA samples were mixed in equal proportions (700 pmol) and fragmented with the RNA Fragmentation Reagents (Ambion) to enhance aRNA hybridization, dried up to 60ul of final volume, and hybridized on INDAC oligonucleotide microarrays.

hyb_protocol: Labeled probes (60 µl) were mixed with 60 µl of 4X hybridization buffer and 120 µl of deionised formamide, denatured at 95°C for 5min and hybridized at 37°C for 12 hours with the Automated Slide Processor (ASP) of Amersham. Slides were successively washed at 37°C in 1X SCC/0.2% SDS for 20 min, in 0.1X SCC/0.2% SDS for 2x10 min, in 0.1X SCC for 10 min, rinsed in isopropanol and air dried.

scan_protocol: Images were obtained with a GenePix 4200AL (Axon Instruments) at 10 um resolution and 5% of laser power. Fluorescence measurements are made using Array Vision quantification software (Imaging Research Inc).

data_processing:
Normalization of primary expression data (from not flagged spots) was performed through two successive steps using both R software packages SMA and LIMMA:
- Lowess normalization to normalize the M-values (Cy3/Cy5) for each array separately (within-array normalization) without prior background correction
- Quantile normalization to the A-values making the density distributions the same across arrays to compare expression intensities between them (between-array normalization).
Final normalized log2 M-values are showed in the VALUE column.

molecule: polyA RNA

organism: Drosophila melanogaster

label_protocol:
20 μg of amino allyl aRNA was labelled according the "Dye Coupling and Labeled aRNA Cleanup" protocol of the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion)
700 pmol of incorporated dye was used for hybridization.

extract_protocol:
Total RNA was extracted from 5 dissected cardiac tubes with Trizol reagent (Invitrogen) in following a modified manufacturer’s experimental protocol adapted to the extraction of small RNA amounts. Dissected cardiac tubes were collected in 300 µl of Trizol and a linear polyacrylamide (GenElute LPA from Sigma) was used as nucleic acid carrier (necessary for small amounts of starting material).
Isolated total RNA (~100 ng) was directly amplified with the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion): the aRNA procedure begins with total RNA that is reverse transcribed using an oligo(dT) primer containing a T7 RNA polymerase promoter sequence. The reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during the second-strand synthesis reaction producing a double-stranded cDNA template for T7 in vitro transcription (IVT). This RNA was subjected to a second round of amplification with a second IVT configured to incorporate the modified nucleotide (amino allyl UTP) into the aRNA during transcription for subsequent indirect labelling with the fluorescent dye Cy3.

value: WT (yw; Canton S)

tag: Development temperature

tag: Stage

value: 42hr APF (pupae)

tag: Hand dissected cardiac tubes

tag: Biological replicate n°4

extract_protocol:
Total RNA was extracted from 5 dissected cardiac tubes with Trizol reagent (Invitrogen) in following a modified manufacturer’s experimental protocol adapted to the extraction of small RNA amounts. Dissected cardiac tubes were collected in 300 µl of Trizol and a linear polyacrylamide (GenElute LPA from Sigma) was used as nucleic acid carrier (necessary for small amounts of starting material).
Isolated total RNA (~100 ng) was directly amplified with the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion): the aRNA procedure begins with total RNA that is reverse transcribed using an oligo(dT) primer containing a T7 RNA polymerase promoter sequence. The reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during the second-strand synthesis reaction producing a double-stranded cDNA template for T7 in vitro transcription (IVT). This RNA was subjected to a second round of amplification with a second IVT configured to incorporate the modified nucleotide (amino allyl UTP) into the aRNA during transcription for subsequent indirect labelling with the fluorescent dye Cy5.

value: 48hr APF (pupae)


title: NCYC_0.3mM Cd_0 min

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 0min

data_processing:
Using GenePixTM Pro 4.0 (Axon) software, spot intensity was quantified for each channel and transferred to Microsoft Excel spreadsheet. All arrays were analyzed using Quintet, an R-based unified cDNA microarray data analysis system with GUI (Choe et al., 2005).
Choe, J.-K., T.-H. Chung, S. Park, H. G. Cho, and C.-G. Hur. 2005. An open source microarray data analysis system with GUI: Quintet. In Slezak D. et al., (Eds) RSFDGrC 2005, LNAI 3642, pp. 392-401, Springer-Verlag Berling Heidelberg.

source_name: Hansenula exposure to 0.3mM cadmium for 0min


title: NCYC_0.3mM Cd_120 min_repeat

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 120min_DYE SWAP

source_name: Hansenula exposure to 0.3mM cadmium for 120min


title: Heart WT 36h 42h APF rep4

value: 36hr APF (pupae)


title: Heart WT 27h 30h APF rep4

value: 27hr APF (pupae)

value: 30hr APF (pupae)


title: Heart WT 24h 27h APF rep4

value: 24hr APF (pupae)


title: Heart WT 33h 36h APF rep4

value: 33hr APF (pupae)


title: Heart WT 48h 21h APF rep4

value: 21hr APF (pupae)


title: Heart WT 21h 24h APF rep4


title: Heart WT 30h 33h APF rep4


title: Heart WT 48h 21h APF rep3

tag: Biological replicate n°3


title: NCYC_0.3mM Cd_120 min

description: Transcriptome profiling of H. polymorpha in response to Cd exposure: 120min


title: Testosterone treated, HIV-1 positive male, day 14 (6)

city: Boston

first: Monty

last: Montano

address: 650 Albany Street, Bldg X, room 640

department: Medicine

institute: Boston Medical Center

description: Sample collected 14d post treatment

source_name: Percutaneous biopsies of vastus lateralis

tag: HIV-1 positive male, 18-60 years old, weight loss of 5-15% in preceding 6 months, stable anti-retroviral therapy. CD4+ T-cells >50/ml, HIV copies =< 10,000/ml, free testosterone <50pg/ml.


title: Testosterone treated, HIV-1 positive male, day 14 (10)

description: Sample collected 14d post treatment


title: Testosterone treated, HIV-1 positive male, day 14 (9)

description: Sample collected 14d post treatment


title: Heart WT 42h 48h APF rep3


title: Heart WT 36h 42h APF rep3


title: Heart WT 48h 21h APF rep2

tag: Biological replicate n°2


title: Testosterone treated, HIV-1 positive male, day 14 (8)

description: Sample collected 14d post treatment


title: Heart WT 30h 33h APF rep3


title: Heart WT 33h 36h APF rep3

extract_protocol:
Total RNA was extracted from 5 dissected cardiac tubes with Trizol reagent (Invitrogen) in following a modified manufacturer’s experimental protocol adapted to the extraction of small RNA amounts. Dissected cardiac tubes were collected in 300 µl of Trizol and a linear polyacrylamide (GenElute LPA from Sigma) was used as nucleic acid carrier (necessary for small amounts of starting material).
Isolated total RNA (~100 ng) was directly amplified with the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion): the aRNA procedure begins with total RNA that is reverse transcribed using an oligo(dT) primer containing a T7 RNA polymerase promoter sequence. The reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during the second-strand synthesis reaction producing a double-stranded cDNA template for T7 in vitro transcription (IVT). This RNA was subjected to a second round of amplification with a second IVT configured to incorporate the modified nucleotide (amino allyl UTP) into the aRNA during transcription for subsequent indirect labelling with the fluorescent dye Cy5


title: Testosterone treated, HIV-1 positive male, day 14 (5)

description: Sample collected 14d post treatment


title: Heart WT 27h 30h APF rep3


title: Heart WT 21h 24h APF rep3


title: Testosterone treated, HIV-1 positive male, day 14 (7)

description: Sample collected 14d post treatment


title: Heart WT 24h 27h APF rep3


title: mPAC cells + neurogenin3 vs bgal expt #1a

city: San Francisco

first: Michael

middle: Scott

last: German

address: 513 Parnassus, HSW 1090

department: Diabetes Center

institute: University of California San Francisco

hyb_protocol: Purified, labeled cDNA were pooled and resuspended in 11 µl of 3xSSC containing 0.75mg/ml polydA (Amersham ref: 27-4110-01), 25mM Hepes and 0.23 % SDS. Before hybridization, the solution was boiled for 2 min and then allowed to cool to room temperature. The solution was applied to the microarray under a cover slip, and the slide was placed in a custom hybridization chamber which was subsequently incubated for 12 to 16 hours in a water bath at 63°C. Before scanning, slides were washed in 0.6xSSC, 0.02% SDS for 1 min, and then 0.05xSSC for 1 min. Slides were dried before scanning by centrifugation at 500 rpm in a Beckman CS-6R centrifuge.

scan_protocol: After hybridization and washing, the microarrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City California, USA) to detect Cy5 and Cy3 fluorescence.

data_processing: Data were acquired and analyzed using Genepix Pro-4 software (Axon instruments). The composite pixel intensity threshold for inclusion into a feature was set to 200 and the background subtraction based on feature local background median.

source_name: mPAC cells + neuroD1

label_protocol: 15 µg of total RNA was primed by 7 ug of a dT(16) oligomer and the mixture was heated to 70°C for 10 min, and then transferred to ice. A premixed solution, consisting of 200 U Superscript II (Gibco), buffer, 100mM DTT and 0.5mM dNTP, was added to the RNA. The reaction was then incubated at 42°C for 2 hours. Nucleotides were used at these final concentrations: 0.5 mM for dATP, dCTP, and dGTP and 0.1 mM for dTTP and 0.4mM for aminoallyl-dUTP (Sigma ref: A0410). NaOH and EDTA were then added and RNA was hydrolyzed by incubation at 65°C for 15min. After neutralization using Hepes, the aminoallyl cDNA was purified using a Bio-spin6 column (BioRad, ref: 732-6002) and concentrated using Centricon-30 microconcentrators (Amicon, ref 42410). NaHCO3 pH9 was added to a final concentration of 0.05M and each cDNA was combined with an aliquot of Cy3 or Cy5 monofunctional dye ester (Amersham, ref: PA25001/2) and incubated for an hour of coupling in the dark. Dye-coupled cDNA was purified using Qiaquick column (Qiagen ref: UB300) and concentrated with a Centricon-30 microconcentrator.

growth_protocol: mPAC cells were routinely maintained in DMEM 4,5g/L glucose supplemented with 10% FBS and antibiotics.

extract_protocol: 350ul of lysis buffer +B-mercaptoethanol lysis buffer was added to each well. Three independent wells per adenovirus treatment were combined into a single tube. Total RNA was extracted following RNeasy kit protocol (Qiagen). RNA samples were treated with RNase-free DNase (Qiagen) to remove contaminating genomic DNA. Purity and quantity of total RNA was assessed with spectrophotometer and ethidium bromide gel analysis.

treatment_protocol: 24h after seeding mPAC cells onto 6-well plates (500,000 cells/well), cells were treated with recombinant adenoviruses (human neurogenin3) at a moi of 50 for 2hours at 37oC. Adenovirus-containing media was then replaced with fresh culture medium. Cells were cultured for 46h additional hours after adenovirus removal

tag: mPAC (Murine Pancreatic Adenocarcinoma) clone L20 derived from pancreatic islets from juvenile mice (2-week old) infected with a retrovirus carrying the polyomavirus middle T oncogene (Yoshida, T. and Hanahan, D. Murine pancreatic ductal adenocarcinoma produced by in vitro transduction of polyoma middle T oncogene into the islets of Langerhans. Am J Pathol 145, 671-684 , 1994)

source_name: mPAC cells + beta-galactosidase exp # 1a

treatment_protocol: 24h after seeding mPAC cells onto 6-well plates (500,000 cells/well), cells were treated with recombinant adenoviruses (betagtalactosidase) at a moi of 50 for 2hours at 37oC. Adenovirus-containing media was then replaced with fresh culture medium. Cells were cultured for 46h additional hours after adenovirus removal


title: mPAC cells + neuroD1 vs bgal expt # 4

source_name: mPAC cells + neuroD1 Expt # 4

treatment_protocol: 24h after seeding mPAC cells onto 6-well plates (500,000 cells/well), cells were treated with recombinant adenoviruses (mouse neuroD1) at a moi of 50 for 2hours at 37oC. Adenovirus-containing media was then replaced with fresh culture medium. Cells were cultured for 46h additional hours after adenovirus removal

source_name: mPAC cells + beta-galactosidase expt #4


title: Testosterone treated, HIV-1 positive male, day 14 (4)

description: Sample collected 14d post treatment


title: mPAC cells + neurogenin3 vs bgal expt # 3

source_name: mPAC cells + neurogenin3 expt #3

extract_protocol: 350ul of lysis buffer +B-mercaptoethanol lysis buffer was added to each well. Three independent wells per adenovirus treatment were combined into a single tube. Total RNA was extracted following RNeasy kit protocol (Qiagen). RNA samples were treated with RNase-free DNase (Qiagen) to remove contaminating genomic DNA. Purity and quantity of total RNA was assessed with spectrophotometer and ethidium bromide gel analysis

source_name: mPAC cells + beta-galactosidase expt # 3

treatment_protocol: 24h after seeding mPAC cells onto 6-well plates (500,000 cells/well), cells were treated with recombinant adenoviruses (betagalactosidase) at a moi of 50 for 2hours at 37oC. Adenovirus-containing media was then replaced with fresh culture medium. Cells were cultured for 46h additional hours after adenovirus removal


title: Heart WT 42h 48h APF rep2


title: mPAC cells + neurogenin3 vs bgal expt# 1b

hyb_protocol: Purified, labeled cDNA were pooled and resuspended in 11 µl of 3xSSC containing 0.75mg/ml polydA (Amersham ref: 27-4110-01), 25mM Hepes and 0.23 % SDS. Before hybridization, the solution was boiled for 2 min and then allowed to cool to room temperature. The solution was applied to the microarray under a cover slip, and the slide was placed in a custom hybridization chamber which was subsequently incubated for 12 to 16  hours in a water bath at 63°C. Before scanning, slides were washed in 0.6xSSC, 0.02% SDS for 1 min, and then 0.05xSSC for 1 min. Slides were dried before scanning by centrifugation at 500 rpm in a Beckman CS-6R centrifuge.

source_name: mPAC cells + neurogenin3 expt # 1b

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer´s protocol. http://www1.qiagen.com/literature/handbooks/PDF/RNAStabilizationAndPurification/FromAnimalAndPlantTissuesBacteriaYeastAndFungi/RNY_Mini/1016272HBRNY_062001WW.pdf
Briefly, 350ul of RLT+B-mercaptoethanol lysis buffer was added to each well. Three independent wells per adenovirus treatment were combined into a single tube. Total RNA was extracted following RNeasy kit protocol (Qiagen). RNA samples were treated with RNase-free DNase (Qiagen) to remove contaminating genomic DNA. Purity and quantity of total RNA was assessed with spectrophotometer and ethidium bromide gel analysis.

source_name: mPAC cells + beta-galactosidase exp # 1b

label_protocol: 15 µg of total RNA was primed by 7 ug of a dT(16) oligomer and the mixture was heated to 70°C for 10 min, and then transferred to ice. A premixed solution, consisting of 200 U Superscript II (Gibco), buffer, 100mM DTT and 0.5mM dNTP, was added to the RNA. The reaction was then incubated at 42°C for 2 hours. Nucleotides were used at thesPurified, labeled cDNA was resuspended in 11 µl of 3xSSC containing 0.75mg/ml polydA (Amersham ref: 27-4110-01), 25mM Hepes and 0.23 % SDS. e final concentrations: 0.5 mM for dATP, dCTP, and dGTP and 0.1 mM for dTTP and 0.4mM for aminoallyl-dUTP (Sigma ref: A0410). NaOH and EDTA were then added and RNA was hydrolyzed by incubation at 65°C for 15min. After neutralization using Hepes, the aminoallyl cDNA was purified using a Bio-spin6 column (BioRad, ref: 732-6002) and concentrated using Centricon-30 microconcentrators (Amicon, ref 42410). NaHCO3 pH9 was added to a final concentration of 0.05M and each cDNA was combined with an aliquot of Cy3 or Cy5 monofunctional dye ester (Amersham, ref: PA25001/2) and incubated for an hour of coupling in the dark. Dye-coupled cDNA was purified using Qiaquick column (Qiagen ref: UB300) and concentrated with a Centricon-30 microconcentrator.

treatment_protocol: 24h after seeding mPAC cells onto 6-well plates (500,000 cells/well), cells were treated with recombinant adenoviruses (B-galactosidase) at a moi of 50 for 2hours at 37oC. Adenovirus-containing media was then replaced with fresh culture medium. Cells were cultured for 46h additional hours after adenovirus removal.


title: mPAC cells + neuroD1 vs bgal expt#5

source_name: mPAC cells + neuroD1 Expt # 5

source_name: mPAC cells + beta-galactosidase expt #5


title: mPAC cells + neurogenin3 vs bgal expt # 2

source_name: mPAC cells + neurogenin3 expt #2

source_name: mPAC cells + beta-galactosidase exp # 2


title: Testosterone treated, HIV-1 positive male, day 14 (3)

description: Sample collected 14d post treatment


title: Placebo treated, HIV-1 positive male, day 14 (9)

description: Sample collected 14d post treatment


title: mPAC cells + neuroD1 vs bgal expt# 3

source_name: mPAC cells + neuroD1 expt # 3

source_name: mPAC cells + beta-galactosidase exp # 3


title: Heart WT 42h 48h APF rep1

tag: Biological replicate n°1


title: Heart WT 24h 27h APF rep2

tag: Strain


title: Testosterone treated, HIV-1 positive male, day 14 (2)

description: Sample collected 14d post treatment


title: Placebo treated, HIV-1 positive male, day 14 (6)

description: Sample collected 14d post treatment


title: Heart WT 36h 42h APF rep2


title: Placebo treated, HIV-1 positive male, day 14 (3)

description: Sample collected 14d post treatment


title: Heart WT 48h 21h APF rep1


title: Placebo treated, HIV-1 positive male, day 14 (7)

description: Sample collected 14d post treatment


title: Heart WT 27h 30h APF rep2


title: Placebo treated, HIV-1 positive male, day 14 (5)

description: Sample collected 14d post treatment


title: Heart WT 36h 42h APF rep1


title: Placebo treated, HIV-1 positive male, day 14 (4)

description: Sample collected 14d post treatment


title: Heart WT 33h 36h APF rep1


title: Placebo treated, HIV-1 positive male, day 14 (8)

description: Sample collected 14d post treatment


title: A549 LKB-KD-3% oxygen

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

description: Agilent

hyb_protocol: Agilent

scan_protocol: Agilent

data_processing: Lowess Normalization

label: A549 LKB-KD-3% oxygen

source_name: A549 LKB-KD-3% oxygen

label_protocol: Agilent

extract_protocol: A549 LKB-KD-3% oxygen

tag: A549 LKB-KD-3% oxygen

label: Common Reference

source_name: Common Reference

extract_protocol: Common Reference

tag: common reference


title: Heart WT 30h 33h APF rep2


title: Heart WT 30h 33h APF rep1


title: Placebo treated, HIV-1 positive male, day 14 (1)

description: Sample collected 14d post treatment

source_name: Percutaneous biopsies of vastus lateralis


title: Placebo treated, HIV-1 positive male, day 14 (2)

description: Sample collected 14d post treatment


title: Heart WT 24h 27h APF rep1


title: Heart WT 21h 24h APF rep1


title: Heart WT 27h 30h APF rep1


title: Testosterone treated, HIV-1 positive male, day 14 (1)

description: Sample collected 14d post treatment


title: Heart WT 21h 24h APF rep2


title: mPAC cells + neurogenin3 vs bgal expt # 4

source_name: mPAC cells + neurogenin3 expt #4


title: Heart WT 33h 36h APF rep2


title: A549 LKB1-WT-3% oxygen

description: Agilent

label: A549 LKB1-WT-3% oxygen

source_name: A549 LKB1-WT-3% oxygen

extract_protocol: A549 LKB1-WT-3% oxygen

tag: A549 LKB1-WT-3% oxygen


title: Normal T-cells, CD3+, donor 5

status: Public on Aug 27 2007

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Gene expression data from immunomagnetically purified CD3+ normal donor derived peripheral blood cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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 1000.

source_name: CD3-purified cells from normal peripheral blood sample. >95% purity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 13.5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: mononuclear cells were isolated from fresh peripheral blood samples (Lyphoprep, Invitrogen, Karlsruhe, Germany). CD3-positive cells were enriched employing anti-CD3 magnetic microbeads (MIdiMACS, Miltenyi, Bergisch-Gladbach, Germany)

tag: Karyotype

value: normal

tag: Age

value: unknown

tag: Gender


title: Normal T-cells, CD3+, donor 6


title: A549 LKB1-WT-21% oxygen

description: Agilent

label: A549 LKB1-WT-21% oxygen

source_name: A549 LKB1-WT-21% oxygen

extract_protocol: A549 LKB1-WT-21% oxygen

tag: A549 LKB1-WT-21% oxygen


title: Normal T-cells, CD3+, donor 7


title: Normal T-cells, CD3+, donor 4


title: Normal T-cells, CD3+, donor 8


title: Normal T-cells, CD3+, donor 3


title: Normal T-cells, CD3+, donor 1


title: T-cell prolymphocytic leukemia, no inv(14)(q11q32), case 8

description: Gene expression data from a highly purified inv(14)-negative T-PLL blood sample

source_name: CD3-purified cells from T-PLL peripheral blood sample. >95% purity

value: 62 years

value: male


title: Normal T-cells, CD3+, donor 2


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 5

description: Gene expression data from a highly purified inv(14)-positive T-PLL blood sample

value: 74 years

value: female


title: Normal Colon 4 Crypt vs. common reference

first: Xin

last: Chen

institute: UCSF

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59034.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 5560; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:34:21; Parameter PMT Volts = 500; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 95062; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:34:21; Parameter PMT Volts = 840; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 94878; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.37; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: SRF

label_protocol: not provided

extract_protocol: not provided

tag: SRF

tag: LabeledExtract


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 2

value: 54 years


title: Normal Colon 8 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59050.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.38; Parameter Scan Time = 09:56:49; Parameter PMT Volts = 520; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.38; Parameter Scan Time = 09:56:49; Parameter PMT Volts = 720; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94655; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 4

value: 90 years


title: Normal Colon 6 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59053.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 11:30:03; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94625; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 11:30:03; Parameter PMT Volts = 670; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94458; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 3

value: 72 years


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 1

value: 49 years


title: Normal Colon 9 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59047.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 11:42:24; Parameter PMT Volts = 480; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 95070; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 11:42:24; Parameter PMT Volts = 920; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 94886; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 7 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59044.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1550, 6000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 11:24:53; Parameter PMT Volts = 520; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 95137; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 11:24:53; Parameter PMT Volts = 880; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 94953; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 5 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59036.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:09:56; Parameter PMT Volts = 430; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 95122; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:09:56; Parameter PMT Volts = 950; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 94937; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.35; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Seasonal bud dormancy Sep vs Oct 2002

status: Public on Aug 24 2007

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Probes were mixed and freeze dried. Pelet was resuspended in 26.4 ul water, 7.65 ul 20XSSC. 7.2 ul 2 % SDS, and 3.75 ul Yeast tRNA (2ug/ul). Probe was heated to 95 C for 5 minutes and placed on array with coverslip. Array was hybridized ON at 60 C.

scan_protocol: An AFFY 428 scanner with Jaguar image analysis software was used.

data_processing: GeneMathsXT program was used to log transform and then loess normalize the intensity ratio.

organism: Euphorbia esula

source_name: Crown buds Sep 2002

label_protocol: 2-step labeling protocol using 30ug total RNA with the invitrogen ARES alexafluor kit.

growth_protocol: Plants were grown in garden plots between greenhouses

extract_protocol: Buds were harvested into liquid nitrogen and ground with a mortar and pestle. RNA was extracted using the pinetree extraction protocol (Chang et al 1993).

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Sep 2002 in Fargo ND.

source_name: Crown buds Oct 2002

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2002 in Fargo ND.


title: Seasonal bud dormancy Sep vs Oct 2006

source_name: Crown buds Sep 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Sep 2006 in Fargo ND.

source_name: Crown buds Oct 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2006 in Fargo ND.


title: Normal Colon 2 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56362.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5230; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 11:03:42; Parameter PMT Volts = 470; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 92110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 11:03:42; Parameter PMT Volts = 850; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 91944; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified SRF

tag: amplified SRF


title: Seasonal bud dormancy Sep vs Oct 2004

source_name: Crown buds Sep 2004

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Sep 2004 in Fargo ND.

source_name: Crown buds Oct 2004

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2004 in Fargo ND.


title: Normal Colon 8 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59049.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1580, 5750; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.41; Parameter Scan Time = 10:04:53; Parameter PMT Volts = 560; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94847; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.41; Parameter Scan Time = 10:04:53; Parameter PMT Volts = 700; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94663; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 1 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56053.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 500; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 92023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 800; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 91857; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.31; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: Amp SRF

tag: Amp SRF


title: Normal Colon 7 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59040.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5370; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 11:17:47; Parameter PMT Volts = 450; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 95129; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 11:17:47; Parameter PMT Volts = 950; Parameter Scan Date = 2005-01-31; Parameter Pixel Size = 10; Parameter Laser on time = 94945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 6 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59052.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 11:09:37; Parameter PMT Volts = 570; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94604; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 11:09:37; Parameter PMT Volts = 710; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94437; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.37; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 3 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56056.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 11:44:10; Parameter PMT Volts = 500; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 92039; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 11:44:10; Parameter PMT Volts = 810; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 91872; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.33; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 1 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56356.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 10:55:16; Parameter PMT Volts = 510; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 92101; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 10:55:16; Parameter PMT Volts = 790; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 91935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 9 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59054.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 5280; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 11:38:50; Parameter PMT Volts = 560; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94634; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 11:38:50; Parameter PMT Volts = 710; Parameter Scan Date = 2005-01-21; Parameter Pixel Size = 10; Parameter Laser on time = 94467; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 2 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56055.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 11:35:55; Parameter PMT Volts = 500; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 92031; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 11:35:55; Parameter PMT Volts = 750; Parameter Scan Date = 2004-10-01; Parameter Pixel Size = 10; Parameter Laser on time = 91864; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.30; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 3 Crypt vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56350.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5040; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.40; Parameter Scan Time = 11:12:15; Parameter PMT Volts = 490; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 92118; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.40; Parameter Scan Time = 11:12:15; Parameter PMT Volts = 800; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 91951; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Seasonal bud dormancy Sep vs Aug 2005

source_name: Crown buds Sep 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Sep 2005 in Fargo ND.

source_name: Crown buds Aug 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Aug 2005 in Fargo ND.


title: Normal Colon 5 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59035.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 11:49:13; Parameter PMT Volts = 500; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 95077; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 11:49:13; Parameter PMT Volts = 860; Parameter Scan Date = 2005-01-28; Parameter Pixel Size = 10; Parameter Laser on time = 94893; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: Normal Colon 4 Top vs. common reference

description:
Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59048.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.38; Parameter Scan Time = 09:49:22; Parameter PMT Volts = 520; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.38; Parameter Scan Time = 09:49:22; Parameter PMT Volts = 720; Parameter Scan Date = 2005-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 94647; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen


title: WT Liver RNA vs. DKO Liver RNA (-) mixed

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.    For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.    Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).

data_processing: Agilent Feature Extraction, log2ratio of normalized Knockout/Wildtype

source_name: WT liver

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

extract_protocol:
Tissues were then homogenized in 4 ml RLT solution in presence of b-mercaptoethanol with a polytron PT 3000 (Brinkmann Instruments, Westbury, NY). The homogenate was loaded into a QIAshredder column (Qiagen, Valencia, CA) and centrifugated at 12,000 x g for 3 min. The supernatant was collected and one volume 50% ethanol added. The mixture was then loaded onto an RNeasy midi column and RNA isolated following the manufacturer’s instructions (Qiagen). The quality and integrity of the RNA was assessed by bioanalyzer (Agilent, Santa Clara, CA) and agarose gel electrophoresis. For each condition, equal amounts of total RNA from several mice were pooled
Tissues were then homogenized in 4 ml RLT solution in presence of b-mercaptoethanol with a polytron PT 3000 (Brinkmann Instruments, Westbury, NY). The homogenate was loaded into a QIAshredder column (Qiagen, Valencia, CA) and centrifugated at 12,000 x g for 3 min. The supernatant was collected and one volume 50% ethanol added. The mixture was then loaded onto an RNeasy midi column and RNA isolated following the manufacturer’s instructions (Qiagen). The quality and integrity of the RNA was assessed by bioanalyzer (Agilent, Santa Clara, CA) and agarose gel electrophoresis. For each condition, equal amounts of total RNA from several mice were pooled

tag: knockout

source_name: RORalpha and gamma DKO liver

treatment_protocol:
The C57/BL6 and AKR/J mice used in the study were maintained on a constant 12 h light:12 h dark cycle with the light cycle beginning at 6 AM. The animals were bred at NIEHS and were supplied ad libitum with NIH-A31 formula and water. Tissues were rapidly dissected and parts either processed in RNA later solution (Ambion, Austin, TX) or flash frozen in liquid nitrogen.
The C57/BL6 and AKR/J mice used in the study were maintained on a constant 12 h light:12 h dark cycle with the light cycle beginning at 6 AM. The animals were bred at NIEHS and were supplied ad libitum with NIH-A31 formula and water. Tissues were rapidly dissected and parts either processed in RNA later solution (Ambion, Austin, TX) or flash frozen in liquid nitrogen.

tag: wildtype


title: WT Liver RNA vs. DKO Liver RNA mixed

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).

extract_protocol: Tissues were then homogenized in 4 ml RLT solution in presence of b-mercaptoethanol with a polytron PT 3000 (Brinkmann Instruments, Westbury, NY). The homogenate was loaded into a QIAshredder column (Qiagen, Valencia, CA) and centrifugated at 12,000 x g for 3 min. The supernatant was collected and one volume 50% ethanol added. The mixture was then loaded onto an RNeasy midi column and RNA isolated following the manufacturer’s instructions (Qiagen). The quality and integrity of the RNA was assessed by bioanalyzer (Agilent, Santa Clara, CA) and agarose gel electrophoresis. For each condition, equal amounts of total RNA from several mice were pooled


title: Seasonal bud dormancy Oct vs Sep 2003

source_name: Crown buds Oct 2003

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2003 in Fargo ND.

source_name: Crown buds Sep 2003

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Sep 2003 in Fargo ND.


title: Seasonal bud dormancy Oct vs Nov 2004

source_name: Crown buds Nov 2004

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2004 in Fargo ND.


title: Seasonal bud dormancy Oct vs Nov 2002

source_name: Crown buds Nov 2002

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2002 in Fargo ND.


title: Seasonal bud dormancy Oct vs Sep 2005

source_name: Crown buds Oct 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2005 in Fargo ND.


title: Seasonal bud dormancy Sep vs Aug 2003

source_name: Crown buds Aug 2003

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Aug 2003 in Fargo ND.


title: Seasonal bud dormancy Nov vs Oct 2003

source_name: Crown buds Nov 2003

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2003 in Fargo ND.


title: Seasonal bud dormancy Nov vs Dec 2004

source_name: Crown buds Dec 2004

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Dec 2004 in Fargo ND.


title: Seasonal bud dormancy Oct vs Nov 2006

source_name: Crown buds Oct 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2006 in Fargo ND.

source_name: Crown buds Nov 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2006 in Fargo ND.


title: WT Liver RNA vs. DKO Liver RNA (-) males 4


title: WT Liver vs. RORgamma KO Liver males 1

source_name: RORgamma KO liver


title: Normal primary thyroid cells, thyroid #3, combined IFN-gamma and IL1-beta treatment

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

source_name: thyroid

label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Normal primary thyroid cells, combined IFN-gamma and IL1-beta treatment


title: Normal primary thyroid cells, thyroid #3, IFN-gamma treatment

tag: Normal primary thyroid cells, IFN-gamma treatment


title: Normal primary thyroid cells, thyroid #1, combined IFN-gamma and IL1-beta treatment


title: Normal primary thyroid cells, thyroid #2, IL1-beta treatment

tag: Normal primary thyroid cells, IL1-beta treatment


title: Normal primary thyroid cells, thyroid #2, IFN-gamma treatment


title: Seasonal bud dormancy Nov vs Dec 2002

source_name: Crown buds Dec 2002

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Dec 2002 in Fargo ND.


title: WT Liver RNA vs. DKO Liver RNA males 2


title: Seasonal bud dormancy Dec vs Nov 2005

source_name: Crown buds Dec 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Dec 2005 in Fargo ND.

source_name: Crown buds Nov 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2005 in Fargo ND.


title: WT Liver vs. RORgamma KO Liver (-) males 1

source_name: WT liver

tag: knockout

tag: wildtype


title: Normal primary thyroid cells, thyroid #3, IL1-beta treatment


title: WT Liver RNA vs. DKO Liver RNA males 4

source_name: RORalpha and gamma DKO liver


title: Seasonal bud dormancy Dec vs Aug 2004

tag: Crown buds of leafy spurge collected in Dec 2004 in Fargo ND.

source_name: Crown buds Aug 2004

tag: Crown buds of leafy spurge collected in Aug 2004 in Fargo ND.


title: Normal primary thyroid cells, thyroid #2, combined IFN-gamma and IL1-beta treatment


title: Normal primary thyroid cells, thyroid #2, control treatment

tag: Normal primary thyroid cells, control (vehicle) treatment


title: Seasonal bud dormancy Nov vs Oct 2005

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Oct 2005 in Fargo ND.


title: Seasonal bud dormancy Dec vs Aug 2006

source_name: Crown buds Dec 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Dec 2006 in Fargo ND.

source_name: Crown buds Aug 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Aug 2006 in Fargo ND.


title: Normal primary thyroid cells, thyroid #1, IFN-gamma treatment


title: Seasonal bud dormancy Dec vs Nov 2003

source_name: Crown buds Dec 2003

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Dec 2003 in Fargo ND.

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2003 in Fargo ND.


title: Normal primary thyroid cells, thyroid #3, control treatment


title: Seasonal bud dormancy Nov vs Dec 2006

tag: Crown buds of leafy spurge (Biotype 1984-ND001) collected in Nov 2006 in Fargo ND.


title: Normal primary thyroid cells, thyroid #4, combined IFN-gamma and IL1-beta treatment

tag: Normal primary thyroid cells, combined IFN-gamma and IL1-beta treatment


title: Normal primary thyroid cells, thyroid #5, control treatment


title: WT Liver vs. RORalpha KO Liver (-) males 3

source_name: RORalpha KO liver


title: Normal primary thyroid cells, thyroid #5, IFN-gamma treatment

tag: Normal primary thyroid cells, IFN-gamma treatment


title: Normal primary thyroid cells, thyroid #4, IL1-beta treatment

tag: Normal primary thyroid cells, IL1-beta treatment


title: Normal primary thyroid cells, thyroid #1, IL1-beta treatment


title: Seasonal bud dormancy Aug vs Dec 2005

source_name: Crown Buds Aug 05

tag: Crown buds of leafy spurge collected on Aug 2005 Fargo ND

source_name: Crown Buds Dec 05

tag: Crown buds of leafy spurge collected in Dec Fargo ND.


title: WT Liver vs. RORalpha KO Liver  males 3


title: Normal primary thyroid cells, thyroid #5, IL1-beta treatment


title: Leafy spurge leaf cy5 vs cassava leaf cy3

hyb_protocol: Mixed labeled cDNAs were freeze dried. Resuspend in 26.4 ul H2O, 7.65 ul 20 X SSC, 7.2 ul 2% SDS, and 3.75 ul yeast tRNA (2ug/ul). Incubated 95 C for 5 minutes, and briefly spun. Placed on chip and covered with cover slip. Hybridized over night in the dark at 60 C. cover slide removed by placing side upside down in 150 ml beaker containing 2XSSC/0.1%SDS for 5 min. Washed 2X in 0.1XSSC/0.1%SDS 5 minutes each and then 2X in 0.1XSSC 5 min each. Spun dry (2k for 2 min is usually sufficient) and scaned.

scan_protocol: Arrays were scanned using an Affy428 scanner and Jaguar software.

data_processing: Raw signal intensities were log transformed and loess normalized using GeneMaths XT software (no background subtraction). The A-values (square root of the product of the log2 of the intensities for both channels) were calculated for each spot. Empty spots, non plant controls, and spots that had A-values of less than the average plus 2 standard deviations of the A-values of the empty spots were deleted from the data set.

source_name: leafy spurge leaf

label_protocol: Labeled cDNA was prepared from 30 ug of total RNA with the use of the Alexa Fluor cDNA labeling kit2 according to manufacture’s protocols.

growth_protocol: Greenhouse grown in 2" cone-tainers, 16 hr day, well watered, collected during day.

extract_protocol: pine tree extraction method (Chang et al. 1993).

treatment_protocol: No treatment

tag: mature leaf from Biotype 1984-ND001

organism: Manihot esculenta

source_name: cassava leaf

growth_protocol: Greenhouse grown in large pots, 16 hr day, well watered, collected during day.

tag: mature leaf from variety TME117


title: Castorbean leaf cy5 vs poinsettia leaf cy3

organism: Ricinus communis

source_name: castorbean leaf

growth_protocol: Greenhouse grown in pots, 16 hr day, well watered, collected during day.

tag: mature leaf

organism: Euphorbia pulcherrima

source_name: Poinsettia leaf

tag: mature leaf from store bought plant


title: Seasonal bud dormancy Aug vs Sep 2006

tag: Crown buds of leafy spurge collected in Aug 2006 in Fargo ND.

source_name: Crown buds Sep 2006

tag: Crown buds of leafy spurge collected in Sep 2006 in Fargo ND.


title: Poinsettia leaf cy5 vs castorbean leaf cy3

source_name: mature poisettia leaf

tag: mature leaf from store-bought plant

source_name: mature castorbean leaf


title: Wild type Kidney C d14 biological rep1	 82

status: Public on Aug 23 2007

city: Konstanz

first: Daniel

last: Dietrich

address: Jakob-Burckhardt-Str. 25

department: Environmental Toxicology

institute: University of Konstanz

description: total RNA from kidney cortex and outer medulla

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA

scan_protocol: The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)

data_processing: Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d14_biological replicate1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix, USA; GeneChip® Expression Analysis, GeneChip sample Cleanup Module, 701194 Rev.1)

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Midi Kit (Qiagen, Cat No. 75144)

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.

tag: Genotype

value: wild type

tag: Gender

tag: Age

value: 10-14 weeks


title: Wild type Kidney C d7 biological rep3	 81

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d7_biological replicate 3

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: WT Liver RNA vs. DKO Liver RNA (-) males 2

source_name: WT liver

tag: knockout

source_name: RORalpha and gamma DKO liver

tag: wildtype


title: Normal primary thyroid cells, thyroid #4, IFN-gamma treatment

source_name: thyroid


title: Seasonal bud dormancy Aug vs Dec 2003

scan_protocol: An AFFY 428 scanner was used with cy5 channel set to 65 and Cy3 channel set to 60.

extract_protocol: Buds were harvested into liquid nitrogen and ground with a mortar and pestle. RNA was extracted using the pinetree extraction protocol.

tag: Crown buds of leafy spurge collected on Aug 11, 2003 in Fargo ND.

tag: Crown buds of leafy spurge collected on Dec 1, 2003 in Fargo ND.


title: Normal primary thyroid cells, thyroid #1, control treatment

tag: Normal primary thyroid cells, control (vehicle) treatment


title: Seasonal bud dormancy Aug vs Sep 2002

scan_protocol: An AFFY 428 scanner with Jaguar image analysis software was used.

source_name: Crown buds Aug 2002

tag: Crown buds of leafy spurge collected in Aug 2002 in Fargo ND.

source_name: Crown buds Sep 2002

tag: Crown buds of leafy spurge collected in Sep 2002 in Fargo ND.


title: Normal primary thyroid cells, thyroid #4, control treatment


title: Normal primary thyroid cells, thyroid #5, combined IFN-gamma and IL1-beta treatment

tag: Normal primary thyroid cells, combined IFN-gamma and IL1-beta treatment


title: Cassava leaf cy5 vs leafy spurge leaf cy3

tag: mature leaf from variety TME117

tag: mature leaf from Biotype 1984-ND001


title: Wild type Kidney C d14 biological rep3	 84

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d14_biological replicate3


title: O103 no.6 (strain PMK5) replicate 1

type: genomic

city: Kiyotake

first: Yoshitoshi

last: Ogura

state: Miyazaki

address: Kihara 5200

department: Frontier science reserch center

country: Japan

institute: University of Miyazaki

hyb_protocol: The Cy5-labeled and the Cy3-labeled DNA preparations (15 µl for each) were mixed with a 90-µl hybridization solution containing 6.4 x SSC, 0.64 % sodium dodecyl sulfate (SDS), and 1.3 mg/ml  yeast tRNA.  After incubation at 96ºC for 2 min, the denatured sample was applied to a microarray slide and incubated on an ArrayBooster hybridization apparatus (Advalytix AG, Brunnthal, Germany) at 50ºC for 16 h.  The slide was then washed twice in 2x SSC/0.2% SDS at room temperature for 10 min, twice in 0.2x SSC/0.2% SDS at 50ºC for 5 min, and twice in 0.2x SSC at room temperature for 10 min.  Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Scanned with a FLA-8000 scanner (Fuji Photofilm, Tokyo, Japan).  The obtained data were analyzed by the ArrayVision 8.0 software (Imaging Research).

data_processing: Spots with reference signal intensities lower than the local background (LBG)  plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG.

molecule: genomic DNA

organism: Escherichia coli

source_name: Genomic DNA from O111 strain PMK5

label_protocol: First, 3 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen).  DNAs were not sheared or digested by restriction enzymes prior to the labeling.  The aminoallyl-labeled DNA was purified by Microcon YM-30 (Millipore), dried in a speed-vac, and resuspended in 10 µl of 50 mM NaHCO3.  After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA.  The fluorescently labeled DNA was finally purified by the Qiaquick PCR purification kit (Qiagen) into 30 µl elution buffer provided by the manufacturer.

growth_protocol: Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium.

extract_protocol: Genomic DNA was purified using the Genomic-tip 100/G and Genomic DNA buffer set (Qiagen) according to the manufacturer's instruction.

tag: Enteroheamorragic E. coli

source_name: O157 strain Sakai


title: Wild type Kidney C d7 biological rep2	 80

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d7_biological replicate 2


title: Wild type Kidney C d14 biological rep2	 83

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d14_biological replicate2


title: O103 no.5 (strain 12009) replicate 2

source_name: Genomic DNA from O111 strain 12009


title: Seasonal bud dormancy Dec vs Aug 2002

source_name: Crown buds Dec 2002

tag: Crown buds of leafy spurge collected in Dec 2002 in Fargo ND.


title: O103 no.4 (strain 11845) replicate 1

source_name: Genomic DNA from O111 strain 11845


title: O103 no.6 (strain PMK5) replicate 2


title: Wild type Kidney C d3 biological rep1	 76

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d3_biological replicate 1

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Wild type Kidney C d7 biological rep1	 79

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_d7_biological replicate 1


title: O103 no.5 (strain 12009) replicate 1


title: O103 no.4 (strain 11845) replicate 2


title: Wild type Kidney C d3 biological rep3	 78

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control for AA and OTA_d3_biological replicate 2


title: O103 no.3 (strain 11711) replicate 1

source_name: Genomic DNA from O111 strain 11711


title: O103 no.3 (strain 11711) replicate 2


title: Wild type Kidney C d1 biological rep2	 74

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_OTA_d1_biological replicate 2

treatment_protocol: Once Gavaged with in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Wild type Kidney C d3 biological rep2	 77

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control  for AA and OTA_biological replicate 2


title: Wild type Kidney C d1 biological rep3	 75

source_name: Kidney cortex and outer medulla_wild type_vehicle control_ for AA and OTA d1_biological replicate 3


title: Wild type Kidney C d1 biological rep1	 73

source_name: Kidney cortex and outer medulla_wild type_time mached vehicle control for AA and OTA_d1_biological replicate 1


title: O103 no.2 (strain 11117) replicate 1

source_name: Genomic DNA from O111 strain 11117


title: O103 no.2 (strain 11117) replicate 2


title: O111 no.6 (strain ED71) replicate 2

source_name: Genomic DNA from O111 strain ED71


title: O103 no.1 (strain 10828) replicate 1

source_name: Genomic DNA from O111 strain 10828


title: O103 no.1 (strain 10828) replicate 2

source_name: O157 strain Sakai


title: Wild type Kidney OTA d14 biological rep2	 71

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d14_biological replicate2

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlate


title: Wild type Kidney OTA d7 biological rep1	 67

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d7_biological replicate 1

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater


title: Wild type Kidney OTA d3 biological rep3	 66

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d3_biological replicate 2

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater


title: Wild type Kidney OTA d14 biological rep3	 72

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d14_biological replicate3


title: Wild type Kidney OTA d7 biological rep2	 68

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d7_biological replicate 2


title: Wild type Kidney OTA d14 biological rep1	 70

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d14_biological replicate1


title: O111 no.6 (strain ED71) replicate 1


title: O111 no.5 (strain 13369) replicate 2

source_name: Genomic DNA from O111 strain 13369


title: O111 no.4 (strain 11788) replicate 1

source_name: Genomic DNA from O111 strain 11788


title: O111 no.3 (strain 11619) replicate 2

source_name: Genomic DNA from O111 strain 11619


title: Wild type Kidney OTA d1 biological rep2	 62

description: total RNA from kindey cortex and outer medulla

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d1_biological replicate 2

treatment_protocol: Gavaged with one single dose OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in


title: Wild type Kidney OTA d7 biological rep3	 69

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d7_biological replicate 3


title: O111 no.3 (strain 11619) replicate 1


title: O111 no.4 (strain 11788) replicate 2


title: O111 no.5 (strain 13369) replicate 1


title: Wild type Kidney AA d7 biological rep3	 57

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA was stained using Phycoerythrin-conjugated Streptavidin

data_processing: Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity of 100.

source_name: Kidney cortex and outer medulla_wild type_AA treated_d7_biological replicate 3

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Wild type Kidney OTA d1 biological rep3	 63

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d1_biological replicate 3


title: Wild type Kidney OTA d3 biological rep2	 65


title: Wild type Kidney AA d14 biological rep1	 58

source_name: Kidney cortex and outer medulla_wild type_AA treated_d14_biological replicate1

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Wild type Kidney OTA d3 biological rep1	 64

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d3_biological replicate 1


title: Wild type Kidney AA d14 biological rep3	 60

source_name: Kidney cortex and outer medulla_wild type_AA treated_d14_biological replicate3


title: Wild type Kidney AA d7 biological rep1	 55

source_name: Kidney cortex and outer medulla_wild type_AA treated_d7_biological replicate 1


title: Wild type Kidney AA d14 biological rep2	 59

source_name: Kidney cortex and outer medulla_wild type_AA treated_d14_biological replicate2


title: Wild type Kidney OTA d1 biological rep1	 61

source_name: Kidney cortex and outer medulla_wild type_OTA treated_d1_biological replicate 1


title: O111 no.2 (strain 11128) replicate 2

source_name: Genomic DNA from O111 strain 11128

source_name: O157 strain Sakai


title: Wild type Kidney AA d3 biological rep2	 53

source_name: Kidney cortex and outer medulla_wild type_AA treated_d3_biological replicate 2

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O111 no.1 (strain 11109) replicate 2

source_name: Genomic DNA from O111 strain 11109


title: O111 no.1 (strain 11109) replicate 1


title: O111 no.2 (strain 11128) replicate 1


title: Wild type Kidney AA d1 biological rep1	 49

source_name: Kidney cortex and outer medulla_wild type_AA treated_d1_biological replicate 1

treatment_protocol: Gavaged with one single dose AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O26 no.7 (strain 13247) replicate 1

source_name: Genomic DNA from O26 strain 13247


title: Wild type Kidney AA d3 biological rep1	 52

source_name: Kidney cortex and outer medulla_wild type_AA treated_d3_biological replicate 1


title: Eker Kidney C d14 biological rep2	 47

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d14_biological replicate2

value: Eker


title: Wild type Kidney AA d1 biological rep3	 51

source_name: Kidney cortex and outer medulla_wild type_AA treated_d1_biological replicate 3


title: O26 no.6 (strain 13065) replicate 2

source_name: Genomic DNA from O26 strain 13065


title: Wild type Kidney AA d1 biological rep2	 50

source_name: Kidney cortex and outer medulla_wild type_AA treated_d1_biological replicate 2


title: Wild type Kidney AA d7 biological rep2	 56

source_name: Kidney cortex and outer medulla_wild type_AA treated_d7_biological replicate 2


title: O26 no.7 (strain 13247) replicate 2


title: Eker Kidney C d7 biological rep3	 45

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d7_biological replicate 3


title: O26 no.8 (strain ED411) replicate 1

source_name: Genomic DNA from O26 strain ED411


title: O26 no.5 (strain 12929) replicate 2

source_name: Genomic DNA from O26 strain 12929


title: Eker Kidney C d3 biological rep1	 40

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d3_biological replicate 1


title: Eker Kidney C d3 biological rep2	 41

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_biological replicate 2


title: Eker Kidney C d14 biological rep1	 46

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d14_biological replicate1


title: O26 no.6 (strain 13065) replicate 1

source_name: O157 strain Sakai


title: Eker Kidney C d7 biological rep2	 44

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d7_biological replicate 2