title: Tissue_BC_Tamoxifen_913

status: Public on Aug 13 2010

city: Woburn

first: Christos

last: Hatzis

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX (MDA) or 3000 (JBI).

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html). MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

source_name: tissue from breast tumor excision

label_protocol: A single-round of T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA was used for cRNA synthesis.

extract_protocol: Total RNA was extracted from fresh frozen tissue specimens from breast cancer patients using Qiagen RNeasy columns.

tag: patient id

tag: profiling lab

value: JBI

value: breast cancer

tag: estrogen receptor (er) status

value: ER+

tag: endocrine therapy

value: Tamoxifen treatment for 5 years

tag: nodal status (0=negative, 1=positive, na=not applicable)

tag: distant relapse (1=dr, 0 censored)

tag: event time (years)


title: Tissue_BC_Tamoxifen_894

type: RNA

state: MA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Tissue_BC_Tamoxifen_928


title: Tissue_BC_Tamoxifen_944


title: Tissue_BC_Tamoxifen_887


title: Tissue_BC_Tamoxifen_890


title: PZ_U133A_2_7-1016

status: Public on Sep 15 2010

city: Boston

first: Lakshmanan

middle: K

last: Iyer

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to manufactuer's instructions on U133A 2 Array. GeneChips were washed and stained as per manufacturer's instructions.

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

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

source_name: bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

tag: cell type

value: CD138-selected plasma cells

tag: cyclin d1 expression level

value: low


title: Tissue_BC_Tamoxifen_837


title: Tissue_BC_Tamoxifen_848


title: Tissue_BC_Tamoxifen_876


title: Tissue_BC_Tamoxifen_638


title: Tissue_BC_Tamoxifen_738


title: Tissue_BC_Tamoxifen_829


title: Tissue_BC_Tamoxifen_705


title: Tissue_BC_Tamoxifen_736


title: Tissue_BC_Tamoxifen_711


title: Tissue_BC_Tamoxifen_700


title: Tissue_BC_Tamoxifen_771


title: Tissue_BC_Tamoxifen_779


title: Tissue_BC_Tamoxifen_742


title: Tissue_BC_Tamoxifen_680


title: Tissue_BC_Tamoxifen_706


title: Tissue_BC_Tamoxifen_669


title: Tissue_BC_Tamoxifen_849


title: Tissue_BC_Tamoxifen_676


title: Tissue_BC_Tamoxifen_595


title: Tissue_BC_Tamoxifen_596


title: Tissue_BC_Tamoxifen_697


title: Tissue_BC_Tamoxifen_630


title: Tissue_BC_Tamoxifen_619


title: Tissue_BC_Tamoxifen_588


title: Tissue_BC_Tamoxifen_55


title: Tissue_BC_Tamoxifen_550


title: Tissue_BC_Tamoxifen_5210


title: Tissue_BC_Tamoxifen_511


title: Tissue_BC_Tamoxifen_427


title: Tissue_BC_Tamoxifen_412


title: Tissue_BC_Tamoxifen_2093


title: Tissue_BC_Tamoxifen_2341


title: Tissue_BC_Tamoxifen_2190


title: Tissue_BC_Tamoxifen_2220


title: Tissue_BC_Tamoxifen_443


title: 14 dpl laser captured CCP replicate 2

status: Public on Oct 22 2010

city: Cambridge

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

country: United Kingdom

institute: Cambridge University

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

data_processing: Data were filtered, removing any non expressed probes according to the detection p-value, then variance stabilization was applied and finally the data were normalised using quantile normalization.

organism: Rattus norvegicus

source_name: Rat caudal cerebellar peduncle

label_protocol: Standard Illumina hybridisation protocol

extract_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

treatment_protocol: Rat caudal cerebellar peduncles (CCP) were demyelinated using 0.1 % ethidium bromide.  The lesioned CCPs were selectively isolated from frozen brains using laser capture microdissections at 5, 14 and 28 days postlesion before RNA extraction and microarray analysis.

tag: strain

value: Sprague Dawley

tag: age

value: 12 weeks at 0 dpl (days post lesion)

value: caudal cerebellar peduncles

tag: time

value: 14  dpl (days post lesion)


title: Tissue_BC_Tamoxifen_2340


title: Tissue_BC_Tamoxifen_2092


title: Tissue_BC_Tamoxifen_3597


title: Tissue_BC_Tamoxifen_429


title: Tissue_BC_Tamoxifen_380


title: Tissue_BC_Tamoxifen_555


title: Tissue_BC_Tamoxifen_375


title: Tissue_BC_Tamoxifen_2188


title: Tissue_BC_Tamoxifen_2069


title: Tissue_BC_Tamoxifen_2027


title: Tissue_BC_Tamoxifen_209


title: Tissue_BC_Tamoxifen_2221


title: Tissue_BC_Tamoxifen_2175


title: Tissue_BC_Tamoxifen_2227


title: Tissue_BC_Tamoxifen_2057


title: Tissue_BC_Tamoxifen_4904


title: Tissue_BC_Tamoxifen_1982


title: Tissue_BC_Tamoxifen_2005


title: Tissue_BC_Tamoxifen_2002


title: Tissue_BC_Tamoxifen_1902


title: Tissue_BC_Tamoxifen_192


title: Tissue_BC_Tamoxifen_1800


title: Tissue_BC_Tamoxifen_1962


title: Tissue_BC_Tamoxifen_1579


title: Tissue_BC_Tamoxifen_1804


title: Tissue_BC_Tamoxifen_1821


title: Tissue_BC_Tamoxifen_1769


title: Tissue_BC_Tamoxifen_1889


title: Tissue_BC_Tamoxifen_1981


title: Tissue_BC_Tamoxifen_1525


title: Tissue_BC_Tamoxifen_1939


title: Tissue_BC_Tamoxifen_1770


title: Tissue_BC_Tamoxifen_1818


title: Tissue_BC_Tamoxifen_1441


title: Tissue_BC_Tamoxifen_1766


title: Tissue_BC_Tamoxifen_1397


title: Tissue_BC_Tamoxifen_1432


title: Tissue_BC_Tamoxifen_1320


title: Tissue_BC_Tamoxifen_1342


title: Tissue_BC_Tamoxifen_1331


title: Tissue_BC_Tamoxifen_1167


title: Tissue_BC_Tamoxifen_1193


title: Tissue_BC_Tamoxifen_1200


title: Tissue_BC_Tamoxifen_1127


title: Tissue_BC_Tamoxifen_1133


title: Tissue_BC_Tamoxifen_1181


title: Tissue_BC_Tamoxifen_124


title: Tissue_BC_Tamoxifen_116


title: Tissue_BC_Tamoxifen_1142


title: Tissue_BC_Tamoxifen_1168


title: Tissue_BC_Tamoxifen_114


title: Tissue_BC_Tamoxifen_1097


title: Tissue_BC_Tamoxifen_1157


title: Tissue_BC_Tamoxifen_1120


title: Tissue_BC_Tamoxifen_1301


title: Tissue_BC_Tamoxifen_1103


title: Tissue_BC_Tamoxifen_1156


title: Tissue_BC_Tamoxifen_1177


title: Tissue_BC_Tamoxifen_1070


title: Pa_PAO1_1

status: Public on May 25 2010

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

hyb_protocol: GeneChips were washed and stained using an Affymetrix fluidics station at the University of Iowa DNA core facility, followed by manufacturer's guideline.

scan_protocol: GeneChips were canned using an Affymetrix fluidics station at the University of Iowa DNA core facility, followed by manufacturer's guideline.

data_processing: We preprocessed microarray .CEL files with the RMA method by using the affy package (Version 1.18.2) in R (Version 2.8.1) with default options (PM probe specific correction, quantile normalization, and expression measure by median polish).

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa strain PA14, replicate 1

label_protocol: The cDNA synthesis products were purified and fragmented by brief incubation with DNase I, and the 3' termini of the fragmentation products were labeled with biotin-ddUTP (Schuster M, et al., J. Bacteriol. 185: 2066-2079)).

growth_protocol: Clinical isolates and the reference strains were routinely grown on Difco blood agar base (BD Sciences) supplemented with 5% sheep’s blood (Remel), brain heart infusion agar (Fisher), or Synthetic Cystic Fibrosis sputum medium (SCFM), which mimics the nutritional environment of the CF lung and was previously described (Palmer KL, et al., J. Bacteriol. 189: 8079-8087). Bacterial growth in liquid media was monitored by measuring the optical density at 600 nm (OD600) during growth at 37°C with shaking at 250 rpm.

extract_protocol: P. aeruginosa isolates were grown in SCFM and cells were harvested at an OD600 of 0.4-0.5. Cultures were mixed 1:1 with RNAlater (Ambion), an RNA stabilizing agent. RNA was isolated using the RNeasy mini kit (Qiagen), and cDNA was prepared for Affymetrix GeneChip microarray analysis as previously described (Schuster M, et al., J. Bacteriol. 185: 2066-2079). PCR amplification of the P. aeruginosa rplU gene was used to detect DNA contamination using the primers rplU-For (5’-CGCAGTGATTGTTACCGGTG-3’) and rplU-Rev (5’-AGGCCTGAATGCCGGTGATC-3’). To assess RNA integrity, samples were subjected to agarose gel electrophoresis.

value: Ref

tag: morphology

value: Classical


title: Tissue_BC_Tamoxifen_1125


title: Pa_C3488D_1

source_name: P. aeruginosa strain C3488D, replicate 1

value: Dwarf


title: Pa_PA14_1

source_name: P. aeruginosa strain PAO1, replicate 1


title: Pa_C3488D_2

source_name: P. aeruginosa strain C3488D, replicate 2


title: Tissue_BC_Tamoxifen_1089


title: Pa_C5623M_1

source_name: P. aeruginosa strain C5623M, replicate 1

value: Mucoid


title: Pa_C5623M_2

source_name: P. aeruginosa strain C5623M, replicate 2


title: Pa_PA14_3

source_name: P. aeruginosa strain PAO1, replicate 2


title: Pa_C2159M_1

source_name: P. aeruginosa strain C2159M, replicate 1


title: Pa_C2159M_2

source_name: P. aeruginosa strain C2159M, replicate 2


title: Pa_C0324C_3

source_name: P. aeruginosa strain C0324C, replicate 2


title: Pa_C0476M_2

source_name: P. aeruginosa strain C0476M, replicate 2


title: Pa_C0476M_1

source_name: P. aeruginosa strain C0476M, replicate 1


title: Pa_PAO1_3

source_name: P. aeruginosa strain PA14, replicate 2


title: Tissue_BC_Tamoxifen_1107


title: Pa_C5913C_2

source_name: P. aeruginosa strain C5913C, replicate 1


title: Pa_C5914M_2

source_name: P. aeruginosa strain C5914M, replicate 2


title: Pa_C0324C_2

source_name: P. aeruginosa strain C0324C, replicate 1


title: Pa_C5914M_1

source_name: P. aeruginosa strain C5914M, replicate 1


title: Pa_C5913C_3

source_name: P. aeruginosa strain C5913C, replicate 2


title: Pa_C4219D_2

source_name: P. aeruginosa strain C4219D, replicate 2


title: Pa_C5912M_2

source_name: P. aeruginosa strain C5912M, replicate 2


title: Pa_C5912M_1

source_name: P. aeruginosa strain C5912M, replicate 1


title: Pa_C4220M_1

source_name: P. aeruginosa strain C4220M, replicate 1


title: Pa_C4220M_2

source_name: P. aeruginosa strain C4220M, replicate 2


title: Pa_C4218C_1

source_name: P. aeruginosa strain C4218C, replicate 1


title: Pa_C4219D_1

source_name: P. aeruginosa strain C4219D, replicate 1


title: Pa_C3639M_2

source_name: P. aeruginosa strain C3639M, replicate 2


title: Pa_C4278M_1

source_name: P. aeruginosa strain C4278M, replicate 1


title: Pa_C3640D_2

source_name: P. aeruginosa strain C3640D, replicate 2


title: Pa_C4278M_2

source_name: P. aeruginosa strain C4278M, replicate 2


title: Pa_C3640D_1

source_name: P. aeruginosa strain C3640D, replicate 1


title: Pa_C1913C_1

source_name: P. aeruginosa strain C1913C, replicate 1


title: Pa_C3470C_2

source_name: P. aeruginosa strain C3470C, replicate 2


title: Pa_C1913C_2

source_name: P. aeruginosa strain C1913C, replicate 2


title: Pa_C2773C_1

source_name: P. aeruginosa strain C2773C, replicate 1


title: Pa_C2773C_3

source_name: P. aeruginosa strain C2773C, replicate 2


title: Pa_C3470C_1

source_name: P. aeruginosa strain C3470C, replicate 1


title: Pa_C3639M_1

source_name: P. aeruginosa strain C3639M, replicate 1


title: Pa_C4218C_2

source_name: P. aeruginosa strain C4218C, replicate 2


title: KIT_307C50 (HG-U133A)

status: Public on Mar 01 2007

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description: Tumor samples from tamoxifen treated primary breast cancer patients.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA Bioconductor

source_name: breast

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

tag: samplename

tag: ID

tag: series

value: KIT

tag: grade

tag: size

tag: er

tag: pgr

tag: node


title: KIT_56A94 (HG-U133A)


title: KIT_96A21 (HG-U133A)


title: KIT_27C82 (HG-U133A)


title: KIT_291C17 (HG-U133A)


title: KIT_7B96 (HG-U133A)


title: KIT_288C57 (HG-U133A)


title: KIT_64A59 (HG-U133A)


title: KIT_40C57 (HG-U133A)


title: KIT_77A50 (HG-U133A)


title: KIT_85A03 (HG-U133A)


title: KIT_79A35 (HG-U133A)


title: KIT_67A43 (HG-U133A)


title: KIT_84A44 (HG-U133A)


title: KIT_41C65 (HG-U133A)


title: KIT_63A62 (HG-U133A)


title: KIT_35C29 (HG-U133A)


title: KIT_71A50 (HG-U133A)


title: KIT_256C45 (HG-U133A)


title: KIT_254C80 (HG-U133A)


title: KIT_298C47 (HG-U133A)


title: KIT_245C22 (HG-U133A)


title: KIT_235C20 (HG-U133A)


title: KIT_244C89 (HG-U133A)


title: KIT_301C66 (HG-U133A)


title: KIT_238C87 (HG-U133A)


title: KIT_53A06 (HG-U133A)


title: KIT_271C71 (HG-U133A)


title: KIT_51A98 (HG-U133A)


title: KIT_230C47 (HG-U133A)


title: KIT_239C32 (HG-U133A)


title: KIT_225C52 (HG-U133A)


title: KIT_191B79 (HG-U133A)


title: KIT_212C21 (HG-U133A)


title: KIT_193B72 (HG-U133A)


title: KIT_203B49 (HG-U133A)


title: KIT_216C61 (HG-U133A)


title: KIT_171B77 (HG-U133A)


title: KIT_17C40 (HG-U133A)


title: KIT_186B22 (HG-U133A)


title: KIT_183B75 (HG-U133A)


title: KIT_165B72 (HG-U133A)


title: KIT_159B47 (HG-U133A)


title: KIT_189B83 (HG-U133A)


title: KIT_169B79 (HG-U133A)


title: KIT_14B98 (HG-U133A)


title: KIT_150B81 (HG-U133A)


title: KIT_166B79 (HG-U133A)


title: KIT_154B42 (HG-U133A)


title: KIT_170B15 (HG-U133A)


title: OXFT_944 (HG-U133A)

value: OXFT


title: KIT_148B49 (HG-U133A)


title: KIT_103B41 (HG-U133A)


title: KIT_112B55 (HG-U133A)


title: KIT_15C94 (HG-U133A)


title: KIT_202B44 (HG-U133A)


title: KIT_130B92 (HG-U133A)


title: OXFT_887 (HG-U133A)


title: OXFT_913 (HG-U133A)


title: OXFT_848 (HG-U133A)


title: OXFT_890 (HG-U133A)


title: OXFT_894 (HG-U133A)


title: KIT_147B19 (HG-U133A)


title: OXFT_829 (HG-U133A)


title: OXFT_771 (HG-U133A)


title: OXFT_876 (HG-U133A)


title: OXFT_849 (HG-U133A)


title: OXFT_729 (HG-U133A)


title: OXFT_697 (HG-U133A)


title: OXFT_779 (HG-U133A)


title: OXFT_705 (HG-U133A)


title: OXFT_676 (HG-U133A)


title: OXFT_550 (HG-U133A)


title: OXFT_555 (HG-U133A)


title: OXFT_5428 (HG-U133A)


title: OXFT_588 (HG-U133A)


title: OXFT_2227 (HG-U133A)


title: OXFT_375 (HG-U133A)


title: OXFT_2175 (HG-U133A)


title: OXFT_1981 (HG-U133A)


title: OXFT_429 (HG-U133A)


title: OXFT_595 (HG-U133A)


title: OXFT_380 (HG-U133A)


title: OXFT_55 (HG-U133A)


title: OXFT_837 (HG-U133A)


title: OXFT_412 (HG-U133A)


title: OXFT_706 (HG-U133A)


title: OXFT_192 (HG-U133A)


title: OXFT_2005 (HG-U133A)


title: OXFT_2002 (HG-U133A)


title: OXFT_1821 (HG-U133A)


title: OXFT_427 (HG-U133A)


title: OXFT_2057 (HG-U133A)


title: OXFT_1962 (HG-U133A)


title: OXFT_1889 (HG-U133A)


title: OXFT_1939 (HG-U133A)


title: OXFT_1818 (HG-U133A)


title: OXFT_1800 (HG-U133A)


title: OXFT_1804 (HG-U133A)


title: OXFT_1662 (HG-U133A)


title: OXFT_1331 (HG-U133A)


title: OXFT_1525 (HG-U133A)


title: OXFT_1766 (HG-U133A)


title: OXFT_1397 (HG-U133A)


title: OXFT_1320 (HG-U133A)


title: OXFT_124 (HG-U133A)


title: OXFT_116 (HG-U133A)


title: OXFT_1193 (HG-U133A)


title: OXFT_1177 (HG-U133A)


title: OXFT_1200 (HG-U133A)


title: OXFT_1181 (HG-U133A)


title: OXFT_1157 (HG-U133A)


title: OXFT_1120 (HG-U133A)


title: OXFT_1167 (HG-U133A)


title: OXFT_1301 (HG-U133A)


title: OXFT_1142 (HG-U133A)


title: OXFT_1127 (HG-U133A)


title: OXFT_1156 (HG-U133A)


title: OXFT_1168 (HG-U133A)


title: OXFT_1103 (HG-U133A)


title: OXFT_1107 (HG-U133A)


title: OXFT_1173 (HG-U133A)


title: OXFT_114 (HG-U133A)


title: OXFT_1089 (HG-U133A)


title: OXFT_1097 (HG-U133A)


title: OXFT_711 (HG-U133A)


status: Public on Jan 10 2007

city: Seattle

first: David

last: Pritchard

state: WA

address: 815 Mercer Street Rm.  418

department: Pathology

institute: University of Washington

description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16048 ; ch1: macroP1: Cy3; ch2: balP1: Cy5

hyb_protocol: For each of the two samples to be compared (A and B), dried Cy3 labeled A and Cy5 labeled B are mixed in 50ul of hyb solution (50% formamide, 5xSSC,5X Denhardt'w, 0.1% SDS, 100ug.ml Cot1DNA and 20ug/ml of polyA73primer) and applied to a slide. The hyb solution is covered with a cover slip and incubated in humid chamber (80-90%) ar 42C for 16 hours. After incubation, the slides were washed with  1) 1xSSC/0.2%SDS, 10 min @54C 2) 0.1xSSC/0.2%SDS 10 min @54C, 2 times 3) 0.1xSSC, 1 min @RT x 2 times(fresh soln on time #2) 4) 2 quick dips in RT dH2O and immediately dried with nitrogen. ; Protocol Type = hybridization; Parameter Chamber type = other[humid chamber]; Parameter Quantity of label target used = 1; Parameter time = 16; Parameter Volume = 50; Parameter temperature = 42;

scan_protocol: Microarrays were scanned at 10um resolution using a GenIII scanner from Molecular Dynamics/Amersham.  Laser and PMT settings were adjusted to minimize saturation and maximize signal-to-noise.; Protocol Type = feature_extraction; Software: Scanning software, type: feature_extraction_software; Hardware: Generation III Array Scanner [Amersham], make: Amersham, model: Generation III Array Scanner, type: array_scanner;

data_processing: raw measurements

source_name: macroP1: Cy3

label_protocol: During the first strand cDNA systhesis from the amplified RNA, 1 ug of Cy3-dCTP are added to the reaction mix of each of the two compared sample pair respectively. The Cy-dye incorporated cDNA are denatured and further purified using 96-well Millipore MAFNNOB DNA purification plate, dried and stored at -20C for later hybridization. ; Protocol Type = labeling; Parameter Amount of nucleic acid labeled = 2; Parameter Label used = Cy3; Parameter Amplification = none;

growth_protocol: Monocyte-derived macrophages were obtained by culturing 3x106 of purified human peripheral blood monocytes with M-CSF. Freshly isolated monocytes  cultured in RPMI 1640 supplemented with both 10% FCS and 10% human AB serum, 2 mM L-glutamine, 25 U/ml penicillin, and 25 µg/ml streptomycin (all from BioWhittaker) in Teflon PFA Vials (Cole-Parmer, Vernon Hills, IL) at 37°C in a humidified 5% CO2 incubator. After 7 days, dead cells were removed by centrifugation over Histopaque-1077. The remaining cells all had macrophage morphology and were >95% viable The cells were harvested on day 7 of culture for RNA isolation.; Protocol Type = grow;

extract_protocol: All cell preparations were pelleted by centrifugation before lysis.  Total RNA was isolated using the QIAGEN RNeasy Mini kit (Qiagen: Hilden,Germany).  The amount of total RNA was quantified by measurement of OD 260 nm.  The quality of the total RNA was determined by capillary electrophoresis analysis using an Agilent 2100 Bioanalyzer (www.Agilent.com)(Agilent: Palo Alto, CA USA).For each different cell type, 1 µg of total RNA was amplified using Arcturus kit (version A), according to the manufacturer’s instruction (www.arctur.com)(Arcturus: Mountain View CA, USA).  The quantity and quality of the amplified RNA were analyzed the same way as the total RNA.; Protocol Type = nucleic_acid_extraction; Parameter Extracted product = total RNA; Parameter Amplification = RNA polymerases;

tag: Age

tag: BioSourceType

tag: DevelopmentalStage

value: adult

tag: DiseaseState

value: healthy

tag: Individual

value: 30 yo Caucasian man

tag: OrganismPart

value: blood

tag: Sex

value: male

tag: TargetedCellType

value: monocyte derived macrophages

source_name: balP1: Cy5

label_protocol: During the first strand cDNA systhesis from the amplified RNA, 1 ug of Cy5-dCTP are added to the reaction mix of each of the two compared sample pair respectively. The Cy-dye incorporated cDNA are denatured and further purified using 96-well Millipore MAFNNOB DNA purification plate, dried and stored at -20C for later hybridization. ; Protocol Type = labeling; Parameter Amount of nucleic acid labeled = 2; Parameter Label used = Cy5; Parameter Amplification = none;

growth_protocol: Primary human alveolar macrophages (AM) were collected by bronchoalveolar lavage of normal volunteers under a standard clinical protocol that was previously approved by the Human Subjects Investigational Review Board of the University of Washington. Subjects were premedicated with 0.4 mg i.v. atropine. The oropharynx and larynx were anesthetized with IO to IS ml atomized 4% lidocaine and a flexible fiberoptic bronchoscope (Pentaxmodel FB- 15X) was passed into the lower airway with instillation of 2 to 10 ml of 2% lidocaine to suppress coughing. A single subsegment of the right middle lobe and then the lingula were each lavaged with five separate 30-1111 aliquots of sterile, pyrogen-free 0.9% NaCl and each aliquot was recovered into a sterile trap by the gentle application of wall suction. The pooled aliquots were transported to the laboratory on ice, strained through sterile gauze to remove mucus, washed twice in cold HBSS without calcium or magnesium, then resuspended at IO6 cells/ml in RPMI 1640 containing 100 U/ml penicillin and 100 yg/ml streptomycin to kill any contaminating oropharyngeal bacteria.as previously described [21].  Isolated AM were greater than 95% viable by trypan blue exclusion, and 95% had macrophage-like morphology by modified Wright-Giemsa staining.; Protocol Type = grow;

value: lung

value: primary alveolar macrophages


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16046 ; ch1: balP1: Cy3; ch2: macroP1: Cy5

source_name: balP1: Cy3

source_name: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16055 ; ch1: macroP2: Cy3; ch2: balP2: Cy5

source_name: macroP2: Cy3

value: 32 yo Asian man

source_name: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16071 ; ch1: macroP4: Cy3; ch2: balP4: Cy5

source_name: macroP4: Cy3

value: 19 yo Asian woman

value: female

source_name: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16054 ; ch1: balP2: Cy3; ch2: macroP2: Cy5

source_name: balP2: Cy3

source_name: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16064 ; ch1: macroP3: Cy3; ch2: balP3: Cy5

source_name: macroP3: Cy3

value: 32 yo Caucasian man

source_name: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16045 ; ch1: balP1: Cy3; ch2: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16063 ; ch1: macroP3: Cy3; ch2: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16062 ; ch1: balP3: Cy3; ch2: macroP3: Cy5

source_name: balP3: Cy3

source_name: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16072 ; ch1: macroP4: Cy3; ch2: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16056 ; ch1: macroP2: Cy3; ch2: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16039 ; ch1: macroP4: Cy3; ch2: monoP4: Cy5

source_name: monoP4: Cy5

growth_protocol: The experimental protocol was approved by the Human Subjects Investigational Review Board of the University of Washington.  Four healthy volunteer subjects were enrolled in this study.  The age and ethnicity of the individuals were as follows: 19 yo Asian woman, 32 yo Caucasian man, 32 yo Asian man and 30 yo Caucasian man.   All individuals were healthy, non-smoking, normal human volunteers who were receiving no medications and had experienced no recent illness at the time of this study.  Fifty (50) ml of peripheral venous blood was drawn from each individual in 1 mM EDTA.  Monocytes were isolated by negative immunoselection using a commercially available bead-based immunoselection kit.  Fifty (50) ìl/ml of RosetteSep cocktail (StemCell Technologies, Inc.) were added to the blood and incubated for 20 min at room temperature.  Blood was then layered on top of Ficoll-Plaque and centrifuged for 20 min at 1200g.  Suspended monocytes were isolated and then platelets were removed by repeated centrifugations.  Greater than 95% of isolated cells were mononuclear, and greater than 90% of these were positive for CD14+ by flow cytometric analysis.  Approximately 1x106 monocytes were used immediately for RNA isolation.  The remainder was used for cultivation of monocyte-derived macrophages (see MonocyteDerivedMacrophages protocol). ; Protocol Type = grow;

value: peripheral blood monocyte


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16053 ; ch1: balP2: Cy3; ch2: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16070 ; ch1: balP4: Cy3; ch2: macroP4: Cy5

source_name: balP4: Cy3

source_name: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16040 ; ch1: macroP4: Cy3; ch2: monoP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16037 ; ch1: monoP4: Cy3; ch2: macroP4: Cy5

source_name: monoP4: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16030 ; ch1: monoP3: Cy3; ch2: macroP3: Cy5

source_name: monoP3: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16029 ; ch1: monoP3: Cy3; ch2: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16031 ; ch1: macroP3: Cy3; ch2: monoP3: Cy5

source_name: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16069 ; ch1: balP4: Cy3; ch2: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16047 ; ch1: macroP1: Cy3; ch2: balP1: Cy5

source_name: macroP1: Cy3

source_name: balP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16024 ; ch1: macroP2: Cy3; ch2: monoP2: Cy5

source_name: macroP2: Cy3

source_name: monoP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16038 ; ch1: monoP4: Cy3; ch2: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16022 ; ch1: monoP2: Cy3; ch2: macroP2: Cy5

source_name: monoP2: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16061 ; ch1: balP3: Cy3; ch2: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16021 ; ch1: monoP2: Cy3; ch2: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16023 ; ch1: macroP2: Cy3; ch2: monoP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16016 ; ch1: macroP1: Cy3; ch2: monoP1: Cy5

source_name: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16032 ; ch1: macroP3: Cy3; ch2: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16057 ; ch1: balP3: Cy3; ch2: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16067 ; ch1: macroP4: Cy3; ch2: balP4: Cy5

source_name: macroP4: Cy3

source_name: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15992 ; ch1: balP2: Cy3; ch2: monoP2: Cy5

source_name: balP2: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16015 ; ch1: macroP1: Cy3; ch2: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16068 ; ch1: macroP4: Cy3; ch2: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15990 ; ch1: monoP2: Cy3; ch2: balP2: Cy5

source_name: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16060 ; ch1: macroP3: Cy3; ch2: balP3: Cy5

source_name: macroP3: Cy3

source_name: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15991 ; ch1: balP2: Cy3; ch2: monoP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16013 ; ch1: monoP1: Cy3; ch2: macroP1: Cy5

source_name: monoP1: Cy3

source_name: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16007 ; ch1: balP4: Cy3; ch2: monoP4: Cy5

source_name: balP4: Cy3

source_name: monoP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15981 ; ch1: monoP1: Cy3; ch2: balP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16058 ; ch1: balP3: Cy3; ch2: macroP3: Cy5

source_name: balP3: Cy3

source_name: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15983 ; ch1: balP1: Cy3; ch2: monoP1: Cy5

source_name: balP1: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16066 ; ch1: balP4: Cy3; ch2: macroP4: Cy5

source_name: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16051 ; ch1: macroP2: Cy3; ch2: balP2: Cy5

source_name: macroP2: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15982 ; ch1: monoP1: Cy3; ch2: balP1: Cy5

source_name: balP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16052 ; ch1: macroP2: Cy3; ch2: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16059 ; ch1: macroP3: Cy3; ch2: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16065 ; ch1: balP4: Cy3; ch2: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15998 ; ch1: monoP3: Cy3; ch2: balP3: Cy5

source_name: monoP3: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15984 ; ch1: balP1: Cy3; ch2: monoP1: Cy5

source_name: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16000 ; ch1: balP3: Cy3; ch2: monoP3: Cy5

source_name: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16008 ; ch1: balP4: Cy3; ch2: monoP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16050 ; ch1: balP2: Cy3; ch2: macroP2: Cy5

source_name: balP2: Cy3

source_name: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15989 ; ch1: monoP2: Cy3; ch2: balP2: Cy5

source_name: monoP2: Cy3

source_name: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15999 ; ch1: balP3: Cy3; ch2: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16014 ; ch1: monoP1: Cy3; ch2: macroP1: Cy5

source_name: monoP1: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16036 ; ch1: macroP4: Cy3; ch2: monoP4: Cy5

source_name: macroP4: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16034 ; ch1: monoP4: Cy3; ch2: macroP4: Cy5

source_name: monoP4: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16027 ; ch1: macroP3: Cy3; ch2: monoP3: Cy5

source_name: macroP3: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16044 ; ch1: macroP1: Cy3; ch2: balP1: Cy5

source_name: macroP1: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16006 ; ch1: macroP4: Cy3; ch2: balP4: Cy5

source_name: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16042 ; ch1: balP1: Cy3; ch2: macroP1: Cy5

source_name: balP1: Cy3

source_name: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15997 ; ch1: monoP3: Cy3; ch2: balP3: Cy5

source_name: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16043 ; ch1: macroP1: Cy3; ch2: balP1: Cy5

source_name: balP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16033 ; ch1: monoP4: Cy3; ch2: macroP4: Cy5

source_name: macroP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16017 ; ch1: monoP2: Cy3; ch2: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16020 ; ch1: macroP2: Cy3; ch2: monoP2: Cy5

source_name: macroP2: Cy3

source_name: monoP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16041 ; ch1: balP1: Cy3; ch2: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16049 ; ch1: balP2: Cy3; ch2: macroP2: Cy5

source_name: balP2: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16026 ; ch1: monoP3: Cy3; ch2: macroP3: Cy5

source_name: monoP3: Cy3

source_name: macroP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16005 ; ch1: monoP4: Cy3; ch2: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16019 ; ch1: macroP2: Cy3; ch2: monoP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16003 ; ch1: balP4: Cy3; ch2: monoP4: Cy5

source_name: balP4: Cy3

source_name: monoP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16018 ; ch1: monoP2: Cy3; ch2: macroP2: Cy5

source_name: monoP2: Cy3

source_name: macroP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16025 ; ch1: macroP3: Cy3; ch2: macroP3: Cy5

source_name: macroP3: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16002 ; ch1: monoP4: Cy3; ch2: balP4: Cy5

source_name: monoP4: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16011 ; ch1: macroP1: Cy3; ch2: monoP1: Cy5

source_name: macroP1: Cy3

source_name: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16009 ; ch1: monoP1: Cy3; ch2: macroP1: Cy5

source_name: monoP1: Cy3

source_name: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16012 ; ch1: macroP1: Cy3; ch2: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16035 ; ch1: macroP4: Cy3; ch2: macroP4: Cy5

source_name: macroP4: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15996 ; ch1: balP3: Cy3; ch2: monoP3: Cy5

source_name: balP3: Cy3

source_name: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15995 ; ch1: balP3: Cy3; ch2: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16010 ; ch1: monoP1: Cy3; ch2: macroP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16004 ; ch1: balP4: Cy3; ch2: monoP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16028 ; ch1: macroP3: Cy3; ch2: monoP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:16001 ; ch1: monoP4: Cy3; ch2: balP4: Cy5

source_name: balP4: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15994 ; ch1: monoP3: Cy3; ch2: balP3: Cy5

source_name: balP3: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15541 ; ch1: balP1: Cy3; ch2: monoP1: Cy5

source_name: balP1: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15985 ; ch1: monoP2: Cy3; ch2: balP2: Cy5

source_name: balP2: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15540 ; ch1: balP1: Cy3; ch2: monoP1: Cy5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15993 ; ch1: monoP3: Cy3; ch2: balP3: Cy5

source_name: monoP3: Cy3


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15988 ; ch1: balP2: Cy3; ch2: monoP2: Cy5

source_name: balP2: Cy3

source_name: monoP2: Cy5


title: OXFT_736

status: Public on Feb 16 2006

description: Tumor samples from Tamoxifen-only treated primary breast cancer patients

source_name: breast

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturer's instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturer's instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

tag: sample name

tag: ggi


title: OXFT_2188


title: OXFT_1579


title: OXFT_619


title: OXFT_2092


title: OXFT_443


title: Anaerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 2

status: Public on Sep 01 2006

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

description: Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

data_processing: background correction, log2 transformation and Loess normalisation were performed using Genesight 4.1 software, copyright BioDiscovery

organism: Escherichia coli

source_name: anaerobic wild type experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

tag: Wild Type Strain MG1655

source_name: anaerobic norR::Tn5 mutant experiment samples in presence of 10 uM each of NOC-5 and NOC-7 for 5 minutes

tag: Strain MG1655, norR::Tn5


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15987 ; ch1: balP2: Cy3; ch2: monoP2: Cy5


title: OXFT_680

tag: grade


title: Anaerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 2 dye swap


title: Anaerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 1 dye swap


title: OXFT_669


title: OXFT_3597


title: OXFT_2069


title: OXFT_638


title: OXFT_4904


title: OXFT_700


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15538 ; ch1: monoP1: Cy3; ch2: balP1: Cy5

source_name: balP1: Cy5


title: OXFT_1432


title: OXFT_742


title: OXFT_596


title: OXFT_511


title: OXFT_1070


title: OXFT_1133


title: OXFT_1982


title: OXFT_738


title: OXFT_5210


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15539 ; ch1: monoP1: Cy3; ch2: balP1: Cy5


title: OXFT_630


title: OXFT_2341


title: OXFT_2338


title: OXFT_1441


title: OXFT_1125


title: OXFT_1342


title: OXFT_2027


title: OXFT_2340


title: OXFT_1770


title: OXFT_1769


title: Anaerobic NO exposed Chemostat Comparison of Wt & norR mutant, Run 1


title: OXFT_928


title: OXFT_2093


title: OXFT_209


title: OXFT_2152


title: OXFT_2190


title: OXFT_1902


title: OXFT_2220


title: OXFT_2221


title: KIT_162B98


title: KIT_135B40


title: KIT_194B60


title: KIT_173B43


title: KIT_252C64


title: KIT_131B79


title: KIT_139B03


title: KIT_72A92


title: KIT_48A46


title: KIT_138B34


description: ebi.ac.uk:MIAMExpress:MeasuredBioAssayData:15986 ; ch1: monoP2: Cy3; ch2: balP2: Cy5

source_name: monoP2: Cy3


title: KIT_55A79


title: KIT_6B85


title: KIT_104B91


title: KIT_114B68


title: KIT_313A87


title: KIT_69A93


title: KIT_76A44


title: KIT_207C08


title: KIT_82A83


title: KIT_311A27


title: KIT_46A25


title: KIT_39C24


title: KIT_289C75


title: 10h-seq-anaero

status: Public on Dec 31 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30533.gif

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)

organism: Campylobacter jejuni

source_name: 1.5 ug RNA pool from each sample

tag: 1.5 ug RNA pool from each sample

source_name: 1.5 ug sequenced 11168 RNA from 10hr anaero


title: 11168 orig vs. seq 1

type: genomic

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28772.gif

molecule: genomic DNA

source_name: 0.5 ug sequenced 11168 DNA

tag: 0.5 ug sequenced 11168 DNA

source_name: 0.5 ug original 11168 DNA

tag: 0.5 ug original 11168 DNA


title: 11168 seq vs. seq 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28771.gif


title: 2h-orig-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30524.gif

source_name: 1.5 ug original 11168 RNA from 2hr micro


title: 6h-seq-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30521.gif

source_name: 1.5 ug sequenced 11168 RNA from 6hr micro


title: 6h-orig-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30525.gif

source_name: 1.5 ug original 11168 RNA from 6hr micro


title: 26h-seq-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30530.gif

source_name: 1.5 ug sequenced 11168 RNA from 26hr anaero


title: 11168 seq vs. seq 1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28770.gif


title: 2h-seq-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30520.gif

source_name: 1.5 ug sequenced 11168 RNA from 2hr micro


title: 11168 orig vs. seq 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28773.gif


title: 26h-seq-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30523.gif

source_name: 1.5 ug sequenced 11168 RNA from 26hr micro


title: 6h-orig-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30534.gif

source_name: 1.5 ug original 11168 RNA from 6hr anaero


title: 2h-seq-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30537.gif

source_name: 1.5 ug sequenced 11168 RNA from 2hr anaero


title: 10h-orig-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30526.gif

source_name: 1.5 ug original 11168 RNA from 10hr micro


title: 26h-orig-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30528.gif

source_name: 1.5 ug original 11168 RNA from 26hr anaero


title: 10h-orig-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30532.gif

source_name: 1.5 ug original 11168 RNA from 10hr anaero


title: 10-seq-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30522.gif

source_name: 1.5 ug sequenced 11168 RNA from 10hr micro


title: 2h-orig-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30536.gif

source_name: 1.5 ug original 11168 RNA from 2hr anaero


title: 26h-orig-micro

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30527.gif

source_name: 1.5 ug RNA pool from each sample

source_name: 1.5 ug original 11168 RNA from 26hr micro


title: 6h-seq-anaero

description:
Simple annotation: Genome comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30535.gif

source_name: 1.5 ug sequenced 11168 RNA from 6hr anaero


title: KIT_8B87

description: Tumor samples from Tamoxifen-only treated primary breast cancer patients

source_name: breast