title: Aromatase KO Lacrimal Male , biological rep 2

description: Lacrimal gland gene expression from male aromatase knockout mice

source_name: Lacrimal glands from male aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Aromatase KO Lacrimal Male


title: Wild Type (Aromatase KO) Lacrimal Female , biological rep 2

status: Public on Feb 01 2009

type: RNA

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

country: USA

institute: Schepens Eye Research Institute

description: Lacrimal gland gene expression from female wild type (aromatase knockout) mice.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse I Bioarray. Bioarrays were washed and stained with streptavidin-Alexa 647 and washed again.

scan_protocol: Bioarrays were scanned with a ScanArray Express HT scanner using ScanArray Express software.

data_processing: Data were analyzed with the CodeLink Image Analysis software using the default settings and normalized using global scaling to a median target intensity  on each array of 1.0.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lacrimal glands from female wild type mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.

extract_protocol: Lacrimal glands: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.  Meibomian glands: RNA was purified with two Trizol extractions.


title: Wild Type (Aromatase KO) Lacrimal Female , biological rep 1


title: Aromatase KO Lacrimal Female , biological rep 3

description: Lacrimal gland gene expression from female aromatase knockout mice

source_name: Lacrimal glands from female aromatase knockout mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

tag: Aromatase KO Lacrimal Female


title: Wild Type (Aromatase KO) Lacrimal Female , biological rep 3


title: Aromatase KO Lacrimal Male , biological rep 3


title: Aromatase KO Lacrimal Female , biological rep 2


title: Wild Type (Aromatase KO) Meibomian Female , biological rep 3

description: Meibomian gland gene expression from female wild type (aromatase knockout) mice.

source_name: Meibomian glands from female wild type mice ( glands pooled from 5-8 mice)


title: Aromatase KO Lacrimal Male , biological rep 1


title: Dll1 C3H_spleen_rep7

status: Public on Jan 01 2009

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Dll1 C3H spleen

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Dll1 C3H, male, spleen, +/-, age

value: 15 weeks, Mouse ID 30051704

source_name: C3H spleen

tag: C3H, male, spleen, age


title: Dll1 C3H_thymus_rep1

source_name: Dll1 C3H thymus

tag: Dll1 C3H, male, thymus, +/-, age

value: 15 weeks, Mouse ID 30051703

source_name: C3H thymus

tag: C3H, male, thymus, age


title: Dll1 C3H_thymus_rep3

value: 15 weeks, Mouse ID 30051706


title: Dll1 C3H_spleen_rep9

value: 15 weeks, Mouse ID 30051707


title: Dll1 C3H_thymus_rep6

value: 15 weeks, Mouse ID 30051705


title: Dll1 C3H_spleen_rep4


title: Dll1 C3H_thymus_rep2


title: Dll1 C3H_liver_rep9

source_name: Dll1 C3H liver

tag: Dll1 C3H, male, liver, +/-, age

source_name: C3H liver

tag: C3H, male, liver, age


title: Dll1 C3H_spleen_rep5


title: Dll1 C3H_spleen_rep6


title: Dll1 C3H_liver_rep7


title: Dll1 C3H_spleen_rep8


title: Dll1 C3H_spleen_rep3


title: Dll1 C3H_thymus_rep4


title: Dll1 C3H_thymus_rep10


title: Dll1 C3H_thymus_rep5


title: Dll1 C3H_thymus_rep8


title: Dll1 C3H_thymus_rep9


title: Dll1 C3H_spleen_rep2


title: Aromatase KO Lacrimal Female , biological rep 1

description: Lacrimal gland gene expression from female aromatase knockout mice.


title: Dll1 C3H_liver_rep10


title: Dll1 C3H_thymus_rep7


title: Dll1 C3H_liver_rep6


title: Dll1 C3H_spleen_rep1


title: Dll1 C3H_liver_rep8


title: Dll1 C3H_liver_rep5


title: Dll1 C3H_liver_rep1


title: Dll1 C3H_liver_rep4


title: Dll1 C3H_liver_rep3


title: Dll1 C3H_liver_rep2


title: Dll1 C3H_brain_rep4

source_name: Dll1 C3H brain

tag: Dll1 C3H, male, brain, +/-, age

source_name: C3H brain

tag: C3H, male, brain, age


title: Dll1 C3H_brain_rep8


title: Dll1 C3H_brain_rep1


title: Dll1 129SvJ/Iso_thymus_rep5

source_name: Dll1 129SvJ/Iso thymus

tag: Dll1 129SvJ/Iso, male, thymus, +/-, age

source_name: 129SvJ/Iso thymus

tag: 129SvJ/Iso, male, thymus, age


title: Dll1 C3H_brain_rep10


title: Dll1 C3H_brain_rep2


title: Dll1 C3H_brain_rep7


title: Dll1 129SvJ/Iso_thymus_rep1


title: Dll1 129SvJ/Iso_thymus_rep2


title: Dll1 129SvJ/Iso_thymus_rep3

value: 16 weeks, RNA pool including Mouse ID:


title: Dll1 129SvJ/Iso_spleen_rep13

source_name: Dll1 129SvJ/Iso spleen

tag: Dll1 129SvJ/Iso, male, spleen, +/-, age

value: 16 weeks, Mouse ID 30015738

source_name: 129SvJ/Iso spleen

tag: 129SvJ/Iso, male, spleen, age


title: Dll1 C3H_brain_rep5


title: Dll1 C3H_brain_rep3


title: Dll1 129SvJ/Iso_spleen_rep12


title: Dll1 129SvJ/Iso_thymus_rep4


title: Dll1 129SvJ/Iso_spleen_rep10

value: 16 weeks, Mouse ID 30015730


title: Dll1 129SvJ/Iso_thymus_rep6


title: Dll1 C3H_brain_rep9


title: Dll1 129SvJ/Iso_spleen_rep14


title: Dll1 129SvJ/Iso_spleen_rep7

value: 16 weeks, Mouse ID      30015740


title: Dll1 129SvJ/Iso_spleen_rep15


title: Dll1 129SvJ/Iso_spleen_rep8

value: 16 weeks, Mouse ID 30015729


title: Dll1 129SvJ/Iso_spleen_rep5

value: 16 weeks, Mouse ID 30015740


title: Dll1 129SvJ/Iso_spleen_rep9


title: Dll1 129SvJ/Iso_spleen_rep6


title: Dll1 129SvJ/Iso_spleen_rep2

value: 16 weeks, Mouse ID 30015734


title: Dll1 129SvJ/Iso_spleen_rep3


title: Dll1 129SvJ/Iso_spleen_rep4


title: Dll1 129SvJ/Iso_liver_rep11

source_name: Dll1 129SvJ/Iso liver

tag: Dll1 129SvJ/Iso, male, liver, +/-, age

source_name: 129SvJ/Iso liver

tag: 129SvJ/Iso, male, liver, age


title: Dll1 129SvJ/Iso_liver_rep9


title: Dll1 129SvJ/Iso_liver_rep7


title: Dll1 129SvJ/Iso_spleen_rep11


title: Dll1 129SvJ/Iso_liver_rep2


title: Dll1 129SvJ/Iso_spleen_rep1


title: Dll1 129SvJ/Iso_liver_rep10


title: Dll1 129SvJ/Iso_liver_rep4


title: Dll1 129SvJ/Iso_liver_rep12


title: Dll1 129SvJ/Iso_liver_rep1


title: Dll1 12SvJ/Iso_brain_rep11

source_name: Dll1 129SvJ/Iso brain

tag: Dll1 129SvJ/Iso, male, brain, +/-, age

source_name: 129SvJ/Iso brain

tag: 129SvJ/Iso, male, brain, age


title: Dll1 129SvJ/Iso_liver_rep5


title: Dll1 12SvJ/Iso_brain_rep14


title: Dll1 12SvJ/Iso_brain_rep13


title: Dll1 12SvJ/Iso_brain_rep12


title: Dll1 129SvJ/Iso_liver_rep8


title: Dll1 129SvJ/Iso_liver_rep3


title: Dll1 12SvJ/Iso_brain_rep10


title: Dll1 129SvJ/Iso_liver_rep6


title: Dll1 12SvJ/Iso_brain_rep6

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen


title: Dll1 12SvJ/Iso_brain_rep5


title: Dll1 12SvJ/Iso_brain_rep8


title: Dll1 12SvJ/Iso_brain_rep4


title: Dll1 12SvJ/Iso_brain_rep7


title: Dll1 12SvJ/Iso_brain_rep9


title: Dll1 12SvJ/Iso_brain_rep1


title: Dll1 12SvJ/Iso_brain_rep2


title: D Caco2 sorted on AC133 negative expression (sort #2)

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina.

scan_protocol: As suggested by illumina using the illumina scanner.

data_processing: cubic spline

label: Streptavidin Cy3

organism: Homo sapiens

source_name: Colon carcinoma cell line (Caco2)

label_protocol: As described in the illumina Human-8 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

growth_protocol:
Caco2: The human colon epithelial cancer cell line Caco2 was obtained from American Type Culture Collection (ATCC, Manassas, VA). Caco2 cells at passage 10 were infected  with a Lentivirus reporter vectors  that contain the mouse Melk promoter driving enhancer green fluorescent protein (MELK-GFP). Individual clones were isolated with the use of glass cloning rings. Two of these clones were used for further experiments. All cells were cultured in DMEM (Mediatech Inc, Manassas, VA) supplemented with 20% fetal bovine serum (Tissue Culture Biologicals, Tulare, CA) and 37 ug/ml Gentamicin (Sigma-Aldrich, St. Louis, MO).
WM115: The melanoma cell line WM115, provided by Boris Fichtman and Zeev Ronai (Burnham Institute for Medical Research, La Jolla, CA), was cultured in 10% FCS in RPMI 1640. In all experiments, cells were cultured in culture dishes (Nunc) at 37ºC in a humidified 5% CO2 incubator.

extract_protocol: Total RNA from AC133 high and negative sorted Caco2 and WM115 cells was extracted using the TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s protocol. Two samples each of two cell lines were analyzed as biological duplicates. Labeled cRNA was prepared from 500 ng RNA using the Illumina® RNA Amplification Kit from Ambion (Austin, TX, USA). The Biotin labeled cRNA (750 ng) was hybridized 18 hr at 58ºC to the HumanRef-8 v2 Expression BeadChip (>22,000 gene transcripts; Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: FACSort: For sorting cells expressing AC133, the cells were removed from the culture dish with 0.05% trypsin and 0.02% EDTA (Invitrogen, Carlsbad, CA), washed in PBS containing 1% FCS, stained with CD133-PE antibody (AC133, Miltenyi Biotec, Auburn, CA ) and resuspended at 106 cells per ml in the same buffer. The cells were filtered through a 35 um nylon filter prior to FACSort. Sorting was performed on a FACSDiVa flow cytometer (Becton Dickinson). Side and forward scatter profiles and propidium iodide (PI) staining were used to eliminate cell doublets and dead cells. The 10% of the cells that expressed the highest AC133 fluorescence and the AC133 negative cells were collected. Cells were recovered in 15ml conical plastic tubes containing 1ml of 100% FCS, and an aliquot was removed at the end of the sort and reanalyzed to evaluate purity.

tag: Caco2  Growth Properties

value: adherent   Organism:Homo sapiens (human)   Morphology:epithelial  Source Organ:colon  Disease:colorectal adenocarcinoma


title: Dll1 12SvJ/Iso_brain_rep3


title: B Caco2 sorted on AC133 negative expression (sort #1)


title: F WM115 cells sorted on AC133 negative expression (sort #1)

source_name: Melanoma cell line (WM 115)

tag: WM115  Growth Properties

value: adherent  Organism:Homo sapiens (human)   Morphology:epithelial  Source Organ:skin  Disease:melanoma


title: C Caco2 sorted on AC133 high expression (sort #2)


title: G WM115 cells sorted on AC133 high expression (sort #2)


title: A Caco2 sorted on AC133 high expression (sort #1)


title: H WM115 cells sorted on AC133 negative expression (sort #2)


title: E WM115 cells sorted on AC133 high expression (sort #1)


title: WT 16 C 40 min |ynr004w 16 C 40 min  (1201_053_20)

status: Public on Dec 31 2008

city: San Francisco

first: Megan

last: Bergkessel

department: Biochemistry

institute: University of California, San Francisco

description: a complete description of the sample collection protocol and source strains can be found in PMID: PENDING EPUB DATE

hyb_protocol: Competitive hybridization at 65oC for 15h

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments). Image analysis was performed using Axon Instruments GenePix Pro version 5.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: Genotype:

tag: Temperature:

tag: Time (min):


title: WT 16 C 25 min |tgs1 16 C 25 min  (1201_048_20)


title: WT 16 C 25 min |ynr004w 16 C 25 min  (1201_052_20)


title: WT log phase steady state|YPR045C log phase steady state (0113_013_20)

tag: Genotype

tag: Temperature

value: logphase

tag: Time (min)

value: steadystate

value: wt


title: ynr004w 16 C 10 min |WT 16 C 10 min  (1201_051_10)


title: WT log phase steady state|csn9 log phase steady state (0707_148_20)


title: WT 16 C 40 min |tgs1 16 C 40 min  (1201_049_20)


title: WT 16 C 10 min |ynr004w 16 C 10 min  (1201_051_20)


title: WT 16 C 10 min |tgs1 16 C 10 min  (1201_047_20)


title: WT 30 C 0 min |ynr004w 30 C 0 min  (1201_050_20)


title: WT log phase steady state|ist3 log phase steady state (0113_014_20)


title: ynr004w 16 C 25 min |WT 16 C 25 min  (1201_052_10)


title: ynr004w 16 C 40 min |WT 16 C 40 min  (1201_053_10)


title: WT log phase steady state|pci8 log phase steady state (0707_149_20)


title: WT 30 C 0 min |tgs1 30 C 0 min  (1201_046_20)


title: tgs1 16 C 40 min |WT 16 C 40 min  (1201_049_10)


title: ynr004w 30 C 0 min |WT 30 C 0 min  (1201_050_10)


title: isy1 log phase steady state|WT log phase steady state (0422_28_10)

value: matched WT for isy1


title: tgs1 16 C 10 min |WT 16 C 10 min  (1201_047_10)


title: tgs1 30 C 0 min |WT 30 C 0 min  (1201_046_10)


title: pci8 log phase steady state|WT log phase steady state (0707_149_10)


title: csn9 log phase steady state|WT log phase steady state (0707_148_10)


title: YPR045C log phase steady state|WT log phase steady state (0113_013_10)


title: csn12 log phase steady state|WT log phase steady state (0113_012_10)


title: 011308_47_10(Dupf1.30C.NA|Dnpl3Dupf1.30C.NA)

first: Tracy

middle: L

last: Kress

address: 600 16th Street, Box 2200

department: Biochemisty and Biophysics

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 5.0.


title: WT log phase steady state|isy1 log phase steady state (0422_28_20)


title: tgs1 16 C 25 min |WT 16 C 25 min  (1201_048_10)


title: ist3 log phase steady state|WT log phase steady state (0113_014_10)


title: WT log phase steady state|csn12 log phase steady state (0113_012_20)


title: 0707_75_10(Dnpl3.37C.15min|Dnpl3Dupf1.37C.15min)


title: 0707_73_10(WT.37C.15min|Dnpl3Dupf1.37C.15min)

value: matched WT for Dnpl3Dupf1


title: 0707_72_10(WT.37C.15min|Dupf1.37C.15min)

value: matched WT for Dupf1


title: 0707_71_10(WT.37C.15min|Dnpl3.37C.15min)

value: matched WT for Dnpl3


title: 1201_079_10(Dnpl3.37C.30min|Dupf1+Dnpl3.37C.30min)


title: 0512_057_10(Dnpl3.30C.NA|Dupf1.30C.NA)


title: 0512_058_10(Dnpl3Dupf1.30C.NA|Dnpl3.30C.NA)


title: 011308_51_20(Dgbp2Dhrb1.37C.30min|WT.37C.30min)

value: matched WT for Dgbp2Dhrb1


title: 011308_44_20(Dgbp2Dhrb1.30C.NA|WT.30C.NA)


title: 0707_85_20(Dhrb1.37C.30min|WT.37C.30min)

value: matched WT for Dhrb1


title: 0707_74_10(Dupf1.37C.15min|Dnpl3.37C.15min)


title: 0119_091_20(Dgbp2.37C.30min|WT.37C.30min)

value: matched WT for Dgbp2


title: 0119_092_20(Dhrb1.37C.30min|WT.37C.30min)


title: 0119_089_20(Dhrb1.30C.NA|WT.30C.NA)


title: 011308_48_20(Dnpl3.37C.30min|WT.37C.30min)


title: 0512_059_10(Dnpl3Dupf1.30C.NA|WT.30C.NA)


title: 011308_45_20(Dgbp2Dhrb1.30C.NA|WT.30C.NA)


title: 011308_19_10(WT.30C.NA|Dnpl3.30C.NA)


title: 011308_50_20(Dgbp2Dhrb1.37C.30min|WT.37C.30min)


title: 0707_84_20(Dgbp2.37C.30min|WT.37C.30min)


title: 0119_088_20(Dgbp2.30C.NA|WT.30C.NA)


title: 011308_23_20(Dnpl3.37C.30min|WT.37C.30min)


title: 0707_56_10(WT.37C.45min|Dnpl3.37C.45min)


title: 0707_80_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0707_81_10(WT.37C.30min|Dnpl3.37C.30min)


title: 011308_42_20(Dnpl3.30C.NA|WT.30C.NA)


title: 0707_51_10(WT.37C.15min|Dnpl3.37C.15min)


title: 1201_078_10(WT.37C.30min|Dupf1.37C.30min)


title: 0707_45_10(WT.37C.30_min|Dnpl3.37C.30_min)


title: 0512_063_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0707_37_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0119_090_10(WT.37C.30min|Dnpl3.37C.30min)


title: 0415_206_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0415_207_10(WT.37C.30min|Dnpl3.37C.30min)


title: 0119_087_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0415_205_10(WT.16C.30min|Dnpl3.16C.30min)


title: 0707_72_20(Dupf1.37C.15min|WT.37C.15min)


title: 0512_058_20(Dnpl3.30C.NA|Dnpl3Dupf1.30C.NA)


title: 1201_079_20(Dupf1+Dnpl3.37C.30min|Dnpl3.37C.30min)


title: 0119_091_10(WT.37C.30min|Dgbp2.37C.30min)


title: 0707_71_20(Dnpl3.37C.15min|WT.37C.15min)


title: 011308_44_10(WT.30C.NA|Dgbp2Dhrb1.30C.NA)


title: 0707_85_10(WT.37C.30min|Dhrb1.37C.30min)


title: 0119_088_10(WT.30C.NA|Dgbp2.30C.NA)


title: 0119_089_10(WT.30C.NA|Dhrb1.30C.NA)


title: 1201_078_20(Dupf1.37C.30min|WT.37C.30min)


title: 0119_092_10(WT.37C.30min|Dhrb1.37C.30min)


title: 0512_059_20(WT.30C.NA|Dnpl3Dupf1.30C.NA)


title: 011308_51_10(WT.37C.30min|Dgbp2Dhrb1.37C.30min)


title: 0707_84_10(WT.37C.30min|Dgbp2.37C.30min)


title: 0707_81_20(Dnpl3.37C.30min|WT.37C.30min)


title: 0512_057_20(Dupf1.30C.NA|Dnpl3.30C.NA)


title: 011308_19_20(Dnpl3.30C.NA|WT.30C.NA)


title: 0707_75_20(Dnpl3Dupf1.37C.15min|Dnpl3.37C.15min)


title: 0707_80_20(Dnpl3.30C.NA|WT.30C.NA)


title: 011308_47_20(Dnpl3Dupf1.30C.NA|Dupf1.30C.NA)


title: 0707_73_20(Dnpl3Dupf1.37C.15min|WT.37C.15min)


title: 0707_56_20(Dnpl3.37C.45min|WT.37C.45min)


title: 0707_45_20(Dnpl3.37C.30_min|WT.37C.30_min)


title: 011308_45_10(WT.30C.NA|Dgbp2Dhrb1.30C.NA)


title: 0707_74_20(Dnpl3.37C.15min|Dupf1.37C.15min)


title: 0707_51_20(Dnpl3.37C.15min|WT.37C.15min)


title: 011308_42_10(WT.30C.NA|Dnpl3.30C.NA)


title: 0707_37_20(Dnpl3.30C.NA|WT.30C.NA)


title: 011308_50_10(WT.37C.30min|Dgbp2Dhrb1.37C.30min)


title: KS C vs Soy C

city: Lausanne

first: Michel

last: Monod

address: Av. de Beaumont 29

department: Dermatology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

description: no additional information

hyb_protocol: Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC,  1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.

scan_protocol: Agilent microarray scanner, 10 μm resolution

data_processing: GenePix Pro 6.0 was used to analyse the images and  generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values.

organism: Trichophyton rubrum

source_name: T. rubrum growm in KS media

label_protocol: 3 µg of total RNA was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, USA). 3 µg of amplified RNA were reverse transcribed into cyanin 3 or cyanin 5 labeled cDNA with the Superscript II reverse transcriptase (Invitrogen) into cDNA using random primers (Invitrogen), purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6147).

growth_protocol: Trichophyton rubrum strain Lau1673  was grown in Sabouraud dextrose medium and, to promote proteolytic activity, in soy liquid medium and keratin-soy medium. Soy medium was prepared by dissolving 2 g soy protein (Supro 1711, Protein Technologies International) in 1 l distilled water. Keratin-soy aliquots of 100 ml were prepared by adding 0.2 g keratin (Merck, Dietikon, Switzerland) and 5 ml soy medium to 95 ml distilled water.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy plant mini kit (Hombrechtikon, Switzerland) according to the instructions of the manufacturer

tag: strong proteolytic activity in the supernatant

source_name: T. rubrum growm in Soy media


title: 0119_087_20(Dnpl3.30C.NA|WT.30C.NA)


title: 0415_206_20(Dnpl3.30C.NA|WT.30C.NA)


title: 0119_090_20(Dnpl3.37C.30min|WT.37C.30min)


title: 0512_063_20(Dnpl3.30C.NA|WT.30C.NA)


title: KS C vs Sab C

description: no additional information

source_name: T. rubrum growm in Sab media

tag: no proteolytic activity in supernatant


title: KS A vs Soy A

description: no additional information


title: Soy B vs Sab B

description: no additional information


title: KS B vs Soy B

description: no additional information


title: 0415_205_20(Dnpl3.16C.30min|WT.16C.30min)


title: Soy A vs Sab A

description: no additional information


title: KS A vs Sab A

description: no additional information


title: Soy C vs Sab C

description: no additional information


title: KS B vs Sab B

description: no additional information


title: wildtype S Cerevisiae treated with 50 microg/ml (MPA) for 30 min

status: Public on Dec 30 2008

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 150 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labeled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 oC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 oC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cnio.es) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=1.0). Normalization method: ratio of medians.

source_name: wild type S. cerevisiae untreated

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (Amersham Biosciences)

growth_protocol: Yeast cells were grown at 28ºC in 10 ml YPD medium to an OD660 of 0.6. The cells were harvested by centrifugation after 30 min, washed once with cold water and dried cells kept at -80ºC until RNA purification

extract_protocol: RNA was extracted by using hot phenol and glass beads as described (Köhrer, K., and Dombey, H. (1991) Methods Enzymol. 194, 398–405).

treatment_protocol: No treatment

tag: Wild type S. cerevisiae BY4741 strain

source_name: wild type S. cerevisiae MPA-treated

growth_protocol: Yeast cells were grown at 28ºC in 10 ml YPD medium to an OD660 of 0.6. The cells were subjected to the treatment and harvested by centrifugation, washed once with cold water and dried cells kept at -80ºC until RNA purification

treatment_protocol: Cells were incubated for 30 min with 50 µg/ml (MPA).

tag: Wild type S. cerevisiae BY4741 strain MPA-treated


title: 011308_48_10(WT.37C.30min|Dnpl3.37C.30min)


title: Colo16 cells_hnRNP A2 shRNA_rep1

status: Public on Dec 01 2008

city: Brisbane

first: Yaowu

last: He

state: Queensland

address: Cooper Road

department: School of Molecular and Microbial Sciences

country: Australia

institute: University of Queensland

description: Washing and staining of probe arrays was carried out on the Affymetrix Fluidics Station 400 operated by the Microarray Suite. Both Test3 Array and HG-U133A GeneChips were washed and stained following a EukGE-WS2 Fluidics Protocol.

hyb_protocol: Hybridization of the fragmented biotin-labeled cRNA to Affymetrix HG-U133A chips was carried out in a buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA and 0.01% Tween-20, in the presence of 50 pM control oligonucleotide B2, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA. A eukaryotic hybridization control mix was used at 1.5, 5, 25, and 100 pM for bioB, bioC, bioD, and cre, respectively. BioB, bioC, and bioD are genes in the biotin synthesis pathway of E. coli. Cre is a recombinase gene from P1 bacteriophage. The hybridization cocktail was heated at 99oC for 5 min, incubated at 45oC for 5 min, and then transferred into the array pre-wetted with the hybridization buffer for 10 min at 45oC. The hybridization was performed for 16 h at 45oC in a rotary incubator. The quality of fragmented cRNA and hybridization performance were confirmed by a preliminary hybridization on Affymetrix Test3 Array chips. The cRNA loads for the Test3 Array and HG-U133A GeneChips were 5, and 15 ug, respectively.

scan_protocol: Probe array scans were performed on a GeneChip Scanner 3000 (Affymetrix) operated by the Microarray Suite, following the manufacturer's instructions

data_processing: The data were processed using the GeneChip Operating Software (GCOS, Affymetrix), which calculated a discrimination score (R) for each probe pair within a probe set (for a gene). ). The probe pair included a perfect-match oligo, giving a signal PM, and a mismatch oligo, giving a signal MM. A global normalization was performed, scaled to 100.

label_protocol: A one-cycle target-labeling protocol supplied by Affymetrix, Inc. (Santa Clara, CA) was followed to label the oligonucleotides to be used in microarray hybridization. Briefly, 3 ug of total RNA sample was spiked with a poly-A RNA control, including lys, phe, thr, and dap at a final concentration of 1:100,000, 1:50,000, 1:25,000, and 1:7,500 (ratio of copy number), to monitor the labeling process. lys, phe, thr, and dap are B. subtilis genes that have been modified by the addition of poly-A-tails. The mRNA was reverse transcribed by SuperScript II to generate the complementary DNA using an oligo dT primer with a T7 promoter leading sequence. The first-strand cDNA was then used as a template to synthesize the second-strand cDNA using E.coli DNA ligase and E.coli DNA polymerase I at 16oC for 2 h, and the original RNA template was eliminated by RNase H at the same time. After incubating the reaction with T4 DNA polymerase for 5 min, the reaction was terminated by adding EDTA to a final concentration of 31 mM. The resultant double-strand cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) following the manufacturer’s protocol. To synthesize the biotin-labeled anti-sense cRNA, the cleaned-up cDNA was used as a template to perform an in vitro transcription using the GeneChip IVT Labeling Kit (Affymetrix). The products were purified using the Sample Cleanup Module (Affymetrix) according to the manufacturer’s instruction. The yield of cRNA was quantified by spectrophotometric analysis at 260 nm. Its purity was assessed by the ratio of A260/A280, and those between 1.9 and 2.1 were kept for further analysis. Prior to hybridization, the length of cRNAs was reduced from 100-2000 bases to 35-200 bases by metal-induced hydrolysis at 94oC for 35 min in a fragmentation buffer supplied by Affymetrix.

growth_protocol: Colo16 cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen)

extract_protocol: Total RNA was isolated from Colo16 cells by using a Qiagen RNeasy Mini kit following the manufacturer’s instructions

treatment_protocol: Cells were transfected with a hnRNP A2-targeting shRNA vector, which was constructed by inserting a firefly sequence (cgtgctgtagcaagagagg) into a pSUPER vector. For transfection, exponentially growing cells were seeded into a 6-well plate at a density of 360,000 cells/well and cultured for 20 h before the medium was replaced with Opti-MEM with 5% FBS. shRNA plasmids (3.0 ug) were mixed with 7.5 ul Lipofectamine 2000 (Invitrogen) and incubated at room temperature for 20 min before being applied to cells. The medium was changed back to RPMI 1640 with 10% FBS 6 h after transfection, and cells were cultured for another 66 h before harvesting.

tag: Species

value: Homo sapiens Gender:female Age:59 Tissue:squamous cell carcinoma Reference:Moore GE, Merrick SB, Woods LK, Arabasz NM. A human squamous cell carcinoma cell line. Cancer Res. 1975 Oct;35(10):2684-8.


title: Colo16 cells_hnRNP A2 shRNA_rep2


title: wildtype S Cerevisiae treated with 75 ng/ml 4-NQO

source_name: wild type S. cerevisiae NQO-treated

treatment_protocol: Cells were incubated for 30 min with 75 ng/ml (4-NQO).

tag: Wild type S. cerevisiae BY4741 strain NQO-treated


title: Colo16 cells_nonspecific shRNA_rep2

extract_protocol: Total RNA was isolated from Colo16 cells by using a Qiagen RNeasy Mini kit following the manufacturer’s instructions.

treatment_protocol: Cells were transfected with a nonspecific control shRNA vector, which was constructed by inserting a firefly sequence (cgtacgcggaatacttcga) into a pSUPER vector. For transfection, exponentially growing cells were seeded into a 6-well plate at a density of 360,000 cells/well and cultured for 20 h before the medium was replaced with Opti-MEM with 5% FBS. shRNA plasmids (3.0 ug) were mixed with 7.5 ul Lipofectamine 2000 (Invitrogen) and incubated at room temperature for 20 min before being applied to cells. The medium was changed back to RPMI 1640 with 10% FBS 6 h after transfection, and cells were cultured for another 66 h before harvesting.


title: Wild type versus mutant rep2

status: Public on Dec 23 2008

city: Randwick

first: Anthony

middle: G.

last: Beckhouse

state: NSW

address: High St

department: BABS

institute: Ramaciotti Centre for Gene Function Analysis

description: Wild type versus mutant rep2

hyb_protocol: Labeled cDNA probes, 53 µg yeast tRNA, 50 µg herring sperm DNA and DIG-Easy hybridisation buffer (Roche) were mixed and the samples were applied to microarray slides within an a-hyb hybridisation station (1 mL/min pump) (Miltenyi Biotec), except for D whe

scan_protocol: Scanned on an Axon Genepix 4200B scanner

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ln processed Red signal/Green signal. GeneSpring V 7.3.1was used

label: Alexa Fluor 647

source_name: Wild type yeast

label_protocol: For A, C, D and E: 20 µg of total RNA was converted into cDNA and labeled using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen)

growth_protocol: Overnight incubation in LZM+Zn (Limiting Zinc Media with Zinc) for 18 hours with shaking (30 °C) to OD 0.5, followed by three washes in water.

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

treatment_protocol: Diluted cells (OD 0.1) were grown up in LZM (Limiting Zinc Media - no zinc) with shaking (30 °C) to an OD of approx 0.5 before the cells were snap-frozen in liquid nitrogen.

tag: Wild type yeast

label: Alexa Fluor 532

source_name: msn2,4 mutant yeast

label_protocol: For B and F: 20 µg of total RNA was primed with 1.5 µL of anchored oligo (dT)20 primer at 65 °C for 5 min, then reversede transcribed at 50 °C for 2.5 h in the presence of 400 U SuperScript III RTase (Invitrogen) and 500 µM dATP, dCTP, dGTP with 125 µM dT

tag: msn2,4 mutant yeast


title: Colo16 cells_nonspecific shRNA-rep1

growth_protocol: Colo16 cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen).

value: Homo sapiens

tag: Gender

value: female

tag: Age

tag: Tissue

value: squamous cell carcinoma

tag: Reference

value: Moore GE, Merrick SB, Woods LK, Arabasz NM. A human squamous cell carcinoma cell line. Cancer Res. 1975 Oct;35(10):2684-8.


title: Wild type versus mutant rep1

description: Wild type versus mutant rep1


title: mutant versus Wild type rep 1

description: mutant versus Wild type rep 1


title: Wild type versus mutant rep3

description: Wild type versus mutant rep3


title: 36082_Endo_180min_exp2

city: Torrance

first: Hyunsook

last: Park

address: 1124 W carson st

department: Infectious Diseases

institute: Los Angeles Biomedical Research Institute at Harbor-UCLA medical center

description: Preparation and labeling of the cDNA and hybrid?ization with the microarrays were performed following standard protocols (http://microarrays.org).  Briefly, 10μg of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, Calif.) in the presence of 5-(3-aminoallyl)-2′-deoxyuridine 5′-triphosphate (aa-dUTP), using both oligo dT and random primers (Stratagene, La Jolla, Calif.).  The cDNAs from the control and experimental conditions were coupled with Cy3 or Cy5 monoreactive dyes (Amersham Biosciences, Piscataway, N.J.), mixed at 1:1 ratio, and concentrated in a Microcon-30 spin column (Millipore, Billerica, Mass.).  The concentrated probes were hybridized with the microarray slide in Hybridization Buffer #3 (Ambion, Austin, Tx.) at 50?C for 16 h. The arrays were visualized with 428TM array scanner (Affymetrix, Santa Clara, Calif.).  At least three hybridizations were performed for each time point, host cell type, and strain of C. albicans.

data_processing: The scanned images of both channels were quantified using ImaGene 5.0 (Biodiscovery, El Segundo, Calif.).  Spots were quantified as the median value of all pixel intensities in the spot region.  The local background values were calculated from the area surrounding each feature and subtracted from respective spot signal values.  The data from each array were normalized by locally weighted linear regression (lowess) analysis using the MIDAS program (http://www.tigr.org/software/).

organism: Candida albicans

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 180min

tag: RNA from Candida albicans 36082 grown on bare plastic for 180min


title: mutant versus Wild type rep 3

description: mutant versus Wild type rep 3


title: 36082_Endo_90min_exp1

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 90min

tag: RNA from Candida albicans 36082 grown on bare plastic for 90min


title: 0415_207_20(Dnpl3.37C.30min|WT.37C.30min)

tag: Genotype

tag: Temperature

tag: Time (min)


title: CAI4_Endo_45min_exp1

description: Preparation and labeling of the cDNA and hybrid¬ization with the microarrays were performed following standard protocols (http://microarrays.org).  Briefly, 10μg of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, Calif.) in the presence of 5-(3-aminoallyl)-2′-deoxyuridine 5′-triphosphate (aa-dUTP), using both oligo dT and random primers (Stratagene, La Jolla, Calif.).  The cDNAs from the control and experimental conditions were coupled with Cy3 or Cy5 monoreactive dyes (Amersham Biosciences, Piscataway, N.J.), mixed at 1:1 ratio, and concentrated in a Microcon-30 spin column (Millipore, Billerica, Mass.).  The concentrated probes were hybridized with the microarray slide in Hybridization Buffer #3 (Ambion, Austin, Tx.) at 50°C for 16 h. The arrays were visualized with 428TM array scanner (Affymetrix, Santa Clara, Calif.).  At least three hybridizations were performed for each time point, host cell type, and strain of C. albicans.

tag: RNA from Candida albicans CAI4-URA grown on HUVEC cells for 45min

tag: RNA from Candida albicans CAI4-URA grown on bare plastic for 45min


title: 36082_Endo_180min_exp1


title: 36082_Endo_45min_exp2

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 45min

tag: RNA from Candida albicans 36082 grown on bare plastic for 45min


title: CAI4_Endo_45min_exp2

tag: RNA from Candida albi ans CAI4-URA grown on HUVEC cells for 45min

tag: RNA from Candida albi ans CAI4-URA grown on bare plastic for 45min


title: CAI4_Endo_180min_exp3

tag: RNA from Candida albicans CAI4-URA grown on HUVEC cells for 180min

tag: RNA from Candida albicans CAI4-URA grown on bare plastic for 180min


title: CAI4_Endo_90min_exp2

tag: RNA from Candida albicans CAI4-URA grown on HUVEC cells for 90min

tag: RNA from Candida albicans CAI4-URA grown on bare plastic for 90min


title: 36082_Endo_45min_exp3


title: CAI4_Endo_45min_exp3


title: CAI4_Endo_180min_exp1


title: mutant versus Wild type rep 2

description: mutant versus Wild type rep 2

tag: msn2,4 mutant yeast

tag: Wild type yeast


title: 7392_Fadu_90min_exp1

tag: RNA from Candida albicans 7392 grown on Fadu oral epithelial cells for 90min

tag: RNA from Candida albicans 7392 grown on bare plastic for 90min


title: CAI4_Endo_90min_exp1


title: 36082_Endo_90min_exp2

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 90min

tag: RNA from Candida albicans 36082 grown on bare plastic for 90min


title: 7392_Fadu_180min_exp1

tag: RNA from Candida albicans 7392 grown on Fadu oral epithelial cells for 180min

tag: RNA from Candida albicans 7392 grown on bare plastic for 180min


title: CAI4_Fadu_90min_exp3

tag: RNA from Candida albicans CAI4-URA grown on Fadu oral epithelial cells for 90min


title: CAI4_Endo_180min_exp2


title: CAI4_Endo_90min_exp3


title: CAI4_Fadu_90min_exp1

data_processing: The scanned images of both channels were quantified using ImaGene 5.0 (Biodiscovery, El Segundo, Calif.).  Spots were quantified as the median value of all pixel intensities in the spot region.  The local background values were calculated from the area surrounding each feature and subtracted from respective spot signal values.  The data from each array were normalized by locally weighted linear regression (lowess) analysis using the MIDAS program (http://www.tigr.org/software/)


title: 7392_Fadu_90min_exp2


title: CAI4_Fadu_180min_exp3

tag: RNA from Candida albicans CAI4-URA grown on Fadu oral epithelial cells for 180min


title: 7392_Fadu_45min_exp2

tag: RNA from Candida albicans 7392 grown on Fadu oral epithelial cells for 45min

tag: RNA from Candida albicans 7392 grown on bare plastic for 45min


title: CAI4_Fadu_180min_exp2

tag: RNAs from Candia albicans CAI4-URA grown on Fadu oral epithelial cells for 180min

tag: RNAs from Candia albicans CAI4-URA grown on bare plastic for 180min


title: CAI4_Fadu_180min_exp1

tag: RNA from Candida albicans CAI4-URA grown on bare plastic for 180min


title: 7392_Fadu_90min_exp3


title: 7392_Fadu_45min_exp3

tag: RNA from Candida albicans 7392 grown on Plastic for 45min


title: 7392_Fadu_45min_exp1


title: 36082_Endo_180min_exp3

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 180min


title: CAI4_Fadu_90min_exp2

tag: RNA from Candida albicans CAI4-URA grwon on Fadu oral epithelial cells for 90min

tag: RNA from Candida albicans CAI4-URA grwon on bare plastic for 90min


title: Saccharomyces cerevisiae; no alpha factor control

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: Total RNA extracted from alpha-factor arrested cells.

hyb_protocol: According to Affymetrix protocol included with Yeast 2.0 arrays.

data_processing: Raw data was normalized using the affy package from Bioconductor.

source_name: Total RNA from mock-treated cells

extract_protocol: Total RNA was extracted using hot acidic phenol. 50 ug of total RNA was treated with Turbo Dnase (Ambion), and checked for integrity using a Bioanalyzer 2100 (Agilent).

tag: Strain info

value: MATa ura3Δ0 leu2Δ0 his3Δ1 met15Δ0 bar1Δ::KanMX


title: Saccharomyces cerevisiae; alpha-factor arrested

scan_protocol: According to Affymetrix protocol included with Yeast 2.0 arrays.

source_name: Total RNA from alpha-factor arrested cells


title: jaw_tcdd_12h_rep2

status: Public on Nov 01 2008

city: Madison

first: Kong

last: Xiong

state: WI

address: 777 Highland Ave, 5208 Rennebohm Hall

department: Biomolecular Chemistry

institute: University of Wisconsin at Madison

description: no additional information

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented and hybridized onto Affymetrix Zebrafish Genechip Arrays following the protocol in the Affymetrix Genechip Expression Analysis Technical Manual.

scan_protocol: Following hybdrization, the arrays were washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400 using the protocol EukGE WS2v4.  Arrays were scanned with an Agilent Gene Array Scanner.

data_processing: Analysis of the relative abundance of each gene transcript was determined using Arrayassist microarray software (Stratagene, La Jolla, CA).  In brief, .CHP files were uploaded into the software and probe intensities were corrected for background noise and normalized across all array replicates with the GC-Robust Multi-Array Average (GC-RMA) algorithm.  Expression levels for each transcript were log2-transformed, and the average log2 value for the TCDD samples was compared to the average value for the DMSO replicates.  Those transcripts that were altered by TCDD by at least 2 fold over DMSO at any of the time points (p < 0.05) were selected for further analysis.  Significant changes were determined by an unpaired t-test.

organism: Danio rerio

source_name: jaw, tcdd treated, 12h

label_protocol: The One-Cycle Target Labeling and Control Reagents kit was used to synthesize cDNA and biotinylated cRNA following the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

extract_protocol: Jaws were microdissected as previously described (Javidan and Schilling, 2004).  Larvae were anesthetized with Tricaine-S (Aquatic EcoSystems, Apopka, FL), positioned onto a microscope slide and a drop of Lebovitz’s L15 media + 10% fetal bovine serum (Invitrogen, Carlsbad, CA) was placed onto each specimen.  With fine forceps (Fine Science Tools, Foster City, CA) the head (anterior of the pectoral fin) was detached from the body then the eyes and brain tissues were removed.  Dissected jaws were placed into a microcentrifuge tube and immediately put into a dry ice bucket.  Jaws were stored at -80°C.

treatment_protocol: AB larvae zebrafish were exposed to TCDD (1 ng/ml; TCDD > 99% purity; Chemsyn, Lenexa, KS) or vehicle [0.1% dimethyl sulfoxide (DMSO)] at 96 hpf for 1 h in water and rinsed with fish water.  Treatment conditions were limited to 10 embryos or fewer per 1 ml treatment volume.  Larvae were raised in 100-mm Petri dishes containing fish water.

tag: AB wild-type strain


title: CAI4_Fadu_45min_exp1

tag: RNA from Candida albicans CAI4-URA grown on Fadu oral epithelial cells for 45min

tag: RNA from Candida albicans CAI4-URA grown on bare plastic for 45min


title: jaw_vehicle control_4h_rep3

description: no additional information

source_name: jaw, vehicle, 4h


title: 7392_Fadu_180min_exp3

tag: RNA from Candida albicans 7392 grown on Fadu oral epithelial cells for 180min


title: CAI4_Fadu_45min_exp2


title: jaw_vehicle control_4h_rep2

description: no additional information


title: jaw_tcdd_2h_rep3

description: no additional information

source_name: jaw, tcdd treated, 2h


title: 7392_Fadu_180min_exp2

tag: RNA from Candida albicans 7392 grown on bare plastic for 180min


title: jaw_tcdd_2h_rep2

description: no additional information


title: jaw_tcdd_4h_rep3

description: no additional information

source_name: jaw, tcdd treated, 4h


title: CAI4_Fadu_45min_exp3


title: jaw_vehicle control_4h_rep1

description: no additional information


title: jaw_tcdd_4h_rep1

description: no additional information


title: jaw_tcdd_4h_rep2

description: no additional information


title: jaw_tcdd_12h_rep1

description: no additional information


title: jaw_tcdd_2h_rep1

description: no additional information


title: jaw_vehicle control_12h_rep1

description: no additional information

source_name: jaw, vehicle, 12h


title: jaw_vehicle control_12h_rep2

description: no additional information


title: jaw_tcdd_1h_rep1

description: no additional information

source_name: jaw, tcdd treated, 1h


title: jaw_tcdd_12h_rep3

description: no additional information


title: jaw_vehicle control_2h_rep3

description: no additional information

source_name: jaw, vehicle, 2h


title: jaw_vehicle control_2h_rep1

description: no additional information


title: jaw_tcdd_1h_rep2

description: no additional information


title: jaw_tcdd_1h_rep3

description: no additional information


title: jaw_vehicle control_12h_rep3

description: no additional information


title: 36082_Endo_90min_exp3

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 90min

tag: RNA from Candida albicans 36082grown on bare plastic for 90min


title: 36082_Endo_45min_exp1

tag: RNA from Candida albicans 36082 grown on HUVEC cells for 45min


title: jaw_vehicle control_1h_rep3

description: no additional information

source_name: jaw, vehicle, 1h


title: jaw_vehicle control_1h_rep2

description: no additional information


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorH)

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

description: Part of series of experiments performed to determine response of S. agalactiae to human blood

hyb_protocol: Overnight 45°C, standard Affymetrix protocol

scan_protocol: Affymetrix Genechip scanner 3000

data_processing: Raw data normalized to total signal intensity of S. agalactiae probes present on the array

label: Biotin

organism: Streptococcus agalactiae

source_name: Growth in blood

label_protocol: Standard Affymetrix

extract_protocol: Each blood with bacterial sample used for RNA isolation was treated with 2 volumes of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA), collected by centrifugation, and stored at –80°C until processing. Red cells were lysez by Erythrocyte Lysis buffer (Qiagen). RNA was extracted using the Lysing Matrix B microtubes containing 0.1 mm silica spheres (Qbiogene, Carlsbad, CA) and 1 mL Trizol (Invitrogen) with the FastPrep FP120 cell disrupter (Qbiogene). RNA extraction was completed with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.

tag: Strain NEM316 grown in blood


title: jaw_vehicle control_1h_rep1

description: no additional information


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorG)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorG)


title: Expression of S. agalatiae genes in blood at time 0 (donorF)

extract_protocol: Each blood with bacteria sample used for RNA isolation was treated with 2 volumes of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA), collected by centrifugation, and stored at –80°C until processing. Red cells were lysed by Erythrocyte Lysis buffer (Qiagen). RNA was extracted using the Lysing Matrix B microtubes containing 0.1 mm silica spheres (Qbiogene, Carlsbad, CA) and 1 mL Trizol (Invitrogen) with the FastPrep FP120 cell disrupter (Qbiogene). RNA extraction was completed with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.


title: jaw_vehicle control_2h_rep2

description: no additional information


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorG)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorG)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorH)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorF)


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorF)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorF)


title: Expression of S. agalatiae genes in blood at time 0 (donorG)


title: Expression of S. agalatiae genes in blood at time 0 (donorH)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorD)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorE)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorE)

data_processing: Raw data normalized to total signal intensity of S. agalactiae to human blood


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorD)


title: Expression of S. agalatiae genes in blood at time 0 (donorE)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorD)


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorE)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorC)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorC)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorC)


title: Expression of S. agalatiae genes in blood at time 0 (donorC)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorD)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorF)


title: Expression of S. agalatiae genes in blood after 90 minutes at 37 degrees (donorB)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorH)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorE)


title: Expression of S. agalatiae genes in blood at time 0 (donorB)

tag: Strain NEM316 grown in human blood


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorB)


title: Expression of S. agalatiae genes in blood after 30 minutes at 40 degrees (donorB)


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorH)


title: Expression of S. agalatiae genes in blood after 30 minutes at 37 degrees (donorC)


title: Expression of S. agalatiae genes in blood after 90 minutes at 40 degrees (donorB)


title: B_GluEarlyStaF1(5)vsGlu&GlyEarlyStaF2(6)

status: Public on Sep 15 2008

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

hyb_protocol: Two individual differentially  labeled cDNAs were  incubated at 95° C for 3'  cooled down to 68° C and  mixed (final-volume 20 µl).  To these mixed cDNAs  180 µl of pre-heated (68°  C) Slidehyb#1 hybridization  buffer (Ambion Austin USA)  was added and the  resulting solution was  applied on a pre-heated  slide (68° C). Slides were  then hybridized at 44° C for  16 hours. Subsequently  slides were washed at  42°C once in 1 x  SSC/0.2% SDS and twice  in 1 x SSC and dried by  centrifugation (1 x SSC is  0.15 M NaCl and 0.15 M  Sodium Citrate).

scan_protocol: Using the Scan Array  Express microarray  scanner. 1.Turn on the  scanner and the computer  (in this order) 2.Login:  scanner 3.Double click the  'ScanArray Express' icon  4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning arrays 5.Click the  'File' button This is to  prevent you from  accidentally turning off the  laser after the 15 minutes  warming-up phase 6.Insert  the slide with the array-side  up and the label towards  the outside. On Agilent  slides the array side is the  side with the label that has  the word Agilent"" on it  7.Press 'Scan | Prescan'  8.Put resolution at 50 m  select both labels used  and set PMT values for  both channels 9.Press  'Start' 10.Press 'Palette '  'Green' as soon as  projection of the image has  started (first dye) select the  red colour as soon as  scanning of the second  layer (second dye) has  started 11.Adjust PMT  values to balance signals  obtained for both  channels. If necessary do  a few low-resolution scans  to obtain a optimal balance  12.Click the 'Scan' button  again 13.Select frame for  high resolution scan adjust  resolution (to 10 m) and  scan the array for both  dyes 14.Press 'File | Save'  to save the files 'Save all'  saves both dye layers ,"  Create a new folder for  each array 'Save all' saves  the signals from both layers  in individual files 15.Switch  off the lasers

data_processing: Microarrays were  normalized by local fitting  of an M-A plot applying the  loess algorithm using the Limma package  in R  (http://www.r-project.org).  Statistical significance was determined from  variation in biological  duplicates by  implementation of the eBayes function included  in Limma (cross-probe  variance estimation) and  false discovery rate adjustment  of the p-values. In order to  characterize the response  of L. reuteri to glycerol,  comparisons were  established (i) during  exponential growth phase (mid-logarithmic  phase response), (ii) during  early stationary growth  phase (early-stationary phase  response), and (iii) by  comparing the differences  between early-stationary and  mid-logarithmic cells  cultured with and without  glycerol (phase shift response). Only  transcripts with an average  absolute log2 (ratio) greater  than 0.585 and a p-value  smaller than 0.05 were  considered for analysis.  The three lists of differentially regulated  genes were projected on  metabolic maps of the  genome-scale model developed in this  study.

organism: Limosilactobacillus reuteri subsp. reuteri F275

label_protocol: Annealing Mix x µl RNA  preparation (=5µg) y µl  nuclease-free water 1 µl  Random Nonamers 11  µl TOTAL 1. mix  Annealing Mix in a 200  µl PCR tube gently by  pipetting up and down  2. incubate for 5’ 70°C  3. cool at room  temperature for 10’  (annealing) 4. spin down  the mixture to the  bottom of the tube 5.  place on ice Reverse  transcription Reverse  Transcription Mix 4 µl 5x  buffer 2 µl 0.1 M DTT 1  µl dNTP-mix 1 µl  AA-dUTP 1 µl TMIII  (keep only briefly  outside 20°C) 20 µl  TOTAL 1. Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.  Incubate for 3 hrs at  42°C (in PCR-machine)  3. Cool on ice for  immediate purification or  place at 20°C for  storage Degradation of  mRNA 1. Add 2 µl 2.5 M  NaOH 2. Mix (vortex)  and spin down 3.  Incubate for 15 min. at  37°C 4. Add 10 µl 2 M  HEPES free acid 5. Mix  (vortex) and spin down  6. Ready for purification  or store at 20°C  Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661 Labelling of  amino allyl-modified  cDNA with CyDye 1.  Add the amino allyl  modified cDNA (in 0.1 M  sodium bicarbonate)  directly into one aliquot  of CyDye NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.  Incubate at room  temperature, in the dark  for 60 to 90 minutes 3.  Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4. Mix  by stirring and incubate  at room temperature, in  the dark, for 15 minutes  5. Proceed directly to  purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed  Ge Healthcare kit  "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA

extract_protocol: Collecting cells  Quenching Buffer 66.7  mM HEPES (pH 6.5)  60%Methanol Extraction  Mixture (Prepared in a  screw-cap tube) -500 µll  phenol/Chloroform -30  µl10% SDS -30 µl3 M  NaAc (pH 5.2) -500 mg  glass-beads (75-150 µm)  -400 µlTE buffer 1.For  each sample prepare a  tube with Extraction  Mixture 2.Harvest cells  and quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of cell culture  3.Mix and store the  sample at -40°C  4.Centrifuge cells at -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix  the cell pellet thoroughly  with Extraction Mixture  by shaking by hand  7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in  the Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary)  9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer  500 µl of the  supernatant to a new  tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with  the "High Pure RNA  Isolation Kit" from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA  in at least 2 aliquots,  one of 20 µl (for  concentration and  quality analysis and  labelling) and one  back-up of 30 µl at  -80°C.

tag: CDM; early stationary phase; fermenter 1

tag: CDM glycerol; early stationary phase; fermenter 2


title: Expression of S. agalactiae genes at 40 degrees at stationary phase (replicate 2)

status: Public on Sep 01 2008

description: Part of the series of experiments performed to determine response of S. agalactiae to growth temperature

hyb_protocol: Overnight at 45C, standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip scanner 3000

source_name: S. agalactiae, 40 degrees at stationary phase (replicate 2)

extract_protocol: 5ml culture was added to 10ml RNA protect (Qiagen), and GBS collected by centrifugation and stored at -80C. RNA was extracted from bacterial cell pellets through mechanical disruption using glass beads (MatrixB tubes) in a FastPrep machine. RNA was purified using TRIZOL extraction and re-purified on Qiagen miRNeasy columns using standard protocol. DNA was removed with DNA-free (Ambion). RNA quality was assessed by bioanalyzer and O.D. measurements.

tag: strain NEM316 grown in THY broth


title: C_Glu&GlyEarlyStaF2(6)vsGlu&GlyExpF2(2)

tag: CDM glycerol; exponential phase; fermenter 2


title: H_Glu&GlyEarlyStaF4(7)vsGluEarlyStaF1(5)

tag: CDM glycerol; early stationary phase; fermenter 4

tag: CDMl; early stationary phase; fermenter 1


title: Expression of S. agalactiae genes at 40 degrees at stationary phase (replicate 3)

source_name: S. agalactiae, 40 degrees at stationary phase (replicate 3)


title: G_Glu&GlyExpF4(4)vsGlu&GlyEarlyStaF4(7)

tag: CDM glycerol; exponential phase; fermenter 4


title: E_Glu&GlyExpF2(2)vsGluExpF3(3)

tag: CDM; exponential phase; fermenter 3


title: Expression of S. agalactiae genes at 40 degrees at late log phase (replicate 1)

source_name: S. agalactiae, 40 degrees at late log phase (replicate 1)


title: Array1GluLateLog5vsGlyLateLog3

description: Array1GluLateLog5vsGlyLateLog3	late exp	LRECDM	2.15

source_name: GlyLateLog

tag: CDM glycerol

source_name: GluLateLog

tag: CDM


title: Expression of S. agalactiae genes at 40 degrees at late log phase (replicate 3)

source_name: S. agalactiae, 40 degrees at late log phase (replicate 3)


title: I_Glu&GlyEarlyStaF2(6)vsGlu&GlyExpF4(4)


title: Array02GluLateLog3vsGlyLateLog5

description: Array02GluLateLog3vsGlyLateLog5	late exp	LRECDM	2.045


title: Expression of S. agalactiae genes at 40 degrees at late log phase (replicate 2)

source_name: S. agalactiae, 40 degrees at late log phase (replicate 2)


title: Expression of S. agalactiae genes at 40 degrees at mid log phase (replicate 3)

source_name: S. agalactiae, 40 degrees at mid log phase (replicate 3)


title: Expression of S. agalactiae genes at 40 degrees at stationary phase (replicate 1)

source_name: S. agalactiae, 40 degrees at stationary phase (replicate 1)


title: A_GluExpF1(1)vsGluEarlyStaF1(5)

tag: CDM; exponential phase; fermenter 1


title: J_Glu&GlyExpF4(4)vsGluExpF3(3)


title: F_GluExpF3(3)vsGlu&GlyExpF4(4)


title: D_Glu&GlyExpF2(2)vsGluExpF1(1)


title: Expression of S. agalactiae genes at 30 degrees at late log phase (replicate 3)

source_name: S. agalactiae, 30 degrees at late log phase (replicate 3)

label_protocol: standard Affymetrix


title: Expression of S. agalactiae genes at 30 degrees at stationary phase (replicate 3)

source_name: S. agalactiae, 30 degrees at stationary phase (replicate 3)


title: Expression of S. agalactiae genes at 30 degrees at late log phase (replicate 2)

source_name: S. agalactiae, 30 degrees at late log phase (replicate 2)


title: Expression of S. agalactiae genes at 40 degrees at mid log phase (replicate 1)

source_name: S. agalactiae, 40 degrees at mid log phase (replicate 1)


title: Expression of S. agalactiae genes at 30 degrees at late log phase (replicate 1)

source_name: S. agalactiae, 30 degrees at late log phase (replicate 1)


title: Expression of S. agalactiae genes at 30 degrees at mid log phase (replicate 2)

source_name: S. agalactiae, 30 degrees at mid log phase (replicate 2)


title: Expression of S. agalactiae genes at 40 degrees at mid log phase (replicate 2)

source_name: S. agalactiae, 40 degrees at mid log phase (replicate 2)


title: Expression of S. agalactiae genes at 30 degrees at stationary phase (replicate 2)

source_name: S. agalactiae, 30 degrees at stationary phase (replicate 2)


title: Expression of S. agalactiae genes at 30 degrees at mid log phase (replicate 3)

source_name: S. agalactiae, 30 degrees at mid log phase (replicate 3)


title: Expression of S. agalactiae genes at 30 degrees at stationary phase (replicate 1)

source_name: S. agalactiae, 30 degrees at stationary phase (replicate 1)


title: Expression of S. agalactiae genes at 30 degrees at mid log phase (replicate 1)

source_name: S. agalactiae, 30 degrees at mid log phase (replicate 1)


title: 3.0_12A_3d3VO

city: Berlin

first: Philipp

last: Hillmeister

state: Berlin

address: Hessische Straße 3-4

department: Center for Cardiovascular Research

institute: Charité Mitte Berlin

description: 3 days upon 3VO surgery analysis of RNA extracted from the posterior cerebral artery

hyb_protocol: Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to a rat expression Affymetrix RAE 230A GeneChip array. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Affymetrix GeneChip Operating Software (GCOS)

label: biotin labeled

organism: Rattus norvegicus

source_name: PCA ipsilateral, 3 days 3VO

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer´s instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL Biol, Berlin, Germany) one to three micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix, Santa Clara, CA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40mM Tris-acetate (pH 8.2), 100mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes.

growth_protocol: Animals were housed under diurnal lighting conditions and allowed food and water ad libitum. Animal housing, care and applications of experimental procedures complied with the permission of state authorities according to the German Law for Protection of Animals, and the National Institute of Health Guidelines for Care and Use of Laboratory Animals. Conditions were in accordance with the recommendations of the Society of Laboratory Animal Science (GV-SOLAS) and the Federation of European Laboratory Animal Science Association (FELASA).

extract_protocol: Posterior cerebral arteries of 8 animals post 3d-3VO were pooled in one sample in RNAlater for RNA extraction.  Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Hilden, Germany)

treatment_protocol: Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. BID for 2 days after surgery. Vascular occlusions were carried out in one session by first electrocoagulating both vertebral arteries, using a paravertebral access (Pulsinelli and Brierley, 1979; Pulsinelli et al., 1983), followed by left common carotid artery ligation. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 3 days postoperatively anesthesia was induced by isoflurane (see above). Thereafter the vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.

tag: strain

value: sprague dawley rat

tag: weight

tag: age

value: 7 weeks


title: Scc1-9PK distribution along the whole genome (+NOC)

status: Public on Oct 01 2008

type: genomic

city: London

first: Maria

last: Ocampo-Hafalla

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK London Research Institute

description: Scc1-9PK distribution along the whole genome in metaphase-arrested cells in the presence of nocodazole. [Figure S1]

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Reference: Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

scan_protocol: The 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

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells in YP + 2% Raffinose were synchronized in G1 with α-factor and released into metaphase arrest with nocodazole.  Cells were then transferred to 37C for one hour.

extract_protocol:
Extraction was performed as previously described (Katou et al. 2003).
Reference:
Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

tag: Strain 2269 = MATa Scc1-9PK-TRP


title: 3.0_11A_3d3VO


title: 3.0_9A_24h_3VO

description: 24 hours upon 3VO surgery analysis of RNA extracted from the posterior cerebral artery

source_name: PCA ipsilateral, 24h 3VO

extract_protocol: Posterior cerebral arteries of 8 animals post 24h-3VO were pooled in one sample in RNAlater for RNA extraction.  Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Hilden, Germany)

treatment_protocol: Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. BID for 2 days after surgery. Vascular occlusions were carried out in one session by first electrocoagulating both vertebral arteries, using a paravertebral access (Pulsinelli and Brierley, 1979; Pulsinelli et al., 1983), followed by left common carotid artery ligation. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 24 hours postoperatively anesthesia was induced by isoflurane (see above). Thereafter the vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: 3.0_14A_intact_control

description: Intact control, analysis of RNA extracted from the posterior cerebral artery

source_name: PCA ipsilateral, intact control

extract_protocol: Posterior cerebral arteries of 8 intact animals were pooled in one sample in RNAlater for RNA extraction.  Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Hilden, Germany)

treatment_protocol: At timepoint 0 intact animals were chosen as control. The vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: 3.0_3A_3d_Sham

description: 3 days upon Sham surgery analysis of RNA extracted from the posterior cerebral artery

source_name: PCA ipsilateral, 3 days Sham

extract_protocol: Posterior cerebral arteries of 8 animals post Sham op were pooled in one sample in RNAlater for RNA extraction.  Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Hilden, Germany)


title: 3.0_13A_intact_control


title: 3.0_4A_24h_3VO


title: 3.0_1A_24h_3VO

treatment_protocol: 3-vessel occlusion (3-VO): Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. Vascular occlusions were carried out in one session by first electrocoagulating both vertebral arteries, using a paravertebral access (Pulsinelli and Brierley, 1979; Pulsinelli et al., 1983), followed by left common carotid artery ligation. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 24h postoperatively anesthesia was induced by isoflurane (see above). The vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: 3.0_10A_3d_Sham

treatment_protocol: Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. BID for 2 days after surgery. Sham operation was carried out in one session by surgically opening tissue and muscle to lay open both vertebral arteries followed by the left common carotid artery without touching the vessels. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 3 days postoperatively anesthesia was induced by isoflurane (see above). Thereafter the vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: 3.0_2A_3d_3VO

treatment_protocol: Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. Vascular occlusions were carried out in one session by first electrocoagulating both vertebral arteries, using a paravertebral access (Pulsinelli and Brierley, 1979; Pulsinelli et al., 1983), followed by left common carotid artery ligation. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 3 days postoperatively anesthesia was induced by isoflurane (see above). Thereafter the vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: 3.0_5A_24h_Sham

description: 24 hours upon Sham surgery analysis of RNA extracted from the posterior cerebral artery

source_name: PCA ipsilateral, 24h Sham

treatment_protocol: Anesthesia was induced and maintained with 2% to 4% isoflurane (in oxygen). Analgesia was achieved by buprenorphine s.c. 0.1mg/kg intraoperatively and 0.05 mg/kg s.c. BID for 2 days after surgery. Sham operation was carried out in one session by surgically opening tissue and muscle to lay open both vertebral arteries followed by the left common carotid artery without touching the vessels. After the wounds were closed animals were returned in pairs to their cages with free access to food and water and allowed to move freely. 24 hours postoperatively anesthesia was induced by isoflurane (see above). Thereafter the vascular system was perfused with latex for visualization under the max. vasodilation by Papaverin. The brain was transferred into RNA Later for surgically extraction of the posterior cerebral artery. Posterior cerebral arteries of 8 animals were pooled for RNA extraction.


title: Gill_cold_30d_rep2

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

country: Japan

institute: Acdemia Sinica

description:
The commercial zebrafish 14K oligonucleotides set (MWG
Biotech AG, Ebersbach, Germany) were obtained and were printed on UltraGAPS Coated slide (Corning, New York, NY ) with use of the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacture’s instructions. The 14,067 oligonucleotides represent 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of this chip is 31 %. The detailed description of the oligonucleotides information can be obtained on the Ocimun Biosolution website (http://www.ocimumbio.com/web/default.asp).

hyb_protocol: The zebrafish 14K OciChip array chip was pretreated with 1% bovine serum albumin (BSA) (fraction V), 4x saline-sodium citrate (SSC), and 1% sodium dodecylsulfate (SDS) at 42 °C for 45 min, and then hybridized overnight in a cocktail containing 5x Denhardt's solution, 6x SSC, 0.5% SDS, 50% formamide, 50 mM sodium phosphate, and 2 µg/µl yeast tRNA. Slides were washed with 2x SSC and 0.1% SDS (5 min), 1x SSC and 0.1% SDS (5 min), 0.5x SSC (5 min), and twice with 0.1x SSC (2 min each).

scan_protocol: Scanning was performed with a Scanarray Gx scanner (PerkinElmer, Waltham, MA). The acquired images were analyzed using ScanArray Express 3.0 (PerkinElmer, Waltham, MA)and Genespring software (Aglient Technologies, Foster City, CA).

data_processing: The measurements of spots were filtered by flags, and the lowest normalization was performed after subtraction of the median background. The VALUE indicated the transformation algorithm of Cy5/Cy3 normalized log10 ratio, which was used to identify the 300 genes which were selected from those with at least 2 of 3 significant signals (ratio > 2 or < 0.5).

source_name: Gill cold treatment for 30 d

label_protocol: cDNA probes were synthesized by reverse transcription of 20 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen).The amine-modified DNA then was incubated with resuspend one aliquot of Cy5 Dye (Amersham Bioscience, Buckinghamshire, UK) at RT in the dark for overnight. Finally, the probe was purified by kit and was eluted with elution EB buffer.

growth_protocol: The experimental protocols were approved by the Academia Sinica Institutional Animal Care and Utilization Committee (approval no. RFiZOOHP2006083).

extract_protocol: Gill tissues dissected from 6 individuals were pooled as a sample and then homogenized in 5 ml Trizol reagent (Invitrogen, Carlsbad, CA). After chloroform extraction, RNA precipitation and ethanol washing, the RNA samples were purified and treated with DNase1 to remove the genomic DNA by using RNeasy Mini Kit (Qiagen, Huntsville, Alabama). The quantity and quality of total RNA were assessed by spectrophotometry and agarose gel electrophoresis, respectively.

treatment_protocol: Adult zebrafish were acclimated to 12 C with a gradually reduced temperature at a gradient of 4 C/h in order to prevent temperature shock and reduce mortality. After 30 d of acclimation, surviving (over an 80% survival rate) fish appeared to be feeding and behaving normally compared with control fish.

tag: The AB strain of zebrafish (D. rerio) was originally obtained from the University of Oregon, and were kept in the zebrafish stock center at Academia Sinica, Taipei, Taiwan.

source_name: Gill normal temperature treatment for 30 d

treatment_protocol: Adult zebrafish were incubated in normal temperature as a control group.


title: 3.0_8A_24h_Sham


title: Gill_cold_1d_rep1

scan_protocol: Scanning was performed with a ScanArray Gx scaner (PerkinElmer, Waltham, MA). The acquired images were analyzed using ScanArray Express 3.0 (PerkinElmer)and Genespring software (Aglient Technologies, Foster City, CA).

source_name: Gill cold treatment for 1 d

extract_protocol: After the low-temperature treatment, gill tissues dissected from 6 individuals were pooled as a sample and then homogenized in 5 ml Trizol reagent (Invitrogen, Carlsbad, CA). After chloroform extraction, RNA precipitation and ethanol washing, the RNA samples were purified and treated with DNase1 to remove the genomic DNA by using RNeasy Mini Kit (Qiagen, Huntsville, Alabama). The quantity and quality of total RNA were assessed by spectrophotometry and agarose gel electrophoresis, respectively.

treatment_protocol: Adult zebrafish were acclimated to 12 C with a gradually reduced temperature at a gradient of 4 C/h in order to prevent temperature shock and reduce mortality. After 1 d of acclimation, surviving (over an 80% survival rate) fish appeared to be feeding and behaving normally compared with control fish.

source_name: Gill normal temperature treatment for 1 d

label_protocol: cDNA probes were synthesized by reverse transcription of 20 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen).The amine-modified DNA then was incubated with resuspend one aliquot of Cy3 Dye (Amersham Bioscience, Buckinghamshire, UK) at RT in the dark for overnight. Finally, the probe was purified by kit and was eluted with elution EB buffer.


title: 3.0_15A_intact_control


title: Gill_cold_1d_rep3

scan_protocol: Scanning was performed with a Genepix scanner (Molecular Devices, Sunnyvale, CA). The acquired images were analyzed using ScanArray Express 3.0 (PerkinElmer, Waltham, MA)and Genespring software (Aglient Technologies, Foster City, CA).

data_processing: The measurements of spots were filtered by flags, and the lowest normalization was performed after subtraction of the median background. The VALUE indicated the transformation algorithm of Cy3/Cy5 normalized log10 ratio, which was used to identify the 300 genes which were selected from those with at least 2 of 3 significant signals (ratio > 2 or < 0.5).


title: 3.0_7A_3d_Sham


title: Wild type SmutansWT_BHI_rep4

status: Public on Aug 30 2008

city: Gainesville

first: Robert

last: Burne

state: FL

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

institute: University of Florida

description: Streptococcus mutans wildtype

hyb_protocol: Hybridizations were carried out in a Maui 4-chamber hybridization system (BioMicro Systems, Salt Lake City, Utah) for 17 h at 42ºC. The slides were then washed according to TIGR protocols (SOT# M008, version 2.1, 11/06).

scan_protocol: The slides were scanned using a GenePix Scanner (Axon Instruments Inc., Union City, CA).

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software and overlayed. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, then the intensity values of each spot were measured. Data was normalized using Microarray data analysis software (MIDAS), by using LOWESS and Iterative Log Mean Centering with default settings.

organism: Streptococcus mutans

source_name: S. mutans UA159 grown in BHI

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Purified cDNAs were coupled with indocarbocyanine (Cy3)-dUTP

growth_protocol:
Growth Media: Brain Heart Infusion
OD600: 0.5

extract_protocol: RNA from S. mutans was isolated from 50 ml cultures that were grown under the desired conditions and harvested by centrifugation at 4ºC. Pelleted cells were resuspended in 400 ml of DEPC-treated water, 800 ml of RNA protect reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were incubated at room temperature for 5 min with vortexing for 10 s at one minute intervals. Cells were then pelleted, resuspended in 500 ml Tris-EDTA (50:10) buffer and transferred to 1.5 ml screw cap tubes containing sterile glass beads (0.1 mm avg. diam.; Biospec, Bartlesville, OK), 100 ml of 1% SDS and 650 ml of acid phenol:chloroform (5:1). The mixture was homogenized in a Bead Beater twice for 40 s and chilled on ice for 2 min between cycles. Samples were centrifuged for 30 min at maximum speed at 4ºC. Two additional hot acid phenol:chloroform extractions were performed followed by one extraction with chloroform:isoamyl-alcohol (24:1). RNA was precipitated in the presence of isopropanol and sodium acetate, pH 5, at -20ºC for 1 h, followed by multiple washes with 70% ethanol, one wash with 99% ethanol, and drying in vacuo. RNA was resuspended in DEPC-treated water and digested with DNAseI (Ambion, Austin, TX). The RNA was re-purified and treated on-column with DNaseI using the RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA), as recommended by the supplier.

tag: S. mutans strain UA159 wildtype

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Reference cDNA was coupled with indodicarbocyanine (Cy5)-dUTP (Amersham Biosciences, Piscataway, NJ).


title: 3.0_6A_24h_Sham


title: Wild type SmutansWT_BHI_rep5

description: Streptococcus mutans wildtype


title: Wild type SmutansWT_BHI_rep7

description: Streptococcus mutans wildtype


title: Wild type SmutansWT_BHI_rep3

description: Streptococcus mutans wildtype


title: Wild type SmutansWT_BHI_rep1

description: Streptococcus mutans wildtype

tag: Strain UA159


title: Wild type SmutansWT_BHI_rep6

description: Streptococcus mutans wildtype


title: Gill_cold_30d_rep3


title: Gill_cold_1d_rep2


title: BrpA deficient mutant SmutansBrpA_BHI_rep5

description: Streptococcus mutans brpA mutant

source_name: S. mutans TW14 grown in BHI

tag: Strain TW14

value: knockout of the brpA gene via insertion of a erythromycin cassette


title: Gill_cold_30d_rep1


title: BrpA deficient mutant SmutansBrpA_BHI_rep2

description: Streptococcus mutans brpA mutant


title: Wild type SmutansWT_BHI_rep2

description: Streptococcus mutans wildtype


title: BrpA deficient mutant SmutansBrpA_BHI_rep3

description: Streptococcus mutans brpA mutant


title: BrpA deficient mutant SmutansBrpA_BHI_rep7

description: Streptococcus mutans brpA mutant


title: BrpA deficient mutant SmutansBrpA_BHI_rep1

description: Streptococcus mutans brpA mutant


title: BrpA deficient mutant SmutansBrpA_BHI_rep6

description: Streptococcus mutans brpA mutant


title: Heart Tissue_Tre1KO/RAG2KO_C

status: Public on Aug 22 2008

city: New Haven

first: Daniel

middle: B

last: Stetson

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

description: Heart ventricle tissue

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix MAS 5.0 software analysis

label_protocol: Affymetrix protocol

extract_protocol: Heart tissue was homogenized in RNABee, and total RNA was prepared using conventional techniques.

tag: Heart tissue from Trex1 KO, RAG2 KO on C57/Bl6 background, 123 days old, male


title: BrpA deficient mutant SmutansBrpA_BHI_rep4

description: Streptococcus mutans brpA mutant


title: Heart Tissue_Trex1KO/RAG2KO_B

description: Heart ventricle tissue

tag: Heart tissue from Trex1 KO, RAG2 KO on C57/Bl6 background, 134 days old, male


title: Heart Tissue_Trex1KO/RAG2KO_A

description: Heart ventricle tissue

tag: Heart tissue from Trex1 KO, RAG2 KO on C57 Bl/6 background, 119 days old, male


title: Heart Tissue_Tre1WT/RAG2KO_C

description: Heart ventricle tissue


title: Sample ID norm1892 normal-cell sample from patient with localized prostate cancer

status: Public on Aug 17 2008

city: Seattle

first: Ilona

middle: N

last: Holcomb

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: On microgram each of tumor and reference DNA labeled with Cy5 and Cy3, respectively, were combined and briefly dried by Speedvac. The samples were resuspended in hybridization mix (50% formamide, 10% dextran sulfate, 3x SSC, 1.5% SDS) and heated to 70°C for 10 minutes, followed by 1-hour incubation at 37°C to allow blocking of repetitive sequences by human Cot-1 DNA. After incubation, samples were applied to the microarray under a coverslip and hybridized at 37°C for 18 hours. After hybridization, the arrays were then washed in 50% formamide and 2x SSC (pH 7.0) for 20 minutes at 45°C, followed by a 7-minute wash at room temperature in 0.1 mol/L NaPO4 (pH 8.0) and 0.1% NP40. After washing, the arrays were dried by centrifugation at 600 rpm for 5 minutes.

scan_protocol: Arrays were scanned with a GenePix 4000A scanner (Axon Instruments, Inc., Union City, CA); fluorescence data were processed with GenePix 3.0 image analysis software (Axon Instruments, Inc.). For each spot, log2 ratio = log2(Cy5/Cy3) and average log2 intensity = [log2(Cy5) + log2(Cy3)]/2 were calculated, where Cy5 and Cy3 refer to the median foreground fluorescent signals of the tumor and reference DNA, respectively. Background subtraction was not used because it conferred no benefit in tests run on cell lines with varying numbers of X chromosome copies.

data_processing: The log2 ratios on each array were normalized and corrected for intensity-based location adjustment with a block-level loess algorithm (as described in Yang YH, Dudoit S, Luu P, Speed TP Normalization for cDNA microarray Bittner ML Chen Y Dorsel AN Dougherty ER eds. . Microarrays: optical technologies and informatics 2001141-52. SPIE, Society for Optical Engineering Bellingham, WA).

source_name: Normal-cell sample collected in parallel with disseminated cells from the bone marrow of a patient with localized prostate cancer.

label_protocol: Array CGH bioprime kit (Invitrogen)

extract_protocol: 10-20 cells amplified directly in collection tube by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499.)

tag: Normal cells detected by CD45 positivity and isolated by micropipetting from the bone marrow of a patient with localized prostate cancer. 10-20 cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. This sample was part of a set of nine normal-cell samples that were used for defining thresholds of chromosomal loss and gain for the disseminated cell arrays.

source_name: normal female reference DNA

extract_protocol: DNA was isolated using a QIAamp DNA Blood Mini Kit (Qiagen)

tag: Normal female genomic DNA isolated from peripheral blood. The DNA equivalent to 10-20 cells was then amplified by  ligation mediated PCR


title: LNCaP_20cellamplification_3

source_name: 20 LNCaP cells amplified by ligation mediated PCR

extract_protocol: LNCaP DNA was amplified in the collection tube by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499).

tag: The sample is the ligation mediated PCR amplified DNA of 10 cells collected and pooled by micropipetting. It was part of a set of five LNCaP arrays that were used to verify the compatability of a small number of cells with array CGH. Specifically, this sample represents a sample of a small number of cells.

tag: Normal female genomic DNA isolated from peripheral blood. The DNA equivalent to 20 cells was then amplified by  ligation mediated PCR


title: Sample ID norm1922 normal-cell sample from patient with localized prostate cancer


title: Sample ID norm1918 normal-cell sample from patient with localized prostate cancer


title: Sample ID norm1923 normal-cell sample from patient with localized prostate cancer


title: Sample ID 1965 disseminated cell sample from patient with advanced prostate cancer

source_name: Disseminated cell sample from patient with advanced prostate cancer.

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was TNM stage M+ and was treated by chemical castration. Bone marrow was collected during the course of treatment.


title: LNCaP_20cellamplification_2

tag: The sample is the ligation mediated PCR amplified DNA of 20 cells collected and pooled by micropipetting. It was part of a set of five LNCaP arrays that were used to verify the compatability of a small number of cells with array CGH. Specifically, this sample represents a sample of a small number of cells.


title: Sample ID 1989 disseminated cell sample from patient with advanced prostate cancer


title: LNCaP_bulkDNAamplification

source_name: LNCaP DNA amplfied by ligation mediated PCR

extract_protocol: LNCaP DNA was isolated by the QIAamp DNA Kit (Qiagen, CA). 200ng of DNA was then amplified by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499).

tag: The sample was an aliquot from the ligation mediated PCR amplified DNA (200ng). It was part of a set of five LNCaP arrays that were used to verify the compatability of a small number of cells with array CGH. Specifically, this sample represented the bulk analysis of LNCaP DNA.

tag: Normal female genomic DNA isolated from peripheral blood.


title: LNCaP_10cellamplification

source_name: 10 LNCaP cells amplified by ligation mediated PCR

tag: Normal female genomic DNA isolated from peripheral blood. The DNA equivalent to 10  cells was then amplified by  ligation mediated PCR


title: LNCaP_20cellamplification_1


title: Sample ID 1877 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 9, TNM stage T3aM+, and received no hormone therapy.


title: Sample ID 1796 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 8, TNM stage T2cM+, treated by radical retropubic prostatectomy (RRP), and received chemical castration. Bone marrow was collected just prior to RRP.


title: Sample ID 1823 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 7, TNM stage T2a, treated by radical retropubic prostatectomy (RRP), and received chemical castration. Bone marrow was collected just prior to RRP.


title: Sample ID 1865 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 9, TNM stage M+, and was treated by chemical castration. Bone marrow was collected during the course of treatment.


title: Sample ID 1696 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 7, TNM stage T4N1, was treated by radical retropubic prostatectomy (RRP), and received no hormone therapy. Bone marrow was collected just prior to RRP.

tag: Normal female genomic DNA isolated from peripheral blood. The DNA equivalent to 10-20 cells was then amplified by  ligation mediated PCR.


title: Sample ID 1856 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 7, TNM stage T3aN1, treated by radical retropubic prostatectomy (RRP), and received no hormone therapy. Bone marrow was collected just prior to RRP.