title: TWT_Doxycycline microarray_Control vs Doxycycline 10xMIC_rep1

status: Public on Sep 07 2006

city: Marseille

first: My-Van

last: La

address: 27 BD Jean Moulin

country: France

institute: Unité des Rickettsies (CNRS-UMR 6020)

description: The data filtering and normalization were then processed with Microsoft Excel software. Spots with background-corrected signal intensity (median) in both channels lower than two-fold the background intensity (median) were excluded from further analysis.

hyb_protocol: Hybridization and washing. Microarrays washed in 0.1% SDS (1 min.) and rinsed with H2O (1 min.) were boiled 3 min in H2O in order to denaturate spotted double-strand DNA. Following prehybridization at 42°C for 45 min. in 5 X SSC, 0.1% SDS and 0.1% BSA solution, microarrays were rinsed in H2O (1 min.) and dried with compressed nitrogen. Hybridization was carried out using twice 7 μg cDNA labeled with Cy3- or Cy5-dCTP pooled and evaporated (SpeedVac™ concentrator) and resuspended in 6 μl of nuclease free H2O. The mixture was heated at 95°C for 2 min, cooled on ice for 30 sec before addition of 7.5 μl of microarray hybridization buffer (supplied in the CyScribe kit (Amersham)) and 15 μl of 100% (v/v) formamide.  The sample was applied to the microarray slide by covering a 24 x 60 mm glass coverslip. Following 18-hrs incubation at 42°C, the slide was washed then dried with compressed nitrogen, and then scanned with ScanArray®Express (Perkin Elmer, Boston, MA, USA). Laser power was set to 100% and Photomultiplicator (PMT) power was set between 55 % and 75 % depending on the slides.

scan_protocol: TIF images containing the data from each fluorescence channel were quantified with the QuantArray® Microarray Analysis Software version 3.0.0.0 (Packard BioScience) to obtain the signal intensity and local background of each spot, and to exclude preliminarily irrelevant values, as flagged.

data_processing: total intensity normalization methods: we discarded the spots with background-corrected signal intensity (median) in both channels lower than two-fold the background intensity (median) using Microsoft Excel. Then, the background-subtracted signals derived from the remaining spots were normalized by the medians of total remaining spot intensities of each channel (control and test, respectively).

organism: Tropheryma whipplei

source_name: Control (reference)

label_protocol: Amplified cDNA labeling. One microgam amplified cDNA was labeled with Cy3- or Cy5-dCTP (Amersham Biosciences) using the BioPrime DNA labeling System (Invitrogen, Carlsbad, CA, USA). The levels of Cy3- and Cy5- incorporation were quantified by absorbance measurement at 550 and 650 nm, and samples processed for hybridization on microarray when incorporation levels are ≥ 50 pmol of fluorochromes per μg cDNA.

growth_protocol: Bacterial strain and growth conditions. T. whipplei strain Twist (La Scola et al., 2001) was grown under axenic conditions in DMEM/F12 medium (Invitrogen Life Technologies, Carlsbad, USA) supplemented with 10% foetal calf serum, 1% L-glutamine and 1% human non-essential amino acids (Invitrogen) as previously described (Renesto et al., 2003). Mid-log cultures (12 day-old) were further incubated or not (control) for 6 hours with two different concentrations of Doxycycline (Vibravenosa, Pfizer): minimum inhibitory concentration (MIC) (0.5µg/µl) and 10 x MIC (5µg/µl), respectively (Boulos et al., 2005).

extract_protocol: RNA extraction, cDNA synthesis and amplification. Following antibiotic treatment (yes/no), bacteria (200 ml) were harvested by centrifugation 16,900 x g for 10 min at 4°C. Resulting pellets were immediately sonicated in 1 ml of Trizol® Reagent (Invitrogen Life Technologies) and then frozen in liquid nitrogen before storage at -80°C. After RNA extraction according to reference protocol, purified RNA samples were treated with RNase-Free DNase Set (QIAGEN) and cleaned-up on to RNeasy column (QIAGEN) to remove eventual DNA contamination. Amount and quality of each RNA sample was monitored using the Bioanalyzer 2100 with RNA Nano LabChips™ (Agilent, Palo Alto, CA, USA). Moreover, the absence of DNA contamination was assessed by reverse transcriptional and standard PCR, as previously described (Crapoulet et al., 2006). Starting from 200 ml T. whipplei culture, the amount of recovered RNA varied from 0.385 µg to 1.918 µg. For each condition, RNA was extracted from at least 3 independent bacterial cultures. Then, 500 ng RNA were used to synthesize cDNA with reverse transcriptase (Superscript II, Invitrogen, Carlsbad, CA, USA). Obtained cDNA (20 ng) was then amplified using the Genomiphi DNA amplification kit (Amersham Biosciences, Piscataway, NJ, USA) and random primers.

tag: Strain Twist

tag: Axenic culture

tag: Exponential growth (Day 12)

tag: Standard condition

source_name: Doxycycline 10xMIC (test)

tag: Doxycycline 10xMIC for 6 hours


title: TWT_Doxycycline microarray_Control vs Control_rep3

type: RNA

molecule: total RNA

source_name: Control (test)


title: TWT_Doxycycline microarray_Control vs Doxycycline 10xMIC_rep2


title: TWT_Doxycycline microarray_Control vs Doxycycline 1xMIC_rep1

source_name: Doxycycline 1xMIC (test)

tag: Doxycycline 1xMIC for 6 hours


title: MAQC_GEH_K_AA_2

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: The samples were randomly labeled and each test site was provided an aliquot of each sample.  To avoid potential confounding factors in experimental implementation, the identity of the RNA samples was kept unknown to the test sites before data were submitted to FDA/NCTR.

scan_protocol: All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.

data_processing: The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.  These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment.  The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background.   Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).

label: biotin

organism: Rattus norvegicus

source_name: Sample type K_AA (Kidney Aristolochic Acid)

label_protocol: 1 ug of total RNA was processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Rat Whole Genome Bioarray (catalog #300031).

treatment_protocol: Groups of six 6-week-old Big Blue rats were gavaged with riddelliine (1 mg/kg body weight) or aristolochic acid (10 mg/kg body weight) five times a week for 12 weeks or Big Blue rats were fed a diet of 8% comfrey roots for 12 weeks.  The animals were sacrificed after 12 weeks of treatment, and the tissues were isolated, frozen quickly in liquid nitrogen and stored at –80 °C.

tag: MAQC rat toxicogenomics samples used in Guo L. et al., Nature Biotechnology, 24(9), 2006.


title: TWT_Doxycycline microarray_Control vs Doxycycline 1xMIC_rep3


title: TWT_Doxycycline microarray_Control vs Doxycycline 10xMIC_rep3


title: TWT_Doxycycline microarray_Control vs Doxycycline 1xMIC_rep2


title: TWT_Doxycycline microarray_Control vs Control_rep2


title: Mouse miRNA Sample 1

status: Public on Sep 06 2006

city: Kobe

first: Anthony

middle: CF

last: Perry

state: Hyogo-ken

address: 2-2-3 Minatojima-minamimachi

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: mouse μParafloTM superfluidic miRNA array

data_processing: Array Pro

organism: Mus musculus

source_name: BCF3, C3H, CBA, C57BL/6, DBA/2 mixed demembranted sperm

treatment_protocol: Epididymidal sperm were extracted with 0.1% TX-100

tag: 10.4ug total RNA


title: MAQC_NCI_1_A1

description: NCI sample-pair convention: A (A/A, Cy3/Cy5), B (B/A, Cy3/Cy5), C (C/A, Cy3/Cy5), and D (D/A, Cy3/Cy5).  MAQC sample A was used as the common reference sample (Cy5; channel 2) in NCI two-color experiments.  Test sites NCI_2 and NCI3 failed in the first round of experiments due to protocol issues.  The failed hybridizations are named as NCI_2Fail and NCI_3Fail.  NCI_2 repeated part of the experiment with 14 hybridizations.

scan_protocol: Slides were scanned using an Axon 4000B instrument at 10 micron resolution.  All scans were performed at 100% laser power, but the PMT setting varied from slide-to-slide depending on the labeling and hybridization outcomes.  Thus, the intensity of the signals among the slides will vary, but the Cy3/Cy5 ratios will be much less variable.

data_processing: Images were processed and quantified using GenePix 4.0 software (Axon Instruments, Union City, CA).  The data were filtered (or flagged) on the basis of signal levels and spot quality.  The raw data were submitted to MAQC and further normalized by using LOWESS.

organism: Homo sapiens

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)

label_protocol: Labeling of probes, hybridization of slides and scanning was done essentially as described [Petersen, D. et al. BMC Bioinformatics 6, 63. 2005]

tag: MAQC sample


title: Slide 802

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep T = 276 days

data_processing: Normalized using a spatial mixed model analysis which includes splines

organism: Ovis aries

source_name: Duodenum, susceptible animal 1025/00

tag: Susceptible to gastrointestinal nematodes

source_name: Duodenum, resistant animal 1041/00

tag: Resistant to gastrointestinal nematodes


title: Slide 801

source_name: Duodenum, susceptible animal 1024/00


title: Slide 799

source_name: Duodenum, susceptible animal 1004/00


title: Slide 800

source_name: Duodenum, susceptible animal 1017/00


title: TWT_Doxycycline microarray_Control vs Control_rep1


title: Slide 773

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep T = 84 days

source_name: Duodenum, resistant animal 1046/02

source_name: Duodenum, susceptible animal 1022/02


title: Slide 774

source_name: Duodenum, susceptible animal 1065/02


title: Slide 770

source_name: Duodenum, susceptible animal 1005/02


title: Slide 771

source_name: Duodenum, susceptible animal 1032/02


title: Slide 768

source_name: Duodenum, resistant animal 1041/02


title: Slide 797

source_name: Duodenum, resistant animal 1032/00


title: Slide 795


title: Slide 769


title: Slide 798


title: Slide 796


title: MAQC_NCI_1_B1

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: Slide 794

source_name: Duodenum, resistant animal 1010/00


title: Slide 791


title: Slide 792


title: Slide 764

source_name: Duodenum, resistant animal 1029/02


title: Slide 790

source_name: Duodenum, resistant animal 1008/00


title: Slide 793


title: Slide 767


title: Slide 766


title: Slide 788


title: Slide 765


title: Slide 789


title: Slide 762

source_name: Duodenum, resistant animal 1001/02


title: Slide 763


title: Slide 635

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep T = 175 days

source_name: Duodenum, susceptible animal 1046/01

source_name: Duodenum, resistant animal 1044/01

tag: Resisant to gastrointestinal nematodes


title: Slide 787


title: Slide 761


title: Slide 759


title: Slide 634

source_name: Duodenum, susceptible animal 1053/01

source_name: Duodenum, resistant animal 1035/01


title: Slide 630

source_name: Duodenum, resistant animal 1003/01


title: Slide 632

source_name: Duodenum, resistant animal 1004/01


title: Slide 629

source_name: Duodenum, susceptible animal 1031/01


title: Slide 760

source_name: Duodenum, susceptible animal 1022/02


title: MAQC_GEH_L_CFY_3

source_name: Sample type L_CFY (Liver Comfrey)


title: Slide 631


title: Slide 633

source_name: Duodenum, susceptible animal 1001/01


title: Slide 626


title: proband k, past exhaustive exercise

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

country: Germany

institute: University Hospital Jena

description: proband k, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2 and GeneSpring 7.1 (Agilent)

source_name: white blood cells

label_protocol: Approximately 3 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 9ml blood were collected and erythrocyte lysis using Qiagen Erythrocyte lysis buffer was performed immediately. White blood cells were washed in icecold PBS two times. Cells were then lysed using Trizol (Invitrogen).Phase lock gel tubes (Eppendorf) were used to extract the RNA containing phase. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: male, healthy, no medicamentation


title: proband k, before moderate exercise

description: proband k, before moderate exercise, white blood cells, male, healthy, no medicamentation


title: proband i, past exhaustive exercise

description: proband i, past exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Slide 625


title: Slide 627


title: Slide 628


title: proband k, past moderate exercise

description: proband k, past moderate exercise, white blood cells, male, healthy, no medicamentation


title: proband i, before moderate exercise

description: proband i, before moderate exercise, white blood cells, male, healthy, no medicamentation


title: Slide 615


title: Slide 623


title: proband i, past moderate exercise

description: proband i, past moderate exercise, white blood cells, male, healthy, no medicamentation


title: proband k, before exhaustive exercise

description: proband k, before exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: proband a, past exhaustive exercise

description: proband a, past exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Slide 624


title: proband a, past moderate exercise

description: proband a, past moderate exercise, white blood cells, male, healthy, no medicamentation


title: proband i, before exhaustive exercise

description: proband i, before exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Slide 605


title: proband g, before moderate exercise

description: proband g, before moderate exercise, white blood cells, male, healthy, no medicamentation


title: proband a, before exhaustive exercise

description: proband a, before exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Mouse miRNA Sample 6

description: mouse μParafloTM superfluidic miRNA array

source_name: C57BL/6 demembranated sperm

treatment_protocol: Cauda epididymidal sperm were extracted with 0.1% Triton X-100

tag: 14.3ug total RNA


title: proband f, before moderate exercise

description: proband f, before moderate exercise, white blood cells, male, healthy, no medicamentation


title: Mouse miRNA Sample 5

source_name: BDF1 demembranated sperm

tag: 9.5ug total RNA


title: proband g, before exhaustive exercise

description: proband g, before exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Mouse miRNA Sample 4

treatment_protocol: Cauda epidydimidal sperm were extracted with 0.1% Triton X-100

tag: 4.5ug total RNA


title: Slide 772

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep T = 84 days

source_name: Duodenum, susceptible animal 1032/02

source_name: Duodenum, resistant animal 1041/02


title: proband g, past exhaustive exercise

description: proband g, past exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: proband a, before moderate exercise

description: proband a, before moderate exercise, white blood cells, male, healthy, no medicamentation


title: Slide 613

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep T = 175 days


title: proband g, past moderate exercise

description: proband g, past moderate exercise, white blood cells, male, healthy, no medicamentation


title: Mouse miRNA Sample 7

tag: 11.6ug total RNA


title: proband f, before exhaustive exercise

description: proband f, before exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: Mouse miRNA Sample 3

source_name: ICR (CD1) demembranated sperm

treatment_protocol: Cauda epididymidal sperm were extracted with 0.1% TX-100


title: Mouse miRNA Sample 2

treatment_protocol: Cauda epidydmidal sperm were extracted with 0.1% Triton X-100

tag: 4.6ug total RNA


title: proband f, past moderate exercise

description: proband f, past moderate exercise, white blood cells, male, healthy, no medicamentation


title: human failing LV myocardium, Ischemic3

status: Public on Sep 05 2006

city: Philadelphia

first: Thomas

last: Cappola

state: PA

address: 6 Penn Tower, 3400 Spruce Street

department: Penn Cardiovascular Institute

country: USA

institute: Univeristy of Pennsylvania School of Medicine

description: Gene expression data from advanced human heart failure due to ischemic cardiomyopathy

hyb_protocol: Following fragmentation cRNA were hybridized with HU133A arrays according to Affymetrix protocol.

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

data_processing: Data were normalized using Robust Multi-Array Analysis (RMA). www.bioconductor.org

source_name: explanted heart tissue at time of cardiac transplantation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

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

treatment_protocol: explanted myocardium snap frozen in liquid nitrogen

tag: systolic heart failure due to ischemic cardiomyopathy


title: human failing LV myocardium, Idiopathic26

description: Gene expression data from advanced human heart failure due to idiopathic dilated cardiomyopathy

tag: systolic heart failure due to idiopathic dilated cardiomyopathy


title: human nonfailing LV myocardium, NonFailing1

description: Gene expression data from nonfailing unused donor heart

source_name: unused donor heart with normal LV function

tag: normally functioning myocardium from unused donor heart


title: human failing LV myocardium, Idiopathic2


title: human failing LV myocardium, Idiopathic29


title: human failing LV myocardium, Ischemic1


title: human failing LV myocardium, Ischemic33


title: human failing LV myocardium, Ischemic2


title: proband f, past exhaustive exercise

description: proband f, past exhaustive exercise, white blood cells, male, healthy, no medicamentation


title: human failing LV myocardium, Idiopathic31


title: human failing LV myocardium, Idiopathic30


title: human failing LV myocardium, Idiopathic28


title: human failing LV myocardium, Idiopathic27


title: human failing LV myocardium, Ischemic39


title: human failing LV myocardium, Idiopathic32


title: human nonfailing LV myocardium, NonFailing10


title: human failing LV myocardium, Ischemic38


title: human failing LV myocardium, Ischemic34


title: human failing LV myocardium, Ischemic41


title: human failing LV myocardium, Ischemic35


title: human failing LV myocardium, Ischemic87


title: human failing LV myocardium, Ischemic6


title: human failing LV myocardium, Ischemic40


title: human failing LV myocardium, Ischemic10


title: human failing LV myocardium, Ischemic86


title: human failing LV myocardium, Ischemic9


title: human failing LV myocardium, Idiopathic1


title: human failing LV myocardium, Idiopathic3


title: human failing LV myocardium, Idiopathic67


title: human failing LV myocardium, Ischemic42


title: human failing LV myocardium, Ischemic14


title: human failing LV myocardium, Idiopathic7


title: human failing LV myocardium, Ischemic16


title: human nonfailing LV myocardium, NonFailing12


title: human failing LV myocardium, Idiopathic8


title: human failing LV myocardium, Ischemic4


title: human failing LV myocardium, Idiopathic10


title: human failing LV myocardium, Ischemic5


title: human failing LV myocardium, Idiopathic5


title: human failing LV myocardium, Ischemic11


title: human failing LV myocardium, Ischemic17


title: human failing LV myocardium, Ischemic7


title: human failing LV myocardium, Ischemic8


title: human failing LV myocardium, Ischemic19


title: human failing LV myocardium, Idiopathic12


title: human failing LV myocardium, Ischemic22


title: human failing LV myocardium, Ischemic21


title: human failing LV myocardium, Ischemic13


title: human failing LV myocardium, Idiopathic4


title: human failing LV myocardium, Ischemic23


title: human failing LV myocardium, Ischemic15


title: human failing LV myocardium, Idiopathic6


title: human failing LV myocardium, Idiopathic9


title: human failing LV myocardium, Ischemic12


title: human failing LV myocardium, Ischemic27


title: human failing LV myocardium, Ischemic18


title: human failing LV myocardium, Idiopathic11


title: human failing LV myocardium, Ischemic31


title: human failing LV myocardium, Idiopathic14


title: human failing LV myocardium, Idiopathic23


title: human failing LV myocardium, Ischemic30


title: human failing LV myocardium, Ischemic32


title: human failing LV myocardium, Idiopathic25


title: human failing LV myocardium, Ischemic24


title: human failing LV myocardium, Ischemic20


title: human failing LV myocardium, Idiopathic13


title: human failing LV myocardium, Ischemic26


title: human failing LV myocardium, Idiopathic20


title: human failing LV myocardium, Idiopathic16


title: human failing LV myocardium, Idiopathic17


title: human failing LV myocardium, Ischemic36


title: human failing LV myocardium, Ischemic28


title: human failing LV myocardium, Idiopathic15


title: human failing LV myocardium, Idiopathic18


title: human nonfailing LV myocardium, NonFailing4


title: human failing LV myocardium, Ischemic25


title: human failing LV myocardium, Ischemic29


title: human nonfailing LV myocardium, NonFailing5


title: human failing LV myocardium, Idiopathic19


title: human failing LV myocardium, Idiopathic21


title: human failing LV myocardium, Idiopathic24


title: human nonfailing LV myocardium, NonFailing3


title: human nonfailing LV myocardium, NonFailing8


title: human nonfailing LV myocardium, NonFailing2


title: human failing LV myocardium, Ischemic43


title: human nonfailing LV myocardium, NonFailing9


title: human nonfailing LV myocardium, NonFailing11


title: human nonfailing LV myocardium, NonFailing6


title: human failing LV myocardium, Idiopathic22


title: human nonfailing LV myocardium, NonFailing7


title: human failing LV myocardium, Ischemic46


title: human failing LV myocardium, Idiopathic35


title: human failing LV myocardium, Ischemic45


title: human failing LV myocardium, Idiopathic34


title: human failing LV myocardium, Ischemic37


title: human failing LV myocardium, Idiopathic37


title: human failing LV myocardium, Idiopathic33


title: human failing LV myocardium, Ischemic50


title: human failing LV myocardium, Ischemic47


title: human failing LV myocardium, Ischemic44


title: human failing LV myocardium, Idiopathic38


title: human failing LV myocardium, Ischemic49


title: human failing LV myocardium, Idiopathic36


title: human failing LV myocardium, Idiopathic42


title: human failing LV myocardium, Ischemic53


title: human failing LV myocardium, Idiopathic43


title: human failing LV myocardium, Ischemic48


title: human failing LV myocardium, Idiopathic39


title: human failing LV myocardium, Ischemic52


title: human failing LV myocardium, Ischemic51


title: human failing LV myocardium, Idiopathic40


title: human failing LV myocardium, Ischemic54


title: human failing LV myocardium, Idiopathic41


title: human failing LV myocardium, Idiopathic46


title: human failing LV myocardium, Idiopathic44


title: human failing LV myocardium, Idiopathic45


title: human failing LV myocardium, Ischemic55


title: human failing LV myocardium, Ischemic56


title: human failing LV myocardium, Idiopathic47


title: human failing LV myocardium, Ischemic61


title: human failing LV myocardium, Ischemic59


title: human failing LV myocardium, Ischemic57


title: human failing LV myocardium, Ischemic60


title: human failing LV myocardium, Ischemic65


title: human failing LV myocardium, Ischemic63


title: human failing LV myocardium, Ischemic66


title: human failing LV myocardium, Ischemic58


title: human failing LV myocardium, Idiopathic50


title: human failing LV myocardium, Idiopathic58


title: human failing LV myocardium, Idiopathic52


title: human failing LV myocardium, Idiopathic55


title: human failing LV myocardium, Ischemic67


title: human failing LV myocardium, Ischemic64


title: human failing LV myocardium, Ischemic68


title: human failing LV myocardium, Ischemic62


title: human failing LV myocardium, Idiopathic49


title: human failing LV myocardium, Idiopathic54


title: human failing LV myocardium, Idiopathic53


title: human failing LV myocardium, Idiopathic57


title: human failing LV myocardium, Idiopathic51


title: human nonfailing LV myocardium, NonFailing13


title: human failing LV myocardium, Ischemic71


title: human failing LV myocardium, Idiopathic48


title: human failing LV myocardium, Ischemic75


title: human failing LV myocardium, Ischemic73


title: human failing LV myocardium, Ischemic69


title: human failing LV myocardium, Idiopathic59


title: human failing LV myocardium, Idiopathic56


title: human failing LV myocardium, Ischemic72


title: human failing LV myocardium, Ischemic76


title: human failing LV myocardium, Idiopathic73


title: human failing LV myocardium, Ischemic74


title: human nonfailing LV myocardium, NonFailing14


title: human failing LV myocardium, Ischemic100


title: human failing LV myocardium, Ischemic77


title: human failing LV myocardium, Ischemic101


title: human failing LV myocardium, Idiopathic75


title: human failing LV myocardium, Ischemic78


title: human failing LV myocardium, Ischemic70


title: human failing LV myocardium, Idiopathic77


title: human failing LV myocardium, Idiopathic79


title: human failing LV myocardium, Idiopathic74


title: human failing LV myocardium, Ischemic99


title: human failing LV myocardium, Ischemic103


title: human failing LV myocardium, Idiopathic78


title: human failing LV myocardium, Ischemic98


title: human failing LV myocardium, Idiopathic76


title: human failing LV myocardium, Idiopathic83


title: human failing LV myocardium, Idiopathic85


title: human failing LV myocardium, Ischemic107


title: human failing LV myocardium, Ischemic104


title: human failing LV myocardium, Ischemic102


title: human failing LV myocardium, Idiopathic80


title: human failing LV myocardium, Ischemic108


title: human nonfailing LV myocardium, NonFailing16


title: human failing LV myocardium, Idiopathic84


title: human failing LV myocardium, Idiopathic81


title: human failing LV myocardium, Idiopathic60


title: human failing LV myocardium, Idiopathic82


title: human failing LV myocardium, Ischemic81


title: human failing LV myocardium, Idiopathic62


title: human failing LV myocardium, Ischemic106


title: human failing LV myocardium, Ischemic80


title: human failing LV myocardium, Ischemic79


title: human failing LV myocardium, Ischemic105


title: human failing LV myocardium, Idiopathic64


title: human failing LV myocardium, Ischemic83


title: human failing LV myocardium, Idiopathic86


title: human failing LV myocardium, Idiopathic61


title: human failing LV myocardium, Ischemic84


title: human failing LV myocardium, Idiopathic66


title: human nonfailing LV myocardium, NonFailing15


title: human failing LV myocardium, Idiopathic68


title: human failing LV myocardium, Ischemic91


title: human failing LV myocardium, Idiopathic65


title: human failing LV myocardium, Ischemic85


title: human failing LV myocardium, Ischemic89


title: human failing LV myocardium, Idiopathic69


title: human failing LV myocardium, Ischemic93


title: human failing LV myocardium, Idiopathic63


title: human failing LV myocardium, Ischemic82


title: human failing LV myocardium, Idiopathic70


title: human failing LV myocardium, Ischemic88


title: human failing LV myocardium, Ischemic90


title: human failing LV myocardium, Ischemic92


title: human failing LV myocardium, Ischemic95


title: human failing LV myocardium, Idiopathic72


title: human failing LV myocardium, Idiopathic71


title: human failing LV myocardium, Ischemic96


title: human failing LV myocardium, Ischemic97


title: NPC_5Day_-GF_rep1

status: Public on Sep 04 2006

city: Harlow

first: Ignacio

last: Munoz-Sanjuan

state: Essex

address: Terlings Park

department: Molecular & Cellular Neuroscience

country: United Kingdom

institute: Merck Sharp & Dohme

description: NPC Cells grown and differentiated by removal of Growth Factors for 5 Days hybridised against a pool of 3 undifferentiated Reference samples

data_processing: Rosetta Resolver Ratio Experiment using a pair of Fluor-Reversed samples normalised using the Rosetta Resolver Agilent Error Model

label: Cy3 / Cy5 Dye Reversal

source_name: Mouse SVZ NPC Reference Pool

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: Undifferentiated Reference Sample Pool (n=3).  Each sample grown in Normal Growth Medium

tag: Strain

tag: Tissue

value: Adult Subventricular Zone Neural Precursor Cells

tag: Sample Type

value: Pool of 3

tag: Differentiation State

value: Undifferentiated

tag: Growth Conditions

value: Normal Growth Media

tag: Time

value: 1 day

source_name: Mouse SVZ NPC 5Day -GF Replicate 1

treatment_protocol: Differentiated Sample grown in Absence of Growth Factors for 5 Days

value: Pool of 1

value: Differentiated

value: No Growth Factors Added

value: 5 day


title: SUP fraction used to normalize Scc1-HA6 ChIP (6th)

status: Public on Sep 02 2006

type: genomic

city: Montpellier

first: Armelle

last: Lengronne

address: 141 rue de la Cardonille

department: Institut de Genetique Humaine

institute: CNRS

description: Sup fraction used to normalize the IP GSM133517

hyb_protocol: Hybridization, blocking and washing were carried out as previously described (Katou et al., 2003, Nature) (Lengronne et al., 2004, Nature). Samples were  hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix).

scan_protocol: Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Sup fraction (equal to Whole Cell Extract)

tag: strain genotype

value: Scc1-HA6 ctf18delta


title: SUP fraction used to normalize Scc1-HA6 ChIP (5th)

description: Sup fraction used to normalize the IP GSM133516

tag: strain background

value: Scc1-HA6 ctf4delta


title: NPC_5Day_-GF_rep2

source_name: Mouse SVZ NPC 5Day -GF Replicate 2


title: SUP fraction used to normalize Flag-PCNA ChIP (2nd)

description: Sup fraction used to normalize the IP GSM133515

value: ctf18delta Flag-PCNA


title: NPC_NGM_rep1

description: NPC Cells grown in fresh Normal Growth Medium for 24 hours hybridised against a pool of 3 undifferentiated Reference samples

source_name: Mouse SVZ NPC NGM Replicate 1

treatment_protocol: Undifferentiated Reference Sample grown in Normal Growth Medium


title: NPC_1Day_Serum_rep3

description: NPC Cells grown and differentiated in presence of Serum for 24 hours hybridised against a pool of 3 undifferentiated Reference samples

source_name: Mouse SVZ NPC 1Day Serum Replicate 3

treatment_protocol: Differentiated Sample grown in presence of Serum for 24 Hours

value: Serum Treated


title: NPC_1Day_-GF_rep3

description: NPC Cells grown and differentiated by removal of Growth Factors for 24 hours hybridised against a pool of 3 undifferentiated Reference samples

source_name: Mouse SVZ NPC 1Day -GF Replicate 3

treatment_protocol: Differentiated Sample grown in Absence of Growth Factors for 24 Hours


title: SUP fraction used to normalize Scc1-HA6 ChIP (2nd)

description: Sup fraction used to normalize the IP GSM133522

tag: Strain genotype

value: scc2-4 Scc1-HA6


title: NPC_1Day_Serum_rep1

source_name: Mouse SVZ NPC 1Day Serum Replicate 1


title: SUP fraction used to normalize Scc1-HA3 ChIP (4th)

description: Sup fraction used to normalize the IP GSM133510 and GSM133511

value: scc2-4 SCC1-Pk9 GAL-SCC1-HA3


title: SUP fraction used to normalize Scc1-PK9 ChIP (1st)

description: Sup fraction used to normalize the IP GSM133521

tag: Wild type strain


title: NPC_1Day_-GF_rep1

source_name: Mouse SVZ NPC 1Day -GF Replicate 1


title: SUP fraction used to normalize Scc1-HA6 ChIP (3rd)

description: Sup fraction used to normalize the IP GSM133518, GSM133519 and GSM133520

value: Scc1-HA6 eco1-1


title: SUP fraction used to normalize Ctf18-HA6 ChIP (2nd)

description: Sup fraction used to normalize the IP GSM133505 and GSM133512

tag: Wild type strain containing Ctf18-HA6 tagged


title: SUP fraction used to normalize Ctf18-HA6 ChIP

description: Sup fraction used to normalize the IP GSM133513

tag: wild type strain contaning Ctf18-HA6 tagged


title: SUP fraction used to normalize Flag-PCNA ChIP (1st)

description: Sup fraction used to normalize the IP GSM133514

tag: Wild type strain contaning Flag-PCNA tagged


title: NPC_5Day_-GF_rep3

source_name: Mouse SVZ NPC 5Day -GF Replicate 3


title: NPC_1Day_-GF_rep2

source_name: Mouse SVZ NPC 1Day -GF Replicate 2


title: NPC_NGM_rep2

source_name: Mouse SVZ NPC NGM Replicate 2


title: NPC_1Day_Serum_rep2

source_name: Mouse SVZ NPC 1Day Serum Replicate 2


title: NPC_Ref_rep2

description: 'Self-Ref' Sample: Single member of reference (undifferentiated) sample hybridised against a pool of 3 such samples

source_name: Mouse SVZ NPC Reference Replicate 2


title: Scc1-HA6 distribution on chromosome VI in scc2-4 cells

description: Scc1-HA6 distribution on chromosome VI in scc2-7 cells arrested in nocodazole at 37°C. The shift from 25°C to 37°C has been done in HU-arrested cells

source_name: Chromatin Immunoprecipitated DNA

value: scc2-4  SCC1-HA6


title: NPC_Ref_rep3

value: Adult Subventricular Zone Neural Precursor Cells

source_name: Mouse SVZ NPC Reference Replicate 3


title: human failing LV myocardium, Ischemic94

description: Gene expression data from advanced human heart failure due to ischemic cardiomyopathy

source_name: explanted heart tissue at time of cardiac transplantation


title: Scc1-HA6 distribution on chromosome VI in eco1-1 cells at 37°C (2nd time point)

description: Scc1-HA6 distribution at 35 min post- HU release on chromosome VI in eco1-1 cells at 37°C

value: eco1-1 Scc1-HA6


description: Scc1-PK distribution on chromosome VI in scc2-4 ctf18-td cells arrested in nocodazole at 37°C. The shift from 25°C to 37°C has been done in HU-arrested cells

value: scc2-4  GAL-HA-UBR1  ctf18-td-myc  SCC1-Pk


title: Input DNA replicate 2

city: Singapore

first: Vinsensius

middle: B

last: Vega

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Input DNA from MCF-7 cells

data_processing: Raw data

source_name: Input DNA from MCF-7

tag: Input DNA


title: Scc1-HA6 distribution on chromosome VI in wild type cells at 37°C

description: Scc1-HA6 distribution at 15 min post- HU release on chromosome VI in wild type cells at 37°C

tag: Wild type strain containing Scc1-HA6


title: Flag-PCNA distribution on chromosome VI in  ctf18 delta cells in HU at 25°C

description: Flag-PCNA distribution on chromosome VI in  ctf18 delta cells arrested in HU at 25°C

value: ctf18delta  Flag3-PCNA


title: Scc1-HA6 distribution on chromosome VI in ctf18 delta cells in G2/M at 25°C

description: Scc1-HA6 distribution on chromosome VI in ctf18 delta cells arrested in G2/M in nocodazole at 25°C

value: ctf18delta SCC1-HA6


title: Scc1-HA6 distribution on chromosome VI in eco1-1 cells at 37°C (1st time point)

description: Scc1-HA6 distribution at 25 min post- HU release on chromosome VI in eco1-1 cells at 37°C


title: Scc1-HA6 distribution on chromosome VI in ctf4 delta cells in G2/M at 25°C

description: Scc1-HA6 distribution on chromosome VI in ctf4 delta cells arrested in G2/M in nocodazole at 25°C

value: ctf4delta SCC1-HA6


title: NPC_Ref_rep1

source_name: Mouse SVZ NPC Reference Pool

value: Pool of 3

value: Undifferentiated

value: Normal Growth Media

value: 1 day

source_name: Mouse SVZ NPC Reference Replicate 1

value: Pool of 1


title: Flag-PCNA distribution on chromosome VI in HU at 25°C

description: Flag-PCNA distribution on chromosome VI in wild type cells arrested in HU at 25°C


title: Scc1 distribution in wild type cells on chromosome VI (in G2/Nocodazole)

description: Distribution of Scc1-HA3 (expressed in HU from the Gal promoter in cells at 37°C)on chromosome VI in wild type cells arrested in nocodazole at 37°C.)

tag: Wild type strain containing SCC1-Pk9 GAL-SCC1-HA3


title: Ctf18-HA6 distribution on chromosome VI in HU at 25°C

description: Ctf18-HA6 distribution on chromosome VI in wild type cells arrested in HU at 25°C


title: Ctf18-HA6 distribution on chromosome VI in HU at 25°C in ctf4 delta cells

description: Ctf18-HA6 distribution on chromosome VI in ctf4 delta cells arrested in HU at 25°C

value: ctf4delta CTF18-HA6


title: SUP fraction used to normalize Ctf4-PK9 ChIPs

description: Sup fraction used to normalize three Ctf4-PK9 ChIPs: GSM133460/1/2

source_name: Sup fraction (equal to Whole Cell Extract)


title: ER ChIP replicate 2

description: ChIP DNA from MCF-7 cells

source_name: ER ChIP DNA from MCF-7

tag: ChIP DNA with ER antibody


description: SUP fraction used to normalize the BrdU ChIP  GSM132931

tag: Wild type strain containing 7 copies of TK gene and CT18-HA6 tagged


title: SUP fraction used to normalize Ctf4-HA6 and Ctf18-HA6 ChIPs

description: Sup fraction used to normalize 2ChIPs: GSM133458 and GSM133459


title: Ctf4-HA6 distribution on chromosome VI, 3rd time point

description: Ctf4-PK9 distribution at 60 min on chromosome VI in wild type cells released from G1 into S phase at 16°C


title: Ctf4-PK9 distribution  on chromosome VI during a time course

description: Ctf4-PK9 distribution at 40 min on chromosome VI in wild type cells released from G1 into S phase at 16°C


title: Scc1 distribution in scc2-4 cells on chromosome VI (in G2/Nocodazole)

description: Distribution of Scc1-HA3 (expressed in HU from the Gal promoter in cells at 37°C)on chromosome VI in scc2-4 cells arrested in nocodazole at 37°C.)

value: scc2-4  SCC1-Pk9  GAL-SCC1-HA3


title: Ctf18-HA6 distribution on chromosome VI in HU

tag: Wild type strain containing 7 copies of the Thymidine Kinase gene


title: Eco1-FLAG distribution on chromosome VI  in HU

description: Eco1-FLAG distribution on chromosome VI in wild type cells arrested in HU at 25°C


title: Ctf4-HA6 distribution on chromosome VI

description: Ctf4-HA6 distribution on chromosome VI in wild type cells arrested in HU at 25°C

tag: wild type strain


title: Ctf4-HA6 distribution on chromosome VI, 2nd time point

description: Ctf4-PK9 distribution at 50 min on chromosome VI in wild type cells released from G1 into S phase at 16°C


title: Input DNA replicate 1

description: Input DNA from MCF-7 cells


title: ER ChIP replicate 1

description: ChIP DNA from MCF-7 cells


title: Dexamethasone 1

city: Augusta

first: Beth

last: Baisden

state: GA

institute: Medical College of Georgia

description: treated sample number 1

data_processing: GCOS

source_name: placenta


title: Dexamethasone 2

description: treated sample number 2


title: Control 2

description: contol sample number 2


title: LightResponse-Rep1

status: Public on Aug 25 2006

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

description: For preparation of RNA for the microarray studies, all replicate for the induced (collected 30 min. after exposure to a 5 min pulse of white light) and non-induced (dark) mycelia was isolated using RNeasy kits (Qiagen Inc. Valencia, CA, USA).

hyb_protocol: Ten micrograms of total RNA for each sample were reverse transcribed and labelled with Cy3 or Cy5 using CyScribe First Strand cDNA Labelling Kit (Amersham Biosciences, Piscataway, NJ, USA). The labelled products were purified with GFX purification columns (CyScribe GFX Purification Kit, Amersham Biosciences). The slides were placed in pre-hybridization solution (1% BSA, 5X SSC, and 0.1% SDS at 45°C) for 2 hours to eliminate non-specific interactions, and then rinsed with 0.1X SSC (22-25°C for 5 min) and HPLC grade water. Each slide was hybridized with a combination of untreated and treated labelled probes at 45°C for 14-16 h in a humidified hybridization chamber (Corning, Acton, MA, USA). After hybridization, the slides were washed once in solutions 1-4 (wash solution 1: 2x SSC, 0.1% SDS at 45ºC; wash solution 2: 0.1x SSC, 0.1% SDS; wash solution 3: 0.1x SSC; wash solution 4: 0.01x SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation in a conical tube for 5 min at 1600 rpm. Three independent replicates of each mycelial treatment, RNA isolation and labelling, and microarray hybridization were performed. To estimate ‘system noise’ that may be due to differences in Cy-dye labelling between samples, we performed a ‘self-to-self’ hybridization, where the same control sample was labelled separately with Cy5 and Cy3, and then hybridized.

data_processing: Data normalization was performed using the GeneSpring 6.1 software package (Silicon Genetics, Redwood, CA, USA) applying the Cross-gene-error-model in combination with a one-way ANOVA (significance level set at p>0.05).  The background fluorescence median values that were less than zero were set to zero and subjected to intensity-dependent LOWESS (locally weighted scatter plot smoother) normalization, in which 20% of the data was used for smoothing (Clevel & Devlin 1998; Yang et al., 2001). This normalization was used to account for differences in overall intensity between slides. Each experimental result was interpreted as the average of the three biological replicates and their corresponding swap replicate. Gene expression profiles were required to be present in all three of the data sets. A signal-to-control channel ratio > 1.8 and a probability t test P<0.05 was defined as up-regulation by the light stimulus. A signal-to-control channel ratio < 0.667 and a probability t test P<0.05 was defined as down-regulation.

organism: Trichoderma atroviride

source_name: LightResponse-Ref-Label (Cy3)-Rep1A

label_protocol:
This protocol can be used to prepare Cy3 or Cy5 labelled cDNA from purified total eukaryotic RNA. In one standard reaction, 2.5 -25 ug of total RNA can be reverse transcribed into fluorescently labelled cDNA. We utilized 10 ug of total RNA in our experiments for each of the conditions (induced mycelia collected 30 min. after exposure to a 5 min pulse of white light and non-induced mycelia growth in total darkness). The final volume recommended for the labelling reaction is 20 ul after addition of all reaction components, therefore, to anneal primers, the volumes corresponding to total RNA (10 ug) and anchored oligo(dT) (2.5 ug) should be adjusted to 11 ul. This reaction mixture it is incubated at 70ºC for 5 min and subsequently let the reaction mixture cool at room temperature for 10 minutes allow the primers to anneal with the total RNA template. Finally the labelling components for the reaction added in the following order: 4 ul for the 5x CyScript buffer, 2 uL 0.1 M DTT, 1 uL dUTP nucleotide mix, 1 uL dUTP CyDye-labelled nucleotide (Cy3 or Cy5), and 1 uL SuperScript II reverse transcriptase, and the reaction mix incubated at 42ºC for 1.5 hours. All the components before mentioned for the reactions from total RNA can be reverse transcribed into fluorescently labelled cDNA form part of the CyScribe First-Strand cDNA labelling kit (cat. Number: RPN6201, Amersham Biosciences).
It is necessary to remove the RNA template for the each sample before the hybridization, from the single-stranded cDNA to promote hybridization of the cDNA probe to immobilized microarray targets and to minimize hybridization with complementary RNA in solution. Removal of unincorporated CyDye-nucleotides is also necessary for minimizing hybridization background and for improving the sensitivity of detection of low abundance targets. The removal of RNA can be achieved in two steps. First RNA is degraded into short oligomers with alkaline treatment (adding 2 uL of 2.5 M NaOH into each microcentrifuge tube containing labelling reactions and incubating the samples at 37ºC for 15 min, subsequently we add 10 uL of 2 M HEPES to neutralize the pH). Then these short oligomers, as well as unincorporated nucleotides, are removed with spin chromatography columns. We use CyScribe GFX Purification kit (Cat. Number: 27-9606-02, Amersham Biosciences). Labelled cDNA tightly bound to the CyScribe GFX column was eluted in 60 ul elution buffer (provided with the kit).

tag: T. atroviride cultures were grown in the dark for 48 h at 27°C on PDYCA plates and used a pre-inoculum. Mycelial plugs were then placed on a washed cellophane sheet overlying a double layer of filter paper (an 8 cm disk of Whatmann 50 was overlaid on a 7 cm disk of Whatmann 1 filter paper in a Petri dish) soaked in 3 ml PDYCB medium (24 g/l of Potato Dextrose Broth, 2 g/l of Yeast Extract and 1.2 g/l of casein hydrolysate medium, all from DIFCO). Cultures were allowed to grow for further 36h in the dark. Total RNA was isolated from colonies  non-induced (kept at all times in the dark). Mycelia were scraped from the surface of the cellophane overlaying the filter paper under red safe-light LEE filter #106 (fluence rate 0.1 mmol/m2s) and immediately frozen in liquid nitrogen for RNA extraction using RNeasy kits (Qiagen Inc. Valencia, CA, USA).

source_name: LightResponse-Test-Label (Cy5)-Rep1A

tag: T. atroviride cultures were grown in the dark for 48 h at 27°C on PDYCA plates and used a pre-inoculum. Mycelial plugs were then placed on a washed cellophane sheet overlying a double layer of filter paper (an 8 cm disk of Whatmann 50 was overlaid on a 7 cm disk of Whatmann 1 filter paper in a Petri dish) soaked in 3 ml PDYCB medium (24 g/l of Potato Dextrose Broth, 2 g/l of Yeast Extract and 1.2 g/l of casein hydrolysate medium, all from DIFCO). Cultures were allowed to grow for further 36h in the dark, and then photoinduced. Total RNA was isolated from colonies that were exposed to white light for five minutes (fluence rate 27 umol/m2s), and placed back in the dark at 27°C for 30 min. Mycelia were scraped from the surface of the cellophane overlaying the filter paper under red safe-light LEE filter #106 (fluence rate 0.1 mmol/m2s) and immediately frozen in liquid nitrogen for RNA extraction using RNeasy kits (Qiagen Inc. Valencia, CA, USA).


title: BR064

status: Public on Aug 23 2006

city: Sendai

first: Shin

last: Takahashi

state: Miyagi

address: 4-1, Seiryo-chou, Aobaku

department: Clinical Oncology

institute: Tohoku Univ.

description: Series of 40 breast cancers

hyb_protocol: An in situ hybridization kit plus (Agilent) was used as a hybridization buffer. After hybridization for 17 h at 60ﾟC, microarrays were washed once in washing solution 1 (6 x SSPE: Amresco and 0.005% N-Lauroylsarcosine: Sigma) for 1 min, once in washing solution 2 (0.06 x SSPE and 0.005% N-Lauroylsarcosine) for 1 min, and then in washing solution 3 (Agilent stabilization and drying solution, Agilent) for 30 s.

scan_protocol: Immediately after the washing process, microarrays were scanned by ScanArray 5000 (GSI Lumonics) at an excitation wavelength of 543 nm (Cy3) and 633 nm (Cy5). Fluorescent intensities of scanned images were quantified by ArrayVision Ver.8 rev.4 (Imaging research).

data_processing: The gene expression data was quantified and analyzed by GeneSpring 6.2 (Silicon Genetics). LOWESS was used for normalization.

source_name: Breast Cancer tissue

label_protocol: RNA from each sample was amplified and labeled using a Low input RNA fluorescent linear amplification kit (Agilent).

extract_protocol: Frozen sections were made from frozen tumor material. From tumor tissue sections, only tumorous cells were microdissected using a Leica AS LMD system (Leica). Tumor cells were collected in 50 μl RLT buffer (Qiagen), containing 1% 2-mercaptoethanol and total RNA was extracted by using RNeasy micro kit (Qiagen). The quality of RNA was confirmed by checking the 28S and 18S ribosomal RNA ratios using a Bioanalyzer (Agilent Technologies).

treatment_protocol: Tumor materials were immediately frozen in liquid nitrogen after surgery and stored at -80ﾟC.

tag: Breast Cancer tissue

source_name: Reference RNA pool

extract_protocol: Reference RNA pool was prepared by mixing 50ng RNA from each RNA sample.

tag: Mixture of 40 breast cancer samples


title: BR062

description: Series of 40 breast cancers

treatment_protocol: Reference RNA pool was prepared by mixing 50ng RNA from each RNA sample.


title: BR054

description: Series of 40 breast cancers


title: BR058

description: Series of 40 breast cancers


title: BR052

description: Series of 40 breast cancers


title: Control 1

description: contol sample number 1


title: BR055

description: Series of 40 breast cancers


title: BR053

description: Series of 40 breast cancers


title: BR063

description: Series of 40 breast cancers


title: BR050

description: Series of 40 breast cancers


title: BR044

description: Series of 40 breast cancers


title: BR046

description: Series of 40 breast cancers


title: BR041

description: Series of 40 breast cancers


title: BR045

description: Series of 40 breast cancers


title: BR043

description: Series of 40 breast cancers


title: BR040

description: Series of 40 breast cancers


title: Dexamethasone 3

description: treated sample number 3


title: BR047

description: Series of 40 breast cancers


title: BR033

description: Series of 40 breast cancers


title: BR048

description: Series of 40 breast cancers


title: BR036

description: Series of 40 breast cancers


title: BR059

description: Series of 40 breast cancers


title: BR024

description: Series of 40 breast cancers


title: BR027

description: Series of 40 breast cancers


title: BR038

description: Series of 40 breast cancers


title: BR035

description: Series of 40 breast cancers


title: BR034

description: Series of 40 breast cancers


title: BR026

description: Series of 40 breast cancers


title: BR016

description: Series of 40 breast cancers


title: BR022

description: Series of 40 breast cancers


title: BR017

description: Series of 40 breast cancers


title: BR021

description: Series of 40 breast cancers


title: BR010

description: Series of 40 breast cancers

treatment_protocol: Tumor materials were immediately frozen in liquid nitrogen after surgery and stored at –80ﾟC.


title: BR011

description: Series of 40 breast cancers


title: BR009

description: Series of 40 breast cancers

hyb_protocol: An in situ hybridization kit plus (Agilent) was used as a hybridization buffer. After hybridization for 17 h at 60ﾟC, microarrays were washed once in washing solution 1 (6 x SSPE: Amresco and 0.005% N-Lauroylsarcosine: Sigma) for 1 min, once in washing solution 2 (0.06 x SSPE and 0.005% N-Lauroylsarcosine) for 1 min, and then in washing solution 3 (Agilent stabilization and drying solution, Agilent) for 30 s.


title: BR019

description: Series of 40 breast cancers


title: Control 3

description: contol sample number 3


title: BR020

description: Series of 40 breast cancers


title: BR005

description: Series of 40 breast cancers

hyb_protocol: An in situ hybridization kit plus (Agilent) was used as a hybridization buffer. After hybridization for 17 h at 60ﾟC, microarrays were washed once in washing solution 1 (6 נSSPE: Amresco and 0.005% N-Lauroylsarcosine: Sigma) for 1 min, once in washing solution 2 (0.06 נSSPE and 0.005% N-Lauroylsarcosine) for 1 min, and then in washing solution 3 (Agilent stabilization and drying solution, Agilent) for 30 s.

treatment_protocol: Tumor materials were immediately frozen in liquid nitrogen after surgery and stored at -80ﾟC


title: BR001

description: Series of 40 breast cancers

hyb_protocol: An in situ hybridization kit plus (Agilent) was used as a hybridization buffer. After hybridization for 17 h at 60ﾟC, microarrays were washed once in washing solution 1 (6 × SSPE: Amresco and 0.005% N-Lauroylsarcosine: Sigma) for 1 min, once in washing solution 2 (0.06 × SSPE and 0.005% N-Lauroylsarcosine) for 1 min, and then in washing solution 3 (Agilent stabilization and drying solution, Agilent) for 30 s.

treatment_protocol: Tumor materials were immediately frozen in liquid nitrogen after surgery and stored at –80ﾟC


title: M. grisea strain (70-15)_total RNA from Vegetative mycelium and Appressorium

status: Public on Aug 18 2006

city: Columbus

first: Mohan

last: Raghupathy

email: mohanbabu_r@yahoo.com, wang.620@osu.edu

state: OH

address: 201 Kottman Hall, 2021 Coffey Rd

department: Department of Plant Pathology

institute: The Ohio State University

description:
The normalized data were then subjected to ANOVA model
using Boenferoni method. False Discovery Rate was calculated based on the p-value (≤0.001) from ANOVA.

hyb_protocol: Agilent hybridization protocols (5184-3568; Agilent).

scan_protocol: Agilent G2565BA microarray scanner as described by Coughlan et al., 2004. The raw TIFF images were analyzed using the Agilent Feature Extraction software v 8.1

data_processing: Data were corrected and normalized Partek Pro v.6.0 software (Partek Inc., Missouri).

label: Cy3 and also carried dye swap for three replicates

organism: Pyricularia grisea

source_name: Vegetative mycelium

growth_protocol:
70-15 was cultured on a liquid medium
[0.2% (w/v) yeast extract and 1% (w/v) sucrose] for 72 h (28°C at 200 rpm). The
harvested mycelia were filtered and grinded for RNA isolation using the TRIzol method
(Invitrogen, CA).

extract_protocol:
TRIzol method
(Invitrogen, CA)

tag: 70-15 was cultured on a liquid medium

tag: (Invitrogen, CA).

label: Cy5 and also carried dye swap for three replicates

source_name: Appressorium

growth_protocol:
The mycelia
of 70-15 were grown for two weeks on oatmeal agar plates and then the conidia were
induced under white fluorescence light for five days. About 2 ml of conidia suspension
(5 x 105 spores ml-1) was sprayed on Falcon Petri plates (150mm x 15mm) (Falcon,
NJ) ,and the lids were covered with moist filter papers. These plates were incubated at
28oC and appressorium formation was monitored under a microscope at 6 h intervals.
Fungal tissue was harvested 24 h after incubation since over 90% of the conidia extended
a germ tube from the basal and/or the apical cell, and differentiated into an appresorium
and produced penetration pegs at this time point.

extract_protocol:
Using a sterile blade, appressoria were
scrapped and transferred quickly to the TRIzol solution, and then the suspension was
centrifuged at 12,000 x g at 5oC for 5 min. About 2 g of appressorium pellet were
collected and subjected for total RNA isolation.

tag: The mycelia


title: Phosphate starvation CC-125 0h vs psr1-1 0h low dye swap 0603

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: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45815.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: Chlamydomonas reinhardtii

source_name: psr1-1 0h

tag: psr1-1 0h


title: BR007

description: Series of 40 breast cancers


title: BR013

description: Series of 40 breast cancers


title: Phosphate starvation CC-125 0h vs psr1-1 24h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46633.gif


title: Phosphate starvation CC-125 0h vs psr1-1 12h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45596.gif


title: Phosphate starvation CC-125 0h vs CC-125 4h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45508.gif


title: Phosphate starvation CC-125 0h vs CC-125 12h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45490.gif


title: Phosphate starvation CC-125 0h vs CC-125 4h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45509.gif


title: Phosphate starvation CC-125 0h vs psr1-1 48h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46632.gif


title: Phosphate starvation CC-125 0h vs psr1-1 48h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45598.gif


title: Phosphate starvation CC-125 0h vs psr1-1 24h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45597.gif


title: Phosphate starvation CC-125 0h vs psr1-1 4h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45595.gif

source_name: psr1-1 4h

tag: psr1-1 4h


title: Phosphate Starvation CC-125 (0h) versus CC-125 (24h) Dye swap Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44053.gif


title: BR008

description: Series of 40 breast cancers


title: Phosphate starvation CC-125 0h vs psr1-1 0h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45599.gif


title: Phosphate starvation CC-125 0h vs CC-125 24h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45489.gif


title: Phosphate starvation CC-125 0h vs psr1-1 0h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45593.gif


title: Phosphate Starvation CC-125 (0h) versus CC-125 (24h) Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44052.gif


title: Phosphate starvation CC-125 0h vs CC-125 24h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45488.gif


title: Phosphate Starvation CC-125 (0h) versus CC-125 (4h) Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44080.gif


title: Phosphate starvation CC-125 0h vs psr1-1 4h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45600.gif


title: Phosphate starvation CC-125 0h vs psr1-1 24h low 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45714.gif


title: Phosphate starvation CC-125 0h vs CC-125 48h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45486.gif


title: Phosphate starvation CC-125 0h vs psr1-1 12h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45601.gif


title: Phosphate Starvation CC-125 (0h) versus CC-125 (4h) Dye swap Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44081.gif


title: Phosphate Starvation CC-125 (0h) versus CC-125 (48h) Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44027.gif


title: Phosphate starvation CC-125 0h vs psr1-1 48h low 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45715.gif


title: Phosphate starvation CC-125 0h vs psr1-1 24h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45602.gif


title: Phosphate starvation CC-125 0h vs psr1-1 0h low 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45711.gif


title: Phosphate starvation CC-125 0h vs psr1-1 4h low 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45712.gif


title: Phosphate starvation CC-125 0h vs CC-125 48h low

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45487.gif


title: Phosphate starvation CC-125 0h vs psr1-1 12h low 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45713.gif


title: Phosphate starvation CC-125 0h vs psr1-1 48h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45603.gif


title: Phosphate starvation CC-125 0h vs CC-125 24h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46583.gif


title: Phosphate Starvation CC-125 (0h) versus CC-125 (12h) Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44061.gif


title: Sample6_111004_II_5+3-

status: Public on Jul 26 2006

city: Dallas

first: Eric

middle: J.

last: Hansen

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: UT Southwestern Medical Center

description: Array hybridized with cDNA labeled with Cy5 (Iron-replete) and Cy3 (Iron-restricted).  cDNA was generated from total RNA with genome-directed primers (GDPs).

data_processing: Gene Pix Pro5.0 and Acuity 4.0

organism: Francisella tularensis

source_name: Ft LVS iron-replete

tag: F.t. LVS grown in MH+ iron-replete condition

source_name: Ft LVS iron-restricted

tag: F.t. LVS grown in MH-/DF iron-restricted condition


title: Phosphate starvation CC-125 0h vs CC-125 48h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46584.gif


title: Phosphate starvation CC-125 0h vs CC-125 12h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46582.gif


title: Phosphate starvation CC-125 0h vs psr1-1 0h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46636.gif


title: Phosphate starvation CC-125 0h vs psr1-1 48h low dye swap 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45819.gif


title: Sample5_110204_5+3-

tag: F. t. LVS grown in MH+ iron-replete condition

tag: F. t. LVS grown in MH-/DF iron restricted condition


title: Phosphate Starvation CC-125 (0h) versus CC-125 (12h) Dye swap Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44060.gif


title: Phosphate starvation CC-125 0h vs psr1-1 24h low dye swap 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45818.gif


title: Sample1_101404_5+3-

tag: F.t. LVS grown in MH-/DF  iron-restricted condition


title: Intact untreated planaria UNTR1

status: Public on Jul 19 2006

city: Pisa

first: Leonardo

last: Rossi

address: Via Volta 4

department: Morfologia Umana e Biologia Applicata

country: Italy

institute: University of Pisa

description: GenePix Pro 4.0 software (Axon Instruments) was used to retrive raw epression data on both channels

scan_protocol: Hybridized arrays were scanned at 10 μm resolution on a GenePix 4000 scanner at variable PMT voltage to obtain maximal signal intensities with less than 1% probe saturation.

data_processing: Data were normalized using the “median ratio over entire array equal to 1” method using BRB-ArrayTools software version 3.2 developed by the Biometric Research Branch of the National Cancer Institute (http://linus.nci.nih.gov/~brb/). The spots with diameter<25 µm, intensity <200 in both channel and missing value > 30% of all experiments were excluded from further analysis

organism: Dugesia japonica

source_name: intact untreated planaria

label_protocol: 3 µg of aRNA were directly labeled by using the non enzymatic method ULS™ aRNA labeling kit (Kreatech) following the manufacturer’s protocol

extract_protocol: Nucleospin RNA II Kit (Macherey-Nagel)

tag: intact untreated

source_name: constant reference

extract_protocol: guanidium thiocyanate/CsCl method

tag: pool of 50 untreated planarians


title: Phosphate starvation CC-125 0h vs psr1-1 4h low dye swap 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45816.gif


title: Phosphate starvation CC-125 0h vs CC-125 4h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46581.gif


title: Phosphate starvation CC-125 0h vs psr1-1 4h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46635.gif


title: Phosphate starvation CC-125 0h vs psr1-1 12h low dye swap 0603

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45817.gif


title: Phosphate starvation CC-125 0h vs psr1-1 12h low B

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46634.gif


title: Auratus goldfish genome project: slide 36; The effects of fluoxetine on female goldfish

status: Public on Aug 04 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Mennigen et al. “The effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)” (to be submitted) and Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17α-EE2 (Physiological Genomics).  Sequence information found at www.auratus.ca

data_processing: Array quality filter test used; Intensity-dependent Lowess normalization

organism: Carassius auratus

source_name: Carassius auratus; hypothalamus; i.p. saline control

tag: Female adult goldfish

tag: tissue

value: hypothalamus

tag: Fish were treated twice a week for 17 days with 0.6%saline

tag: Sexually regressed animals (December)

tag: Adults approx. 2-3 years of age

tag: dye swap with slide 39

source_name: Carassius auratus; hypothalamus; i.p injection fluoxetine

tag: Fish were treated twice a week for 17 days with 5 μg fluoxetine/g of body weight


title: CD8+H7aTet+_01

status: Public on Jul 12 2006

city: Montreal

first: Etienne

last: Caron

state: Quebec

address: 5415 Boul. L'Assomption

department: Recherche

country: Canada

institute: Hopital Maisonneuve Rosemont

description: B10.C-H7b(47N)/SN female mice were immunized by i.p. co-injection of C57BL/10Snj male and B10.C-H7b(47N)/SN male spleen cells. Fourteen days later, single-cell suspensions were prepared from the spleen of immunized mice. CD8+H7aTet+, CD8+HYTet+ and CD8+Tet- cells were sorted using a FACSVantage SE with Diva option (BD Biosciences, San Jose). Purity of sorted cell populations was always ≥ 98%. Tet+ populations containing between 8-300 thousand cells and Tet- population containing 2-3 million cells were obtained for each mouse and processed separately.

scan_protocol: Pixel Size 1.56 Filter 570 Scan Temperature Scan Date Aug 30 2004 05:59PM Scanner ID 50207280 Number of Scans 1 Scanner Type M10

label: biotin + R-phycoerythrin strepta

source_name: Spleen Tcells day 14

label_protocol: Labeling of samples was performed according to standard Affymetrix protocol

extract_protocol: Total RNA was isolated from sorted populations using TRIzol (Invitrogen/Life Technologies)

treatment_protocol: Immunization of a female B10.C-H7b(47N)/SN with splenocytes from male B10.C-H7b(47N)/SN + male C57BL/10Snj

tag: Strain

tag: Gender

value: Female

tag: Age


title: Canine_Temporal lobe_Gpaez_rep1

status: Public on Jul 06 2006

first: Gerardo

middle: L.

last: Paez

address: 3900 Delancey Street

department: Clinical Studies Philadelphia

institute: University of Pennsylvania

description: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and further purified by Rneasy mini kit (Qiagen, Valencia, CA). Purity and RNA quality were evaluated by absorbance at 260 nm and by denaturing formaldehyde agarose gel electrophoresis. High quality RNAs with A260/280 ratio over 1.8 and intact 28S and 18S RNA bands were used for microarray analysis. To generate an RNA reference sample for microarray hybridizations, we pooled equal amounts of total RNA from the occipital, temporal, and frontal brain regions collected from three 16-week-old beagles to achieve a homogeneous pool of transcripts. The pooled RNA was divided into aliquots (2μg/μl) and stored at -80 °C until use. For the purpose of this work, four tissue groups have been established, containing five biological replicates for normal retina and three for each respective brain region. After initial validation of reproducibility, only one microarray experiment was used for each sample.

data_processing: loess subgrid normalization

organism: Canis lupus familiaris

source_name: Temporal Brain tissue

tag: total RNA extracted from temporal brain tissue from dogs aged at 16 weeks

source_name: Brain pool

tag: Brain pool tissue made by adding equal amounts of Frontal Temporal and occipital total RNA cortices


title: CD8+HYTet+_01

label: biotin + R-phycoerythrin streptavidin


title: CD8+Tet-_05


title: CD8+Tet-_03


title: CD8+Tet-_02


title: ID: N1369A

status: Public on Jul 01 2006

city: Cincinnati

first: Bruce

middle: J

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

description: Sample type: Human colorectal carcinomas and normal adult human colon tissue.

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing:  Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm.

scan_protocol: The image file was captured on an Affymetrix Gene Chip Scanner 3000

data_processing:
Processed with Microarray suite 5.0 (Affymetrix) to generate .CEL files that were subject to RMA normalization (Irizarry et al 2003) using Bioconductor.org software.
Standard Affymetrix internal control genes, overall percent present call genes and signal to noise estimates were used to check the quality of the assay per chip. Quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3 were used. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. The Raw CEL files were processed using the RMA (Robust Multichip Average) from Bioconductor.org. Then, depending on the biological question to be addressed, the samples were referenced either to the median gene expression value across all the samples or to the expression levels of normal control adult colon samples.

source_name: Human colorectal tissue

label_protocol: Standard protocal fro 2 microgram total RNA using oligo dT primers was used.

extract_protocol:
The human investigations were performed after approval by the University of South Florida Institutional Review Board and in accord with an assurance filed with and approved by the Department of Health and Human Services. A waiver of informed consent was filed. All tumors and normal tissues were meticulously harvested under an identical, rigorous procurement protocol whereby tissues were macrodissected for purity and snap frozen in liquid nitrogen within 20 min of surgical extirpation. Human colorectal tumor samples (n=100) were microdissected (80% tumor cells) by frozen section guidance. Normal mucosal samples (n=5) were harvested from zones greater than 10 cm away from the gross tumor specimen and subjected to the same procedures as were the tumor samples.
Quality control steps:   RNA quality was assessed by using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: refer to Series supplementary file for sample characteristics


title: ID: N552G


title: CD8+Tet-_04

description: B10.C-H7b(47N)/SN  female mice were immunized by i.p. co-injection of C57BL/10Snj  male and B10.C-H7b(47N)/SN male spleen cells. Fourteen days later, single-cell suspensions were prepared from the spleen of immunized mice. CD8+H7aTet+, CD8+HYTet+ and CD8+Tet- cells were sorted using a FACSVantage SE with Diva option (BD Biosciences, San Jose). Purity of sorted cell populations was always ≥ 98%. Tet+ populations containing between 8-300 thousand cells and Tet- population containing 2-3 million cells were obtained for each mouse and processed separately.

source_name: Spleen T cells day 14


title: CD8+HYTet+_04


title: CD8+H7aTet+_03


title: WT differentiated brown fat cells (rep1)

city: Boston

first: Marc

last: Uldry

state: MA

address: 1 Jimmy Fund Way

institute: Dana Farber Cancer Institute

description: Cells immortalized through SV40 driven largeT antigen expression.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

label: biotinylation

source_name: brown fat cells differentiated for seven days

tag: immortalized cells derived from brown fat tissue of mouse of mixed background.

tag: passage number


title: CD8+HYTet+_03


title: Auratus goldfish genome project: The effects of fluoxetine on the reproductive axis of female goldfish

description: Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Mennigen et al. “The effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)” (to be submitted) and Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17α-EE2(in press, Physiological Genomics).  Sequence information found at www.auratus.ca

source_name: Carassius auratus; telencephalon; i.p. saline control

source_name: Carassius auratus; telencephalon; i.p injection fluoxetine


title: ID: N2367A


title: ID: N773A1


title: ID: N1102A


title: ID: T4354H


title: CD8+HYTet+_02


title: CD8+H7aTet+_04

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Aug 30 2004 05:59PM Scanner ID	50207280 Number of Scans	1 Scanner Type	M10

label: biotin + R-phycoerythrin steptavidin


title: ID: T4257A


title: ID: T4174A


title: ID: T420A


title: ID: T433A


title: CD8+Tet-_01


title: ID: T4360A2


title: ID: T4373B1


title: ID: T4360A3


title: ID: T4373B3


title: ID: T4373B2


title: Phosphate Starvation CC-125 (0h) versus CC-125 (48h) Dye swap Low

description:
Simple annotation: Environmental conditions, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44050.gif


title: ID: T4449E4


title: ID: T4449E2


title: ID: T4376A


title: ID: T4452A


title: ID: T4449E3


title: ID: T4449E1


title: ID: T4475A1


title: ID: T4452A1


title: ID: T4508A1


title: ID: T4448A


title: ID: T4452A2


title: ID: T4489A1


title: ID: T4491A2


title: ID: T4491A1


title: ID: T4452A3


title: ID: T4550B


title: ID: T4573A1


title: ID: T4452A4


title: ID: T4555A1


title: ID: T4541A1


title: ID: T451A


title: ID: T4544A1


title: ID: T4603A1


title: CD8+H7aTet+_02


title: ID: T4611B1


title: ID: T4612A1


title: ID: T4644B1


title: ID: T4660A1


title: ID: T462A


title: ID: T4695A1


title: ID: T4834A1


title: ID: T4750A1


title: ID: T4799A1


title: ID: T4919A1


title: ID: T4920A1


title: ID: T4701A1


title: ID: T4984A1


title: ID: T4948A2


title: ID: T5002A1


title: ID: T5102A1


title: ID: T4667A1


title: ID: T4956A1


title: ID: T5024A1


title: ID: T4926A1


title: ID: T5162A1


title: ID: T5107B1


title: ID: T5139A1


title: ID: T5133A


title: ID: T4975A1


title: ID: T519A


title: ID: T5063A


title: ID: T521B


title: ID: T4980A1


title: ID: T5164A1


title: ID: T5287A1


title: Phosphate starvation CC-125 0h vs CC-125 12h low dye swap

description:
Simple annotation: Environmental conditions, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45494.gif


title: ID: T5266A1


title: ID: T5261B1


title: ID: T5513A1


title: ID: T552G


title: ID: T5389A1


title: ID: T551C


title: ID: T5430A1


title: ID: T5565A1


title: ID: T5573A1


title: ID: T5245A1


title: ID: T5376A1


title: ID: T5536C4


title: ID: T565A


title: ID: T5811A1


title: ID: T789A


title: ID: T656A


title: ID: T625A


title: ID: T771A


title: ID: T740A


title: ID: T573A


title: ID: T694C


title: ID: T5589B1


title: ID: T645A


title: ID: T773A1


title: ID: T74A


title: ID: T672A


title: ID: T6190A1


title: ID: T826A


title: ID: T866D


title: ID: T902A


title: PBMCs from an HIV positive transmitter mother in Botswana (11)

first: Monty

last: Montano

address: 650 Albany Street, Bldg X, room 640

department: Medicine

institute: Boston Medical Center

description:
HIV seropositive and drug naive
HIV seropositive transmitter mothers

data_processing: Data scaled with GCOS

label: Biotin

source_name: Human peripheral blood mononuclear cells (PBMCs) from an HIV positive Batswana woman

tag: Botswana mother between 17 and 44 years old. HIV positive. Transmitted virus to child.


title: PBMCs from an HIV positive non-transmitter mother in Botswana (14)

description:
HIV seropositive and drug naive
HIV seropositive nontransmitter mothers

tag: Botswana mother between 17 and 44 years old. HIV positive.  Did not transmit virus to child.


title: PBMCs from an HIV positive non-transmitter mother in Botswana (13)


title: ID: T932B1


title: ID: T924C


title: PBMCs from an HIV positive non-transmitter mother in Botswana (11)


title: ID: T801A1


title: PBMCs from an HIV positive non-transmitter mother in Botswana (12)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (10)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (7)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (4)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (1)


title: ID: T949B


title: ID: T981A


title: PBMCs from an HIV positive non-transmitter mother in Botswana (9)


title: PBMCs from an HIV positive transmitter mother in Botswana (10)

tag: Botswana mother between 17 and 44 years old. HIV positive.  Transmitted virus to child.


title: PBMCs from an HIV positive transmitter mother in Botswana (7)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (8)


title: ID: T940A


title: PBMCs from an HIV positive non-transmitter mother in Botswana (6)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (3)


title: PBMCs from an HIV positive transmitter mother in Botswana (6)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (5)


title: PBMCs from an HIV positive transmitter mother in Botswana (9)


title: PBMCs from an HIV positive non-transmitter mother in Botswana (2)


title: PBMCs from an HIV positive transmitter mother in Botswana (5)


title: PBMCs from an HIV positive transmitter mother in Botswana (4)


title: PBMCs from an HIV positive transmitter mother in Botswana (3)


title: NFIA E18WT3

status: Public on Mar 30 2007

city: Hamburg

first: Yong Wee

last: Wong

address: 94 Falkenried Str

institute: Center for Molecular Neurobiology

description: total RNA extracted from mouse brain

hyb_protocol: Procedures for cDNA synthesis, labeling and hybridization were carried out according to the manufacturer's protocol (Affymetrix). All experiments were performed using Affymetrix mouse genome Genechip U74A version 2. Briefly, 15mg of total RNA were used for first strand cDNA synthesis with an HPLC-purified T7-(dT)24 primer. Synthesis of biotin-labeled cRNA was carried out using the ENZO RNA transcript labeling kit (Affymetrix). For hybridization, 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45oC for 16 hours. Genechips were washed and stained with streptavidin-phycoerythrin using the microfluidic workstation™ (Affymetrix) and scanned with a laser scanner (Agilent Technologies).

data_processing: RMA, nomralised to 50th percentile

source_name: NFIA E18WT3

extract_protocol: Total RNA was extracted from the entire brain of NF-I-A-deficient and wild-type control mice (n=3 each) using TRIzol (Invitrogen) according to the manufacturer’s instructions. Further purification of RNA was performed with the RNeasy Mini Kit (Qiagen). Total RNA concentration was determined using a spectrophotometer at 260 nm and 280 nm wavelength. To check RNA integrity, total RNA was separated in a 1% agarose gel containing formaldehyde, and the intensity ratio of 28S and 18S ribosomal RNA bands was assessed after ethidium bromide staining.

tag: cRNA

tag: embryonic day 18

tag: WT


title: PBMCs from an HIV negative mother in Botswana (6)

description: HIV seronegative

source_name: Human peripheral blood mononuclear cells (PBMCs) from an HIV negative Batswana woman

tag: Botswana mother between 18 and 38 years old.  HIV negative.


title: PBMCs from an HIV negative mother in Botswana (18)

description: HIV seronegative


title: PBMCs from an HIV positive transmitter mother in Botswana (2)


title: PBMCs from an HIV positive transmitter mother in Botwana (1)


title: PBMCs from an HIV negative mother in Botswana (17)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (19)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (14)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (16)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (13)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (7)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (5)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (10)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (3)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (4)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (9)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (8)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (2)

description: HIV seronegative


title: PBMCs from an HIV negative mother in Botswana (15)

description: HIV seronegative


title: PBMCs from an HIV positive transmitter mother in Botswana (8)


title: PBMCs from an HIV negative mother in Botswana (1)

description: HIV seronegative


title: cplxpro30 - mat

status: Public on Jun 08 2006

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

institute: Institut National de la Recherche Agronomique

description: Nylon array protocol

data_processing: Low oligonucleotide signals (lower than three times the background level) were excluded from the analysis.  At this step, signal processing was performed using the vector oligonucleotide data to correct each spot signal by the actual amount of DNA present in each spot.  After correction, signal was normalized by dividing each gene expression value by the median value of the array.

organism: Oncorhynchus mykiss

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO30  Autumn-spawning strain

tag: Ovarian stage

value: oocyte maturation


title: cplxpro25 - mat

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO25  Autumn-spawning strain


title: PBMCs from an HIV negative mother in Botswana (11)

description: HIV seronegative


title: cplxpro15-fv

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO15  Autumn-spawning strain

value: post-vitellogenesis


title: cplxpro31-fv

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO31  Autumn-spawning strain


title: cplxpro14-fv

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Germinal vesicle (GV) in periphery  Female #PRO14  Autumn-spawning strain


title: cplxpro29 - mat

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO29  Autumn-spawning strain


title: cplxpro26 - mat

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO26  Autumn-spawning strain


title: cplxpro13-fv

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Post Vitellogenesis  Female #PRO13  Autumn-spawning strain


title: cplxpro3 - vit

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO3  Autumn-spawning strain

value: late-vitellogenesis


title: cplxpro2 - vit

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO2  Autumn-spawning strain


title: cplxpro27 - mat

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO27  Autumn-spawning strain


title: cplxpro28 - mat

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO28  Autumn-spawning strain


title: cplxpro4 - vit

description: Nylon array protocol

source_name: Preovulatory ovary  Full ovarian tissue  Female #PRO4  Autumn-spawning strain


title: Basal epidermal cells (e/e) (2) vs. Reference

status: Public on May 24 2006

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25945.gif

source_name: Reference (brain, liver, neonate, whole dorsal skin) (50ug)

source_name: Basal epidermal cells e/e (2) (50ug)

tag: Basal epidermal cells e/e (2) (50ug)


title: Whole skin (E+/E+) (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17835.gif

tag: Reference (brain, liver, neonate, whole dorsal skin) (50ug)

source_name: Whole skin (E+/E+) (3) (50ug)

tag: Whole skin (E+/E+) (3) (50ug)


title: Whole skin (e/e) (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17663.gif

source_name: Whole skin e/e (2) (50ug)

tag: Whole skin e/e (2) (50ug)


title: Whole epidermis (E+/E+) (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17815.gif

source_name: Whole epidermis E+/E+ (2) (50ug)

tag: Whole epidermis E+/E+ (2) (50ug)


title: PBMCs from an HIV negative mother in Botswana (12)

description: HIV seronegative

source_name: Human peripheral blood mononuclear cells (PBMCs) from an HIV negative Batswana woman


title: Basal epidermal cells (E+/E+) (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25940.gif

source_name: Basal epidermal cells E+/E+ (3) (50ug)

tag: Basal epidermal cells E+/E+ (3) (50ug)


title: Whole skin (E+/E+) (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17818.gif

source_name: Whole skin (E+/E+) (2) (50ug)

tag: Whole skin (E+/E+) (2) (50ug)


title: melan-a (4) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16057.gif

source_name: melan-a (4) (50ug)

tag: melan-a (4) (50ug)


title: Basal epidermal cells (E+/E+) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25931.gif

source_name: Basal epidermal cells E+/E+ (1) (50ug)

tag: Basal epidermal cells E+/E+ (1) (50ug)


title: Whole epidermis (E+/E+) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17814.gif

source_name: Whole epidermis E+/E+ (1) (50ug)

tag: Whole epidermis E+/E+ (1) (50ug)


title: Whole epidermis (e/e) (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17812.gif

source_name: Whole epidermis e/e (3) (50ug)

tag: Whole epidermis e/e (3) (50ug)


title: Whole skin (e/e) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17662.gif

source_name: Whole skin e/e (1) (50ug)

tag: Whole skin e/e (1) (50ug)


title: melan-a (3) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16056.gif

source_name: melan-a (3) (50ug)

tag: melan-a (3) (50ug)


title: Basal epidermal cells (E+/E+) (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25935.gif

source_name: Basal epidermal cells E+/E+ (2) (50ug)

tag: Basal epidermal cells E+/E+ (2) (50ug)


title: Basal epidermal cells (e/e) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25942.gif

source_name: Basal epidermal cells e/e (1) (50ug)

tag: Basal epidermal cells e/e (1) (50ug)


title: Whole skin (E+/E+) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17817.gif

source_name: Whole skin (E+/E+) (1) (50ug)

tag: Whole skin (E+/E+) (1) (50ug)


title: melan-a (6) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16055.gif

source_name: Reference (brain, liver, neonate, whole dorsal skin) (50ug)

source_name: melan-a (6) (50ug)

tag: melan-a (6) (50ug)


title: Whole epidermis (E+/E+) (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17816.gif

source_name: Whole epidermis E+/E+ (3) (50ug)

tag: Whole epidermis E+/E+ (3) (50ug)


title: melan-a (5) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16053.gif

tag: Reference (brain, liver, neonate, whole dorsal skin) (50ug)

source_name: melan-a (5) (50ug)

tag: melan-a (5) (50ug)


title: Whole skin (e/e) (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17666.gif

source_name: Whole skin e/e (3) (50ug)

tag: Whole skin e/e (3) (50ug)


title: B CELLS M2 (-)     *auto_grid

status: Public on May 23 2006

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41070.gif

source_name: 3 ug Stratagene 2 rounds (from AW & SP 12/2001)

source_name: B CELLS 0408 (-) 6 ug

tag: B CELLS 0408 (-) 6 ug


title: melan-a (1) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16058.gif

source_name: melan-a (1) (50ug)

tag: melan-a (1) (50ug)


title: melan-a (2) vs. Reference

description:
Simple annotation: Pigmentation, Melanoma cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16054.gif

source_name: melan-a (2) (50ug)

tag: melan-a (2) (50ug)


title: Whole epidermis (e/e) (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17810.gif

source_name: Whole epidermis e/e (2) (50ug)

tag: Whole epidermis e/e (2) (50ug)


title: PBMC F2A     *auto_grid

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41064.gif

tag: 3 ug Stratagene 2 rounds (from AW & SP 12/2001)

source_name: PBMC 0226 6 ug

tag: PBMC 0226 6 ug


title: B CELLS F1B (+)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40848.gif

source_name: B CELLS 0301 (+) 6 ug

tag: B CELLS 0301 (+) 6 ug


title: B CELLS M3 (-)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41071.gif

source_name: B CELLS 0219 (-) 6 ug

tag: B CELLS 0219 (-) 6 ug


title: Pax F2B     *auto_grid

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41063.gif

source_name: Pax 0328 6 ug

tag: Pax 0328 6 ug


title: Whole epidermis (e/e) (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17809.gif

source_name: Whole epidermis e/e (1) (50ug)

tag: Whole epidermis e/e (1) (50ug)


title: High nitrogen 33hrs. vs. high nitrogen 85hrs.

description:
Simple annotation: Stress, Nitrogen
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/7999.gif

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

source_name: High nitrogen 33hrs

tag: High nitrogen 33hrs

source_name: High nitrogen 85hrs

tag: High nitrogen 85hrs


title: CD8 F1A (-)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40843.gif


title: Pax M5     *auto_grid

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41085.gif

source_name: Pax 0314 6 ug

tag: Pax 0314 6 ug


title: CD4 M1 (-)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40838.gif


title: PBMC M1     *auto_grid

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41087.gif

source_name: PBMC 0402 6 ug

tag: PBMC 0402 6 ug


title: CD8 M2 (-)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40842.gif


title: B CELLS F1A (-)     *auto_grid

description:
Simple annotation: Normal tissue, Blood cell subtype
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40845.gif

source_name: B CELLS 0221 (-) 6 ug

tag: B CELLS 0221 (-) 6 ug


title: Low Nitrogen (40mg/L) 38 hours vs. 85 hours

description:
Simple annotation: Stress, Nitrogen
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/7893.gif

source_name: Low Nitrogen 33 hours

tag: Low Nitrogen 33 hours

source_name: Low Nitrogen 85 hours

tag: Low Nitrogen 85 hours