title: TG016_C4

status: Public on Jan 01 2009

type: RNA

city: Dayton

first: Oleg

last: Paliy

state: OH

address: 3640 Col. Glenn Hwy

country: USA

institute: Wright State University

description: Used affymetrix GeneChip Fluidics Stations to follow staining and washing protocol

hyb_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

scan_protocol: GeneChip® Scanner 3000

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4

label: biotin

molecule: total RNA

organism: Escherichia coli

source_name: E. coli K12 strain NCM3722

growth_protocol: Grown with aeration in K medium containing 10 or 20 mM glucose as described by Balaji et al., (2005) Appl Environ Microbiol 71, 8273-8283

extract_protocol: Total RNA was extracted using a hot phenol-chloroform method

treatment_protocol: E.coli grown in K medium at 43º C and harvested during mid log phase (OD=0.4-0.5)to extract RNA

tag: A wild type commensal strain


title: TG018_C6

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

treatment_protocol: E.coli grown in K medium at 43º C with added 0.3 M NaCl  and harvested during mid log phase (OD=0.4-0.5)to extract RNA. Gycine betaine (GB) was added to a final concentration of 1 mM.


title: TG09_F3

treatment_protocol: E.coli grown in K medium at 30º C with added 0.3 M NaCl  and harvested during mid log phase (OD=0.4-0.5)to extract RNA. Gycine betaine (GB) was added to a final concentration of 1 mM.


title: TG12_F6


title: TG05_E5

treatment_protocol: E.coli grown in K medium at 43º C with added 0.3 M NaCl and harvested during mid log phase (OD=0.4-0.5)to extract RNA


title: TG017_D5


title: TG04-E4


title: TG015_D3


title: TG03_E3

treatment_protocol: E.coli grown in K medium at 30º C with added 0.3 M NaCl and harvested during mid log phase (OD=0.4-0.5)to extract RNA


title: SELT-2

status: Public on Dec 25 2008

city: Taipei

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

description: Human hepatocellular carcinoma cells, namely, HuH7 were seeded. Samples were cultured in 0.1 μM sodium selenite-containing medium for 15 passages (SELT) or in serum-free medium for 30 h (SF30) or in the regular complete medium containing 10 % fetal calf serum (HUH7) for 30 h. All the samples were collected at the time indicated above. The total RNA were reverse transcried and hybridized to Human 8K-1 (Egenomix Technology Corp., Taiwan). The hybridization time and temperature was 16 h and 62℃, respectively. SELT and HUH7 samples were labeled with Cy5 while SF30 sample was labeled with Cy3. Local background correction and interchip global normalization were accomplished by GenePix Pro 5.0 (Molecular Devices, Sunnyvale, CA ).  Genes with differential up- or down-regulation by 1.5 fold with respect to the SF30 cells were obtained using GeneSpring software 7.0 (Silicon Genetics, Agilent Technologies).

organism: Homo sapiens

source_name: Human hepatocellular carcinoma cells HuH7 (control or cultured with 0.1 μM sodium selenite)

tag: HuH7 were cultured in 0.1 μM sodium selenite-containing medium for 15 passages (SeLT). Total RNA was purified from cultured cells using an RNeasy kit (Qiagen, Valencia, CA).

source_name: Human hepatocellular carcinoma cells HuH7 (cultured in serum-free medium for 30 h)

tag: HuH7 were cultured in serum-free medium for 30 h (SF30). Total RNA was purified from cultured cells using an RNeasy kit (Qiagen, Valencia, CA).


title: TG013_F1

treatment_protocol: E.coli grown in K medium at 30º C and harvested during mid log phase (OD=0.4-0.5)to extract RNA


title: SELT-1

data_processing: Local background correction and interchip global normalization were accomplished by GenePix Pro 5.0 (Molecular Devices, Sunnyvale, CA )

tag: HuH7 were cultured in 0.1 μM sodium selenite-containing medium for 15 passages (SELT). Total RNA was purified from cultured cells using an RNeasy kit (Qiagen, Valencia, CA).


title: MDCK_E47_2_CY5

status: Public on Dec 21 2008

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: cDNA CNIO Oncochip Array. MDCK epithelial cells transfectant hybridized against MDCK-CMV control.

hyb_protocol: All of the samples were labeled and hybridized against to reference sample (CMV control cells)

scan_protocol: After hybridization, slides were scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively, to obtain 10-m resolution image

data_processing: GenePix 6.0 - log2 ratio

organism: Canis lupus familiaris

source_name: MDCK cells

label_protocol: Three um from amplified RNA was used to generate fluorescence antisense RNAs by transcriptional synthesis using SuperScript enzyme protocol (Life Technologies).

extract_protocol: MDCK-E47_2 CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

tag: MDCK cells treated with E47

extract_protocol: MDCK-CMV CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

tag: MDCK CMV CONTROL CELLS CY3


title: HUH7-3

tag: HuH7 were cultured in the regular complete medium containing 10 % fetal calf serum (HUH7) for 30 h. Total RNA was purified from cultured cells using an RNeasy kit (Qiagen, Valencia, CA).


title: TG014_C2


title: TG11_F5


title: MDCK E22B_CY5

extract_protocol: MDCK-CONTROL CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

tag: MDCK CMV CONTROL CELLS

extract_protocol: MDCK-E22B CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

tag: MDCK E22B transfectants


title: E47_CY5_1

extract_protocol: MDCK-E47_1 CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.


title: MDCK_E47_2_CY3

tag: MDCK CMV CONTROL CELLS CY5


title: TG10_F4

treatment_protocol: E.coli grown in K medium at 43º C and harvested during mid log phase (OD=0.4-0.5)to extract RNA.


title: TG07_E1


title: MDCK_E22B_CY3


title: TG08_E2


title: TG06_E6


title: TG02_D2


title: MDCK_E22A_CY3

tag: MDCK-CMV CONTROL CELLS

tag: MDCK E22A transfectants


title: MDCK_EE2A_CY5

extract_protocol: MDCK-E22A CELLS WERE cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

tag: MDCK-CMV CONTROL CELLS CY5


title: OE-B, biological rep3

status: Public on Dec 20 2008

city: Seoul

first: Jung

last: Kwang Wook

address: Anam-dong 1-ga

country: South Korea

institute: Korea university

description: Gene expression data from unopened flowers of wild-type plant

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45? on Arabidopsis ATH1 Genome Array. After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25? followed by a stringent wash buffer at 50?. After washing, the arrays were stained with a streptavidin-phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner, controlled by GCOS Affymetrix software.

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software. For normalization, data from each expression array were scaled, so that the overall fluorescence intensity across each chip was equivalent (average target intensity set at 500). The One-Sided Wilcoxon's Signed Rank test was employed to generate the Detection p-value.

organism: Arabidopsis thaliana

source_name: LEJ1-overexpressed unopened flowers when the anthers are not yet opened.

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

growth_protocol: unopened flower buds of 5-week-old wild-type grown under LD conditions at 24?.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then purified with the RNeasy Mini kit.

tag: LEJ1-overexpressed Arabidopsis

tag: Flowers with anther stage from 1 to 12


title: OE-OF, biological rep3

source_name: LEJ1-overexpressed open flowers when anthesis occurs.

growth_protocol: open flowers of 5-week-old wild-type grown under LD conditions at 24?.

tag: Flowers with anther stage from 13 to 14


title: TG01_D1

treatment_protocol: Growth at 30 C until mid-log phase (30oC, no NaCl)


title: OE-B, biological rep2


title: KO-OF, biological rep1

source_name: lej1 open flowers when anthesis occurs.

tag: LEJ1 knock-out line (lej1)


title: WT-B, biological rep3

source_name: Arabiodopsis wild-type unopened flowers when the anthers are not yet opened.

tag: wild-type (ecotype Col-0)


title: KO-B, biological rep1

source_name: lej1 unopened flowers when the anthers are not yet opened.


title: HUH7-2


title: SELT-3


title: KO-B, biological rep2


title: KO-OF, biological rep3


title: OE-OF, biological rep2


title: KO-OF, biological rep2


title: KO-B, biological rep3


title: small airways, smoker 058

status: Public on Dec 19 2008

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ethnic group

value: black

tag: Smoking status

value: smoker, 80 pack-years


title: WT-OF, biological rep2

source_name: Arabiodopsis wild-type open flowers when anthesis occurs.


title: small airways, smoker 033

value: white

value: smoker, 15 pack-years


title: small airways, smoker 001

value: F

value: smoker, 23 pack-years


title: small airways, non-smoker 015

value: non-smoker


title: WT-OF, biological rep3


title: HUH7-1

tag: HuH7 were cultured in serum-free medium for 30 h (SF30). Total RNA was purified from cultured cells using an RNeasy kit (Qiagen, Valencia, CA).


title: small airways, non-smoker 013

value: hispanic


title: WS_CLF_Pulldown_07

type: genomic

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: Genomic DNA enriched for CLF binding sites

hyb_protocol: Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: Quantile Normalization

molecule: genomic DNA

source_name: 10-14 day old seedlings

label_protocol: The sample was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Plants were grown under 16 h light on 1/2 X MS media

extract_protocol: sample was prepared by ChIP using an antibody against GFP from a CLF-GFP line

treatment_protocol: Untreated


title: OE-OF, biological rep1


title: WS_CLF_Pulldown_08

tag: Genomic DNA enriched for CLF binding sites


title: WS_CLF_Pulldown_06


title: WS_CLF_Pulldown_05


title: WT-B, biological rep2


title: OE-B, biological rep1


title: WT-OF, biological rep1


title: small airways, early-COPD 021

value: early-COPD, 30 pack-years


title: small airways, early-COPD 045

value: early-COPD, 31 pack-years


title: small airways, smoker 044

value: smoker, 38 pack-years


title: small airways, early-COPD 012

value: early-COPD, 12 pack-years


title: small airways, smoker 049


title: small airways, COPD 020

value: COPD, GOLD-II, 20 pack-years


title: small airways, non-smoker 021


title: WT-B, biological rep1


title: small airways, smoker 027

value: smoker, 45 pack-years


title: small airways, early-COPD 054

value: early-COPD, 50 pack-years


title: small airways, early-COPD 009

value: early-COPD, 20 pack-years


title: small airways, non-smoker 005

value: M


title: small airways, early-COPD 037

value: early-COPD, 42.5 pack-years


title: small airways, early-COPD 086

value: black


title: R120G-6 month-rep6

status: Public on Dec 12 2008

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

hyb_protocol: Arrays hybridized at 42C, then washed in wash buffer at 42C, followed by washes at rooom temperature, dried with compressed air.

scan_protocol: Arrays scanned on Axon GenePix 4000A scanner at 532 and 635 nm.

data_processing: Images processed using ImaGene software, version 6.0. No BG subtraction, spots flagged as 'bad' (flag=3) removed, lowess normalized with print-tip scope using AROMA software, log(base 2) transformed, replicate spots averaged.

organism: Mus musculus

source_name: cardiac ventricle-6 month old human R120G CryAB transgenic mouse

label_protocol: C  dyes were incorporated by reverse transcription using Invitrogen Superscript II.

growth_protocol: Nontransgenic and Transgenic mice, housed in barrier facility, 12 hr dark/light cycle, 22°C, food/water ad lib.

extract_protocol: QIAGEN RNA Easy miniprep, including proteinase K and on-column DNase 1 treatment

treatment_protocol: no treatment other than cardiac specific expression of transgene (alpha-myosin heavy chain promoter)

tag: Strain

value: C57BL/6, Gender:male, Age:6 months, Tissue:cardiac

source_name: UMRR

tag: Universal Mouse Reference RNA, Stratagene


title: R120G-6 month-rep1


title: R120G-6 month-rep2


title: R120G-6 month-rep7


title: R120G-6 month-rep3


title: R120G-3 month-rep6

source_name: cardiac ventricle-3 month old human R120G CryAB transgenic mouse

value: C57BL/6, Gender:male, Age:3 months, Tissue:cardiac


title: Small airways, non-smoker 035

status: Public on Dec 16 2008

description: small airways, non-smoker

value: white


title: small airways, COPD 012

value: COPD, GOLD-II, 33 pack-years


title: small airways, non-smoker 004

value: non-smoker


title: R120G-6 month-rep4


title: R120G-6 month-rep5


title: small airways, early-COPD 064

value: early-COPD, 90 pack-years


title: R120G-3 month-rep5


title: R120G-3 month-rep3


title: R120G-3 month-rep2


title: WT-6 month-rep5

source_name: cardiac ventricle-6 month old wt human CryAB transgenic mouse


title: R120G-3 month-rep4


title: R120G-3 month-rep1


title: WT-6 month-rep6


title: WT-3 month-rep6

source_name: cardiac ventricle-3 month old wt human CryAB transgenic mouse


title: Brown Fat WT vs. Brown Fat DKO

status: Public on Dec 18 2008

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.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

data_processing: Data were retrieved with the Agilent Feature Extraction software (v7.5), using defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.  The resulting data were processed using the Rosetta Resolver® system (version 5.1) (Rosetta Biosoftware, Kirkland, WA). The Resolver system combines ratio profiles to create ratio experiments using an error-weighted average. P-values are generated and propagated throughout the system and represent the probability that a given gene is significantly expressed.  Genes with a p value less than 0.001 were considered statistically, differentially expressed.

source_name: Brown Fat WT

label_protocol: Total RNA (100 ng) from WT mice was amplified and labeled with Cy3 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture’s protocol.

extract_protocol: Total RNAs were extracted using RNeasy mini kits (Qiagen, Valencia, CA) following the manufacturer’s instructions. The quality of the purified RNA was determined by agarose gel and using a BioAnalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Interscapular brown adipose tissue was isolated from 4 C57BL/6 WT male mice (2-3 months old) around circadian time 20.

source_name: Brown Fat DKO

label_protocol: Total RNA (100 ng) from DKO mice was amplified and labeled with Cy5 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture’s protocol.

treatment_protocol: Interscapular brown adipose tissue was isolated from 4 C57BL/6 RORa-/- RORg-/- male mice (2-3 months old) around circadian time 20.

value: RORa-/- RORg-/- C57BL/6, Gender:Male, Age:2-3 months, Tissue:Interscapular brown adipose tissue


title: WT-6 month-rep1


title: Control-6 month-rep5

source_name: cardiac ventricle-6 month old nontransgenic mouse


title: WT-6 month-rep2


title: WT-3 month-rep5


title: WT-3 month-rep3


title: WT-3 month-rep1


title: Brown Fat DKO vs. Brown Fat WT

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: Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.

label_protocol: Total RNA (100 ng) from DKO mice was amplified and labeled with Cy3 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture’s protocol.

label_protocol: Total RNA (100 ng) from WT mice was amplified and labeled with Cy5 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture’s protocol.

value: C57BL/6, Gender:Male, Age:2-3 months, Tissue:Interscapular brown adipose tissue


title: Control-6 month-rep3


title: WT-6 month-rep4


title: WT-3 month-rep2


title: Control-6 month-rep4


title: WT-6 month-rep3


title: Control-6 month-rep1


title: Control-6 month-rep2


title: WT-3 month-rep4


title: Control-3 month-rep3

source_name: cardiac ventricle-3 month old nontransgenic mouse


title: 14028_Promoterlibmix_stable+unstable_sort2_mouseTumor(+)(-)(+)_115249_1

type: other

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Date of Scan Jul 12 2007

hyb_protocol: overnight hyb on Nimblegen custom made whole genome slides at 42°C in water bath

scan_protocol: Axon scanner, image acquisition with GenePix 4000B software, spot quantification using NimbleScan 2.0 software

data_processing: used ONLY SalmP probes of the array for processing, normalized based on total signal of all SalmP probes for each channel, VALUE data obtained from log of normalized ch1/ch2 signal.

molecule: other

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 14028s Promoterlibmix_stable+unstable, sort2, GFP(+) in human PC3 tumors of nude mouse, GFP(-) in LBAmp, GFP(+) in human PC3 tumors of nude mouse

label_protocol: incorporation of dye using Klenow enzyme and Cy3-endlabeled nonamers

extract_protocol: plasmid extraction from recovered clones, followed by PCR amplification of plasmid inserts (Taq DNA Pol)

tag: Salmonella typhimurium 14028s mix of promoter libraries of stable and unstable GFP variants (180,000 clones), sort2

value: GFP(+) cells recovered from human PC3 tumors 2 days after IT injection of 10^7 into tumors of five nude mice, then GFP(-) cells recovered from overnight growth in LB Amp, then GFP(+) cells recovered from human PC3 tumors 2 days after IT injection of 10^7 into tumors of five nude mice

source_name: 14028s Promoterlibmix_stable+unstable

label_protocol: incorporation of dye using Klenow enzyme and Cy5-endlabeled nonamers


title: Control-3 month-rep4


title: 14028_Promoterlibmix_stable+unstable_sort1_mouseTumor(+)(-)(+)_115249_2

description: Date of Scan Sep 05, 2007

source_name: 14028s Promoterlibmix_stable+unstable, sort1: GFP(+) in human PC3 tumors of nude mouse, GFP(-) in LBAmp, GFP(+) in human PC3 tumors of nude mouse

tag: Salmonella typhimurium 14028s mix of promoter libraries of stable and unstable GFP variants (180,000 clones), sort1


title: GGS27_BR1_2S_12896678annot_MDS_MDS.tav.refIsIA.out

status: Public on Dec 09 2008

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: Information covered in other sections

hyb_protocol: Prehybridization: 1. Prepare prehybridization buffer containing 5x SSC, 0.1% SDS and 1% bovine serum albumin. Place slides to be analyzed into a Coplin jar  fill with prehybridization buffer, and incubate at 42 degree Celsius for 45 minutes. 2. Wash slides in distilled water 4-8 times to remove excess prehybridization buffer. 3. Dip the slides in room temperature isoproponol 10 times and dry in slide spinner. 4. Slides should be used immediately following prehybridization. We have found that hybridization efficiency decreases rapidly if the slides are allowed to dry for more than one hour. Hybridization: 1. Resuspend the probe in 70ul hybridization buffer (50% formamide, 5x SSC, 1mg/ml salmon sperm DNA, syringe filtered). 2. Incubate at 98 degree Celsius for 15 minutes to resuspend as much probe as possible and spin for 5 minutes at maximum angular velocity to collect any remaining solid at the bottom of the tube. 3. Place a polyethylene hydrophobic lifterslip on each prehybridized slide so that it covers the array. 4. Apply the probe to one end of the coverslip and allow capillary action to draw the liquid through to cover the whole array.  Place the slide in a sealed hybridization chamber, add 20 ul of 20x SSC to the chamber at each end of the slide. 5. Place the sealed chamber in a 42 degree Celsius water bath and incubate for a minimum 18-20 hours. 6. Remove the array from the hybridization chamber, taking care not to disturb the coverslip. 7. Place the slide in a staining dish with low-stringency wash buffer containing 1x SSC and 0.2% SDS at 42 degree Celsius. 8. Gently remove the coverslip while the slide is in solution and agitate for 2-4 minutes. Wash again in 1xSSC and 0.2% SDS for 2-4 minutes. 9. Wash the slide twice at high-stringency in a staining dish containing 0.1x SSC and 0.2% SDS at room temperature, agitating for 2-4 minutes. 10. Wash the slide twice in 0.1x SSC, agitating for 2-4 minutes. 11. Provide one final wash by dipping each slide 6-7 times in a 0.05x SSC solution immediately prior to drying. 12. Dry the slide in a slide spinner.

scan_protocol: Slides were promptly scanned post-hybridization at a 10 um resolution using an Axon 4000B scanner with GenePix 4.0 software. PMT values were optimized during scanning to balance channel intensities.

data_processing: Processing of 16-bit TIFF images from hybridized arrays were produced using the TIGR TM4 package (www.tm4.org). Intensity values for Cy3 and Cy5 channels were obtained using TIGR-Spotfinder software. Normalization was performed using the LOWESS algorithm available in TIGR-MIDAS using block mode and a smooth parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis and replicate reporter intensities on one slide (one technical replicate) were reduced to a single value by computing the geometric mean.

organism: Geobacter sulfurreducens

source_name: Geobacter sulfurreducens strain DL1 cell cultures in chemostats under conditions of acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor

label_protocol: cDNA was labeled from total RNA with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5) via an indirect coupling method. First cDNA was synthesized from total RNA with aminoallyl-dUTP incorporated into the first strand cDNA to which Cy-3 and Cy-5 fluorescent dye molecules are subsequently coupled.

growth_protocol: General growth conditions of the G. sulfurreducens DL1 cells were that they were cultured anaerobically in chemostats.  Two growth conditions were tested. In the first, the electron donor (acetate 5mM) was limiting and fumarate was the electron acceptor. In the second condition, acetate as sole electron donor was provided in excess and fumarate was the limiting substrate. A dilution rate of 0.05 per hour was used for all chemostats. Additional details concerning the growth of G. sulfurreducens are given in the following reference: Esteve-Nunez, A., M. Rothermich, M. Sharma, and L. D. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.

extract_protocol: Total RNA was extracted as previously described by first mechanically disrupting cells using a FastPrep instrument (Qbiogene, Carlsbad, CA) with Lysing Matrix B (Qbiogene, Carlsbad, CA), followed by nucleic acid extraction with TRIzol reagent (Invitrogen, Carlsbad, CA) (a monophasic solution of phenol and guanidine isothiocyanate) (Methe et al. 2005). Any residual DNA was removed using RNase-free DNase according to the manufacturer’s instructions  (Ambion, Austin, TX), and treated RNA was subsequently cleaned and concentrated with RNeasy minicolumns (QIAGEN Inc., Valencia, CA). The quality of total RNA was assessed by agarose-formaldehyde gel electrophoresis and the oncentration determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: G. sulfurreducens was anaerobically cultured in chemostats under two conditions: 1) in which acetate was the sole electron donor and the limiting growth substrate, and fumarate was the sole electron acceptor and 2) acetate was the sole electron donor and supplied in excess while fumarate was the sole electron acceptor and the substrate that limited growth.

tag: Strain DL1, grown under steady state conditions in chemostats

tag: Reference

source_name: Geobacter sulfurreducens strain DL1 cell cultures in chemostats under conditions of acetate was supplied in excess with fumarate supplied as the sole electron acceptor and limiting factor

tag: Query


title: Control-3 month-rep1


title: Time: Processed Normally, Treatment: Control, Type: Radical Prostatectomy (030025_PR)

status: Public on Dec 01 2008

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Human Prostate 030025_PR from Human hybridized against Reference

hyb_protocol: We prepared and hybridized spotted cDNA microarrays as previously described (Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563- 571, 2005)  using RNA from a single batch of reference standard for each hybridization.

scan_protocol: Fluorescence array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA), and GenePix Pro 4.1 software was used to grid and extract image intensity data.

data_processing: Spots of poor quality, as determined by visual inspection, were removed from further analysis. To normalize log-ratio data, a print-tip specific Lowess curve was fit to the log-intensity versus log-ratio plot, using 20.0% of the data to calculate the fit at each point. This curve was used to center the log-ratio for each spot. Data were filtered to exclude poorly hybridized cDNAs by removing values with average foreground-minus-background intensity levels less than 300. We used the average of the two duplicatecDNAsspotsoneach microarray chip in subsequent analyses. Data were filtered to include clones returning data for at least 75% of the samples in both presurgery and postsurgery groups, which reduced the initial list of 6,751 clones to 5,753 clones.

source_name: Reference

extract_protocol: Biopsy cores were embedded individually in polyethylene glycol freezing media (Tissue-Tek OCT Compound, Sakura Finetek, Torrance, CA) and placed in isopentane that was precooled in liquid nitrogen. Specimens were then placed at 80°C until laser-capture microdissection (LCM). At time of LCM, 8-um frozen sections were obtained and immediately fixed in cold 95% ethanol. Sections were briefly (5 to 10 seconds) stained with hematoxylin using the Arcturus HistoGene Staining Solution (Arcturus Bioscience, Mountain View, CA) and dehydrated in 100% ethanol followed by xylenes (described in the Arcturus HistoGene LCM Frozen Section Staining Kit protocol). Five thousand epithelial cells from histologically benign glands were obtained by LCM using the Arcturus PixCell II instrument (modified from Emmert-Buck as described in Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563-571, 2005). Digital photos were taken of tissue sections before, during, and after LCM and assessed by an experienced genitourinary pathologist (B.S.K.) to confirm the histology of the laser captured cells. Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were 55mWbeam, 1.5 ms pulse, and 15um spot size. Cells were lysed in Arcturus RNA Extraction Buffer, RNA was isolated using the Arcturus PicoPure RNA Isolation Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNAse Set (Qiagen Inc, Valencia, CA). RNA was amplified for two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), and sample quality and quantity were assessed by agarose gel electrophoresis and absorbance at A260. To provide a reference standard RNA for use on cDNA microarrays, we isolated total RNA from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640-1640 medium supplemented with 10% fetal bovine serum (FBS; Life Technologies, Rockville, MD). RNA was purified using Trizol (Life Technologies) following the manufacturer’s protocol.

source_name: Human Prostate 030025_PR treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030025_PR. Specimen_ID

value: 030025_PR; Age (years):68; Race/Ethnicity:White; PSA (ng/dL):4.7; Total Operative Time (minutes) :185; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):78; Nerve Sparing:None; Patient Number:3; Type:Radical Prostatectomy; Ischemia Time (minutes):40; Estimated Blood Loss (mL):"1,000";


title: Control-3 month-rep2


title: Time: Before Intervention, Treatment: Low-fat/lowglycemic load, Type: Needle (030022_BI)

description: Human Prostate 030022_BI from Human hybridized against Reference

label_protocol: We prepared and hybridized spotted cDNA microarrays as previously described (Moore S, Knudsen B, True LD, et al: Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma. Int J Cancer 114:563- 571, 2005)  using RNA from a single batch of reference standard for each hybridization.

source_name: Human Prostate 030022_BI treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030022_BI. Specimen_ID

value: 030022_BI; Age (years):64; Race/Ethnicity:White; PSA (ng/dL):8.2; Total Operative Time (minutes) :187; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:8; pStage:T2aN1; Prostate Volume (mL):39; Nerve Sparing:Unilateral; Patient Number:2; Type:Needle; Ischemia Time (minutes):33; Estimated Blood Loss (mL):600;


title: Time: Before Intervention, Treatment: None, Type: Needle (030113_BI)

description: Human Prostate 030113_BI from Human hybridized against Reference

source_name: Human Prostate 030113_BI treated with None

tag: Human Prostate 030113_BI. Specimen_ID

value: 030113_BI; Age (years):67; Race/Ethnicity:African American; PSA (ng/dL):6; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):31; Nerve Sparing:Bilateral; Patient Number:9; Type:Needle; Ischemia Time (minutes):26; Estimated Blood Loss (mL):950;


title: 14028_Promoterlibmix_stable+unstable_sort2_mouseSpleen(+)_115218_1

description: Date of Scan Jul 12 2007

source_name: 14028s Promoterlibmix_stable+unstable, sort2, GFP(+) in spleens of nude mouse

value: GFP(+) cells recovered from spleen 2 days after IV passage of 10^7 through five nude mice

tag: Salmonella typhimurium 14028s mix of promoter libraries of stable and unstable GFP variants (180,000 clones)


title: Time: Processed Normally, Treatment: None, Type: Radical Prostatectomy (030113_PR)

description: Human Prostate 030113_PR from Human hybridized against Reference

source_name: Human Prostate 030113_PR treated with None

tag: Human Prostate 030113_PR. Specimen_ID

value: 030113_PR; Age (years):67; Race/Ethnicity:African American; PSA (ng/dL):6; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):31; Nerve Sparing:Bilateral; Patient Number:9; Type:Radical Prostatectomy; Ischemia Time (minutes):26; Estimated Blood Loss (mL):950;


title: Time: Processed Normally, Treatment: None, Type: Radical Prostatectomy (030020_PR)

description: Human Prostate 030020_PR from Human hybridized against Reference

source_name: Human Prostate 030020_PR treated with None

tag: Human Prostate 030020_PR. Specimen_ID

value: 030020_PR; Age (years):67; Race/Ethnicity:White; PSA (ng/dL):5.6; Total Operative Time (minutes) :180; Treatment:None; Gleason Sum:7; pStage:T3aN0; Prostate Volume (mL):43; Nerve Sparing:None; Patient Number:1; Type:Radical Prostatectomy; Ischemia Time (minutes):36; Estimated Blood Loss (mL):"1,100";


title: Time: Processed Normally, Treatment: Control, Type: Radical Prostatectomy (030133_PR)

description: Human Prostate 030133_PR from Human hybridized against Reference

source_name: Human Prostate 030133_PR treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030133_PR. Specimen_ID

value: 030133_PR; Age (years):69; Race/Ethnicity:White; PSA (ng/dL):5; Total Operative Time (minutes) :196; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):65; Nerve Sparing:Bilateral; Patient Number:10; Type:Radical Prostatectomy; Ischemia Time (minutes):29; Estimated Blood Loss (mL):800;


title: Time: Before Intervention, Treatment: Control, Type: Needle (030025_BI)

description: Human Prostate 030025_BI from Human hybridized against Reference

source_name: Human Prostate 030025_BI treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030025_BI. Specimen_ID

value: 030025_BI; Age (years):68; Race/Ethnicity:White; PSA (ng/dL):4.7; Total Operative Time (minutes) :185; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):78; Nerve Sparing:None; Patient Number:3; Type:Needle; Ischemia Time (minutes):40; Estimated Blood Loss (mL):"1,000";


title: Time: at Radical Prostatectomy, Treatment: None, Type: Needle (030113_PL)

description: Human Prostate 030113_PL from Human hybridized against Reference

source_name: Human Prostate 030113_PL treated with None

tag: Human Prostate 030113_PL. Specimen_ID

value: 030113_PL; Age (years):67; Race/Ethnicity:African American; PSA (ng/dL):6; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):31; Nerve Sparing:Bilateral; Patient Number:9; Type:Needle; Ischemia Time (minutes):26; Estimated Blood Loss (mL):950;


title: Time: at Radical Prostatectomy, Treatment: Control, Type: Needle (030025_PL)

description: Human Prostate 030025_PL from Human hybridized against Reference

source_name: Human Prostate 030025_PL treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030025_PL. Specimen_ID

value: 030025_PL; Age (years):68; Race/Ethnicity:White; PSA (ng/dL):4.7; Total Operative Time (minutes) :185; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):78; Nerve Sparing:None; Patient Number:3; Type:Needle; Ischemia Time (minutes):40; Estimated Blood Loss (mL):"1,000";


title: Time: at Radical Prostatectomy, Treatment: Low-fat/lowglycemic load, Type: Needle (030070_PL)

description: Human Prostate 030070_PL from Human hybridized against Reference

source_name: Human Prostate 030070_PL treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030070_PL. Specimen_ID

value: 030070_PL; Age (years):62; Race/Ethnicity:White; PSA (ng/dL):2.5; Total Operative Time (minutes) :203; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):37; Nerve Sparing:Bilateral; Patient Number:6; Type:Needle; Ischemia Time (minutes):27; Estimated Blood Loss (mL):650;


title: Time: Before Intervention, Treatment: Low-fat/lowglycemic load, Type: Needle (030107_BI)

description: Human Prostate 030107_BI from Human hybridized against Reference

source_name: Human Prostate 030107_BI treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030107_BI. Specimen_ID

value: 030107_BI; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):3.5; Total Operative Time (minutes) :210; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2aN0; Prostate Volume (mL):50; Nerve Sparing:Bilateral; Patient Number:8; Type:Needle; Ischemia Time (minutes):30; Estimated Blood Loss (mL):"1,600";


title: Time: at Radical Prostatectomy, Treatment: Low-fat/lowglycemic load, Type: Needle (030167_PL)

description: Human Prostate 030167_PL from Human hybridized against Reference

source_name: Human Prostate 030167_PL treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030167_PL. Specimen_ID

value: 030167_PL; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):4.6; Total Operative Time (minutes) :201; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):49; Nerve Sparing:Bilateral; Patient Number:12; Type:Needle; Ischemia Time (minutes):19; Estimated Blood Loss (mL):800;


title: Time: Processed Normally, Treatment: Low-fat/lowglycemic load, Type: Radical Prostatectomy (030022_PR)

description: Human Prostate 030022_PR from Human hybridized against Reference

source_name: Human Prostate 030022_PR treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030022_PR. Specimen_ID

value: 030022_PR; Age (years):64; Race/Ethnicity:White; PSA (ng/dL):8.2; Total Operative Time (minutes) :187; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:8; pStage:T2aN1; Prostate Volume (mL):39; Nerve Sparing:Unilateral; Patient Number:2; Type:Radical Prostatectomy; Ischemia Time (minutes):33; Estimated Blood Loss (mL):600;


title: Time: Processed Normally, Treatment: Control, Type: Radical Prostatectomy (030077_PR)

description: Human Prostate 030077_PR from Human hybridized against Reference

source_name: Human Prostate 030077_PR treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030077_PR. Specimen_ID

value: 030077_PR; Age (years):65; Race/Ethnicity:White; PSA (ng/dL):16; Total Operative Time (minutes) :237; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):149; Nerve Sparing:Bilateral; Patient Number:7; Type:Radical Prostatectomy; Ischemia Time (minutes):35; Estimated Blood Loss (mL):"2,100";


title: Time: Processed Normally, Treatment: Control, Type: Radical Prostatectomy (030157_PR)

description: Human Prostate 030157_PR from Human hybridized against Reference

tag: Reference

source_name: Human Prostate 030157_PR treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030157_PR. Specimen_ID

value: 030157_PR; Age (years):59; Race/Ethnicity:African American; PSA (ng/dL):5.4; Total Operative Time (minutes) :164; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:8; pStage:T2bN0; Prostate Volume (mL):35; Nerve Sparing:None; Patient Number:11; Type:Radical Prostatectomy; Ischemia Time (minutes):25; Estimated Blood Loss (mL):"1,500";


title: Time: Before Intervention, Treatment: Low-fat/lowglycemic load, Type: Needle (030167_BI)

description: Human Prostate 030167_BI from Human hybridized against Reference

source_name: Reference

source_name: Human Prostate 030167_BI treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030167_BI. Specimen_ID

value: 030167_BI; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):4.6; Total Operative Time (minutes) :201; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):49; Nerve Sparing:Bilateral; Patient Number:12; Type:Needle; Ischemia Time (minutes):19; Estimated Blood Loss (mL):800;


title: Time: Processed Normally, Treatment: Low-fat/lowglycemic load, Type: Radical Prostatectomy (030167_PR)

description: Human Prostate 030167_PR from Human hybridized against Reference

source_name: Human Prostate 030167_PR treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030167_PR. Specimen_ID

value: 030167_PR; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):4.6; Total Operative Time (minutes) :201; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):49; Nerve Sparing:Bilateral; Patient Number:12; Type:Radical Prostatectomy; Ischemia Time (minutes):19; Estimated Blood Loss (mL):800;


title: Time: at Radical Prostatectomy, Treatment: None, Type: Needle (030020_PL)

description: Human Prostate 030020_PL from Human hybridized against Reference

source_name: Human Prostate 030020_PL treated with None

tag: Human Prostate 030020_PL. Specimen_ID

value: 030020_PL; Age (years):67; Race/Ethnicity:White; PSA (ng/dL):5.6; Total Operative Time (minutes) :180; Treatment:None; Gleason Sum:7; pStage:T3aN0; Prostate Volume (mL):43; Nerve Sparing:None; Patient Number:1; Type:Needle; Ischemia Time (minutes):36; Estimated Blood Loss (mL):"1,100";


title: Time: Processed Normally, Treatment: Low-fat/lowglycemic load, Type: Radical Prostatectomy (030107_PR)

description: Human Prostate 030107_PR from Human hybridized against Reference

source_name: Human Prostate 030107_PR treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030107_PR. Specimen_ID

value: 030107_PR; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):3.5; Total Operative Time (minutes) :210; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2aN0; Prostate Volume (mL):50; Nerve Sparing:Bilateral; Patient Number:8; Type:Radical Prostatectomy; Ischemia Time (minutes):30; Estimated Blood Loss (mL):"1,600";


title: Time: at Radical Prostatectomy, Treatment: Control, Type: Needle (030157_PL)

description: Human Prostate 030157_PL from Human hybridized against Reference

source_name: Human Prostate 030157_PL treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030157_PL. Specimen_ID

value: 030157_PL; Age (years):59; Race/Ethnicity:African American; PSA (ng/dL):5.4; Total Operative Time (minutes) :164; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:8; pStage:T2bN0; Prostate Volume (mL):35; Nerve Sparing:None; Patient Number:11; Type:Needle; Ischemia Time (minutes):25; Estimated Blood Loss (mL):"1,500";


title: Time: Before Intervention, Treatment: Control, Type: Needle (030157_BI)

description: Human Prostate 030157_BI from Human hybridized against Reference

source_name: Human Prostate 030157_BI treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030157_BI. Specimen_ID

value: 030157_BI; Age (years):59; Race/Ethnicity:African American; PSA (ng/dL):5.4; Total Operative Time (minutes) :164; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:8; pStage:T2bN0; Prostate Volume (mL):35; Nerve Sparing:None; Patient Number:11; Type:Needle; Ischemia Time (minutes):25; Estimated Blood Loss (mL):"1,500";


title: Time: at Radical Prostatectomy, Treatment: Low-fat/lowglycemic load, Type: Needle (030107_PL)

description: Human Prostate 030107_PL from Human hybridized against Reference

source_name: Human Prostate 030107_PL treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030107_PL. Specimen_ID

value: 030107_PL; Age (years):60; Race/Ethnicity:White; PSA (ng/dL):3.5; Total Operative Time (minutes) :210; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2aN0; Prostate Volume (mL):50; Nerve Sparing:Bilateral; Patient Number:8; Type:Needle; Ischemia Time (minutes):30; Estimated Blood Loss (mL):"1,600";


title: 14028_Promoterlibmix_stable+unstable_sort2_mouseTumor(+)_110997_2

description: Date of Scan Sep 05 2007

source_name: 14028s Promoterlibmix_stable+unstable, GFP(+) in human PC3 tumors of nude mouse

tag: Salmonella typhimurium 14028s mix of promoter libraries of stable and unstable GFP variants (180,000 clones), sort2

value: GFP(+) cells recovered from human PC3 tumors 2 days after IT injection of 10^7 into tumors of five nude mice

source_name: 14028s Promoterlibmix_stable+unstable


title: Time: at Radical Prostatectomy, Treatment: Low-fat/lowglycemic load, Type: Needle (030022_PL)

description: Human Prostate 030022_PL from Human hybridized against Reference

source_name: Human Prostate 030022_PL treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030022_PL. Specimen_ID

value: 030022_PL; Age (years):64; Race/Ethnicity:White; PSA (ng/dL):8.2; Total Operative Time (minutes) :187; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:8; pStage:T2aN1; Prostate Volume (mL):39; Nerve Sparing:Unilateral; Patient Number:2; Type:Needle; Ischemia Time (minutes):33; Estimated Blood Loss (mL):600;


title: Time: Before Intervention, Treatment: Low-fat/lowglycemic load, Type: Needle (030070_BI)

description: Human Prostate 030070_BI from Human hybridized against Reference

source_name: Human Prostate 030070_BI treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030070_BI. Specimen_ID

value: 030070_BI; Age (years):62; Race/Ethnicity:White; PSA (ng/dL):2.5; Total Operative Time (minutes) :203; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):37; Nerve Sparing:Bilateral; Patient Number:6; Type:Needle; Ischemia Time (minutes):27; Estimated Blood Loss (mL):650;


title: Time: Before Intervention, Treatment: None, Type: Needle (030020_BI)

description: Human Prostate 030020_BI from Human hybridized against Reference

source_name: Human Prostate 030020_BI treated with None

tag: Human Prostate 030020_BI. Specimen_ID

value: 030020_BI; Age (years):67; Race/Ethnicity:White; PSA (ng/dL):5.6; Total Operative Time (minutes) :180; Treatment:None; Gleason Sum:7; pStage:T3aN0; Prostate Volume (mL):43; Nerve Sparing:None; Patient Number:1; Type:Needle; Ischemia Time (minutes):36; Estimated Blood Loss (mL):"1,100";


title: Time: at Radical Prostatectomy, Treatment: Control, Type: Needle (030077_PL)

description: Human Prostate 030077_PL from Human hybridized against Reference

source_name: Human Prostate 030077_PL treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030077_PL. Specimen_ID

value: 030077_PL; Age (years):65; Race/Ethnicity:White; PSA (ng/dL):16; Total Operative Time (minutes) :237; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):149; Nerve Sparing:Bilateral; Patient Number:7; Type:Needle; Ischemia Time (minutes):35; Estimated Blood Loss (mL):"2,100";


title: Time: at Radical Prostatectomy, Treatment: None, Type: Needle (030031_PL)

description: Human Prostate 030031_PL from Human hybridized against Reference

source_name: Human Prostate 030031_PL treated with None

tag: Human Prostate 030031_PL. Specimen_ID

value: 030031_PL; Age (years):53; Race/Ethnicity:White; PSA (ng/dL):6.3; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):43; Nerve Sparing:Bilateral; Patient Number:4; Type:Needle; Ischemia Time (minutes):25; Estimated Blood Loss (mL):450;


title: Time: Processed Normally, Treatment: None, Type: Radical Prostatectomy (030031_PR)

description: Human Prostate 030031_PR from Human hybridized against Reference

source_name: Human Prostate 030031_PR treated with None

tag: Human Prostate 030031_PR. Specimen_ID

value: 030031_PR; Age (years):53; Race/Ethnicity:White; PSA (ng/dL):6.3; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):43; Nerve Sparing:Bilateral; Patient Number:4; Type:Radical Prostatectomy; Ischemia Time (minutes):25; Estimated Blood Loss (mL):450;


title: Time: at Radical Prostatectomy, Treatment: None, Type: Needle (030061_PL)

description: Human Prostate 030061_PL from Human hybridized against Reference

source_name: Human Prostate 030061_PL treated with None

tag: Human Prostate 030061_PL. Specimen_ID

value: 030061_PL; Age (years):69; Race/Ethnicity:Hispanic; PSA (ng/dL):4.2; Total Operative Time (minutes) :176; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):36; Nerve Sparing:Bilateral; Patient Number:5; Type:Needle; Ischemia Time (minutes):20; Estimated Blood Loss (mL):700;


title: HKE-1, noncancerous

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

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

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description: mortal lifespan

hyb_protocol: The synthesized 10 microgram of cRNA, quantified by spectrometry and qualified using an Agilent 2100 Bioanalyzer, was then fragmented and hybridized to each array. After 16hr hybridization, arrays were rinsed with 0.75 x TNT buffer for 1 h, labeled with Streptavidin-Cy5 at room temperature for 30 min, rinsed again with TNT buffer and 0.05% Tween 20, and dried by centrifugation.

scan_protocol: Each microarray was scanned using an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by CodeLink Expression Analysis Software (GE Healthcare) and normalized to the median expression value of the whole array spots using GeneSpringTM GX (Agilent Technologies).

source_name: human esophageal epithelia

label_protocol: The first-strand cDNA was generated from 1 microgram of total RNA using reverse transcriptase and a T7 primer using the CodeLink Expression Assay Reagent Kit, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotin-11-UTP.

growth_protocol: Cells were cultured in Keratinocyte SFMTM medium with growth supplement containing 2.5 mg EGF and 25 mg bovine pituitary extract in 500 ml liquid basal medium (GIBCO BRL, Rockville, MD) in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from the frozen cultured cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), respectively, according to the manufacturer's protocols. The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human noncancerous esophageal epithelial cell primary culture


title: Time: Before Intervention, Treatment: None, Type: Needle (030031_BI)

description: Human Prostate 030031_BI from Human hybridized against Reference

source_name: Reference

tag: Reference

source_name: Human Prostate 030031_BI treated with None

tag: Human Prostate 030031_BI. Specimen_ID

value: 030031_BI; Age (years):53; Race/Ethnicity:White; PSA (ng/dL):6.3; Total Operative Time (minutes) :221; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):43; Nerve Sparing:Bilateral; Patient Number:4; Type:Needle; Ischemia Time (minutes):25; Estimated Blood Loss (mL):450;


title: Time: Before Intervention, Treatment: Control, Type: Needle (030133_BI)

description: Human Prostate 030133_BI from Human hybridized against Reference

source_name: Human Prostate 030133_BI treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030133_BI. Specimen_ID

value: 030133_BI; Age (years):69; Race/Ethnicity:White; PSA (ng/dL):5; Total Operative Time (minutes) :196; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):65; Nerve Sparing:Bilateral; Patient Number:10; Type:Needle; Ischemia Time (minutes):29; Estimated Blood Loss (mL):800;


title: HEEC-1, noncancerous

description: mortal lifespan

tag: cultured human noncancerous esophageal epithelial cell


title: Time: Before Intervention, Treatment: Control, Type: Needle (030077_BI)

description: Human Prostate 030077_BI from Human hybridized against Reference

source_name: Human Prostate 030077_BI treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030077_BI. Specimen_ID

value: 030077_BI; Age (years):65; Race/Ethnicity:White; PSA (ng/dL):16; Total Operative Time (minutes) :237; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:7; pStage:T2bN0; Prostate Volume (mL):149; Nerve Sparing:Bilateral; Patient Number:7; Type:Needle; Ischemia Time (minutes):35; Estimated Blood Loss (mL):"2,100";


title: Time: Before Intervention, Treatment: None, Type: Needle (030061_BI)

description: Human Prostate 030061_BI from Human hybridized against Reference

source_name: Human Prostate 030061_BI treated with None

tag: Human Prostate 030061_BI. Specimen_ID

value: 030061_BI; Age (years):69; Race/Ethnicity:Hispanic; PSA (ng/dL):4.2; Total Operative Time (minutes) :176; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):36; Nerve Sparing:Bilateral; Patient Number:5; Type:Needle; Ischemia Time (minutes):20; Estimated Blood Loss (mL):700;


title: Time: Processed Normally, Treatment: None, Type: Radical Prostatectomy (030061_PR)

description: Human Prostate 030061_PR from Human hybridized against Reference

source_name: Human Prostate 030061_PR treated with None

tag: Human Prostate 030061_PR. Specimen_ID

value: 030061_PR; Age (years):69; Race/Ethnicity:Hispanic; PSA (ng/dL):4.2; Total Operative Time (minutes) :176; Treatment:None; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):36; Nerve Sparing:Bilateral; Patient Number:5; Type:Radical Prostatectomy; Ischemia Time (minutes):20; Estimated Blood Loss (mL):700;


title: Human Prostate 686

description: Human Prostate 686 from Human hybridized against Reference

hyb_protocol: Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.

scan_protocol: Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.

data_processing: Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.

label_protocol: Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.

extract_protocol: Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.

source_name: Human Prostate 686 treated with Immediate Radical Prostatectomy

tag: Human Prostate 686. #

value: 686; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Time: at Radical Prostatectomy, Treatment: Control, Type: Needle (030133_PL)

description: Human Prostate 030133_PL from Human hybridized against Reference

source_name: Human Prostate 030133_PL treated with Control - 35% energy from fat and total daily glycemic load >200

tag: Human Prostate 030133_PL. Specimen_ID

value: 030133_PL; Age (years):69; Race/Ethnicity:White; PSA (ng/dL):5; Total Operative Time (minutes) :196; Treatment:Control - 35% energy from fat and total daily glycemic load >200; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):65; Nerve Sparing:Bilateral; Patient Number:10; Type:Needle; Ischemia Time (minutes):29; Estimated Blood Loss (mL):800;


title: Human Prostate 690

description: Human Prostate 690 from Human hybridized against Reference

source_name: Human Prostate 690 treated with Immediate Radical Prostatectomy

tag: Human Prostate 690. #

value: 690; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate 650

description: Human Prostate 650 from Human hybridized against Reference

source_name: Human Prostate 650 treated with Neoadjuvant hormone suppression for 6 mo

tag: Human Prostate 650. #

value: 650; Treatment:Neoadjuvant hormone suppression for 6 mo; Reference:HGSv5;


title: Human Prostate 646

description: Human Prostate 646 from Human hybridized against Reference

source_name: Human Prostate 646 treated with Neoadjuvant hormone suppression for 6 mo

tag: Human Prostate 646. #

value: 646; Treatment:Neoadjuvant hormone suppression for 6 mo; Reference:HGSv5;


title: Human Prostate 643

description: Human Prostate 643 from Human hybridized against Reference

source_name: Human Prostate 643 treated with Neoadjuvant hormone suppression for 3-6 mo

tag: Human Prostate 643. #

value: 643; Treatment:Neoadjuvant hormone suppression for 3-6 mo; Reference:HGSv5;


title: Human Prostate GSK-60

description: Human Prostate GSK-60 from Human hybridized against Reference

label_protocol: Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCaP, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.

extract_protocol: Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.

source_name: Human Prostate GSK-60 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-60. Specimen ID

value: GSK-60; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-46

description: Human Prostate GSK-46 from Human hybridized against Reference

source_name: Human Prostate GSK-46 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-46. Specimen ID

value: GSK-46; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate 689

description: Human Prostate 689 from Human hybridized against Reference

source_name: Human Prostate 689 treated with Neoadjuvant hormone suppression for 6 mo

tag: Human Prostate 689. #

value: 689; Treatment:Neoadjuvant hormone suppression for 6 mo; Reference:HGSv5;


title: Human Prostate 587

description: Human Prostate 587 from Human hybridized against Reference

source_name: Human Prostate 587 treated with Neoadjuvant hormone suppression for 3-6 mo

tag: Human Prostate 587. #

value: 587; Treatment:Neoadjuvant hormone suppression for 3-6 mo; Reference:HGSv5;


title: Human Prostate GSK-16

description: Human Prostate GSK-16 from Human hybridized against Reference

tag: Reference

source_name: Human Prostate GSK-16 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-16. Specimen ID

value: GSK-16; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-25

description: Human Prostate GSK-25 from Human hybridized against Reference

source_name: Reference

source_name: Human Prostate GSK-25 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-25. Specimen ID

value: GSK-25; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-42

description: Human Prostate GSK-42 from Human hybridized against Reference

source_name: Human Prostate GSK-42 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-42. Specimen ID

value: GSK-42; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-59

description: Human Prostate GSK-59 from Human hybridized against Reference

source_name: Human Prostate GSK-59 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-59. Specimen ID

value: GSK-59; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-36

description: Human Prostate GSK-36 from Human hybridized against Reference

source_name: Human Prostate GSK-36 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-36. Specimen ID

value: GSK-36; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-53

description: Human Prostate GSK-53 from Human hybridized against Reference

source_name: Human Prostate GSK-53 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-53. Specimen ID

value: GSK-53; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate 687

description: Human Prostate 687 from Human hybridized against Reference

source_name: Human Prostate 687 treated with Immediate Radical Prostatectomy

tag: Human Prostate 687. #

value: 687; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-38

description: Human Prostate GSK-38 from Human hybridized against Reference

source_name: Human Prostate GSK-38 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-38. Specimen ID

value: GSK-38; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-23

description: Human Prostate GSK-23 from Human hybridized against Reference

source_name: Human Prostate GSK-23 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-23. Specimen ID

value: GSK-23; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-5

description: Human Prostate GSK-5 from Human hybridized against Reference

source_name: Human Prostate GSK-5 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-5. Specimen ID

value: GSK-5; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-6

description: Human Prostate GSK-6 from Human hybridized against Reference

source_name: Human Prostate GSK-6 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-6. Specimen ID

value: GSK-6; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate 514

description: Human Prostate 514 from Human hybridized against Reference

source_name: Human Prostate 514 treated with Neoadjuvant hormone suppression for 3-6 mo

tag: Human Prostate 514. #

value: 514; Treatment:Neoadjuvant hormone suppression for 3-6 mo; Reference:HGSv5;


title: Human Prostate GSK-49

description: Human Prostate GSK-49 from Human hybridized against Reference

source_name: Human Prostate GSK-49 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-49. Specimen ID

value: GSK-49; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-11

description: Human Prostate GSK-11 from Human hybridized against Reference

source_name: Human Prostate GSK-11 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-11. Specimen ID

value: GSK-11; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-10

description: Human Prostate GSK-10 from Human hybridized against Reference

source_name: Human Prostate GSK-10 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-10. Specimen ID

value: GSK-10; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-4

description: Human Prostate GSK-4 from Human hybridized against Reference

source_name: Human Prostate GSK-4 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-4. Specimen ID

value: GSK-4; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-12

description: Human Prostate GSK-12 from Human hybridized against Reference

tag: Reference

source_name: Human Prostate GSK-12 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-12. Specimen ID

value: GSK-12; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-37

description: Human Prostate GSK-37 from Human hybridized against Reference

source_name: Reference

source_name: Human Prostate GSK-37 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-37. Specimen ID

value: GSK-37; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-39

description: Human Prostate GSK-39 from Human hybridized against Reference

source_name: Human Prostate GSK-39 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-39. Specimen ID

value: GSK-39; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-47

description: Human Prostate GSK-47 from Human hybridized against Reference

source_name: Human Prostate GSK-47 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-47. Specimen ID

value: GSK-47; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-29

description: Human Prostate GSK-29 from Human hybridized against Reference

source_name: Human Prostate GSK-29 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-29. Specimen ID

value: GSK-29; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-14

description: Human Prostate GSK-14 from Human hybridized against Reference

source_name: Human Prostate GSK-14 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-14. Specimen ID

value: GSK-14; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-26

description: Human Prostate GSK-26 from Human hybridized against Reference

source_name: Human Prostate GSK-26 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-26. Specimen ID

value: GSK-26; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Time: Processed Normally, Treatment: Low-fat/lowglycemic load, Type: Radical Prostatectomy (030070_PR)

description: Human Prostate 030070_PR from Human hybridized against Reference

source_name: Human Prostate 030070_PR treated with Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100

tag: Human Prostate 030070_PR. Specimen_ID

value: 030070_PR; Age (years):62; Race/Ethnicity:White; PSA (ng/dL):2.5; Total Operative Time (minutes) :203; Treatment:Low-fat/lowglycemic load - <20% energy from fat and total daily glycemic load <100; Gleason Sum:6; pStage:T2bN0; Prostate Volume (mL):37; Nerve Sparing:Bilateral; Patient Number:6; Type:Radical Prostatectomy; Ischemia Time (minutes):27; Estimated Blood Loss (mL):650;


title: Human Prostate GSK-58

description: Human Prostate GSK-58 from Human hybridized against Reference

source_name: Human Prostate GSK-58 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-58. Specimen ID

value: GSK-58; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-18

description: Human Prostate GSK-18 from Human hybridized against Reference

source_name: Human Prostate GSK-18 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-18. Specimen ID

value: GSK-18; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-45

description: Human Prostate GSK-45 from Human hybridized against Reference

source_name: Human Prostate GSK-45 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-45. Specimen ID

value: GSK-45; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-20

description: Human Prostate GSK-20 from Human hybridized against Reference

source_name: Human Prostate GSK-20 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-20. Specimen ID

value: GSK-20; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-21

description: Human Prostate GSK-21 from Human hybridized against Reference

source_name: Human Prostate GSK-21 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-21. Specimen ID

value: GSK-21; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-8

description: Human Prostate GSK-8 from Human hybridized against Reference

source_name: Human Prostate GSK-8 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-8. Specimen ID

value: GSK-8; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-19

description: Human Prostate GSK-19 from Human hybridized against Reference

source_name: Human Prostate GSK-19 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-19. Specimen ID

value: GSK-19; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: CUTLL1_CompE_2

first: Adolfo

middle: A

last: Ferrando

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Second replica of duplicate CompE treatment

hyb_protocol: Standard Affymetix protocol

scan_protocol: Standard Affymetix protocol

label: Standard Affymetix labeling

source_name: CUTLL1 cell line

label_protocol: Standard Affymetix protocol

growth_protocol: RPMI 20% FBS Pen/Strep, 37C, 5%CO2

extract_protocol: RNAqueous RNA extraction kit (Ambion)

treatment_protocol: Gamma-secretase inhibitor (CompE 100nM) treatment for 24 hours

tag: T-cell lymphoblastic lymphoma cell line


title: Human Prostate GSK-2

description: Human Prostate GSK-2 from Human hybridized against Reference

tag: Reference

source_name: Human Prostate GSK-2 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-2. Specimen ID

value: GSK-2; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: CUTLL1_DEXA_2

description: SEcond replica of duplicate dexamethasone treatment

treatment_protocol: Glucocorticoid (Dexamethasone 1 microM) treatment for 24 hours


title: Human Prostate GSK-28

description: Human Prostate GSK-28 from Human hybridized against Reference

source_name: Reference

source_name: Human Prostate GSK-28 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-28. Specimen ID

value: GSK-28; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: CUTLL1_DEXA+CompE_1

description: First replica of duplicate dexamethasone plus CompE  cotreatment

treatment_protocol: Glucocorticoid (Dexamethasone 1 microM) plus gamma-secretase inhibitor (CompE 100 nM) treatment for 24 hours


title: Human Prostate GSK-7

description: Human Prostate GSK-7 from Human hybridized against Reference

source_name: Human Prostate GSK-7 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-7. Specimen ID

value: GSK-7; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: CUTLL1_DEXA+CompE_2

description: SEcond replica of duplicate dexamethasone plus CompE  cotreatment


title: CUTLL1_Control_2

description: Second replica of duplicate vehicle-only treatment controls

treatment_protocol: Vehicle only(DMSO) treatment


title: CUTLL1_CompE_1

description: First replica of duplicate CompE treatment


title: CUTLL1_DEXA_1

description: First replica of duplicate dexamethasone treatment


title: Human Prostate GSK-27

description: Human Prostate GSK-27 from Human hybridized against Reference

source_name: Human Prostate GSK-27 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-27. Specimen ID

value: GSK-27; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-22

description: Human Prostate GSK-22 from Human hybridized against Reference

source_name: Human Prostate GSK-22 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-22. Specimen ID

value: GSK-22; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-40

description: Human Prostate GSK-40 from Human hybridized against Reference

source_name: Human Prostate GSK-40 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-40. Specimen ID

value: GSK-40; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-3

description: Human Prostate GSK-3 from Human hybridized against Reference

source_name: Human Prostate GSK-3 treated with Immediate Radical Prostatectomy

tag: Human Prostate GSK-3. Specimen ID

value: GSK-3; Treatment:Immediate Radical Prostatectomy; Reference:HGSv5;


title: Human Prostate GSK-9

description: Human Prostate GSK-9 from Human hybridized against Reference

source_name: Human Prostate GSK-9 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-9. Specimen ID

value: GSK-9; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: Human Prostate GSK-1

description: Human Prostate GSK-1 from Human hybridized against Reference

source_name: Human Prostate GSK-1 treated with 0.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-1. Specimen ID

value: GSK-1; Treatment:0.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: TcLr34_7dpi_mock_rep3

status: Public on Nov 01 2008

city: St. Paul

first: David

last: Garvin

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Plant Science Research Unit

institute: USDA

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip wheat Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data analysis was conducted using the Expressionist software version Pro 3.1 (Genedata AG, CH-4016 Basel, Switzerland).  The probe set values from all experiments were condensed together using the MAS 5.0 algorithm (Affymetrix, I. Statistical Algorithms Description Document. 2002.).  The MAS 5.0 signal data were normalized to a median target intensity of 500 as follows: P. triticina- and mock-inoculated data were normalized together for each genotype at each timepoint for a total of six comparisons.  The experiment was a randomized complete block design with three replicates for each genotype, and employed univariate analysis (t-tests) between mock- and P. triticina-inoculated plants within each genotype at each timepoint, for a total of six comparisons across the entire experiment.

organism: Triticum aestivum

source_name: Wheat flag leaves, 7 dpi, mock

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

growth_protocol: Seed of each genotype were stratified on wet filter paper for 4 days, and then planted three to a pot in 6 inch round plastic pots (Belden Plastics, Roseville, MN) filled with a potting mixture of field soil, compost, and sand.  20 grams of Nutricote 100 day slow release 13-13-13 pellets with micronutrients (SunGro, Vancouver, British Columbia, Canada) was placed into each pot.  Pots were placed in a growth chamber (Conviron PGW36, Conviron, Winnipeg, Canada) initially set at 18°C day 16°C night, with 16 h day/8 h night light regime.  The pots were laid out in a split plot with three reps.  Genotypes were the main effect, and the subplots were treatments (mock-inoculated or pathogen-inoculated).  For each rep, 6 pots (3 plants per pot) were planted per genotype.  Pots were watered on an as-needed basis.  After one month, the temperature was dropped to 15°C day/13°C night temperature to help ensure synchronized flowering, and subsequently the temperature was gradually stepped up to 20°C day/17°C night temperatures (16°C day/14°C night 9 days after setting to 15°C day/13°C night, 17°C/15°C two days later, 18°C/16°C two days later, and 20°C/17°C 9 days later).  Pots were also watered thoroughly with a fertilizer solution (1.86 g L-1 Peters 20-20-20 soluble fertilizer) three weeks and 8 weeks after planting, and with a more dilute solution (0.62 g L-1) of the same soluble fertilizer 6 weeks after planting.  Two months after sowing, plants were ready for inoculation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, treated with RNase-free DNase, and further purified using RNeasy columns (Promega, Madison, WI) according to manufacturer's instructions.

treatment_protocol: Tillers at anthesis (+/- two days) on each plant were tagged prior to inoculation.  Flag leaves of each tiller were individually inoculated on the adaxial face either with Soltrol oil alone or with a suspension of P. triticina race 1 (BBB) spores in Soltrol oil (18 mg spores ml-1 oil).  Inoculations employed two passes across the leaf surface with an atomizer nozzle.  Spore densities applied to leaves were determined by inoculating 6 microscope slides during the course of the inoculations and then counting the number of spores in a defined area (2.67 mm2) on each slide under a microscope.  Using this method, the average spore density on inoculated leaf surfaces was determined to be 592 spores cm-1.  Spore germination was assessed by spraying water agar plates lightly with inoculum and then determining the percentage of spores that had germinated after 4 h.  By this method, 75% of spores had germinated (germination tube evident), while a significant portion of the other spores were oblong in shape, indicating that they were in the early process of germinating.   After allowing oil to dry off of leaf surfaces for 1.5 h, pots were placed in mist chambers (one rep per chamber) and subjected to 30 min initial misting.  A 30 min mist/4 min no mist cycle was then employed for three h, followed by a mist cycle of 10 min on/10 min off for 5 h, and finally a mist regime of 6 min on/10 min off for 10 h 45 min.  The temperature in the mist chamber during the mist period was 21ºC +/- 1ºC.  Plant were then removed from the mist chambers and allowed to dry, and they were placed back into the growth chamber.

tag: Genotype

value: Thatcher-Lr34, Growth stage:anthesis


title: Human Prostate GSK-30

description: Human Prostate GSK-30 from Human hybridized against Reference

source_name: Human Prostate GSK-30 treated with 3.5 mg PO qDay Dutasteride

tag: Human Prostate GSK-30. Specimen ID

value: GSK-30; Treatment:3.5 mg PO qDay Dutasteride; Reference:HGSv5;


title: TcLr34_7dpi_inoculated_rep3

source_name: Wheat flag leaves, 7 dpi, inoculated


title: Tc_7dpi_inoculated_rep3

value: Thatcher, Growth stage:anthesis


title: TcLr1_7dpi_mock_rep3

value: Thatcher-Lr1, Growth stage:anthesis


title: TcLr1_7dpi_inoculated_rep3


title: Tc_7dpi_mock_rep3


title: TcLr34_7dpi_inoculated_rep2


title: Tc_3dpi_inoculated_rep3

source_name: Wheat flag leaves, 3 dpi, inoculated


title: TcLr1_7dpi_inoculated_rep2


title: TcLr1_7dpi_inoculated_rep1


title: Tc_3dpi_mock_rep3

source_name: Wheat flag leaves, 3 dpi, mock


title: TcLr1_7dpi_mock_rep1


title: TcLr34_7dpi_mock_rep2


title: TcLr1_7dpi_mock_rep2


title: Tc_7dpi_inoculated_rep1


title: TcLr34_3dpi_inoculated_rep2


title: TcLr34_3dpi_mock_rep3


title: Tc_7dpi_mock_rep2


title: TcLr1_3dpi_mock_rep2


title: TcLr1_3dpi_mock_rep3


title: Tc_7dpi_inoculated_rep2


title: TcLr34_3dpi_inoculated_rep3


title: TcLr34_7dpi_inoculated_rep1


title: TcLr1_3dpi_inoculated_rep3


title: Tc_7dpi_mock_rep1


title: TcLr34_3dpi_mock_rep2


title: TcLr1_3dpi_inoculated_rep2


title: TcLr34_3dpi_mock_rep1


title: TcLr34_7dpi_mock_rep1


title: CUTLL1_Control_1

description: First replica of duplicate vehicle-only treatment controls


title: Tc_3dpi_inoculated_rep2


title: TcLr1_3dpi_inoculated_rep1


title: Tc_3dpi_mock_rep2


title: Tc_3dpi_inoculated_rep1


title: Tc_3dpi_mock_rep1


title: TcLr1_3dpi_mock_rep1


title: sua5D 12th-3

status: Public on Oct 01 2008

city: shanghai

first: feilong

last: meng

address: 320 yuyang road

department: SIBCB

country: China

institute: Shanghai institutes for biology sciences

description: performed following Affymetrix standard protocols

hyb_protocol: Hybridization Control Kit Affymetrix

scan_protocol: Gene array Scanner3000 Affymetrix

data_processing: GCOS1.2 Affymetrix

organism: Saccharomyces cerevisiae

source_name: sua5D 300 generations after sporulation

label_protocol: IVT Labeling Kit  Affymetrix

growth_protocol:
innoculate in 5ml YPD liquid medium
harvest at mid-log phase

extract_protocol: the RNeasy Mini Kit (Qiagen) and on-column DNase Digestion Kit (Qiagen)

tag: background

value: dissection sproe of BY4743 MAT a

tag: sua5 disruption

tag: restreak on YPD plate 12 times, innoculate in 5ml YPD liquid medium

tag: harvest at mid-log phase


title: BY4742 -3

treatment_protocol:
innoculate in 5ml YPD liquid medium
harvest at mid-log phase

tag: BY4742 wildtype


title: BY4742 wildtype

tag: wildtype strain BY4742


title: sua5D 12th-1

source_name: sua5D 300generation after sporulation


title: Macgoren-Abnornal karyotype-S4v12_3

first: Su

last: Hong

department: Life Science Institute

institute: Macrogen Inc.

description: Amplified RNA synthesized from limited quantities of heterogenous cDNA (Van Gelder et al., 1990) was performed using the Illumina RNA Amplification kit (Ambion, Inc., Austin, TX) following the Manufacturer instructions.

hyb_protocol: Labeled, amplified material (700 ng per array) was hybridized to the Illumina HumanRef-6 BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner according to the Manufacturer's instructions.

data_processing: Array data processing and analysis was performed using Illumina BeadStudio software.

source_name: SNUhESC-4 12 variant sample #3

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP (Perkin Elmer Life and Analytical Sciences, Boston, MA) present at a ratio of 1:1 with unlabeled UTP.

extract_protocol:
Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorlessupper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization.
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8°C. The RNA precipitate,
often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8°C.
At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes). Do not dry the RNA by centrifugation under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples
have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

tag: Cell line

tag: Status

value: chromosome 12 trisomy


title: sua5D 12th-2


title: Macgoren-Abnornal karyotype-S4v12_2

source_name: SNUhESC-4 12 variant sample #2


title: Macgoren-Abnornal karyotype-H1_3

source_name: H1 normal sample #3

value: Normal


title: sua5D 1st-3

source_name: sua5D 35generation after sporulation

tag: restreak on YPD plate once, innoculate in 5ml YPD liquid medium


title: sua5D 1st-4


title: Macgoren-Abnornal karyotype-H1_1

source_name: H1 normal sample #1


title: Macgoren-Abnornal karyotype-S4_3

source_name: SNUhESC-4 normal sample #3


title: Macgoren-Abnornal karyotype-S4_1

source_name: SNUhESC-4 normal sample #1


title: sua5D 1st-1


title: Macgoren-Abnornal karyotype-S4v12_1

source_name: SNUhESC-4 12 variant sample #1

value: Chromosome 12 trisomy


title: Macgoren-Abnornal karyotype-S3v12_2

source_name: SNUhESC-3 variable 12 sample #2

value: 12 chromosome trisomy


title: BY4742 -2

source_name: BY4742 wildtype

tag: BY4742 wildtye


title: Macgoren-Abnornal karyotype-S3v12_1

source_name: SNUhESC-3 varient 12 #1


title: Macgoren-Abnornal karyotype-S3vX_2

source_name: SNUhESC-3 X variation sample #2

value: X chromosome variation


title: Macgoren-Abnornal karyotype-S4_2

source_name: SNUhESC-4 normal sample #2


title: Macgoren-Abnornal karyotype-H1_2

source_name: H1 normal sample #2


title: Macgoren-Abnornal karyotype-S3_2

source_name: SNUhESC-3 normal sample #2


title: Macgoren-Abnornal karyotype-S3vX_1

source_name: SNUhESC-3 X variable sample #1

value: X chromosome variable


title: Macgoren-Abnornal karyotype-S3_1

source_name: SNUhESC-3 normal sample #1


title: TcLr34_3dpi_inoculated_rep1

source_name: Wheat flag leaves, 3 dpi, inoculated


title: TL2_14028s_IP_mouse5_LibB5_5D730_2

status: Public on Sep 01 2008

description:
User - CSantiviago
Date_of_Scan = Tue Feb 15 14:51:08 2005

data_processing: Quantarray 3.0, adaptive quantitation, protocol STv5_SP040504_adapforsmallpins_040817

source_name: 14028s Tn5 lib IP passaged through mouse 05 (Library B#5)

extract_protocol: arbitrarily primed sampling (DOPR) + specific PCR amplification + T7 in vitro transcription + RT labeling (Cy3-dCTP)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#05

source_name: 14028s Tn5 lib grown in LB broth (Library 0 Mice)

extract_protocol: arbitrarily primed sampling (DOPR) + specific PCR amplification + T7 in vitro transcription + RT labeling (Cy5-dCTP)

tag: Salmonella typhimurium 14028s Transposon library grown in Luria-Bertani broth (kanamycin 50ug/ml), O/N at 37°C with aeration


title: TL2_14028s_IP_mouse_pool_LibBPool_5D703_3

description:
User - CSantiviago
Date_of_Scan = Wed Feb 09 16:17:21 2005

source_name: 14028s Tn5 lib IP passaged through mouse; pool of 6 samples (Library B Pool)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mice; pool of 6 samples


title: TL2_14028s_IP_mouse1_LibB1_5D704_3

description:
User - CSantiviago
Date_of_Scan = Mon Feb 14 14:14:32 2005

source_name: 14028s Tn5 lib IP passaged through mouse 01 (Library B#1)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#01


title: TL2_14028s_IP_mouse5_LibB5_5D730_1


title: TL2_14028s_IP_mouse1_LibB1_5D704_1


title: TL2_14028s_IP_mouse2_LibB2_5D705_3

description:
User - CSantiviago
Date_of_Scan = Mon Feb 14 14:45:35 2005

source_name: 14028s Tn5 lib IP passaged through mouse 02 (Library B#2)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#02


title: TL2_14028s_IP_mouse2_LibB2_5D705_2


title: TL2_14028s_IP_mouse3_LibB3_5D729_1

description:
User - CSantiviago
Date_of_Scan = Tue Feb 15 13:58:33 2005

source_name: 14028s Tn5 lib IP passaged through mouse 03 (Library B#3)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#03


title: TL2_14028s_IP_mouse3_LibB3_5D729_2


title: TL2_14028s_IP_mouse4_LibB4_5D701_1

description:
User - CSantiviago
Date_of_Scan = Wed Feb 09 15:16:02 2005

source_name: 14028s Tn5 lib IP passaged through mouse 04 (Library B#4)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#04


title: TL2_14028s_IP_mouse1_LibB1_5D704_2


title: TL2_14028s_IP_mouse6_LibB6_5D702_3

description:
User - CSantiviago
Date_of_Scan = Wed Feb 09 15:52:39 2005

source_name: 14028s Tn5 lib IP passaged through mouse 06 (Library B#6)

tag: Salmonella typhimurium 14028s Transposon library recovered from spleen after IP passage of 2x10^6 through BALB/c mouse#06


title: TL2_14028s_IP_mouse3_LibB3_5D729_3


title: TL2_14028s_IP_mouse_pool_LibBPool_5D703_2


title: TL2_14028s_IP_mouse4_LibB4_5D701_3


title: TL2_14028s_IP_mouse6_LibB6_5D702_1


title: TL2_14028s_IP_mouse_pool_LibBPool_5D703_1


title: TL2_14028s_IP_mouse5_LibB5_5D730_3


title: TL2_14028s_IP_mouse2_LibB2_5D705_1


title: TL2_14028s_IP_mouse4_LibB4_5D701_2


title: TL2_14028s_M9+arabinose_sample3_LibAra3_5D670_3

description:
User - CSantiviago
Date_of_Scan = Fri Jan 21 21:28:35 2005

source_name: 14028s Tn5 lib grown in M9 arabinose, sample3 (Library Ara#3)

tag: Salmonella typhimurium 14028s Transposon library grown in M9 minimal medium (arabinose 0.4%), O/N at 37°C with aeration, sample3

source_name: 14028s Tn5 lib (Library 0)

tag: Salmonella typhimurium 14028s Transposon library. The initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C


title: TL2_14028s_IP_mouse6_LibB6_5D702_2


title: TL2_14028s_M9+arabinose_sample3_LibAra3_5D670_1


title: TL2_14028s_M9+arabinose_sample2_LibAra2_5D669_2

description:
User - CSantiviago
Date_of_Scan = Fri Jan 21 20:52:10 2005

source_name: 14028s Tn5 lib grown in M9 arabinose, sample2 (Library Ara#2)

tag: Salmonella typhimurium 14028s Transposon library grown in M9 minimal medium (arabinose 0.4%), O/N at 37°C with aeration, sample2


title: TL2_14028s_M9+arabinose_sample1_LibAra1_5D668_3

description:
User - CSantiviago
Date_of_Scan = Fri Jan 21 20:09:24 2005

source_name: 14028s Tn5 lib grown in M9 arabinose, sample1 (Library Ara#1)

tag: Salmonella typhimurium 14028s Transposon library grown in M9 minimal medium (arabinose 0.4%), O/N at 37°C with aeration, sample1


title: TL2_14028s_M9+arabinose_sample3_LibAra3_5D670_2


title: TL2_14028s_M9+arabinose_sample2_LibAra2_5D669_3


title: TL2_14028s_invA::cam_IP_mouse2_LibS2invA_7DS108_2

description: biological replicate, Date of Scan Fri May 05 09:47:25 2006

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 02 (Library S2 invA)

label_protocol: incorporation of Cy3-dCTP with Reverse Transcriptase

extract_protocol: arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7)

tag: Salmonella typhimurium 14028s invA::cam Transposon library recovered from spleen 2 days after IP passage of 2.2 x 10^6 through BALB/c mouse 02

source_name: 14028s invA::cam Tn5 lib grown in LB broth (Library 0 invA Mice)

label_protocol: incorporation of Cy5-dCTP with Reverse Transcriptase

tag: Salmonella typhimurium 14028s invA::cam Transposon library grown in Luria-Bertani broth (kanamycin 50ug/ml), O/N at 37°C with aeration


title: TL2_14028s_invA::cam_IP_mouse5_LibS5invA_7DS111_3

description: biological replicate, Date of Scan Mon May 08 10:11:14 2006

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 05 (Library S5 invA)

tag: Salmonella typhimurium 14028s invA::cam Transposon library recovered from spleen 2 days after IP passage of 2.2 x 10^6 through BALB/c mouse 05


title: TL2_14028s_invA::cam_IP_mouse2_LibS2invA_7DS108_1


title: TL2_14028s_invA::cam_IP_mouse5_LibS5invA_7DS111_1


title: TL2_14028s_M9+arabinose_sample1_LibAra1_5D668_1


title: TL2_14028s_M9+arabinose_sample2_LibAra2_5D669_1