title: Comparison of WT Vs NaS1-/- ileum 4

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

description:
Followed protocol described in:
	PMID: 15998744

data_processing:
Scanned using Agilent Scanner.
Image analysis performed using Imagene5.0 Normalised via print tip Loess (R application from Limma) and between arrrays (R application fro SMA)

source_name: WT ileum

label_protocol: Ambion Messageamp IVT

extract_protocol: Qiagen RNeasy total RNA extraction

tag: pool of 4 week old male tissue (n=14)

source_name: NaS1-/- ileum


title: Comparison of WT Vs NaS1-/- ileum

status: Public on Sep 01 2008

type: RNA

description:
Followed protocol described in:
PMID: 15998744

data_processing:
Scanned using Agilent Scanner.
Image analysis performed using Imagene5.0
Normalised via print tip Loess (R application from Limma) and between arrrays (R application fro SMA)

molecule: total RNA

organism: Mus musculus

source_name: WT Ileum

source_name: NaS1-/- ileum.


title: TL2_14028s_invA::cam_IP_mouse3_LibS3invA_7DS109_2

type: other

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri May 05 10:27:30 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.

molecule: other

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 03 (Library S3 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 03

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_M9+arabinose_sample1_LibAra1_5D668_2

type: genomic

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

data_processing: Quantarray 3.0, adaptive quantitation, protocol STv5_SP040504_adapforsmallpins_040817

molecule: genomic DNA

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

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

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

source_name: 14028s Tn5 lib (Library 0)

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

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_invA::cam_IP_mouse4_LibS4invA_7DS110_3

description: biological replicate, Date of Scan Mon May 08 09:48:54 2006

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 04 (Library S4 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 04


title: TL2_14028s_invA::cam_IP_mouse3_LibS3invA_7DS109_1


title: TL2_14028s_invA::cam_IP_mouse5_LibS5invA_7DS111_2

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_mouse6_LibS6invA_7DS112_3

description: biological replicate, Date of Scan Mon May 08 10:45:25 2006

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 06 (Library S6 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 06


title: TL2_14028s_invA::cam_IP_mouse6_LibS6invA_7DS112_1


title: TL2_14028s_invA::cam_IP_mouse6_LibS6invA_7DS112_2


title: TL2_14028s_invA::cam_IP_mouse3_LibS3invA_7DS109_3


title: Comparison of WT Vs NaS1-/- ileum 2

hyb_protocol: Followed protocol described in: PMID: 15998744


title: TL2_14028s_invA::cam_IP_mouse4_LibS4invA_7DS110_2


title: Comparison of WT Vs NaS1-/- ileum 3

scan_protocol: Followed protocol described in: PMID: 15998744


title: TL2_14028s_invA::cam_IP_mouse1_LibS1invA_7DS107_3

description: biological replicate, Date of Scan Fri May 05 14:53:26 2006

source_name: 14028s invA::cam Tn5 lib IP passaged through mouse 01 (Library S1 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 01


title: TL2_14028s_invA::cam_IP_mouse1_LibS1invA_7DS107_2


title: TL2_14028s_invA::cam_IP_mouse2_LibS2invA_7DS108_3

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

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


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 3 MG-U74C

status: Public on Jul 31 2008

city: Amherst

first: D.

middle: Joseph

last: Jerry

state: MA

address: 161 Holdsworth Way

department: Veterinary & Animal Scineces

institute: University of Massachusetts

description: Mammary gland mRNA expression data from mice treated with progesterone.

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U74A GeneChip.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  The trimmed mean target intensity of each array was set to 150.

label: biotin

source_name: mammary gland

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

treatment_protocol: ovariectomized animals were injected daily with 2ug 17-Beta-estrogen + 1 mg progesterone for 4 days

tag: eight week old virgin BALB/cJ mice were ovariectomized followed by a period of one week before treatment to clear endogenous hormones

tag: lymph node-free mammary gland


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 2 MG-U74C


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 4 MG-U74C

treatment_protocol: ovariectomized animals were injected daily with 100ul sesame oil for 4 days


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 3 MG-U74C


title: TL2_14028s_invA::cam_IP_mouse4_LibS4invA_7DS110_1


title: TL2_14028s_M9+arabinose_(3_passages)_sample2_LibM9(2-3)_7DS061_3

description: biological replicate, Date of Scan Wed Feb 22 12:36:48 2006

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

source_name: 14028s Tn5 lib grown in M9 arabinose (3 consecutive rounds to late log ), sample 2 (Library M9 2-3)

label_protocol: incorporation of  Cy3-dCTP with Reverse Transcriptase

tag: Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, sample 2

source_name: 14028s Tn5 lib (Library 0 Exp.2)

label_protocol: incorporation of  Cy5-dCTP with Reverse Transcriptase

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


title: TL2_14028s_M9+arabinose_(3_passages)_sample1_LibM9(1-3)_7DS060_2

description: biological replicate, Date of Scan Wed Feb 22 10:40:32 2006

source_name: 14028s Tn5 lib grown in M9 arabinose (3 consecutive rounds to late log ), sample 1 (Library M9 1-3)

tag: Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, sample 1


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 2 MG-U74C


title: TL2_14028s_invA::cam_IP_mouse1_LibS1invA_7DS107_1


title: TL2_14028s_M9+arabinose_(3_passages)_sample1_LibM9(1-3)_7DS060_1


title: TL2_14028s_M9+arabinose_(3_passages)_sample2_LibM9(2-3)_7DS061_1


title: TL2_14028s_M9+arabinose_(3_passages)_sample2_LibM9(2-3)_7DS061_2


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 2 MG-U74C


title: TL2_14028s_M9+arabinose_(3_passages)_sample1_LibM9(1-3)_7DS060_3


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 4 MG-U74C


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 1 MG-U74C


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 3 MG-U74C


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 2 MG-U74C

extract_protocol: Ultraspec for RNA extraction (Biotexc, Houston, TX)

treatment_protocol: ovariectomized animals were injected daily with 1 mg progesterone for 4 days


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 4 MG-U74C


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 3 MG-U74C


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 5 MG-U74C


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 1 MG-U74C


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 1 MG-U74C


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 1 MG-U74C

description: Mammary gland mRNA expression data from mice treated with estrogen.

treatment_protocol: ovariectomized animals were injected daily with 2ug 17-Beta-estrogen for 4 days


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 3 MG-U74B


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 4 MG-U74B


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 2 MG-U74B


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 3 MG-U74B


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 2 MG-U74B


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 1 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 4 MG-U74C


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 1 MG-U74B


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 5 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 2 MG-U74C


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic repl. 1 MG-U74C


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 2 MG-U74B


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 3 MG-U74B


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 1 MG-U74B


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 3 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 3 MG-U74C


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 4 MG-U74B


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 4 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 3 MG-U74B


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 2 MG-U74B


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 1 MG-U74B


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 1


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 4 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 2 MG-U74B


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 1 MG-U74B


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 3


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 4


title: mammary gland-epithelial-free fat pad-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 2


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 5


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 1


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 3


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 4


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 3


title: mammary gland-vehicle treated-100ul sesame oil intraperitoneally-biologic replicate 2


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 2


title: mammary gland-2ug 17-beta-estrogen + 1mg progesterone intraperitoneally-biologic replicate 1


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 4


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 3


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 2


title: mammary gland-1mg progesterone intraperitoneally-biologic replicate 1


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 2


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 3


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 4


title: LS3 strain replicate 2

status: Public on Jul 15 2008

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2XSSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantization background subtracted

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

source_name: LS3 strain growing in exponential phase replicate 2

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

extract_protocol: Total RNA from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

tag: Total RNA from LS3 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. cerevisiae mitochondrial DNA.

tag: Hybridization on macrochip F22.


title: 11204x7070.1 strain replicate 1

source_name: 11204x7070.1 strain growing in exponential phase replicate 1

tag: Total RNA from 11204x7070.1 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. cerevisiae mitochondrial DNA.

tag: Hybridization on macrochip F19.


title: 11204x11502.1 strain replicate 2

data_processing: Raw image quantization background subtracted.

source_name: 11204x11502.1 strain growing in exponential phase replicate 2

tag: Total RNA from 11204x11502.1 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. uvarum mitochondrial DNA.


title: mammary gland-2ug estrogen intraperitoneally-biologic replicate 1


title: 11204x7070.1 strain replicate 2

source_name: 11204x7070.1 strain growing in exponential phase replicate 2


title: genomic V2-L2-F19

organism: Saccharomyces cerevisiae

source_name: 3002 strain

label_protocol:
Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol).
The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987). Ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli (Gene 57:267-272).

tag: V2-L2-F19 filter hybridization with labeled yeast genomic (3002) DNA. DNA labeling by random priming procedure and 33P-dCTP


title: 12233x6213.1 strain replicate 3

source_name: 12233x6213.1 strain growing in exponential phase replicate 3

tag: Total RNA from 12233x6213.1 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. uvarum mitochondrial DNA.

tag: Hybridization on macrochip F24.


title: genomic V2-L2-F22

tag: V2-L2-F22 filter hybridization with labeled yeast genomic (3002) DNA. DNA labeling by random priming procedure and 33P-dCTP


title: LS3 strain replicate 1

source_name: LS3 strain growing in exponential phase replicate 1


title: 12233x6213.1 strain replicate 1

source_name: 12333x6213.1 strain growing in exponential phase replicate 1


title: 11204x11502.1 strain replicate 3

source_name: 11204x11502.1 strain growing in exponential phase replicate 3


title: LS3 strain replicate 3

source_name: LS3 strain growing in exponential phase replicate 3


title: genomic V2-L2-F24

tag: V2-L2-F24 filter hybridization with labeled yeast genomic (3002) DNA. DNA labeling by random priming procedure and 33P-dCTP


title: 12233x6213.1 strain replicate 2

source_name: 12233x6213.1 strain growing in exponential phase replicate 2


title: epithelium_15: 24h; Air

status: Public on Jul 01 2008

city: Greensboro

first: Elizabeth

middle: Sherman

last: Roberts

state: NC

address: 3200 Northline Ave, Suite 300

institute: Novartis Animal Health US

description: ER_15_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

organism: Rattus rattus

source_name: 24h; Air

extract_protocol:
Extraction Method: PicoPure Nucleic acid spin column
Additional Purification Method: Ribo Amp OA and Affymetrix IVT label

treatment_protocol: in vivo Treatment: Air, Treatment Duration: 3, Units of Duration: hr, Treatment Time: 1, Units of Treatment Time: exposure, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: Additional Information

value: All 18 samples will be available 12/16/05.  RNA was isolated from LCM samples using Arcturus\' PicoPure Isolation kit.  Samples went through two amplifications using Arcturus\' Ribo Amp OA kit with an Affymetrix IVT label.

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ug

tag: Ratio

tag: Technical Replicate

value: norvegicus

tag: Strain or Line

value: Sprague-Dawley rat

tag: NCBI Taxonomy ID

tag: Developmental State

value: adult

tag: Sacrifice Method

value: 60 mg/kg sodium pentbarbital IP

tag: Sex

value: male

tag: Age

tag: Units of Age

value: days


title: 11204x7070.1 strain replicate 3

source_name: 11204x7070.1 strain growing in exponential phase replicate 3

tag: Total RNA from 11204x7070.1 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. cerevisiae mitochondrial DNA.


title: 11204x11502.1 strain replicate 1

source_name: 11204x11502.1 strain growing in exponential phase replicate 1

tag: Total RNA from 11204x11502.1 hybrid wine yeast strain growing in exponential phase in YPD. This hybrid contains S. uvarum mitochondrial DNA.

tag: Hybridization on macrochip F19.


title: epithelium_16: 24h; Air

description: ER_16_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: RNA Integrity Number


title: epithelium_13: 24h; H2S

description: ER_13_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

treatment_protocol: in vivo Treatment: H2S , Treatment Duration: 3, Units of Duration: hr, Treatment Time: 1, Units of Treatment Time: exposure, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: Additional Information


title: epithelium_17: 24h; Air

description: ER_17_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Array Type


title: epithelium_11: 24h; H2S

description: ER_11_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Amount to Core


title: epithelium_14: 24h; H2S

description: ER_14_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

treatment_protocol: in vivo Treatment: H2S, Treatment Repeat: 5, Units of Treatment Repeat: days, Treatment Duration: 3, Units of Duration: hr, Treatment Time: 1, Units of Treatment Time: exposure, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: Units of Amount


title: epithelium_12: 24h; H2S

description: ER_12_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Ratio


title: epithelium_24: 144h; H2S

description: ER_24_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Technical Replicate


title: epithelium_10: 6h; H2S

description: ER_10_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

source_name: 6h; H2S

extract_protocol:
Extraction Method: PicoPure Nucleic acid spin column
Additional Purification Method: Ribo Amp OA and IVT label

tag: Strain or Line


title: epithelium_23: 144h; H2S

description: ER_23_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: NCBI Taxonomy ID


title: epithelium_25: 144h; H2S

description: ER_25_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Developmental State


title: epithelium_8: 6h; H2S

description: ER_8_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Sacrifice Method


title: epithelium_22: 144h; Air

description: ER_22_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

source_name: 144h; Air

treatment_protocol: in vivo Treatment: Air, Treatment Repeat: 5, Units of Treatment Repeat: days, Treatment Duration: 3, Units of Duration: hr, Treatment Time: 1, Units of Treatment Time: exposure, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: Sex


title: epithelium_4: 3h; H2S

description: ER_4_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

source_name: 3h; H2S

tag: Age


title: epithelium_3: 3h; H2S

description: ER_3_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.

tag: Units of Age


title: epithelium_20: 144h; Air

description: ER_20_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_18: 24h; Air

description: ER_18_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_9: 6h; H2S

description: ER_9_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_21: 144h; Air

description: ER_21_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_19: 144h; Air

description: ER_19_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_5: 3h; H2S

description: ER_5_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_6: 3h; H2S

description: ER_6_Rat230_2_IMF RT 0023: frozen sample for laser capture microdissection and RNA microarray analysis.


title: epithelium_26: 144h; H2S

description: ER_26_Rat230_2_IMF RT 0023:frozen sample for laser capture microdissection and RNA microarray analysis.


title: M-Prostate_rep3_R

status: Public on Jun 01 2008

city: São Paulo

first: Eduardo

last: Reis

address: Av. professor Lineu Prestes, 748

department: Departamento de Bioquímica

country: Brazil

institute: Instituto de Química da Universidade de São Paulo

description: Hybridization included external mRNA spikes for quality control of the experiment (Lucidea Microarray ScoreCard. Raw images were analyzed using the ArrayVision software (Version 8.0, Imaging Research Inc.). An array template (or grid) was first automatically aligned to locate the position of each spot in the array, and subsequently manually adjusted to obtain the best possible alignment.

hyb_protocol: Labeled targets were ressuspended in 250 (l of 1 x hybridization buffer (25% formamide, 12.5% of proprietary Microarray Hybridization Buffer Version 2 from Amersham Biosciences cat. RPK0325) denatured for 2 min at 92 ºC and centrifuged at 13,000 rpm for 5 min. All slide processing steps (blocking, hybridization, washing) were carried out on an automated slide processor (ASP) from Amersham Biosciences. The slides were incubated for 16h at 42ºC and subsequently washed at room temperature in 1xSSC/0.2%SDS for 5min, 0.1xSSC/0.2%SDS for 5 min and in 0.1XSSC for 3 min. After the washing steps, slides were flushed with isopropanol and dried with an air flush at 42ºC.

scan_protocol: Images were obtained from each channel by laser scanning using a Generation III Scanner (Amersham Biosciences). Slides were scanned with the following parameters: excitation wave length: 633 nm (Cy5-labeled targets); emission filter: 675 nm (Cy5-labeled targets); PMT voltage: 700 volts (Cy5-labeled targets).

data_processing: We employed in our analyses the Artifact-Removed density value (ARM) calculated for each spot by ArrayVision. The ARM value represents the average of all the pixels remaining in the spot, after first removing pixels with density values that exceed four median absolute deviations (MADs) from the median. The ARM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels).The raw data of each spot was compared to the value of hibridization background using the Lucidea Microarray Scorecard to determine which spots have a signal above or below the detection limit of each hybridization, where the background was given by the signal measured on a negative control (plant cDNA). The 3,686 unique probes are duplicated in each slide (Left and Right sides of the slide), and each transcript was considered as expressed in one side of the slide if its probe intensity was equal to or higher than the mean intensity of the Negative Controls plus three standard deviation in the same sub array. The gene was considered detected in the slide if it was positive on both sides (Left and Right) and was considered as expressed in the tissue if it was detected in all three slides. It was considered as detected in each species if it was detected in at least one tissue. The intensities of all spots of each slide were normalized among the different experiments using the 40% trimmed average intensity of a set of six different housekeeping genes (spotted at 264 different places in each slide) as reference.

source_name: Prostate pool

label_protocol: Labeled targets for hybridizations were generated from total RNA in reverse transcription reactions using oligo dT as RT primer, following strictly the protocol accompanying the CyScribe First-Strand labeling kit (Amersham Biosciences, Piscataway, NJ). In short, 15 (g total RNA was combined with primers in a total volume of 11 (l, denatured at 70°C for 10 minutes, put on ice for 30 seconds, spin down and placed at room temperature for 10 minutes. Nine microliters of a premix solution was added containing 5X Superscript II reaction buffer (5X), 200 U Superscript II reverse transcriptase,  0.1 M DTT, dNTP mix (2 mM dATP, 2 mM dGTP, 2 mMdTTP ,1 mM dCTP) and 1 mM of Cy5-dCTP. After addition of the premix, the reaction was kept at room temperature for 10 minutes and then incubated at 42°C for 1.5 hr. RNA templates were removed by alkaline hydrolysis by adding 2 (l of 2.5 M sodium hydroxide and incubating the mixture at 37° C for 15 minutes.  The labeling reaction was neutralized with 10 (l 2 M MOPS free acid and labeled targets were purified using 96-well Millipore Multiscreen filter plates as follows: 5 volumes of 5.3 M Guanidine-HCl: 150 mM KOAc were added to labeling reactions. The mixture was applied on the plate and washed 4X with 80% EtOH by centrifugation at 3500 rpm for 5 min. Residual EtOH was spin out by an additional centrifugation at 3500 rpm for 5 minutes. Labeled targets were eluted in 50 (l 10mM Tris pH 8.5, by spinning at 3000 rpm for 5 minutes, dried on a SpeedVac and kept at -20°C, protected from light until use.

extract_protocol: Total RNA was purified from cell extracts using Trizol (Invitrogen). Total RNA was treated with of RNAse-free DNAse (RNeasy - Qiagen) for 15min to minimize genomic DNA contaminants. Purity of the isolated RNA was estimated by measuring the ratio A 260/A 280. Integrity of total RNA was checked by electrophoresis using the Bio Sizing total RNA Nano assay in the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Total RNA purified using Trizol from frozen prostate tissues were treated with RNAse-free DNAse (RNeasy – Qiagen) for 15 minute to reduce the levels of genomic DNA contaminant.

tag: Tissues from liver, prostate and kidney from five adult male mice of the Balb/c strain were obtained and frozen in liquid nitrogen.


title: M-Prostate_rep3_L


title: M-Prostate_rep2_R


title: LB DMF 7h suspension cells

status: Public on Jun 30 2008

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

institute: Texas A&M University

description: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100.  For P. aeruginosa with 7-hydroxyindole and indole, 500 mM 7-hydroxyindole in 250 mL DMF, 1000 mM indole in 250 mL DMF, or 250 mL DMF alone were added to cells grown in LB.  The cells were shaken at 250 rpm and 30oC (for indole experiment) or 37oC (for 7-hydroxyindole experiment) for 7 h or 24 h to form biofilms on the glass wool, and RNA was isolated from the suspension cells and the biofilm.

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip P. aeruginosa Genome Array (Affymetrix, P/N 900339) at 50°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa PAO1

source_name: Channel 1

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from suspension cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB and 0.1 % DMF with glass wool at 37oC


title: M-Prostate_rep1_R


title: M-Prostate_rep2_L


title: M-Prostate_rep1_L


title: M-Liver_rep3_R

source_name: Liver pool

treatment_protocol: Total RNA purified using Trizol from frozen liver tissues were treated with RNAse-free DNAse (RNeasy – Qiagen) for 15 minute to reduce the levels of genomic DNA contaminant.


title: M-Liver_rep3_L


title: M-Liver_rep2_R


title: M-Liver_rep1_R


title: M-Liver_rep2_L


title: M-Kidney_rep3_R

source_name: Kidney pool

treatment_protocol: Total RNA purified using Trizol from frozen kidney tissues were treated with RNAse-free DNAse (RNeasy – Qiagen) for 15 minute to reduce the levels of genomic DNA contaminant.


title: M-Liver_rep1_L


title: M-Kidney_rep3_L


title: M-Kidney_rep2_R


title: M-Kidney_rep2_L


title: M-Kidney_rep1_R


title: M-Kidney_rep1_L


title: H-Prostate_rep3_R

organism: Homo sapiens

tag: Five non-tumor samples of human prostate, kidney or liver from our tumor bank were selected. All samples were obtained from patients who signed informed consent, and approval was received from the ethics committees of the hospitals.


title: H-Prostate_rep3_L


title: TMK27_WT_I

city: East Lansing

first: Sookyung

last: Oh

state: MI

department: Horticulture

institute: Michigan State University

description: Enriched for DNA associated with trimethylation of H3 K27

hyb_protocol: Following fragmentation, DNA was hybridized  for 16 hr on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained in the Affymetrix Fluidics Station according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using The GeneChip Scanner 3000 7G

data_processing: Quantile Normalization using TileMap package

organism: Arabidopsis thaliana

source_name: 14 day old seedlings

label_protocol: Biotinylated DNA was prepared according to the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (P/N 702238 Rev. 2, Affymetrix).

growth_protocol: Plants were grown under 16h light on soil

extract_protocol: Chromatin immunoprecipitation using anti-trimethylation of H3 K27 antibody (Upstate)

treatment_protocol: Untreated

tag: Aerial parts of 14 day old seedlings


title: H-Prostate_rep2_L


title: H-Prostate_rep1_R


title: H-Prostate_rep1_L


title: TMK27_WT_II

tag: Enriched for DNA associated with trimethylation of H3 K27


title: Input_vip3_II

description: Input control DNA

extract_protocol: Input control DNA

tag: Input control DNA


title: TMK27_vip3_I


title: diMK36_WT_II

description: Enriched for DNA associated with dimethylation of H3 K36

extract_protocol: Chromatin immunoprecipitation using anti-dimethylation of H3 K36 antibody (Upstate)


title: H-Liver_rep3_R


title: H3_vip3_II

description: Enriched for DNA associated with H3

extract_protocol: Chromatin immunoprecipitation using anti-H3 antibody (Upstate)

tag: Enriched for DNA associated with H3


title: H-Liver_rep2_R


title: H-Liver_rep3_L


title: H-Liver_rep2_L


title: H-Kidney_rep3_R


title: H-Liver_rep1_R


title: H-Liver_rep1_L


title: Input_WT_I

description: Input control DNA


title: H-Prostate_rep2_R


title: H3_WT_I

description: Enriched for DNA associated with H3


title: TMK27_vip3_II


title: H-Kidney_rep2_R


title: H-Kidney_rep3_L


title: diMK27_WT_II

description: Enriched for DNA associated with dimethylation of H3 K27

extract_protocol: Chromatin immunoprecipitation using anti-dimethylation of H3 K27 antibody (Upstate)


title: diMK27_vip3_I

tag: Enriched for DNA associated with dimethylation of H3 K27


title: H-Kidney_rep2_L


title: H3_WT_II

description: Enriched for DNA associated with H3


title: H-Kidney_rep1_R


title: H3_vip3_I

description: Enriched for DNA associated with H3


title: TMK4_vip3_II

description: Enriched for DNA associated with trimethylation of H3 K4

extract_protocol: Chromatin immunoprecipitation using anti-trimethylation of H3 K4 antibody (Upstate)


title: diMK36_vip3_I

tag: Enriched for DNA associated with dimethylation of H3 K36


title: Input_WT_II

description: Input control DNA


title: Input_vip3_I

description: Input control DNA


title: H-Kidney_rep1_L


title: TMK4_vip3_I

tag: Enriched for DNA associated with trimethylation of H3 K4


title: Cell line resistant to Vitamin D vs. sensitive line (MCF7 x MCF7 DR)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: see Costa et all for additional information

hyb_protocol: cDNA was incubated at room temperature for 1 hour with fluorolink monofunctional Cy5 or Cy3 dye (Amersham, Roosendaal, The Netherlands) followed by 15 minutes of 4 mol/L hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen, Leusden, The Netherlands) and mixed with 12 µg poly(dA) (Amersham), 60 µg yeast tRNA (Sigma-Aldrich Chemie, Zwijndrecht, The Netherlands), and 24 µg Cot-1 DNA (Invitrogen). The labeled target was dissolved in 127-µL hybridization mixture containing 46% formamide (Invitrogen), 9.5% dextran sulfate (U.S. Biochemical Corp., Cleveland, USA), 2x SSC, and 0.2% SDS. The labeled target was heated to 70°C for 10 minutes and annealed at 37°C for 1 hour. Slides were hybridized at 37°C overnight (14h). After hybridization, the slides were washed in the HybArray 12, with 50% formamide (Fluka, Sigma-Aldrich Chemie), 2x SSC (pH 7) at 35°C for 15 minutes followed by PI buffer (0.1 mol/L sodium phosphate, 0.1% Igepal Ca630 (pH 8)) at room temperature and three washes of 0.2x SSC, 0.1x SSC, and 0.01x SSC at room temperature followed by centrifugation.

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spot analysis and quality control were fully automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK) and spots with quality flag <1 or confidence value <0.1 were excluded from further analysis. After scanning and data acquisition, genes with spots flagged in more than one array were excluded from further analysis. For the remaining genes, the value of a flagged spot was imputed using K nearest neighbors’ imputation as implemented in the R-package “impute”. Curvature in the MA plots was limited but nevertheless normalized using lowess as implemented in the R-package “MAAnova”. In typical conditions a normal distribution of the ratios is expected. By blocking the degradation of nonsense mRNAs an accumulation of genes with mutations is expected, which can be measured by a “skew” in the “normal” distribution plot towards the positive side.

label_protocol: cDNA probes were generated from 30μg of total RNA, with an oligo(dT) [(dT)20-VN] primer (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with incorporation of dUTP, and indirectly labeled with cyanine-5 dCTP and cyanine-3 dCTP (Perkin-Elmer). cDNA was incubated at room temperature for 1 hour with fluorolink monofunctional Cy5 or Cy3 dye (Amersham, Roosendaal, The Netherlands) followed by 15 minutes of 4 mol/L hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen, Leusden, The Netherlands).

extract_protocol: Cells were incubated with the drug Emetine (Fluka), which inhibits the NMD pathway, hereby blocking the degradation of non-sense mRNAs. Approximately 4x106 cells at 70% confluence were treated with 100 μg/ml emetine for 10 hours (10). Following incubation with emetine, cells were directly lyzed by the addition of TRIzol (Invitrogen). Nucleic acids were quantified using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, USA) and quality was visually confirmed by gel electrophoresis.

tag: Human breast cancer cell line

source_name: MCF7 DR

tag: Human breast cancer cell line resistant to Vitamin D


title: diMK27_WT_I


title: Cell line resistant to Vitamin D vs. sensitive line 31_26_MCF7DRAxMCF7P38

hyb_protocol: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

data_processing: Spot analysis and quality control were fully automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK) and spots with quality flag <1 or confidence value <0.1 were excluded from further analysis. Log2ratios were normalized to their average value. For interpretation and visualization purposes, smoothing was performed with lambda set to 3.0.

source_name: MCF7 DRA

label_protocol:
DNA labeling protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol: Cells (70-80% confluent) cultured in 75 cm2 flasks were harvested using 1 ml/10 cm2 of TRIzol reagent (Invitrogen) and stored at -80ºC until use. RNA and DNA were extracted using TRIzol reagent and according to the manufacturers protocols. Nucleic acids were quantified using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, USA) and quality was visually confirmed by gel electrophoresis.

source_name: MCF7 P38


title: Cell line resistant to Vitamin D vs. sensitive line 31_27_MCF7D3RExMCF7P38

source_name: MCF7 D3RE


title: TMK4_WT_II


title: Cell line resistant to Vitamin D vs. sensitive line 131_25_MCF7_DRxMCF7


title: TMK4_WT_I


title: diMK36_WT_I


title: Cell line resistant to Vitamin D vs. sensitive line (MCF7 x MCF7 VDr)

source_name: MCF7 VDr


title: Cell line resistant to Vitamin D vs. sensitive line (MCF7 D3RE x MCF7)


title: diMK27_vip3_II


title: diMK36_vip3_II


title: MCF7 (2) X MCF7 VDr (2)

data_processing: Spot analysis and quality control were fully automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK) and spots with quality flag <1 or confidence value <0.1 were excluded from further analysis. After scanning and data acquisition, genes with spots flagged in more than one array were excluded from further analysis. For the remaining genes, the value of a flagged spot was imputed using K nearest neighbors’ imputation as implemented in the R-package “impute”. Curvature in the MA plots was limited but nevertheless normalized using lowess as implemented in the R-package “MAAnova”.


title: MCF7 DRA (2) X MCF7 P38 (2)


title: MCF7 X MCF7 DR


title: MCF7 X MCF7 VDr


title: MCF7 P38 (2) X MCF7 D3RE (2)


title: MCF7 X MCF7 DRA


title: MCF7 DR X MCF7

description: see Costa et all for additional informations.


title: Cell line resistant to Vitamin D vs. sensitive line (MCF7 DRA x MCF7 P38)


title: MCF7 VDr X MCF7


title: MCF7 VDr (2) X MCF7 (2)


title: MCF7 P38 (2) X MCF7 DRA (2)


title: MCF7 D3RE X MCF7 P38


title: MCF7 P38 X MCF7 D3RE


title: p21M3_cy5_slide743_041806

city: Birmingham

first: William

middle: J

last: Britt

email: thad007@uab.edu, wbritt@peds.uab.edu

state: AL

address: 1600 6th Ave S

department: Pediatrics, Division Infectious Disease

institute: University of Alabama at Birmingham

description: sample part of larger series

hyb_protocol: The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station (BioMicro Systems, Inc., 4 chamber model).

scan_protocol: Following post hybridization washes, all arrays were scanned on an AXON 4000b scanner.

data_processing: Quantile-Quantile normalization, which ranks each observation on the chip based on expression value and then converts to the value of a deviation that would be expected from the standard normal distribution based on the observation rank. Quantile-quantile normalization results in data from each chip with a mean of zero and standard deviation of 1.0.

source_name: uninfected day 21 post-natal cerebellum

label_protocol: Amino-allyl tagged dUTP (Sigma, A0410).  Additonally, RNA Spike- In controls (Ambion, cat#1780) were added at concentrations ranging from 0 – 200pg per spike per Reverse Transcriptase reaction.  These 8 control spike-ins hybridize to the Ambion control spots on VMSR arrays. Final concentrations of dNTP's in the reaction were 200uM dA,dG,dC, 51uM dT, and 149uM AAdUTP (Sigma A 0410).  cDNA targets generated were incubated with NaOH to hydrolyze any remaining total RNA, then neutralized with HCl, and cleaned over Qiaquick PCR Purification columns (Qiagen, 28106) following manufacturer’s protocol with the exception of the following:  Two washes were completed with 80% ETOH instead of PE buffer and the elution was completed with nuclease-free H2O instead of EB buffer.  The targets were dried to completion and then coupled to either ester-linked Cy5 or Cy3 dyes (Amersham PA23001 Cy3, and PA25001 Cy 5) in 0.1M Sodium Bicarbonate, pH. 9.0 for 60 minutes in a 6ul volume to facilitate the coupling reaction. After quenching of unbound dye with 4M Hydroxylamine (Aldrich 43,136-2) Cy3 and Cy5 pairs were combined and the target pairs were cleaned up over Qiaquick columns again (Qiagen, 28106) and then dried to completion in a speed-vac. The targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target.

extract_protocol: rotor homogenize and phenol chlorophorm extraction

tag: uninfected day 21 post-natal balb-c mouse cerebellum


title: p21infected3_cy3_slide743_041806

description: sample part of larger series

source_name: uninfected day 5 post-natal cerebellum

tag: uninfected day 5 post-natal balb-c mouse cerebellum


title: MCF7 D3RE (2) X MCF7 P38 (2)


title: MCF7 DRA X MCF7 P38

tag: Human breast cancer cell line resistant to vitamin D


title: p21infected4_cy5_slide744_041806

description: sample part of larger series

source_name: infected day 21 post-natal cerebellum

tag: infected day 21 post-natal balb-c mouse cerebellum


title: p21M4_cy3_slide744_041806

description: sample part of larger series


title: p21M2_cy5_slide742_041806

description: sample part of larger series


title: p12mock5_cy3_slide741_041806

description: sample part of larger series

source_name: uninfected day 12 post-natal cerebellum

tag: uninfected day 12 post-natal balb-c mouse cerebellum


title: p12infected5_cy5_slide741_041806

description: sample part of larger series

source_name: infected day 12 post-natal cerebellum

tag: infected day 12 post-natal balb-c mouse cerebellum


title: p12mok4_cy5_slide740_041806

description: sample part of larger series


title: p12infected3_cy3_slide739_041806

description: sample part of larger series


title: p12mok3_cy5_slide739_041806

description: sample part of larger series


title: p8infected5_cy5_slide738_041806

description: sample part of larger series

source_name: infected day 8 post-natal cerebellum

tag: infected day 8 post-natal balb-c mouse cerebellum


title: p8mock5_cy3_slide738_041806

description: sample part of larger series

source_name: uninfected day 8 post-natal cerebellum

tag: uninfected day 8 post-natal balb-c mouse cerebellum


title: Cell line resistant to Vitamin D vs. sensitive line 31_24_MCF7_VDr_DKxMCF7_DK


title: p12infected_cy3_slide580_091305

description: sample part of larger series


title: p8infected2_cy3_slide577_091305

description: sample part of larger series


title: p8infected4_cy3_slide737_041806

description: sample part of larger series


title: p12Mok2_cy5_slide582_091305

description: sample part of larger series


title: p5Minfected_cy3_slide575_091305

description: sample part of larger series

source_name: infected day 5 post-natal cerebellum

tag: infected day 5 post-natal balb-c mouse cerebellum


title: p8infected3_cy3_slide578_091305

description: sample part of larger series


title: p21infected_cy3_slide579_091305

description: sample part of larger series


title: p12infected2_cy3_slide582_091305

description: sample part of larger series


title: p5M_cy5_slide574_091305

description: sample part of larger series


title: p21infected_cy3_slide742_041806

description: sample part of larger series


title: p21M_cy5_slide579_091305

description: sample part of larger series


title: p8infected_cy3_slide576_091305

description: sample part of larger series


title: 96 UTF exp2

status: Public on May 01 2008

city: RTP

first: Edward

last: Karoly

address: MD 58D

department: HSD

institute: U.S. EPA

description: We profiled gene expression of human primary epithelial cells exposed to coarse, fine and ultrafine Chapel Hill particles (250ug/ml) or vehicle for 6h.

hyb_protocol: see affymetrix protocol

scan_protocol: see affymetrix protocol

data_processing: GCOS, raw value with no transformation

label: enzo biotin label

source_name: Human primary epithelial cells

label_protocol: see affymetrix protocol

extract_protocol: RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturer's protocols.  Total RNA was resuspended in RNase free water and assessed with the Agilent 2100 Bioanalyzer and RNA 6000 Nano assay (Agilent Technologies, Palo Alto, CA).  All RNA samples were stored at -80C prior to shipment on dry ice to Expression Analysis Inc, (Durham, NC).

tag: Human primary epithelial cells.  Treatment

value: 6h ultrafine particle (250ug/ml).  Biological replicate 2.


title: p12infected4_cy3_slide740_041806

description: sample part of larger series


title: 99 fine exp3

value: 6h fine particle (250ug/ml).  Biological replicate 3.


title: p8mock_cy5_slide737_041806

description: sample part of larger series


title: 100 UTF exp3

value: 6h ultrafine particle (250ug/ml).  Biological replicate 3.


title: p8mock3_cy5_slide578_091307

description: sample part of larger series


title: p8mok_cy5_slide576_091305

description: sample part of larger series


title: p8mock_cy5_slide577_091307

description: sample part of larger series


title: p5mock_cy5_slide575_091305

description: sample part of larger series


title: 98 coarse exp3

value: 6h coarse particle (250ug/ml).  Biological replicate 3.


title: p5_MCMV infected_cerebellum

description: sample part of larger series

source_name: MCMV infected day 5 post-natal cerebellum

treatment_protocol: rotor homogenize and

tag: MCMV infected day 5 post-natal balb-c mouse cerebellum


title: 97 control exp3

value: 6h control.  Biological replicate 3.


title: p5M_cy5_slide573_091305

description: sample part of larger series


title: 93 control exp2

value: 6h control.  Biological replicate 2.


title: p12M_cy5_slide580_091305

description: sample part of larger series


title: 90 coarse exp1

source_name: human primary epithelial cells

value: 6h coarse particle (250ug/ml)


title: TGH9011 Replicate 1

status: Public on Apr 21 2008

city: Lethbridge

middle: N

last: Taboada

state: Alberta

address: PO Box 640, TWP Rd. 9-1

country: Canada

institute: Public Health Agency of Canada

description: CGH analysis of Strain TGH9011 vs. Strain NCTC_11168

hyb_protocol: Equivalent amounts of Cy-3 labelled experimental and Cy-5 labelled control genomic DNAs with similar dye incorporation efficiencies were pooled and co-hybridized overnight to the microarray at 37ºC in DIG-easy hyb solution (Roche). Washes performed as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

scan_protocol: Microarrays were scanned using a Chipreader laser scanner (BioRad, Mississauga, ON) according to the manufacturer’s recommendations.  Laser power and gain were adjusted to obtain balanced scans on control spots.

data_processing: Features were extracted using ArrayPro Analyzer version 4.5 and imported into the BioArray Software Environment (BASE version 1.2). Spots flagged due to poor spot morphology or low signal intensity (less than 3 X local background) were filtered out. After print-tip Loess normalization, data was used to calculate the average log ratio [log2(Signal Experimental / Signal Control)] of replicate spots

organism: Campylobacter jejuni

source_name: TGH9011 genomic DNA

label_protocol: Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

growth_protocol: Cells from each strain were grown as a confluent lawn on  Mueller-Hinton agar plates at 42ºC  for 36 Hrs. under microaerophilic conditions prior to genomic DNA isolation

extract_protocol: Approximately 1X10^10 cells were harvested and genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

tag: Strain TGH9011

source_name: NCTC_11168 genomic DNA

tag: Strain NCTC_11168


title: RM1221 Replicate 1

description: CGH analysis of Strain RM1221 vs. Strain NCTC_11168

source_name: RM1221 genomic DNA

tag: Strain RM1221


title: 89 control exp1

value: 6h control, exp 1.


title: PC72 Replicate 1

description: CGH analysis of Strain PC72 vs. Strain NCTC_11168

source_name: PC72 genomic DNA

tag: Strain PC72


title: 95 fine exp2

value: 6h fine particle (250ug/ml).  Biological replicate 2.


title: NZ_T0157 Replicate 1

description: CGH analysis of Strain NZ_T0157 vs. Strain NCTC_11168

source_name: NZ_T0157 genomic DNA

tag: Strain NZ_T0157


title: NZ_Pstt2 Replicate 1

description: CGH analysis of Strain NZ_Pstt2 vs. Strain NCTC_11168

source_name: NZ_Pstt2 genomic DNA

tag: Strain NZ_Pstt2


title: NZ_Pstau Replicate 1

description: CGH analysis of Strain NZ_Pstau vs. Strain NCTC_11168

source_name: NZ_Pstau genomic DNA

tag: Strain NZ_Pstau


title: PC69 Replicate 1

description: CGH analysis of Strain PC69 vs. Strain NCTC_11168

source_name: PC69 genomic DNA

tag: Strain PC69


title: NZ_Pst1 Replicate 1

description: CGH analysis of Strain NZ_Pst1 vs. Strain NCTC_11168

source_name: NZ_Pst1 genomic DNA

tag: Strain NZ_Pst1


title: NZ_tau330 Replicate 1

description: CGH analysis of Strain NZ_tau330 vs. Strain NCTC_11168

source_name: NZ_tau330 genomic DNA

tag: Strain NZ_tau330


title: NCTC_13266 Replicate 1

description: CGH analysis of Strain NCTC_13266 vs. Strain NCTC_11168

source_name: NCTC_13266 genomic DNA

tag: Strain NCTC_13266


title: 92 UTF exp1

value: 6h ultrafine particle (250ug/ml).  Biological replicate 1.


title: p5infected_cy3_slide574_091305

description: sample part of larger series


title: NZ_T0346b Replicate 1

description: CGH analysis of Strain NZ_T0346b vs. Strain NCTC_11168

source_name: NZ_T0346b genomic DNA

tag: Strain NZ_T0346b


title: NCTC_13264 Replicate 1

description: CGH analysis of Strain NCTC_13264 vs. Strain NCTC_11168

source_name: NCTC_13264 genomic DNA

tag: Strain NCTC_13264


title: NZ_T1012 Replicate 1

description: CGH analysis of Strain NZ_T1012 vs. Strain NCTC_11168

source_name: NZ_T1012 genomic DNA

tag: Strain NZ_T1012


title: NZ_T0446b Replicate 1

description: CGH analysis of Strain NZ_T0446b vs. Strain NCTC_11168

source_name: NZ_T0446b genomic DNA

tag: Strain NZ_T0446b


title: 91 fine exp 1

tag: Human primary epithelial cells.  Treatment

value: 6h fine particle (250ug/ml). Biological replicate 1.


title: NZ_T1018 Replicate 1

description: CGH analysis of Strain NZ_T1018 vs. Strain NCTC_11168

source_name: NZ_T1018 genomic DNA

tag: Strain NZ_T1018


title: NCTC_13262 Replicate 1

description: CGH analysis of Strain NCTC_13262 vs. Strain NCTC_11168

source_name: NCTC_13262 genomic DNA

tag: Strain NCTC_13262


title: NCTC_13261 Replicate 1

description: CGH analysis of Strain NCTC_13261 vs. Strain NCTC_11168

source_name: NCTC_13261 genomic DNA

tag: Strain NCTC_13261

tag: Strain NCTC_11168


title: NCTC_13259 Replicate 1

description: CGH analysis of Strain NCTC_13259 vs. Strain NCTC_11168

source_name: NCTC_13259 genomic DNA

tag: Strain NCTC_13259

source_name: NCTC_11168 genomic DNA


title: NCTC_13257 Replicate 1

description: CGH analysis of Strain NCTC_13257 vs. Strain NCTC_11168

source_name: NCTC_13257 genomic DNA

tag: Strain NCTC_13257


title: NCTC_13260 Replicate 1

description: CGH analysis of Strain NCTC_13260 vs. Strain NCTC_11168

source_name: NCTC_13260 genomic DNA

tag: Strain NCTC_13260


title: MK104 Replicate 1

description: CGH analysis of Strain MK104 vs. Strain NCTC_11168

source_name: MK104 genomic DNA

tag: Strain MK104


title: K569 Replicate 1

description: CGH analysis of Strain K569 vs. Strain NCTC_11168

source_name: K569 genomic DNA

tag: Strain K569


title: IcelandH51 Replicate 1

description: CGH analysis of Strain IcelandH51 vs. Strain NCTC_11168

source_name: IcelandH51 genomic DNA

tag: Strain IcelandH51


title: NCTC_11168 Replicate 1

description: CGH analysis of Strain NCTC_11168 vs. Strain NCTC_11168

source_name: NCTC_11168 genomic DNA genomic DNA


title: NCTC_13254 Replicate 1

description: CGH analysis of Strain NCTC_13254 vs. Strain NCTC_11168

source_name: NCTC_13254 genomic DNA

tag: Strain NCTC_13254


title: NCTC_11351 Replicate 1

description: CGH analysis of Strain NCTC_11351 vs. Strain NCTC_11168

source_name: NCTC_11351 genomic DNA

tag: Strain NCTC_11351


title: NCTC_13255 Replicate 1

description: CGH analysis of Strain NCTC_13255 vs. Strain NCTC_11168

source_name: NCTC_13255 genomic DNA

tag: Strain NCTC_13255


title: NCTC_13258 Replicate 1

description: CGH analysis of Strain NCTC_13258 vs. Strain NCTC_11168

source_name: NCTC_13258 genomic DNA

tag: Strain NCTC_13258


title: IcelandH23 Replicate 1

description: CGH analysis of Strain IcelandH23 vs. Strain NCTC_11168

source_name: IcelandH23 genomic DNA

tag: Strain IcelandH23


title: Iceland1102 Replicate 1

description: CGH analysis of Strain Iceland1102 vs. Strain NCTC_11168

source_name: Iceland1102 genomic DNA

tag: Strain Iceland1102


title: GBS_PG836 Replicate 1

description: CGH analysis of Strain GBS_PG836 vs. Strain NCTC_11168

source_name: GBS_PG836 genomic DNA

tag: Strain GBS_PG836


title: Iceland1861 Replicate 1

description: CGH analysis of Strain Iceland1861 vs. Strain NCTC_11168

source_name: Iceland1861 genomic DNA

tag: Strain Iceland1861


title: IcelandH21 Replicate 1

description: CGH analysis of Strain IcelandH21 vs. Strain NCTC_11168

source_name: IcelandH21 genomic DNA

tag: Strain IcelandH21


title: 94 coarse exp2

description: We profiled gene expression of human primary epithelial cells exposed to coarse, fine and ultrafine Chapel Hill particles (250ug/ml) or vehicle for 6h.

source_name: Human primary epithelial cells

tag: Human primary epithelial cells.  Treatment

value: 6h coarse particle (250ug/ml).  Biological replicate 2.


title: CCUG_7800 Replicate 1

description: CGH analysis of Strain CCUG_7800 vs. Strain NCTC_11168

source_name: CCUG_7800 genomic DNA

tag: Strain CCUG_7800

source_name: NCTC_11168 genomic DNA

tag: Strain NCTC_11168


title: F-M_F08 Replicate 1

description: CGH analysis of Strain F-M_F08 vs. Strain NCTC_11168

source_name: F-M_F08 genomic DNA

tag: Strain F-M_F08


title: IcelandH40 Replicate 1

description: CGH analysis of Strain IcelandH40 vs. Strain NCTC_11168

source_name: IcelandH40 genomic DNA

tag: Strain IcelandH40


title: F-M_C089 Replicate 1

description: CGH analysis of Strain F-M_C089 vs. Strain NCTC_11168

source_name: F-M_C089 genomic DNA

tag: Strain F-M_C089


title: CNET_109 Replicate 1

description: CGH analysis of Strain CNET_109 vs. Strain NCTC_11168

source_name: CNET_109 genomic DNA

tag: Strain CNET_109


title: ATCC_43431 Replicate 1

description: CGH analysis of Strain ATCC_43431 vs. Strain NCTC_11168

source_name: ATCC_43431 genomic DNA

tag: Strain ATCC_43431


title: CNET_025 Replicate 1

description: CGH analysis of Strain CNET_025 vs. Strain NCTC_11168

source_name: CNET_025 genomic DNA

tag: Strain CNET_025


title: CNET_043 Replicate 1

description: CGH analysis of Strain CNET_043 vs. Strain NCTC_11168

source_name: CNET_043 genomic DNA

tag: Strain CNET_043


title: CNET_031 Replicate 1

description: CGH analysis of Strain CNET_031 vs. Strain NCTC_11168

source_name: CNET_031 genomic DNA

tag: Strain CNET_031


title: ATCC_33560 Replicate 1

description: CGH analysis of Strain ATCC_33560 vs. Strain NCTC_11168

source_name: ATCC_33560 genomic DNA

tag: Strain ATCC_33560


title: CNET_106 Replicate 1

description: CGH analysis of Strain CNET_106 vs. Strain NCTC_11168

source_name: CNET_106 genomic DNA

tag: Strain CNET_106


title: ATCC_29428 Replicate 1

description: CGH analysis of Strain ATCC_29428 vs. Strain NCTC_11168

source_name: ATCC_29428 genomic DNA

tag: Strain ATCC_29428


title: Esophageal tissue from Sprague-Dawley rat treated with OSU-HDAC42

status: Public on Mar 20 2008

city: Columbus

first: Laura

middle: A

last: Kresty

state: OH

address: CCC Building, Rm 302B

department: Internal Medicine

institute: The Ohio State University

description: Gene expression data from esophageal tissue of Sprague-Dawley rats treated with OSU-HDAC42

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the 230 2.0 chip (Affymetrix).  Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

organism: Rattus norvegicus

source_name: Sprague-Dawley rat

label_protocol: Biotinylated cRNA were prepared from a minimum of 1 ug total RNA.

growth_protocol: Male Sprague-Dawley rats 5-6 weeks of age were purchased from Taconic (Germantown, NY).

extract_protocol: Trizol extraction of total RNA was performed per the manufacterer's instructions.

treatment_protocol: Seven doses of OSU-HDAC42 (50 mg/kg body weight) or vehicle were delivered by gavage to the rats over 15 days (thrice weekly plus one additional dose), for a total dose of 350 mg/kg.  On day 15 (24 hours post the final administration of OSU-HDAC42), the rats were euthanized by CO2 asphyxiation, blood was drawn, gross necropsy performed,  and multiple organs harvested for protein isolation and histopathologic evaluation.

tag: Male Sprague-Dawley rats 5-7 weeks of age treated with OSU-HDAC42


title: Esophagel tissue from Sprague-Dawley rat treated with vehicle

description: Gene expression data from esophageal tissue of Sprague-Dawley rats treated with vehicle

tag: Male Sprague-Dawley rats 5-7 weeks of age treated with vehicle


title: UP28 Basal vs REF

status: Public on Mar 01 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 50% formamide/GE healthcare hyb buffer, 42 degrees for 3 nights.

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 ul hybridisation mix (19 ul Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150ul aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,500. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

source_name: UP28 Basal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Basal epithelial cells (KRT14+ve) isolated by Palm Microbeam (Zeiss) system. )

label_protocol: Total RNA (4 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Extraction of RNA from low cell numbers.  Column based.

tag: gender

tag: tissue type

value: normal

source_name: Human Pooled Universal Reference_Jennifer.Knight_06-06-14(Human Pooled Universal reference (BD Biosciences) amplified 2 rounds with AmpTec GmBH TRinucleotide kit for degraded RNA. )

extract_protocol: Purchased from BD Biosciences

tag: subset

value: Pooled human reference


title: PNB21 CD133- cult vs REF

description: Cohybridised with 5ug of Human Reference RNA.

scan_protocol: Scanner: Axon4000A. Voltage: 10. Resolution (micrometers): 430,370.

source_name: PNB21 CD133- cult(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)

value: tumor

source_name: Human Pooled Reference RNA(BD Biosciences Human Pooled Reference RNA. )


title: Low calorie diet and stabilization N9

status: Public on Mar 26 2008

city: Paris

first: Karine

last: Clement

address: place du parvis Notre-Dame

department: Service de Medecine et Nutrition

country: France

institute: Hotel-Dieu

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57443.gif

hyb_protocol: Cy3 (before) and Cy5 (after weight reduction) probes from the same subject were purified and hybridized as described in Viguerie et al, J Clin Endocrinol Metab 89: 2000-2014 (2004).

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 4720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement

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

source_name: before weight loss program

label_protocol: Fluorescent probes were synthesized from 1 ug of aRNA using the CyScribe First Strand cDNA Labelling Kit (Amersham Biosciences, Orsay, France)

extract_protocol:
Total RNA preparation and amplification: Total RNA from frozen biopsies was prepared and amplified as previously described (Viguerie et al, J Clin Endocrinol Metab 89: 2000?2014, 2004). Total and amplified RNA (aRNA) concentration as well as quality check was performed using the Agilent 2100 bioanalyzer and RNA 6000 labChip Kit (Agilent Technologies, Massy, France)
Total RNA was extracted using the RNA STAT-60 isolation reagent (Tel-Test, Friendswood, TX). Total RNA quantity and quality were assessed using the Agilent 2100 bioanalyzer and RNA 6000 labChip kit (Agilent Technologies, Massy, France).Amplified RNA (aRNA) were prepared using the Message Amp aRNA kit (Ambion, Cambridgeshire, UK) (14, 15). Briefly, 400 ng total RNA were used for an RT reaction containing a T7 promoter sequence primer. After second-strand cDNA synthesis, in vitro transcription wasperformed overnight resulting in an approximately 1000-fold yield in aRNA. aRNA quantity and quality were assessed using the Agilent 2100 bioanalyzer.; Protocol Type = Extract preparation; Performer: Karine,,Clement
Total RNA was extracted using the RNA STAT-60 isolation reagent (Tel-Test, Friendswood, TX). Total RNA quantity and quality were assessed using the Agilent 2100 bioanalyzer and RNA 6000 labChip kit (Agilent Technologies, Massy, France).Amplified RNA (aRNA) were prepared using the Message Amp aRNA kit (Ambion, Cambridgeshire, UK) (14, 15). Briefly, 400 ng total RNA were used for an RT reaction containing a T7 promoter sequence primer. After second-strand cDNA synthesis, in vitro transcription wasperformed overnight resulting in an approximately 1000-fold yield in aRNA. aRNA quantity and quality were assessed using the Agilent 2100 bioanalyzer.; Protocol Type = Extract preparation; Performer: Karine,,Clement

tag: Viguerie_Subjects and study design; Six obese Caucasian premenopausal women were submitted to a weight loss program including three phases. The first one was a 4-wk very low calorie liquid formula diet (3.3 MJ/day, GAYELORD HAUSER?). The second phase was a 3 to 6-wk low calorie diet (4 to 5 MJ/day) until reaching a loss of 10% of the initial body weight. The last phase was a 4-wk isocaloric diet (mean 5.8 MJ/day), planned to stabilize the new body weight. Percutaneous biopsy of the vastus lateralis muscle was obtained in obese women before and after the weight loss program.; Protocol Type = Biological Sample; Performer

value: Karine,,Clement

source_name: after weight loss program


title: UP64 CD133- cult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 635,532. Resolution (micrometers): 10.

source_name: UP64 CD133- cultured(Cultured prostate primary epithelial cells. CD133-cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)

value: male

source_name: Human Pooled Universal Reference_Chris_09-2006(Human pooled reference RNA (BD Biosciences) amplified 2 rounds using the RiboAmp HS kit. )


title: UP23 Basal vs REF

description: 50% formamide/GE healthcare hyb buffer, 42 degrees for 3 nights

scan_protocol: Scanner: Axon4000B-1. Voltage: 580,520. Resolution (micrometers): 10.

source_name: UP23 Basal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Basal epithelial cells (KRT14+ve) isolated by Palm Microbeam (Zeiss) system. )


title: UP45 Luminal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 520,520. Resolution (micrometers): 10.

source_name: UP45 Luminal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Luminal epithelial cells (KRT14-ve) isolated by Palm Microbeam (Zeiss) system.  )


title: Low calorie diet and stabilization N7

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57353.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 4830; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement

extract_protocol:
Total RNA preparation and amplification: Total RNA from frozen biopsies was prepared and amplified as previously described (Viguerie et al, J Clin Endocrinol Metab 89: 2000?2014, 2004). Total and amplified RNA (aRNA) concentration as well as quality check was performed using the Agilent 2100 bioanalyzer and RNA 6000 labChip Kit (Agilent Technologies, Massy, France)
Total RNA was extracted using the RNA STAT-60 isolation reagent (Tel-Test, Friendswood, TX). Total RNA quantity and quality were assessed using the Agilent 2100 bioanalyzer and RNA 6000 labChip kit (Agilent Technologies, Massy, France).Amplified RNA (aRNA) were prepared using the Message Amp aRNA kit (Ambion, Cambridgeshire, UK) (14, 15). Briefly, 400 ng total RNA were used for an RT reaction containing a T7 promoter sequence primer. After second-strand cDNA synthesis, in vitro transcription wasperformed overnight resulting in an approximately 1000-fold yield in aRNA. aRNA quantity and quality were assessed using the Agilent 2100 bioanalyzer.; Protocol Type = Extract preparation; Performer: Karine,,Clement


title: UP45 Basal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 560,540. Resolution (micrometers): 10.

source_name: UP45 Basal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Basal epithelial cells (KRT14+ve) isolated by Palm Microbeam (Zeiss) system. )


title: Low  calorie diet and stabilization N12

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57891.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement


title: PNB13A CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 540,390. Resolution (micrometers): 10.

source_name: PNB13A CD133- cultured(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: PNB6 CD133+

scan_protocol: Scanner: Axon4000B-1. Voltage: 550,530. Resolution (micrometers): 10.

source_name: PNB6 CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP28 Luminal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 10. Resolution (micrometers): 510,480.

source_name: UP28 Luminal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Luminal epithelial cells (KRT14-ve) isolated by Palm Microbeam (Zeiss) system. )


title: PNB10 Cd133- cult vs REF

description: Labelled 5ug of amplified RNA with Cy5.

scan_protocol: Scanner: Axon4000B-1. Voltage: 390,350. Resolution (micrometers): 10.

source_name: PNB 10 CD133- cultured(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP43 Luminal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 580,590. Resolution (micrometers): 10.

source_name: UP43 Luminal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Luminal epithelial cells (KRT14-ve) isolated by Palm Microbeam (Zeiss) system. )


title: UP43 Basal

scan_protocol: Scanner: Axon4000B-1. Voltage: 590,570. Resolution (micrometers): 10

source_name: UP43 Basal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Basal epithelial cells (KRT14+ve) isolated by Palm Microbeam (Zeiss) system. )


title: PNB20 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 570,530. Resolution (micrometers): 10.

source_name: PNB20 CD133- cultured(Cultured prostate primary epithelial cells. CD133-cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system    )


title: UP41 Luminal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 450,500. Resolution (micrometers): 10.

source_name: UP41 Luminal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Luminal epithelial cells (KRT14-ve) isolated by Palm Microbeam (Zeiss) system. )

source_name: Human Pooled Universal Reference_Jennifer.Knight_06-06-14(Human Pooled Universal reference (BD Biosciences) amplified 2 rounds with AmpTec GmBH TRinucleotide kit for degraded RNA. )


title: UP50 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 500,520. Resolution (micrometers): 10.

source_name: UP50 CD133+ cult(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)

source_name: Human Pooled Reference RNA(BD Biosciences Human Pooled Reference RNA. )


title: Low calorie diet and stabilization N6

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57021.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement

source_name: before weight loss program

source_name: after weight loss program


title: UP57 CD133- cultured vs REF #3

source_name: UP57 CD133- cultured(Cultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB20 CD133+ cult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 500,410. Resolution (micrometers): 10.

source_name: PNB20 CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP41 Basal vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 510,480. Resolution (micrometers): 10.

source_name: UP41 Basal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Basal epithelial cells (KRT14+ve) isolated by Palm Microbeam (Zeiss) system. )


title: Low calorie diet and stabilization N11

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57877.gif


title: UP23 Luminal vs REF

source_name: UP23 Luminal(Frozen BPH human tissue sections, stained with haematoxylin, antibody stained for KRT14 and DAB to visualise. Luminal epithelial cells (KRT14-ve) isolated by Palm Microbeam (Zeiss) system. )


title: PNB6 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 510,460. Resolution (micrometers): 10.

source_name: PNB6 CD133- cultured(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB13A CD133+ vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 635,532. Resolution (micrometers): 10.

source_name: PNB13A CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: Low calorie diet and stabilization N10

description:
Simple annotation: Normal tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57725.gif

hyb_protocol: not provided


title: UP57 CD133+ cult vs REF

source_name: UP57 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP46 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,410. Resolution (micrometers): 10.

source_name: UP46 CD133- cultured(Cultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP48 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 510,390. Resolution (micrometers): 10.

source_name: UP48 CD133- cultured(Cultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP55 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 470,410. Resolution (micrometers): 10.

source_name: UP55 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP55 CD133- cult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 470,400. Resolution (micrometers): 10.

source_name: UP55 CD133- cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP64 CD133+ cultured vs REF

source_name: UP64 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP46 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 510,410. Resolution (micrometers): 10.

source_name: UP46 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP55 CD133+ uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 430,470. Resolution (micrometers): 10.

source_name: UP55 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP43 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 470,370. Resolution (micrometers): 10.

source_name: UP43 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)

source_name: Human Pooled Reference RNA(BD Biosciences Human Pooled Reference RNA. )


title: PNB 21 CD133+ cult vs REF

description: Invitrogen system. 5ug each RNA.

scan_protocol: Scanner: Axon4000A. Voltage: 420,390. Resolution (micrometers): 10.

source_name: PNB 21 CD133+ cult(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB 10 CD133+ cult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 420,350. Resolution (micrometers): 10.

source_name: PNB10 CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system. )


title: UP64 CD133- uncult vs REF

source_name: UP64 CD133- uncultured(Uncultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system    )

source_name: Human Pooled Universal Reference_Chris_09-2006(Human pooled reference RNA (BD Biosciences) amplified 2 rounds using the RiboAmp HS kit. )


title: UP48 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 500,380. Resolution (micrometers): 10.

source_name: UP48 CD133+ cultured(Cultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP50 CD133- uncult vs REF

source_name: UP50 CD133- uncultured(Uncultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP43 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 490,400. Resolution (micrometers): 10.

source_name: UP43 CD133- cultured(Cultured prostate primary epithelial cells. CD133-cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP55 CD133- uncult vs REF

description: Labelled 5ug of amplified RNA with Cy5. Invitrogen post labelling system.

scan_protocol: Scanner: Axon4000B-1. Voltage: 570,520. Resolution (micrometers): 10.

source_name: UP55 CD133- uncultured(Uncultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP64 CD133+ uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 500,460. Resolution (micrometers): 10.

source_name: UP64 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: UP57 CD133+ uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 510,450. Resolution (micrometers): 10.

source_name: UP57 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP57 CD133- uncultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 530,500. Resolution (micrometers): 10.

source_name: UP57 CD133- cultured(Cultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB9 CD133+ cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 420,350. Resolution (micrometers): 10

source_name: PNB9 CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB9 CD133- cultured vs REF

source_name: PNB9 CD133- cultured(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB11 CD133+ cult vs REF

description: Labelled 5ug of amplified RNA with Cy5.

scan_protocol: Scanner: Axon4000A. Voltage: 390,350 . Resolution (micrometers): 10.

source_name: PNB11 CD133+ cultured(Cultured prostate needle biopsy. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP35 CD133+ uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 600,500. Resolution (micrometers): 10.

source_name: UP35 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP35 CD133- uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 500,400. Resolution (micrometers): 10.

source_name: UP35 CD133- uncultured(Uncultured prostate primary epithelial cells. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: PNB11 Cd133- cult vs REF

scan_protocol: Scanner: Axon4000A. Voltage: 1450,390. Resolution (micrometers): 10.

source_name: PNB 11 CD133- cultured(Cultured prostate needle biopsy. CD133- cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)

source_name: Human Pooled Reference RNA(BD Biosciences Human Pooled Reference RNA. )


title: UP50 CD133- cultured vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,350. Resolution (micrometers): 10.

source_name: UP50 CD133- cultured(Cultured prostate primary epithelial cells. CD133-cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system.)


title: SDJP3

status: Public on Feb 15 2008

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: All data are derived from the same batch of human ES cells (line H9, WA-09). With the exception of the “UD” file all files represent neural cell types derived from the undifferentiated hESCs. Following mechanical isolation, rosettes were maintained for various passages in the presence of defined growth factors and morphogen factors as indicated below at the R-NSC stage. Cells at the NSCFGF/EGF stage were derived from mechanically isolated neural rosettes that were purified and long-term expanded as attached monolayer cultures in serum free medium in the presence of FGF2/EGF.

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: MAS5.0.  Global intensity targetted to 500

source_name: human ES cells (line H9, WA-09).

label_protocol: Ambion Message Amp.

extract_protocol: Trizol and RNEasy

tag: Passage 3 R-NSC stage cells maintained in the presence of SHH, Dll4, and Jagged 1


title: UP43 CD133- uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,390. Resolution (micrometers): 10.

source_name: UP43 CD133- uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: UP50 CD133+ uncult vs REF

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,470. Resolution (micrometers): 10.

source_name: UP50 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)


title: FL_Late

source_name: human ES cells (line H9, WA-09)

tag: NSCsFGF/EGF stage cells after long-term expansion in the presence of FGF2 and EGF


title: M3a - W83_MDS

status: Public on Feb 01 2008

city: Gainesville

first: Paulo

last: Rodrigues

state: FL

address: 1600 Archer Rd

department: Oral Biology

institute: University of Florida

description: Biological replicate 4 of 4. Control W83 cells, untreated, harvested at late-log growth phase.

hyb_protocol: Four individual Cy3-labeled cDNA samples originating from four different cultures of W83 or W830593 grown in broth without antibiotics, were hybridized to the arrays along with Cy5-labeled reference cDNA samples, for a total of 8 slides.  Hybridizations were carried out in a MAUI 4-bay hybridization system (BioMicro Systems) for 16 h at 42ºC.

scan_protocol: GenePix scanner (Axon) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel) with a Cy3:Cy5 ratio of 1:1.

data_processing: 16-bit TIFF single-channel images were stored and later loaded into TIGR Spotfinder software (http://www.tm4.org/spotfinder.html). The intensity values of each spot were measured and then normalized using LOWESS (LocFit Normalization – mode: global) and Interlog Mean (Interactive Log Mean Centering Normalization) using the default settings, but with the following modification: one bad channel tolerance: generous; followed by in-slide replicate analysis using TIGR MIDAS software (http://www.tm4.org/midas.html). Spots that were flagged as faulty, due to either low intensity values or signal saturation, were automatically discarded. Final statistical analysis was carried out using BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). A total of 1902 genes passed the filtering criteria after the analysis by the BRB software. Class prediction was then, determined at p value of 0.005.

organism: Porphyromonas gingivalis

source_name: Total RNA from W83 (control) labeled with Cyanine-3 (green)

label_protocol: Reverse transcription reactions were performed according to the protocol provided by The Institute of Genomic Research (TIGR) at http://pfgrc.tigr.org/protocols.shtml with the following minor modifications: Superscript III (Invitrogen) was used as the reverse transcriptase, the amount of RNA used was increased to 5.0 µg, and the molar ratio of aa-dUTP:dTTP used was 2:1. Purified W83 and LY2003 cDNAs were then, coupled with Cy3, while reference cDNAs were coupled with Cy5

growth_protocol: P. gingivalis wild type W83 and strain W830593 were grown in 40 ml of TSB to an optical density of 2.0 at 600 nm

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

tag: strain W83

source_name: Total RNA isolated from W83 cells grown in TSB to an optical density of 0.5, 1.0, 1.5 and 2.0 at 600 nm, pooled and labeled with Cyanine-5 (green).


title: UD-Undifferentiated

tag: undifferentiated human ES cells (line H9, WA-09)


title: BASFP2

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

label: Biotin

label_protocol: Ambion message Amp.

extract_protocol: Trizol+RNEasy

tag: Passage 2 R-NSC stage cells maintained in the presence of SHH and FGF8


title: FM_Early

tag: Passage 1 R-NSC stage cells following FACS mediated isolation of Forse1- cells


title: M6a - W83_MDS

description: Biological replicate 2 of 4. Control W83 cells, untreated, harvested at late-log growth phase.


title: M7a - W83_MDS

description: Biological replicate 1 of 4. Control W83 cells, untreated, harvested at late-log growth phase.


title: M4a - W83_MDS

description: Biological replicate 3 of 4. Control W83 cells, untreated, harvested at late-log growth phase.


title: M5a - htrA_MDS

description: Biological replicate 4 of 4. htrA mutant cells, untreated, harvested at late-log growth phase.

source_name: Total RNA from htrA mutant labeled with Cyanine-3 (green)

tag: htrA mutant strain W83


title: BASFP3

tag: Passage 3 R-NSC stage cells maintained in the presence of SHH and FGF8


title: FP_early

tag: Passage 1 R-NSC stage cells following FACS mediated isolation of Forse1+ cells


title: M8a - htrA_MDS

description: Biological replicate 3 of 4. htrA mutant cells, untreated, harvested at late-log growth phase.