title: tympanic membrane_perforated_24hr_group4

city: Perth

first: Peter

middle: Luke

last: Santa Maria

state: WA

address: 2nd floor M Block, QE II Medical Centre, Nedlands

department: Ear Sciences

country: Australia

institute: University of Western Australia

description: Gene expression in rat tympanic membrane 24 hours after perforation with 23 gauge needle

hyb_protocol: Hybridization was performed according to standard protocols for 17 hours.

scan_protocol: Scanning was performed using an Agilent DNA Microarray Scanner and Agilent's Feature Extraction 9.5.3 Software.

data_processing: After the microarray data was compiled by the feature extraction software, further analysis was performed using GeneSpring GX9 (Agilent). One microarray (in the day 6 timepoint) was rejected as it appeared to be an outlier in the quality control metrics plot produced by GeneSpring. Further analysis was carried out by GeneSpring on genes identified as either present or marginal. Genes with statistically different expression (p<0.05) between sequential timepoints were identified using a One Way Anova (analysis of variance) test with the Benjamin and Hochberg multiple testing correction and Tukey Post-hoc test.

source_name: Tympanic Membrane, Perforated, 24hr, group4

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (version 1.0.1) was followed, which included use of Agilent One Colour RNA Spike-In Kit, cDNA synthesis and amplification, and cRNA purification.

extract_protocol: Whenever possible, RNA extraction was completed on the day of tissue collection. If not possible due to time constraints it was extracted as soon as possible. The RNeasy minikit (Qiagen catalog number 74104) was used and the accompanying protocol followed after removing the tubes from liquid nitrogen and removing excess RNA later. All samples were then analysed using a NanoDrop 1000 (Thermoscientific) spectrophotometer to confirm the presence of good quality RNA before sending by overnight courier in dry ice to the Victorian Agribiosciences Centre at the Latrobe University in Bundoora, Victoria. On arrival in Victoria, before proceeding to the pooling stage, samples were again assessed using a NanoDrop 1000 (Thermoscientific) and also an Agilent 2100 Bioanalyzer. The accuracy of the NanoDrop 1000 (Thermoscientific) was first confirmed using 1ug/ul 1kb plus DNA ladder (Invitrogen cat 10787-026). Samples were rejected if they returned an RIN of 6 or less on the Agilent 2100 Bioanalyzer. In cases where the RIN was reported as N/A because of low RNA concentration, the profile was visually inspected and if it contained two obvious peaks similar to other samples in the same timepoint with a passing RIN, these samples also passessed. Samples were randomly pooled into 3 groups (biological replicate groups) per timepoint. There were 18 individuals per timepoint meaning 6 samples were pooled per group. They were pooled so that equal amounts of RNA were taken from each sample. Pooled groups were then assessed using a NanoDrop 1000 (Thermoscientific) and also an Agilent 2100 Bioanalyzer. Pooled groups were rejected using the same criteria as above.

treatment_protocol: Rats were randomly selected as either controls or in the perforation group. Perforations were created unilaterally (left ear) in the upper outer quadrant of the pars tensa of rats’ tympanic membranes using sterile 23 gauge needles by the first author.  Perforations were created while the rat was under general anaesthesia using an inhalational technique with Isoflurane (Oxygen and Isoflurane mixture of approximately 2ml/min Oxygen and 5ml/min (induction) or 2.5ml/min (maintenance) Isoflurane). The tympanic membrane was approached using a 2mm ear speculum using an operating otomicroscope (Zeiss). Before perforation, both ears were examined for signs of inflammation, trauma or disease. No rats were excluded for these reasons.  Rats were then randomly allocated into timepoint groups to be sacrificed at either 12, 24, or 36 hours, or 2, 3, 4, 5, 6, or 7 days.  At the point of microarray, there were 18 rats per timepoint group and 18 controls. A rat was sacrificed at 12, 24, 36 hours and on day 2, 3, 4, 5, 6, 7. Control rats were also sacrificed. Rats were sacrificed under general anaesthesia (technique above) with 2mls of intracardiac pentobarb. The pars tensa of the tympanic membrane was extracted bilaterally immediately after confirmation of death. To extract the pars tensa, first a postauricular incision was made which was extended to include transection of the ear canal at the bony cartilaginous junction. An incision was then made between the skull base and skin of neck anteriorly allowing exsanguination to occur and provide minimal blood in the field. Soft tissue was dissected off the tympanic bulla using a periosteal elevator and canal skin was removed using a round knife. Using curved needles the pars tensa was dissected from the handle of the malleus and the annulus.  Samples were immediately added to tubes containing RNA later and the tubes placed in liquid nitrogen.

tag: time post-perforation

value: 24 hours

tag: number of rats per group

tag: sex

value: male

tag: weight

value: tympanic membrane, pars tensa


title: Human3_PCB126_9

status: Public on Aug 19 2009

type: RNA

city: Niskayuna

first: Erik

middle: A

last: Carlson

state: NY

address: 1 Research Circle

country: USA

institute: General Electric

description: Human donor 3, (ZYZ), IVT Lot MHU-L-0730044, was a 46 year-old African-American male who died from anoxia (http://www.celsis.com/characterisation.html).

hyb_protocol: GeneChips were hybridized according to the standard Affymetrix protocol

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol

data_processing: All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Donor 3, -9logM PCB126

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

growth_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519

tag: Organism

value: Human

tag: Tissue

value: Liver

tag: Gender

value: Male

tag: Age

tag: Chemical

value: PCB 126

tag: Dose


title: Human3_PCB126_6

source_name: Human Donor 3, -6logM PCB126

extract_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519


title: tympanic membrane_perforated_12hr_group5

description: Gene expression in rat tympanic membrane 12 hours after perforation with 23 gauge needle

organism: Rattus norvegicus

source_name: Tympanic Membrane, Perforated, 12hr, group5

value: 12 hours

tag: tissue


title: Rat2_TCDD_11

description: Rat Pool 2, -11logM TCDD

source_name: Rat Pool 2, -11logM TCDD

treatment_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519

value: Sprague Dawley Rats

tag: Strain

value: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA

value: Female

value: TCDD


title: Rat2_PCB126_9

description: Rat Pool 2, -9logM PCB 126

source_name: Rat Pool 2, -9logM PCB 126


title: Human3_PCB126_5

source_name: Human Donor 3, -5logM PCB126


title: tympanic membrane_perforated_72hr_group4

description: Gene expression in rat tympanic membrane 72 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 72hr, group4

value: 72 hours


title: tympanic membrane_perforated_36hr_group4

description: Gene expression in rat tympanic membrane 36 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 36hr, group4

value: 36 hours


title: Human3_TCDD_14

source_name: Human Donor 3, -14logM TCDD


title: tympanic membrane_control_group6

description: Gene expression in rat tympanic membrane without perforation

source_name: Tympanic Membrane, control, group6

value: 0 hours


title: tympanic membrane_perforated_12hr_group4

source_name: Tympanic Membrane, Perforated, 12hr, group4


title: tympanic membrane_control_group4

source_name: Tympanic Membrane, control, group4


title: Human3_TCDD_12

source_name: Human Donor 3, -12logM TCDD


title: tympanic membrane_perforated_144hr_group4

description: Gene expression in rat tympanic membrane 144 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 144hr, group4

value: 144 hours


title: Human3_TCDD_11

source_name: Human Donor 3, -11logM TCDD


title: tympanic membrane_control_group5

source_name: Tympanic Membrane, control, group5


title: tympanic membrane_perforated_168hr_group3

description: Gene expression in rat tympanic membrane 168 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 168hr, group3

value: 168 hours


title: tympanic membrane_perforated_120hr_group4

description: Gene expression in rat tympanic membrane 120 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 120hr, group4

value: 120 hours


title: Human3_TCDD_9

source_name: Human Donor 3, -9logM TCDD


title: Human3_TCDD_8

source_name: Human Donor 3, -8logM TCDD


title: tympanic membrane_perforated_168hr_group2

source_name: Tympanic Membrane, Perforated, 168hr, group2

value: male


title: Human3_TCDD_6.5

source_name: Human Donor 3, -6.5logM TCDD


title: Human3_TCDD_10

source_name: Human Donor 3, -10logM TCDD


title: tympanic membrane_perforated_144hr_group3

source_name: Tympanic Membrane, Perforated, 144hr, group3

value: tympanic membrane, pars tensa


title: Human2_PCB126_12

description: Human donor 2, (RFA), IVT Lot FHU-L-072004, was a 56 year-old Caucasian female who died from a cerebrovascular accident (http://www.celsis.com/characterisation.html).

source_name: Human Donor 2, -12logM PCB126

value: Human


title: Human3_Control_0

source_name: Human Donor 3, vehicle control

value: Liver

value: Vehicle Control (0.5% DMSO)


title: Human2_PCB126_11

source_name: Human Donor 2, -11logM PCB126

value: PCB 126


title: tympanic membrane_perforated_144hr_group1

source_name: Tympanic Membrane, Perforated, 144hr, group1


title: tympanic membrane_perforated_120hr_group3

source_name: Tympanic Membrane, Perforated, 120hr, group3


title: tympanic membrane_perforated_120hr_group2

source_name: Tympanic Membrane, Perforated, 120hr, group2


title: Human2_PCB126_9

source_name: Human Donor 2, -9logM PCB126


title: tympanic membrane_perforated_120hr_group1

source_name: Tympanic Membrane, Perforated, 120hr, group1


title: tympanic membrane_perforated_96hr_group2

description: Gene expression in rat tympanic membrane 96 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 96hr, group2

value: 96 hours


title: Human2_PCB126_8

source_name: Human Donor 2, -8logM PCB126


title: tympanic membrane_perforated_96hr_group3

source_name: Tympanic Membrane, Perforated, 96hr, group3


title: Human2_PCB126_6

source_name: Human Donor 2, -6logM PCB126


title: Human2_TCDD_14

source_name: Human Donor 2, -14logM TCDD


title: Human2_TCDD_12

source_name: Human Donor 2, -12logM TCDD


title: Human2_TCDD_11

source_name: Human Donor 2, -11logM TCDD


title: Human2_PCB126_5

source_name: Human Donor 2, -5logM PCB126


title: tympanic membrane_perforated_96hr_group1

source_name: Tympanic Membrane, Perforated, 96hr, group1


title: tympanic membrane_perforated_72hr_group2

source_name: Tympanic Membrane, Perforated, 72hr, group2


title: tympanic membrane_perforated_72hr_group3

source_name: Tympanic Membrane, Perforated, 72hr, group3


title: Human2_TCDD_10

source_name: Human Donor 2, -10logM TCDD


title: tympanic membrane_perforated_48hr_group2

description: Gene expression in rat tympanic membrane 48 hours after perforation with 23 gauge needle

source_name: Tympanic Membrane, Perforated, 48hr, group2

value: 48 hours


title: Human2_TCDD_9

source_name: Human Donor 2, -9logM TCDD


title: tympanic membrane_perforated_72hr_group1

source_name: Tympanic Membrane, Perforated, 72hr, group1


title: tympanic membrane_perforated_48hr_group1

source_name: Tympanic Membrane, Perforated, 48hr, group1


title: Human2_TCDD_8

source_name: Human Donor 2, -8logM TCDD


title: tympanic membrane_perforated_36hr_group3

source_name: Tympanic Membrane, Perforated, 36hr, group3


title: Human2_Control_0

source_name: Human Donor 2, vehicle control


title: Human1_PCB126_10

description: Human donor 1, (WRG), IVT Lot MHU-L-052004, was a 41 year-old Caucasian male who died from an astrocytoma ( http://www.celsis.com/characterisation.html).

source_name: Human Donor 1, -10logM PCB126

value: Male


title: Human2_TCDD_6.5

source_name: Human Donor 2, -6.5logM TCDD

value: Female


title: Human1_PCB126_12

source_name: Human Donor 1, -12logM PCB126


title: tympanic membrane_perforated_24hr_group2

source_name: Tympanic Membrane, Perforated, 24hr, group2

value: 24 hours


title: tympanic membrane_perforated_36hr_group1

source_name: Tympanic Membrane, Perforated, 36hr, group1


title: Human1_PCB126_8

source_name: Human Donor 1, -8logM PCB126


title: tympanic membrane_perforated_24hr_group1

source_name: Tympanic Membrane, Perforated, 24hr, group1


title: tympanic membrane_perforated_12hr_group3

source_name: Tympanic Membrane, Perforated, 12hr, group3

value: 12 hours


title: Human1_PCB126_5

source_name: Human Donor 1, -5logM PCB126


title: Human1_PCB126_6

source_name: Human Donor 1, -6logM PCB126


title: tympanic membrane_perforated_24hr_group3

source_name: Tympanic Membrane, Perforated, 24hr, group3


title: tympanic membrane_perforated_12hr_group2

source_name: Tympanic Membrane, Perforated, 12hr, group2


title: tympanic membrane_perforated_12hr_group1

source_name: Tympanic Membrane, Perforated, 12hr, group1


title: tympanic membrane_control_group3

source_name: Tympanic Membrane, control, group3


title: Human1_TCDD_12

source_name: Human Donor 1, -12logM TCDD

value: TCDD


title: Human1_TCDD_8

source_name: Human Donor 1, -8logM TCDD


title: tympanic membrane_control_group2

source_name: Tympanic Membrane, control, group2

value: 0 hours


title: Human1_TCDD_14

source_name: Human Donor 1, -14logM TCDD


title: Human1_TCDD_10

source_name: Human Donor 1, -10logM TCDD


title: tympanic membrane_control_group1

source_name: Tympanic Membrane, control, group1


title: Human1_TCDD_6.5

source_name: Human Donor 1, -6.5logM TCDD


title: tympanic membrane_perforated_144hr_group2

source_name: Tympanic Membrane, Perforated, 144hr, group2

value: 144 hours


title: Human1_Control_0

source_name: Human Donor 1, vehicle control


title: Ricin Sham_96h_3

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

description: no additional information

hyb_protocol: Test and control RNA was resuspended in 250ul of hybridisation buffer supplied by the microarray slide manufacturer (MWG Biotech, Ebersberg, Germany). Slides were hybridised overnight in hybridisation chambers (Qiagen, Crawley, West Sussex) for 16 hours at 42C in the dark and then washed in 3 different wash buffers for 5 minutes each wash. Wash buffer 1 consisted of 2 x SSC (buffered solution of sodium chloride and trisodium citrate), 0.1% SDS (Sigma, Poole), wash buffer 2 consisted of 1 x SSC and wash buffer 3 consisted of 0.5% SSC. All wash buffers were filter sterilised to prevent contaminating debris. The slides were dried by centrifugation at 500 x g for 5 minutes.

scan_protocol: Scanning was performed using a 428 nm scanner (GenePix 4000B, Axon, US) using the appropriate gain settings and filters for the Cy3 and Cy5 dyes (Cy3 = 532nm, 17mW, Cy5 = 635nm, 10mW).

data_processing: Image analysis was carried out using BlueFuse image analysis software (BlueGnome, Cambridge, UK). Statistical analysis of the array data was performed using GeneSpring software, version GX7.3 (Agilent Technologies, Berks, UK). Data were normalised using a Lowess curve fit to log-intensity versus log ratio plot, where 20% of the data were used for the Lowess normalisation. Agent data were then normalised to the respective sham time-matched control expression level for every spot on the chip (1509) using the “normalise to specific sample” algorithm within GeneSpring version GX7.3 (i.e. 24 hour ricin normalised to 24 hour sham).

organism: Mus musculus

label_protocol: RNA was labelled using the LabelStar Array Kit (Qiagen, Crawley, West Sussex, UK). 3mg of test RNA (ricin or sham exposed) was labelled with Cyanine 3-dNTP (Cy3) (Ambion, Cambridgeshire, UK) and 3mg of universal mouse reference RNA (Stratagene Europe, Netherlands) labelled with Cyanine 5-dNTP (Cy5) (Ambion, Cambridgeshire, UK).

extract_protocol: Total RNA was extracted from each of the six lung tissue samples, after homogenisation with a rotor stator homogeniser, using the RNeasy Mini Kit (Qiagen, Crawley, West Sussex, UK) following the manufacturer’s protocol.

treatment_protocol: Ricin or PBS aerosol exposure

tag: strain

value: Balb/c

tag: gender

value: Lung

tag: agent

value: Sham (PBS)

tag: time

source_name: Stratagene Universal Reference RNA

tag: cell line

value: Mixture of 11 cell lines


title: Ricin_96h_2

description: no additional information

value: Ricin


title: Ricin Sham_96h_2

description: no additional information


title: Jurkat Postactivation 12hr Transcriptome rep3

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

description:
Total mRNA
Biological Replicate 3 of 3. Tranacriptome IP. 12hr Postactivation

hyb_protocol: Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems).

scan_protocol: Arrays were scanned on a GenePix 4000B microarray scanner (Axon Instruments).

data_processing: All arrays were subject to loess normalization within each array and scale normalization across all arrays using the Array Magic package in R. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates. In order to be considered for subsequent analysis, a probe had to be twofold above local background in all three biological replicates for any of the RIPs or the totals at any time point.

molecule: polyA RNA

label_protocol: RNA from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, Jurkat derived RNA samples were labeled with Cy3 and reference samples were labeled with Cy5.

growth_protocol: Human acute T cell leukemia Jurkat cells were cultured in RPMI 1640 supplemented with 10% FBS (GIBCO/BRL).

extract_protocol: RIPs utilized 100 μL pre-swollen and packed Protein-A Sepharose beads (Sigma) loaded with 30 μg of anti-HuR (3A2), anti-PABP, IgG1 (BD PharMingen) or normal rabbit sera immunoglobulin.  Antibody loaded beads were incubated with 3 mg (total protein) cell lysate for four hours at 4ºC, washed 4 times with ice-cold NT2 buffer (50mM Tris pH 7.4/150mM NaCl/1 mM MgCl2/0.05% Nonidet P-40) followed by 3 washes with ice-cold NT2 supplemented with 1M Urea. Extraction of associated RNA was performed as described, and total RNA was isolated using the Trizol reagent (Invitrogen).

treatment_protocol: Mitogenic activation: cells were cultured in the presence of 50 ng/ml PMA and 2 μg/ml PHA (Calbiochem/EMD).

tag: Jurkat Cells 12hr Postactivation with PMA and PHA, Transcriptome

source_name: Reference mRNA

tag: Reference mRNA from Stratagene


title: Jurkat Postactivation 4hr Transcriptome rep1

description:
Total mRNA
Biological Replicate 1 of 3. Tranacriptome IP. 4hr Postactivation

tag: Jurkat Cells 4hr Postactivation with PMA and PHA, Transcriptome


title: Jurkat Postactivation 0hr Transcriptome rep3

description:
Total mRNA
Biological Replicate 3 of 3. Tranacriptome IP. 0hr Postactivation

tag: Jurkat Cells 0hr Postactivation with PMA and PHA, Transcriptome


title: tympanic membrane_perforated_168hr_group1

source_name: Tympanic Membrane, Perforated, 168hr, group1

tag: time post-perforation

value: 168 hours

tag: number of rats per group

tag: sex

value: male

tag: weight

value: tympanic membrane, pars tensa


title: tympanic membrane_perforated_36hr_group2

source_name: Tympanic Membrane, Perforated, 36hr, group2

value: 36 hours


title: tympanic membrane_perforated_48hr_group3

source_name: Tympanic Membrane, Perforated, 48hr, group3

value: 48 hours


title: Ricin_96h_1

description: no additional information


title: Jurkat Postactivation 4hr Transcriptome rep2

description:
Total mRNA
Biological Replicate 2 of 3. Tranacriptome IP. 4hr Postactivation

source_name: Jurkat Cells 4hr Postactivation with PMA and PHA


title: Jurkat Postactivation 0hr Transcriptome rep2

description:
Total mRNA
Biological Replicate 2 of 3. Tranacriptome IP. 0hr Postactivation

source_name: Jurkat Cells 0hr Postactivation with PMA and PHA


title: Jurkat Postactivation 12hr Transcriptome rep2

description:
Total mRNA
Biological Replicate 2 of 3. Tranacriptome IP. 12hr Postactivation

source_name: Jurkat Cells 12hr Postactivation with PMA and PHA


title: Ricin_96h_3

description: no additional information


title: Jurkat Postactivation 12hr Transcriptome rep1

description:
Total mRNA
Biological Replicate 1 of 3. Tranacriptome IP. 12hr Postactivation


title: Jurkat Postactivation 0hr Transcriptome rep1

description:
Total mRNA
Biological Replicate 1 of 3. Tranacriptome IP. 0hr Postactivation


title: Jurkat Postactivation 12hr NEG-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. Neg IP. 12hr Postactivation

tag: Jurkat Cells 12hr Postactivation with PMA and PHA, NEG IP


title: Ricin Sham_96h_1

description: no additional information


title: Jurkat Postactivation 4hr Transcriptome rep3

description:
Total mRNA
Biological Replicate 3 of 3. Tranacriptome IP. 4hr Postactivation


title: 2f_Healthy swine_2006

status: Public on Aug 29 2009

type: genomic

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

description: 2f_Healthy swine_2006

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42oC using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 05ZYH33 and from each test SS2 strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.

molecule: genomic DNA

organism: Streptococcus suis

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for Suis test strains and Cy5 for reference strain 05ZYH33) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)

growth_protocol: Cells were cultured in Todd-Hewitt broth (THB)(Difco Laboratories, Detroit, MI) medium.

extract_protocol: Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)

tag: origin

value: Jiangsu, China

tag: pathogenicity

value: Avirulent

source_name: Reference DNA from 05ZYH33

value: Virulent


title: Jurkat Postactivation 12hr NEG-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. Neg IP. 12hr Postactivation


title: Jurkat Postactivation 4hr NEG-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. Neg IP. 4hr Postactivation

tag: Jurkat Cells 4hr Postactivation with PMA and PHA, NEG IP


title: Ricin_7h_4

description: no additional information

tag: strain

value: Female

tag: tissue


title: Ricin_7h_2

description: no additional information

tag: gender

tag: agent


title: Ricin Sham_7h_3

description: no additional information

tag: time

tag: cell line


title: Jurkat Postactivation 12hr NEG-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. Neg IP. 12hr Postactivation

tag: Reference mRNA from Stratagene


title: Jurkat Postactivation 0hr NEG-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. Neg IP. 0hr Postactivation

tag: Jurkat Cells 0hr Postactivation with PMA and PHA, NEG IP


title: Ricin Sham_7h_2

description: no additional information


title: Ricin_7h_3

description: no additional information


title: Jurkat Postactivation 4hr NEG-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. Neg IP. 4hr Postactivation


title: Ricin Sham_4h_3

description: no additional information


title: Jurkat Postactivation 0hr NEG-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. Neg IP. 0hr Postactivation


title: Jurkat Postactivation 0hr NEG-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. Neg IP. 0hr Postactivation


title: Jurkat Postactivation 12hr PABP-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. PABP IP. 12hr Postactivation

tag: Jurkat Cells 12hr Postactivation with PMA and PHA, PABP IP


title: Jurkat Postactivation 4hr PABP-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. PABP IP. 4hr Postactivation

tag: Jurkat Cells 4hr Postactivation with PMA and PHA, PABP IP


title: Jurkat Postactivation 4hr NEG-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. Neg IP. 4hr Postactivation


title: Ricin Sham_7h_1

description: no additional information


title: Jurkat Postactivation 12hr PABP-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. PABP IP. 12hr Postactivation


title: Jurkat Postactivation 4hr PABP-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. PABP IP. 4hr Postactivation


title: Jurkat Postactivation 12hr PABP-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. PABP IP. 12hr Postactivation


title: Jurkat Postactivation 4hr PABP-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. PABP IP. 4hr Postactivation


title: Ricin Sham_4h_2

description: no additional information


title: Jurkat Postactivation 0hr PABP-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. PABP IP. 0hr Postactivation

tag: Jurkat Cells 0hr Postactivation with PMA and PHA, PABP IP


title: Jurkat Postactivation 0hr PABP-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. PABP IP. 0hr Postactivation


title: Ricin Sham_4h_1

description: no additional information


title: Ricin_4h_4

description: no additional information


title: Jurkat Postactivation 12hr HuR-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. HuR IP. 12hr Postactivation

tag: Jurkat Cells 12hr Postactivation with PMA and PHA, HuR IP


title: Jurkat Postactivation 0hr PABP-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. PABP IP. 0hr Postactivation


title: Jurkat Postactivation 12hr HuR-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. HuR IP. 12hr Postactivation


title: Jurkat Postactivation 4hr HuR-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. HuR IP. 4hr Postactivation

tag: Jurkat Cells 4hr Postactivation with PMA and PHA, HuR IP


title: Ricin_4h_3

description: no additional information


title: Jurkat Postactivation 0hr HuR-IP rep2

description:
Immunoprecipitated mRNA
Biological Replicate 2 of 3. HuR IP. 0hr Postactivation

tag: Jurkat Cells 0hr Postactivation with PMA and PHA, HuR IP


title: Jurkat Postactivation 12hr HuR-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. HuR IP. 12hr Postactivation


title: Ricin_4h_2

description: no additional information


title: Jurkat Postactivation 0hr HuR-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. HuR IP. 0hr Postactivation


title: Ricin Sham_48h_3

description: no additional information


title: Jurkat Postactivation 4hr HuR-IP rep3

description:
Immunoprecipitated mRNA
Biological Replicate 3 of 3. HuR IP. 4hr Postactivation


title: Ricin_48h_3

description: no additional information


title: Jurkat Postactivation 4hr HuR-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. HuR IP. 4hr Postactivation


title: Ricin Sham_48h_2

description: no additional information


title: Ricin_48h_2

description: no additional information


title: Ricin_48h_1

description: no additional information


title: Jurkat Postactivation 0hr HuR-IP rep1

description:
Immunoprecipitated mRNA
Biological Replicate 1 of 3. HuR IP. 0hr Postactivation


title: Ricin Sham_48h_1

description: no additional information


title: Gallus gallus bursal IFE_rep1

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description: Bursa of Fablicius was dissected from the rectum and soaked in Hank's Buffered Salt Solution (HBSS) (GIBCO) containing black ink for 5 min at room temperature to visualize FAE. After incubation, the tissue was treated with 40 mM EDTA/25 mM Hepes (pH 7.4) in HBSS for 5min at room temperature to collect bursal FAE or 30 min at 37ºC for bursal IFE. Bursal FAE and IFE were collected with a fine 29G needle under stereomicroscope monitoring.

hyb_protocol: Affymetrix standard procedures

scan_protocol: using GeneChip Scanner 3000

data_processing: Raw signals are from MAS5. Normalized data from GeneSpring 7.3.1.

organism: Gallus gallus

source_name: bursal FAE

label_protocol: Two-Cycle Target Labeling and Control Reagents

extract_protocol: Total RNA extracted with commercial kit.

tag: source type

value: isolated cell

tag: organism part

value: bursa of Fablicius

tag: cell type

value: interfollicular epithelium

tag: strain[background]

value: Line-M

tag: developmental stage

value: chick

tag: age

value: 19 days

tag: microbial condition

value: SPF

tag: disease state

value: healthy


title: Gallus gallus bursal IFE_rep2


title: Ricin_24h_3

description: no additional information

tag: strain

value: Balb/c

tag: gender

tag: tissue

value: Lung

tag: agent

value: Ricin

tag: time

tag: cell line

value: Mixture of 11 cell lines


title: Gallus gallus bursal FAE_rep1

value: follicle-associated epithelium


title: Gallus gallus bursal FAE_rep2


title: Pod-Cre, PTIP-, rep6

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

institute: University of Michigan

hyb_protocol: 10 ug of cRNA was hybridized for 16h at 46oC. Washing and staining were performed using the Affymetrix fluidics staion 400.

scan_protocol: Affymetrix scanner 3000 was used to scan arrays.

data_processing: The data were analyzed using the limma and affy bioconductor packages implemented in the R statistical programming environment. Normalization was done using RMA.

source_name: kidney

label_protocol: Biotinylated UTP and CTP were used as specified by Affymetrix in standard protocols.

growth_protocol: Mice were raised in approved housing and fed 5008 chow after weaning. Light-dark cycles were 12h each. Mice were euthanized by CO2 inhalation at 4 weeks of age.

extract_protocol: Kidneys were dissected free, encapsulated and washed in PBS. Tissue was homogneized using a fresh razor blade until a consistent pulp was achieved. Homgenate was pushed through a 91 micron nylon mesh. Glomeruli were then captured on a 41 micron nylon mesh and washed with PBS. RNA was isolated using the RNeasy Tissue Micro Kit (Qiagen, Valencia, CA) as recommended by the manufacturer.

value: kidney

value: glomerulus

value: 14 month old

tag: genome/variation

value: Pod-Cre, PTIP-


title: Pod-Cre, PTIP-, rep10

value: 18 month old


title: Pod-Cre, PTIP-, rep9

value: 17 month old


title: Pod-Cre, PTIP-, rep7

value: 15 month old


title: Ricin Sham_24h_3

description: no additional information

value: Female

value: Sham (PBS)


title: Pod-Cre, PTIP-, rep3

value: 11 month old


title: Pod-Cre, PTIP-, rep1

value: 9 month old


title: Pod-Cre, PTIP-, rep8

value: 16 month old


title: Pod-Cre, PTIP-, rep5

value: 13 month old


title: Ricin_24h_2

description: no additional information

value: Balb/c

value: Lung


title: Ricin Sham_24h_2

description: no additional information

value: Mixture of 11 cell lines


title: wild-type, PTIP+, rep6

value: 6 month old

value: wild type, PTIP+


title: wild-type, PTIP+, rep8

value: kidney

value: glomerulus

value: 8 month old


title: wild-type, PTIP+, rep7

value: 7 month old


title: Ricin Sham_24h_1

description: no additional information


title: Ricin_1h_3

description: no additional information

value: Ricin


title: PLX4720 24 hr

city: London

first: Leisl

middle: M

last: Packer

address: 237 Fulham Rd

department: Cell and molecular biology

institute: Institute of Cancer Research

description: A375P melanoma cells treated with PLX4720 for 24 hours

hyb_protocol: See detailed protocol in WT_sense_target_prep_v2.0_1ug.pdf at The Paterson Institute Microarray Service website of The Paterson Institute of Cancer Research

data_processing: We background corrected and quantile normalised probe level signals  and generated core and extended gene level signal estimates using  robust multi-array average (RMA) (Irizarry et al., 2003) implemented  in APT version 1.10.0 from Affymetrix (switch '-a rma'). Gene-level analysis of the probesets was performed. This process  was carried out for the inhibitor treatment and BRAF siRNA groups  separately. In the case of the BRAF/MEK inhibition experiment, we  removed genes with a coefficient of variance of less than or equal to  0.05 from further analysis. We setup contrasts of drug treatment    (PD184352 and PLX4720) verses DMSO control for each time point (2, 6,  and 24 hours). A linear model was fitted to the data and F-statistics    moderated by empirical Bayes shrinkage of the standard errors towards  a common value. We identified contrast specific inhibitor dependent    effects on expression using a nested F selection procedure with a 0.05  false discovery rate (FDR) threshold. We identified genes differential    in both treatment groups at 6 and 24 hours. These 56 genes are  presented in the accompanying heatmap. The analysis was carried out    using Limma from Bioconductor (Gentleman et al., 2004) version 2.16.2  running within R version 2.8.0.

source_name: A375P melanoma cells

growth_protocol: A375P cells were grown in DMEM supplemented with 10% FBS, penicillin, streptomycin.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit with on-column Dnase treatment.

treatment_protocol: Cells were plated at 6x105 cells per 10cm dish. Cells were treated with DMSO, 1uM PD184352 or 0.4uM PLX4720 for 2, 6, or 24 hours.

tag: treatment

tag: timepoint


title: Ricin_24h_1

description: no additional information


title: wild-type, PTIP+, rep5

value: 5 month old


title: Pod-Cre, PTIP-, rep4

value: 12 month old

value: Pod-Cre, PTIP-


title: wild-type, PTIP+, rep3

value: 3 month old


title: PLX4720 6 hr

description: A375P melanoma cells treated with PLX4720 for 6 hours

scan_protocol: See detailed protocol in WT_sense_target_prep_v2.0_1ug.pdf at The Paterson Institute Microarray Service website of The Paterson Institute of Cancer Research


title: PLX4720 2 hr

description: A375P melanoma cells treated with PLX4720 for 2 hours

label_protocol: See detailed protocol in WT_sense_target_prep_v2.0_1ug.pdf at The Paterson Institute Microarray Service website of The Paterson Institute of Cancer Research


title: wild-type, PTIP+, rep4

value: 4 month old


title: PD184352 24 hr

description: A375P melanoma cells treated with PD184352 for 24 hours


title: wild-type, PTIP+, rep1

value: 1 month old


title: Ricin_1h_4

description: no additional information

value: Female


title: PD184352 6 hr

description: A375P melanoma cells treated with PD184352 for 6 hours


title: Ricin Sham_1h_3

description: no additional information

value: Balb/c

value: Sham (PBS)


title: Ricin_1h_2

description: no additional information

value: Lung

value: Mixture of 11 cell lines


title: mouse dendritic cells treated with anti-DC-HIL mAb, 2

city: Dallas

first: Kiyoshi

last: Ariizumi

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern Medical Center

description: cDNA prepared from mRNA of mouse dendritic cells treated with anti-DC-HIL mAb

hyb_protocol: The GeneFilters were prehybridized for 2 h at 60 C with GEAhyb hybridization solution (SuperArray) and added 4 mg of biotin-labeled cDNA in 2 ml of GEAhyb hybridization solution and then hybridized for 15 h at 60 C, hyridization signals were then detected using chemiluminescent detection kit.

scan_protocol: The raw data were scaled in individual hybridization intensities. Image acquisition were performed by ImageQuant 400 (GE Healthcare).

data_processing: Analysis of data were performed by ImageQuant 400 (GE Healthcare). The raw data were scaled in individual hybridization intensities. Normalized signal intensity using GAPDH.

label_protocol: 2 mg of total RNA was reverse-transcribed using biotinylated 16-UTP (Roche Applied Science) and  the GeneBiotin-labeled cDNA probes were prepared using the TrueLabeling-AMPTM 2.0 kit (SuperArray), according to the manufacturer’s recommendations.

growth_protocol: Bone marrow-derived dendritic cells (BM-DC) were cultured in 96-well plate (1 x 105 cells/well).

extract_protocol: After 6 h of culture at 37 C, total RNA was isolated from treated cells (1 x 106) using ArrayGrade total RNA isolation kit (SuperArray).

treatment_protocol: BM-DC were cross-linked with UTX-103 mAb or control IgG (20 mg/ml).

value: dendritic cells

value: anti-DC-HIL mAb


title: PD184352 2 hr

description: A375P melanoma cells treated with PD184352 for 2 hours


title: Pod-Cre, PTIP-, rep2

value: kidney

value: glomerulus

value: 10 month old


title: DMSO 24 hr

description: A375P melanoma cells treated with DMSO control for 24 hours

value: DMSO


description: cDNA prepared from mRNA of mouse dendritic cells treated with control IgG

value: control IgG


title: mouse dendritic cells treated with anti-DC-HIL mAb, 1

source_name: cDNA prepared from mRNA of mouse dendritic cells treated with anti-DC-HIL mAb


title: Ricin Sham_1h_2

description: no additional information


description: cDNA prepared from mRNA of mouse dendritic cells treated with anti-DC-HIL mAb or control IgG

source_name: cDNA prepared from mRNA of mouse dendritic cells treated with control IgG and anti-DC-HIL mAb

label_protocol: 2 microgram of total RNA was reverse-transcribed using biotinylated 16-UTP (Roche Applied Science) and  the GeneBiotin-labeled cDNA probes were prepared using the TrueLabeling-AMPTM 2.0 kit (SuperArray), according to the manufacturer’s recommendations.

growth_protocol: Bone marrow-derived dendritic cells were cultured in 96-well plate (1 x 105 cells/well).

treatment_protocol: Bone marrow-derived dendritic cells were cross-linked with UTX-103 anti-DC-HIL mAb or control IgG (20 microgram/ml).

tag: agents

value: control IgG and anti-DC-HIL mAb


title: Ricin Sham_1h_1

description: no additional information


title: Lung, 9 days post Ganciclovir, Replicate 4

status: Public on Aug 18 2009

first: Barry

middle: R

last: Stripp

address: 106 Research Drive, DUMC Box 103000

department: Medicine

description:
Replicate 4 of 4.
GCV10_169

hyb_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.

data_processing: Raw data were log2 transformed and normalized by the geometric mean across all groups.

source_name: left lung, 9d post Ganciclovir

extract_protocol: Phenol Chloroform (Chomczynski and sacchi 1987).

treatment_protocol: RNA from Control (N = 4) or mice exposed to Naphthalene and recovered for 1, 2, 3, or 6 days (N = 4 per timepoint), in addition to mice expressing HSV-tk under the control of the mouse CCSP promoter, exposed to GCV, and recovered for 3, 6, or 9 days (N = 4 per timepoint), was isolated and used for screening Codelink Mouse 20K Bioarrays.  More details can be found in the published manuscripts (PMIDs:  18978301 and 18757308).

value: CCtk (+) FVB/N

value: lung

value: male

value: adult

value: Ganciclovir

tag: treatment time

value: 9 days


title: Lung, 9 days post Ganciclovir, Replicate 2

description:
Replicate 2 of 4.
GCV10_166

scan_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.


title: Lung, 6 days post Ganciclovir, Replicate 4

description:
Replicate 4 of 4.
GCV6_163

source_name: left lung, 6d post Ganciclovir

label_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.

value: 6 days


title: Lung, 3 days post Ganciclovir, Replicate 3

description:
Replicate 3 of 4.
GCV3_158

source_name: left lung, 3d post Ganciclovir

value: 3 days


title: Lung, 6 days post Ganciclovir, Replicate 3

description:
Replicate 3 of 4.
GCV6_162


title: Lung, 9 days post Ganciclovir, Replicate 1

description:
Replicate 1 of 4.
GCV10_165


title: Lung, 9 days post Ganciclovir, Replicate 3

description:
Replicate 3 of 4.
GCV10_168


title: DMSO 2 hr

description: A375P melanoma cells treated with DMSO control for 2 hours


title: Lung, 3 days post Ganciclovir, Replicate 4

description:
Replicate 4 of 4.
GCV3_159


title: Lung, 3 days post Ganciclovir, Replicate 2

description:
Replicate 2 of 4.
GCV3_157


title: DMSO 6 hr

description: A375P melanoma cells treated with DMSO control for 6 hours


title: Lung, 6 days post Ganciclovir, Replicate 2

description:
Replicate 2 of 4.
GCV6_161


title: Lung, 3 days post Ganciclovir, Replicate 1

description:
Replicate 1 of 4.
GCV3_156


title: Lung, 6 days post Ganciclovir, Replicate 1

description:
Replicate 1 of 4.
GCV6_160


title: Lung, 6 days post naphthalene, Replicate 4

description:
Replicate 4 of 4.
N6_154

source_name: left lung, 6d post naphthalene

value: FVB/N

value: naphthalene


title: Lung, 6 days post naphthalene, Replicate 3

description:
Replicate 3 of 4.
N6_153


title: shRNA-TAK1-2 (HuT-102 cells + shRNA-TAK1)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: HuT-102 cells, a human cutaneous T cell lymphoma, were stably transfected with shRNA expression vectors against human MAP3K7 (TAK1) or firefly luciferase (Luc). HuT-102 cells stably transfected with pSUPER-gfp+neo (firefly luciferase) served as a control. HuT-102 cells stably transfected with pSUPER-gfp+neo (human MAP3K7) were server as shRNA-TAK1. The cells were maintained in media containing 0.5 mg/ml G418. For the experiment, the cells were incubated in media without G418 for 36 h at 37°C.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed, and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: Human cutaneous T cell lymphoma HuT-102 cells, shRNA-TAK1

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: cell type

value: human cutaneous T cell lymphoma cells

tag: transfection vector

value: shRNA expression vector against TAK1


title: Control-2 (HuT-102 cells + vector only)

source_name: Human cutaneous T cell lymphoma HuT-102 cells, vector control

value: shRNA expression vector against Luc


title: shRNA-TAK1-1 (HuT-102 cells + shRNA-TAK1)


title: Control-1 (HuT-102 cells + vector only)


title: Lung, 6 days post naphthalene, Replicate 2

description:
Replicate 2 of 4.
N6_152

tag: developmental stage


title: Lung, 3 days post naphthalene, Replicate 3

description:
Replicate 3 of 4.
N3_148

source_name: left lung, 3d post naphthalene


title: Lung, 6 days post naphthalene, Replicate 1

description:
Replicate 1 of 4.
N6_150


title: Lung, 3 days post naphthalene, Replicate 1

description:
Replicate 1 of 4.
N3_145


title: MCF7_siER24h_array1

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  siRNA for ERα at 20 nM, and incubated for 24h.

hyb_protocol: 1.5 µg each cRNA sample was hybridized to Illumina’s Sentrix Human-6 V2 Epression Bead Chips at 58 °C overnight (19 h) according to Illumina 11225598_WGGEX_IntelliHyb_Seal_SystemManual_RevA.pdf.

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%).

data_processing: The numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction. The data was preprocessed by Bioconductor lumi package (version 1.8.3). It was vst transformed and quantile normalized.

source_name: MCF-7 cells

label_protocol: Illumina Total Prep RNA Amplification kit (Ambion). In vitro transcription reaction overnight (14h) and during it cRNA was biotinylated. The cRNA concentrations where checked with Nanodrop ND-1000 and cRNA quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: MCF-7 cells were grown at normal growth conditions.

extract_protocol: The total cellular RNAs were isolated with MiRVana™ total RNA isolation kit (Ambion).

tag: atcc® number

tag: designations

value: Female

tag: growth properties

value: adherent

tag: morphology

value: epithelial

tag: organ

value: mammary gland; breast

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion


title: MCF7_scramble24h_array2

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  Ambion pre-miR™ negative control #1 (scrambled pre-miR) at 20 nM, and incubated for 24h.

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with Ambion pre-miR™ negative control #1 (scrambled pre-miR) at 20 nM, and incubated for 24h.

tag: gender


title: MCF7_20624h_array2

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  Ambion pre-miR™ construct for miR-206 at 20 nM, and incubated for 24h.

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with Ambion pre-miR™ construct for miR-206 at 20 nM, and incubated for 24h.


title: MCF7_302c24h_array2

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  Ambion pre-miR™ construct for miR-302c at 20 nM, and incubated for 24h.

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with Ambion pre-miR™ construct for miR-302c at 20 nM, and incubated for 24h.


title: Lung, 2 days post naphthalene, Replicate 4

description:
Replicate 4 of 4.
N2_144

source_name: left lung, 2d post naphthalene

tag: strain

tag: tissue

value: lung

value: male

tag: agent

value: 2 days


title: Lung, 3 days post naphthalene, Replicate 4

description:
Replicate 4 of 4.
N3_149

value: adult


title: MCF7_scramble24h_array1


title: MCF7_302c24h_array1


title: Lung, 2 days post naphthalene, Replicate 1

description:
Replicate 1 of 4.
N2_140


title: Lung, 2 days post naphthalene, Replicate 3

description:
Replicate 3 of 4.
N2_143


title: MCF7_193b24h_array2

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  Ambion pre-miR™ construct for miR-193b at 20 nM, and incubated for 24h.

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with Ambion pre-miR™ construct for miR-193b at 20 nM, and incubated for 24h.


title: MCF7_193b24h_array1


title: wild-type, PTIP+, rep2

value: kidney

value: glomerulus

value: 2 month old

tag: genome/variation

value: wild type, PTIP+


title: Lung, 1 day post naphthalene, Replicate 4

description:
Replicate 4 of 4.
N1_139

source_name: left lung, 1d post naphthalene

value: FVB/N

value: naphthalene

value: 1 day


title: Lung, 1 day post naphthalene, Replicate 3

description:
Replicate 3 of 4.
N1_138


title: Lung, 1 day post naphthalene, Replicate 1

description:
Replicate 1 of 4.
N1_136


title: Lung, 1 day post naphthalene, Replicate 2

description:
Replicate 2 of 4.
N1_137


title: Cow #2829, right rear mammary gland, gland cistern, E. coli 12 hr

city: Beltsville

first: Anthony

middle: V.

last: Capuco

state: MD

address: 10300 Baltimore Ave., Bldg 200, Rm 14

department: Beltsville Agricultural Research Center

institute: USDA-ARS

description:
Mammary gland of lactating cow was infused with 400 CFU of E. coli (P4 isotype) suspended in 4 ml of phosphate-buffered saline 12 hr prior to euthanasia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.

hyb_protocol: single dye

scan_protocol: Axon GenePix 4000B at 5 um resolution

data_processing: The data presented are average fluorescence intensity from either 4 or 8 perfect match oligos that represent a single unique sequence.  These data are usually log transformed and subject to quantile normalization method using the R package before analyzed.  See Li & Li, BMC Genomics 2006, 7:234.

organism: Bos taurus

label_protocol: incorporation

extract_protocol: Trizol followed by DNase digestion and Qiagen RNeasy purification.

tag: breed

value: Holstein

value: right rear mammary gland, gland cistern


title: Lung, Control, Replicate 2

description:
Replicate 2 of 4.
C_172

source_name: left lung, control


title: Lung, Control, Replicate 3

description:
Replicate 3 of 4.
C_173


title: MCF7_18a24h_array2

description: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an  Ambion pre-miR™ construct for miR-18a at 20 nM, and incubated for 24h.

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with Ambion pre-miR™ construct for miR-18a at 20 nM, and incubated for 24h.

value: Female

value: adherent

value: epithelial


title: Lung, 2 days post naphthalene, Replicate 2

description:
Replicate 2 of 4.
N2_142

tag: treatment time


title: Lung, Control, Replicate 1

description:
Replicate 1 of 4.
C_171


title: Lung, Control, Replicate 4

description:
Replicate 4 of 4.
C_174


title: Cow #2829, right front mammary gland, Furstenburg's rosette, E. coli 24 hr

description:
Mammary gland of lactating cow was infused with 400 CFU of E. coli (P4 isotype) suspended in 4 ml of phosphate-buffered saline 24 hr prior to euthanasia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.


title: Cow #2829, right rear mammary gland, lobuloalveolar, E. coli 12 hr


title: Cow #2829, right rear mammary gland, teat cistern, E. coli 12  hr

value: right rear mammary gland, teat cistern


title: Lung, 3 days post naphthalene, Replicate 2

description:
Replicate 2 of 4.
N3_147

value: lung

value: 3 days


title: Cow #2829, right front mammary gland, teat cistern, E. coli 24 hr

value: right front mammary gland, teat cistern


title: MCF7_siER24h_array2

treatment_protocol: MCF-7 cells (300 000 per well on 6-well plates) were transfected with an siRNA for ERα at 20 nM, and incubated for 24h.

value: mammary gland; breast

value: adenocarcinoma

value: pleural effusion

tag: cell type


title: RAD4 30 min rep1

city: Charlottesville

first: Kunal

last: Poorey

state: VA

address: 1340 Jefferson Park Avenue

department: Biomedical Sciences: Biochemistry, Molecular Biology & Genetics

institute: University of Virginia Health System

description: Gene expression data for rad4Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

hyb_protocol: Hybridization of labelled, fragmented cRNA to Affymetrix Yeast Genome 2.0 arrays was performed using Affymetrix GeneChip reagents according to the manufacturer's instructions.

scan_protocol: Scanning was done on the Affymetrix GeneChip System according to the manufacturer's instructions.

data_processing: The data was quantile normalized and expression estimates were generated using the Bioconductor GCRMA (version 2.10.0) package in R (version 2.6.2).

organism: Saccharomyces cerevisiae

source_name: rad4Δ cells 30 minutes after irradiation

label_protocol: cDNA synthesis, cRNA synthesis, biotin labelling and fragmentation were performed using Affymetrix GeneChip reagents according to the manufacturer's instructions.

growth_protocol: Cells were grown overnight in liquid YPD with shaking at 30ºC to an OD600 = 1.0.

extract_protocol: Total RNA was extracted using a hot acid phenol method followed by sodium acetate/ethanol precipitation.

treatment_protocol: Cells were briefly resuspended in water and irradiated (or mock treated for unirradiated samples) with 100 J/m2 UV-C light with a Stratalinker 1800 (Stratagene). Cells were then resuspended in fresh YPD and allowed to recover for the indicated times by incubation with shaking at 30ºC.

tag: strain background

tag: genotype


title: RAD4 60 min rep1

description: Gene expression data for rad4Δ yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: rad4Δ cells 60 minutes after irradiation


title: RAD4 60 min rep2


title: Cow #2829, left front mammary gland, Furstenburg's rosette, PBS 24 hr

description:
Mammary gland of lactating cow was infused with 4 ml of phosphate-buffered saline 24 hr prior to euthanzia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.


title: RAD4 ND rep1

description: Gene expression data for log-phase rad4Δ yeast cells

source_name: rad4Δ cells prior to irradiation


title: Cow #2829, left front mammary gland, gland cistern, PBS 24 hr

value: left front mammary gland, gland cistern


title: Cow #2829, right front mammary gland, gland cistern, E. coli 24 hr


title: Cow #2661, left front mammary gland, teat cistern, E. coli 12 hr

value: left front mammary gland, teat cistern


title: MCF7_18a24h_array1

description: MCF-7 cells (300 000 per well on 6-well plates) with Ambion pre-miR™ construct for miR-18a at 20 nM, and incubated for 24h.

tag: atcc® number


title: Cow #2661, left front mammary gland, lobuloalveolar, E. coli 12 hr


title: SNF-RAD 60 min rep2

description: Gene expression data for snf1Δ rad23Δ yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ rad23Δ cells 60 minutes after irradiation

value: snf1Δ rad23Δ


title: Cow #2829, left front mammary gland, teat cistern, PBS 24 hr


title: Cow #2661, left front mammary gland, gland cistern, E. coli 12 hr


title: Cow #2829, right rear mammary gland, Furstenburg's rosette, E. coli 12 hr


title: Cow #2661, left front mammary gland, Furstenburg's rosette, E. coli 12 hr


title: Cow #2829, left front mammary gland, lobuloalveolar, PBS 24 hr


title: Cow #2661, left rear mammary gland, Furstenburg's rosette, E. coli 24 hr


title: SNF-RAD 60 min rep1


title: Cow #2661, left rear mammary gland, lobuloalveolar, E. coli 24 hr

value: left rear mammary gland, lobuloalveolar


title: SNF-RAD ND rep2

description: Gene expression data for log-phase snf1Δ rad23Δ yeast cells

source_name: snf1Δ rad23Δ cells prior to irradiation


title: SNF-RAD 30 min rep1

description: Gene expression data for snf1Δ rad23Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ rad23Δ cells 30 minutes after irradiation


title: Cow #2661, left rear mammary gland, teat cistern, E. coli 24 hr

source_name: Left rear mammary gland, teat cistern, E. coli 24 hr

value: left rear mammary gland, teat cistern


title: SNF-RAD ND rep1


title: RAD 60 min rep2

description: Gene expression data for rad23Δ yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: rad23Δ cells 60 minutes after irradiation


title: RAD 30 min rep1

description: Gene expression data for rad23Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: rad23Δ cells 30 minutes after irradiation


title: RAD 60 min rep1


title: RAD 30 min rep2


title: Cow #2661, right rear mammary gland, teat cistern, PBS 24 hr

source_name: Right rear mammary gland, teat cistern, PBS 24 hr

value: Holstein


title: Cow #2661, right rear mammary gland, lobuloalveolar, PBS 24 hr

source_name: Right rear mammary gland, lobuloalveolar, PBS 24 hr


title: Cow #2851, left rear mammary gland, Furstenburg's rosette, E. coli 12 hr

source_name: Left rear mammary gland, Furstenburg's rosette, E. coli 12 hr


title: Cow #2661, right rear mammary gland, gland cistern, PBS 24 hr

source_name: Right rear mammary gland, gland cistern, PBS 24 hr

value: right rear mammary gland, gland cistern


title: RAD ND rep2

description: Gene expression data for log-phase rad23Δ yeast cells

source_name: rad23Δ cells prior to irradiation


title: Cow #2661, left rear mammary gland, gland cistern, E. coli 24 hr

value: left rear mammary gland, gland cistern


title: RAD ND rep1


title: SNF 60 min rep2

description: Gene expression data for snf1Δ yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ cells 60 minutes after irradiation


title: SNF 60 min rep1


title: RAD4 ND rep2


title: Cow #2851, left rear mammary gland, lobuloalveolar, E. coli 12 hr

source_name: Left rear mammary gland, lobuloalveolar, E. coli 12 hr


title: Cow #2661, right rear mammary gland, Furstenburg's rosette, PBS 24 hr

source_name: Right rear mammary gland, Furstenburg's rosette, PBS 24 hr


title: Cow #2851, left rear mammary gland, gland cistern, E. coli 12 hr

source_name: Left rear mammary gland, gland cistern, E. coli 12 hr


title: Cow #2851, left front mammary gland, Furstenburg's rosette, E. coli 24 hr

description:
Mammary gland of lactating cow was infused with 400 CFU of E. coli (P4 isotype) suspended in 4 ml of phosphate-buffered saline 24 hr prior to euthanzia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.

source_name: Left front mammary gland, Furstenburg's rosette, E. coli 24 hr


title: Cow #2851, left rear mammary gland, teat cistern, E. coli 12 hr

source_name: Left rear mammary gland, teat cistern, E. coli 12 hr


title: SNF 30 min rep2

description: Gene expression data for snf1Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ cells 30 minutes after irradiation


title: SNF 30 min rep1


title: SNF 15 min rep1

description: Gene expression data for snf1Δ yeast cells 15 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ cells 15 minutes after irradiation


title: SNF 15 min rep2


title: MIG 60 min rep1

description: Gene expression data for mig3Δ yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: mig3Δ cells 60 minutes after irradiation


title: Cow #2851, left front mammary gland, gland cistern, E. coli 24 hr

description:
Mammary gland of lactating cow was infused with 400 CFU of E. coli (P4 isotype) suspended in 4 ml of phosphate-buffered saline 24 hr prior to euthanasia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.

source_name: Left front mammary gland, gland cistern, E. coli 24 hr


title: SNF ND rep1

description: Gene expression data for log-phase snf1Δ yeast cells

source_name: snf1Δ cells prior to irradiation


title: Cow #2851, left front mammary gland, teat cistern, E. coli 24 hr

source_name: Left front mammary gland, teat cistern, E. coli 24 hr


title: SNF ND rep2


title: Cow #2851, right front mammary gland, Furstenburg's rosette, PBS 24 hr

source_name: Right front mammary gland, Furstenburg's rosette, PBS control at 24 hr


title: Cow #2851, right front mammary gland, teat cistern, PBS control 24 hr

source_name: Right front mammary gland, teat cistern, PBS control at 24 hr


title: MIG 15 min rep1

description: Gene expression data for mig3Δ yeast cells 15 minutes after UV irradiation (100 J/m2)

source_name: mig3Δ cells 15 minutes after irradiation


title: MIG 30 min rep1

description: Gene expression data for mig3Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: mig3Δ cells 30 minutes after irradiation


title: MIG 30 min rep2


title: MIG ND rep2

description: Gene expression data for log-phase mig3Δ yeast cells

source_name: mig3Δ cells prior to irradiation


title: MIG ND rep1


title: MIG 60 min rep2


title: Cow #2851, right front mammary gland, lobuloalveolar region, PBS 24 hr

description:
Mammary gland of lactating cow was infused with 4 ml of phosphate-buffered saline 24 hr prior to euthanzia.  Tissue collected when cow was euthanized.
See:  Li & Li, BMC Genomics 2006, 7:234.

source_name: Right front mammary gland, lobuloalveolar region, PBS 24 hr


title: Cow #2851, left front mammary gland, lobuloalveolar, E. coli 24 hr

source_name: Left front mammary gland, lobuloalveolar, E. coli 24 hr


title: Cow #2851, right front mammary gland, gland cistern, PBS 24 h

source_name: Right front mammary gland, gland cistern, PBS control at 24 hr


title: Cow #2829, right front mammary gland, lobuloalveolar, E. coli 24 hr


title: WT 60 min rep2

description: Gene expression data for WT yeast cells 60 minutes after UV irradiation (100 J/m2)

source_name: WT cells 60 minutes after irradiation

value: WT


title: WT 60 min rep1


title: WT 30 min rep2

description: Gene expression data for WT yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: WT cells 30 minutes after irradiation


title: WT ND rep2

description: Gene expression data for log-phase WT yeast cells

source_name: WT cells prior to irradiation


title: WT 15 min rep2

description: Gene expression data for WT yeast cells 15 minutes after UV irradiation (100 J/m2)

source_name: WT cells 15 minutes after irradiation


title: WT 15 min rep1


title: WT 30 min rep1


title: RAD4 30 min rep2

description: Gene expression data for rad4Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: rad4Δ cells 30 minutes after irradiation


title: SNF-RAD 30 min rep2

description: Gene expression data for snf1Δ rad23Δ yeast cells 30 minutes after UV irradiation (100 J/m2)

source_name: snf1Δ rad23Δ cells 30 minutes after irradiation


title: 4042KO

city: Bethesda

first: WeiPing

last: Chen

address: Building 8 room 1a11

department: Genomic Core Lab

institute: NIDDK/NIH

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

source_name: KO

label_protocol: Affymetrix standard protocol

growth_protocol: Mice were grow in NIDDK animal core facility with the standard protocol

extract_protocol: kit from Qiagen:RNeasy Protect MiniKits

treatment_protocol: Mice lacking or with  the Stat5a and 5b genes in blood cells, treated with GH or not.

tag: KO


title: WT ND rep1


title: 4038WT

source_name: WT

tag: WT


title: 4063WT


title: 4035KO


title: 4060WT


title: 4036KO


title: M43KO+GH

source_name: KO+GH

tag: KO+GH


title: M50WT+GH

source_name: WT+GH

tag: WT+GH


title: totRNA_MNNG_5

city: Oslo

first: Gard

last: Thomassen

state: Oslo

address: Rikshospitalet University Hospital

department: Molecular microbiology

country: Norway

institute: Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology

description: single colony and culture parallell to totRNA_DMSO_5 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)

hyb_protocol: Fragmented and labelled cDNA were hybridized to arrays overnight at 45°C according to the Affymetrix 'Prokaryotic sample and array processing' protocol version 701029 Rev. 4.

scan_protocol: The arrays were scanned using GeneChip Skanner 3000 7G with settings appropriate to the array type.

data_processing: Data processed according to novel method described in Thomassen et al. 2008 (submitted)

label: Biotin

organism: Escherichia coli str. K-12 substr. MG1655

source_name: total RNA extracted after 60 min induction of the adaptive response by MNNG

label_protocol: Fragmented cDNA was terminal labelled with Biotin according to the Affymetrix 'Prokaryotic sample and array processing' protocol version 701029 Rev. 4.

growth_protocol: Escherichia coli K-12 MG1655 single colony from overnight cultures were diluted 1:500 in 100 ml K-medium (1xM9, 1.2% glucose, 1.25% casamino acids (dCAA), 1 mM MgSO4, 0.1 mM CaCl2) and grown at 37°C with aeration by rotary shaking until OD600=0.5.

extract_protocol: 1 ml trizol was added pr 106 cells and incubated at room temperature for 5 minutes. 0.2 ml chloroform was added pr ml Trizol and the sample was mixed for 15 seconds before 15 minutes centrifutgation (12000 g 4°C). The aqueous phase was slowly added 1:1(vol) to 70% EtOH and further loaded to a RNeasy column (QIAGEN), washed and DNase treated according to RNeasy protocol (QIAGEN).

treatment_protocol: 50 ml culture of Escherichia coli K-12 MG1655 was added 1 µg ml-1 MNNG at OD600 = 0.5. The culture was further harvested by centrifugation 60 minutes after exposure to MNNG.(sample 6-10)

tag: cell culture

value: mid-log phase


title: M47WT+GH


title: totRNA_MNNG_2

description: single colony and culture parallell to totRNA_DMSO_2 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: M48KO+GH


title: totRNA_DMSO_4

description: single colony and culture parallell to totRNA_MNNG_4 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)

source_name: total RNA extracted after 60 min growth with DMSO as a reference to the induction of the adaptive response

treatment_protocol: 50 ml culture of Escherichia coli K-12 MG1655 was added 10 µl DMSO at OD600 = 0.5. The culture was further harvested by centrifugation 60 minutes after exposure to DMSO.(Sample 1-5)


title: totRNA_DMSO_5

description: single colony and culture parallell to totRNA_MNNG_5 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: M42KO+GH


title: totRNA_MNNG_3

description: single colony and culture parallell to totRNA_DMSO_3 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: totRNA_MNNG_1

description: single colony and culture parallell to totRNA_DMSO_1 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: totRNA_DMSO_3

description: single colony and culture parallell to totRNA_MNNG_3 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: totRNA_DMSO_2

description: single colony and culture parallell to totRNA_MNNG_2 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: totRNA_MNNG_4

description: single colony and culture parallell to totRNA_DMSO_4 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: totRNA_DMSO_1

description: single colony and culture parallell to totRNA_MNNG_1 (the culture was split in two, half induced by MNNG the other half as reference was added DMSO)


title: Breast_tumor_T402

status: Public on Aug 17 2009

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Lowess global normalization, non-background subtracted data obtained from log2 of processed Cy5/Cy3 signal. Agilent Feature Extraction software was used (version 9.5)

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]

extract_protocol:
RNA isolation. We used 30 sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with RNAzolB, and finally dissolved in RNase-free H2O. Twenty-five micrograms of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 µg/µl.
A reference cRNA pool was made by pooling equal amounts of amplified cRNA from 106 primary breast tumors selected from patients from the clinical validation series ( N Engl J Med 2002; 347:1999-2009, Dec 19, 2002) to give a proportional distribution between good and poor outcome patients.

value: female

value: breast

tag: tumor type

value: early-stage breast cancer

source_name: breast cancer reference sample

value: breast cancer reference sample


title: Breast_tumor_T404

description: A reference cRNA pool was made by pooling equal amounts of amplified cRNA from 106 primary breast tumors selected from patients from the clinical validation series ( N Engl J Med 2002; 347:1999-2009, Dec 19, 2002) to give a proportional distribution between good and poor outcome patients.

tag: gender


title: Breast_tumor_T399


title: Breast_tumor_T401


title: Breast_tumor_T403


title: Breast_tumor_T400


title: Breast_tumor_T398


title: Breast_tumor_T397


title: Breast_tumor_T396


title: Breast_tumor_T395


title: Breast_tumor_T394


title: Breast_tumor_T392


title: Breast_tumor_T386


title: Breast_tumor_T390


title: Breast_tumor_T391


title: Breast_tumor_T388


title: Breast_tumor_T387


title: Breast_tumor_T393


title: Breast_tumor_T389


title: M44WT+GH


title: Breast_tumor_T385


title: Breast_tumor_T384


title: Breast_tumor_T379


title: Breast_tumor_T383


title: Breast_tumor_T382


title: Breast_tumor_T381


title: Breast_tumor_T380


title: Breast_tumor_T377


title: Breast_tumor_T375


title: Breast_tumor_T378


title: Breast_tumor_T373


title: Breast_tumor_T376


title: Breast_tumor_T372


title: Breast_tumor_T374


title: Breast_tumor_T370


title: Breast_tumor_T371


title: Breast_tumor_T368


title: Breast_tumor_T365


title: Breast_tumor_T358


title: Breast_tumor_T362


title: Breast_tumor_T361


title: Breast_tumor_T364


title: Breast_tumor_T359


title: Breast_tumor_T363


title: Breast_tumor_T360


title: Breast_tumor_T366


title: Breast_tumor_T369


title: Breast_tumor_T357


title: Breast_tumor_T356


title: Breast_tumor_T352


title: Breast_tumor_T354


title: Breast_tumor_T355


title: Breast_tumor_T349


title: Breast_tumor_T351


title: Breast_tumor_T353


title: Breast_tumor_T350


title: Breast_tumor_T348


title: Breast_tumor_T345


title: Breast_tumor_T341


title: Breast_tumor_T347


title: Breast_tumor_T338


title: Breast_tumor_T343


title: Breast_tumor_T344


title: Breast_tumor_T342


title: Breast_tumor_T339


title: Breast_tumor_T346


title: Breast_tumor_T340


title: Breast_tumor_T335


title: Breast_tumor_T367


title: Breast_tumor_T331


title: Breast_tumor_T334


title: Breast_tumor_T332


title: Breast_tumor_T333


title: Breast_tumor_T330


title: Breast_tumor_T328


title: Breast_tumor_T336


title: Breast_tumor_T329


title: Breast_tumor_T337


title: Breast_tumor_T327


title: Breast_tumor_T326


title: Breast_tumor_T318


title: Breast_tumor_T320


title: Breast_tumor_T315


title: Breast_tumor_T319


title: Breast_tumor_T316


title: Breast_tumor_T322


title: Breast_tumor_T321


title: Breast_tumor_T325


title: Breast_tumor_T317


title: Breast_tumor_T324


title: Breast_tumor_T310


title: Breast_tumor_T313


title: Breast_tumor_T312


title: Breast_tumor_T323


title: Breast_tumor_T314


title: Breast_tumor_T309


title: Breast_tumor_T311


title: Breast_tumor_T308


title: Breast_tumor_T306


title: Breast_tumor_T305


title: Breast_tumor_T307


title: Breast_tumor_T304


title: Breast_tumor_T299


title: Breast_tumor_T301


title: Breast_tumor_T302


title: Breast_tumor_T303


title: Breast_tumor_T296


title: Breast_tumor_T295


title: Breast_tumor_T300


title: Breast_tumor_T297


title: Breast_tumor_T293


title: Breast_tumor_T287


title: Breast_tumor_T290


title: Breast_tumor_T289


title: Breast_tumor_T291


title: Breast_tumor_T288


title: Breast_tumor_T285


title: Breast_tumor_T231


title: Breast_tumor_T232


title: Breast_tumor_T284


title: Breast_tumor_T230


title: Breast_tumor_T233


title: Breast_tumor_T227


title: Breast_tumor_T292


title: Breast_tumor_T226


title: Breast_tumor_T223


title: Breast_tumor_T222


title: Breast_tumor_T221


title: Breast_tumor_T224


title: Breast_tumor_T225


title: Breast_tumor_T218


title: Breast_tumor_T219


title: Breast_tumor_T286


title: Breast_tumor_T200


title: Breast_tumor_T197


title: Breast_tumor_T196


title: Breast_tumor_T203


title: Breast_tumor_T198


title: Breast_tumor_T202


title: Breast_tumor_T199


title: Breast_tumor_T204


title: Breast_tumor_T194


title: Breast_tumor_T190


title: Breast_tumor_T186


title: Breast_tumor_T220


title: Breast_tumor_T193


title: Breast_tumor_T201


title: Breast_tumor_T187


title: Breast_tumor_T185


title: Breast_tumor_T195


title: Breast_tumor_T189


title: Breast_tumor_T192


title: Breast_tumor_T294


title: Breast_tumor_T183


title: Breast_tumor_T180


title: Breast_tumor_T184


title: Breast_tumor_T178


title: Breast_tumor_T298


title: Breast_tumor_T182


title: Breast_tumor_T173


title: Breast_tumor_T176


title: Breast_tumor_T171


title: Breast_tumor_T172


title: Breast_tumor_T177


title: Breast_tumor_T175


title: Breast_tumor_T161


title: Breast_tumor_T166


title: Breast_tumor_T169


title: Breast_tumor_T160


title: Breast_tumor_T170


title: Breast_tumor_T167


title: Breast_tumor_T158


title: Breast_tumor_T165


title: Breast_tumor_T174


title: Breast_tumor_T179


title: Breast_tumor_T151


title: Breast_tumor_T155


title: Breast_tumor_T163


title: Breast_tumor_T154


title: Breast_tumor_T150


title: Breast_tumor_T159


title: Breast_tumor_T146


title: Breast_tumor_T138


title: Breast_tumor_T148


title: Breast_tumor_T153


title: Breast_tumor_T145


title: Breast_tumor_T156


title: Breast_tumor_T149


title: Breast_tumor_T147


title: Breast_tumor_T140


title: Breast_tumor_T139


title: Breast_tumor_T133


title: Breast_tumor_T144


title: Breast_tumor_T134


title: Breast_tumor_T142


title: Breast_tumor_T143


title: Breast_tumor_T135


title: Breast_tumor_T137


title: Breast_tumor_T152


title: Breast_tumor_T136


title: Breast_tumor_T181


title: Breast_tumor_T129


title: Breast_tumor_T120


title: Breast_tumor_T130


title: Breast_tumor_T127


title: Breast_tumor_T126


title: Breast_tumor_T283


title: Breast_tumor_T128


title: Breast_tumor_T123


title: Breast_tumor_T132


title: Breast_tumor_T125


title: Breast_tumor_T280


title: Breast_tumor_T121


title: Breast_tumor_T281


title: Breast_tumor_T278


title: Breast_tumor_T275


title: Breast_tumor_T131


title: Breast_tumor_T124


title: Breast_tumor_T116


title: Breast_tumor_T273


title: Breast_tumor_T271


title: Breast_tumor_T255


title: Breast_tumor_T261


title: Breast_tumor_T247


title: Breast_tumor_T265


title: Breast_tumor_T242


title: Breast_tumor_T252


title: Breast_tumor_T266


title: Breast_tumor_T244


title: Breast_tumor_T251


title: Breast_tumor_T258


title: Breast_tumor_T246


title: Breast_tumor_T238


title: Breast_tumor_T260


title: Breast_tumor_T236


title: Breast_tumor_T235


title: Breast_tumor_T229


title: Breast_tumor_T264


title: Breast_tumor_T141


title: Breast_tumor_T215


title: Breast_tumor_T217


title: Breast_tumor_T162


title: Breast_tumor_T168


title: Breast_tumor_T207


title: Breast_tumor_T209


title: Breast_tumor_T211


title: Breast_tumor_T118


title: Breast_tumor_T112


title: Breast_tumor_T108


title: Breast_tumor_T113


title: Breast_tumor_T122


title: Breast_tumor_T110


title: Breast_tumor_T101


title: Breast_tumor_T117


title: Breast_tumor_T103


title: Breast_tumor_T106


title: Breast_tumor_T274


title: Breast_tumor_T096


title: Breast_tumor_T100


title: Breast_tumor_T094


title: Breast_tumor_T081


title: Breast_tumor_T091


title: Breast_tumor_T090


title: Breast_tumor_T092


title: Breast_tumor_T086


title: Breast_tumor_T076


title: Breast_tumor_T069


title: Breast_tumor_T078


title: Breast_tumor_T085


title: Breast_tumor_T087


title: Breast_tumor_T072


title: Breast_tumor_T089


title: Breast_tumor_T067


title: Breast_tumor_T205


title: Breast_tumor_T074


title: Breast_tumor_T079


title: Breast_tumor_T066


title: Breast_tumor_T063


title: Breast_tumor_T054


title: Breast_tumor_T056


title: Breast_tumor_T049


title: Breast_tumor_T053


title: Breast_tumor_T050


title: Breast_tumor_T043


title: Breast_tumor_T034


title: Breast_tumor_T045


title: Breast_tumor_T061


title: Breast_tumor_T047


title: Breast_tumor_T055


title: Breast_tumor_T042


title: Breast_tumor_T033


title: Breast_tumor_T035


title: Breast_tumor_T029


title: Breast_tumor_T039


title: Breast_tumor_T213


title: Breast_tumor_T026


title: Breast_tumor_T018


title: Breast_tumor_T024


title: Breast_tumor_T011


title: Breast_tumor_T028


title: Breast_tumor_T004


title: Breast_tumor_T021


title: Breast_tumor_T008


title: Breast_tumor_T014


title: Breast_tumor_T279


title: Breast_tumor_T277


title: Breast_tumor_T015


title: Breast_tumor_T002


title: Breast_tumor_T009


title: Breast_tumor_T071


title: Breast_tumor_T020


title: Breast_tumor_T282


title: Breast_tumor_T272


title: Breast_tumor_T276


title: Breast_tumor_T270


title: Breast_tumor_T267


title: Breast_tumor_T250


title: Breast_tumor_T269


title: Breast_tumor_T263


title: Breast_tumor_T259


title: Breast_tumor_T245


title: Breast_tumor_T253


title: Breast_tumor_T257


title: Breast_tumor_T241


title: Breast_tumor_T240


title: Breast_tumor_T239


title: Breast_tumor_T256


title: Breast_tumor_T249


title: Breast_tumor_T234


title: Breast_tumor_T243


title: Breast_tumor_T228


title: Breast_tumor_T237


title: Breast_tumor_T212


title: Breast_tumor_T268


title: Breast_tumor_T216


title: Breast_tumor_T208


title: Breast_tumor_T107


title: Breast_tumor_T206


title: Breast_tumor_T188


title: Breast_tumor_T105


title: Breast_tumor_T111


title: Breast_tumor_T164


title: Breast_tumor_T119


title: Breast_tumor_T191


title: Breast_tumor_T157


title: Breast_tumor_T114


title: Breast_tumor_T104


title: Breast_tumor_T115


title: Breast_tumor_T109


title: Breast_tumor_T099


title: Breast_tumor_T098


title: Breast_tumor_T102


title: Breast_tumor_T097


title: Breast_tumor_T093


title: Breast_tumor_T082


title: Breast_tumor_T083


title: Breast_tumor_T077


title: Breast_tumor_T073


title: Breast_tumor_T075


title: Breast_tumor_T088


title: Breast_tumor_T068


title: Breast_tumor_T070


title: Breast_tumor_T095


title: Breast_tumor_T248


title: Breast_tumor_T064


title: Breast_tumor_T080


title: Breast_tumor_T062


title: Breast_tumor_T065


title: Breast_tumor_T060


title: Breast_tumor_T262


title: Breast_tumor_T052


title: Breast_tumor_T059


title: Strain 2221ΔPEL in THY, stationary, sample C

status: Public on Aug 25 2009

city: Reno

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description: 2221ΔPEL T2 C

hyb_protocol: Labeled cDNA was hybridized to a custom array for 16h at 40 degrees C.  GeneChips were washed and stained using  the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

organism: Streptococcus pyogenes

source_name: PEL mutant, stationary phase

label_protocol: RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin.

growth_protocol: GAS strains were grown in THY broth to O.D. 600 of 0.5 (exponential phase) or 1.7 (stationary phase).

extract_protocol: Total RNA was extracted via mechanical disruption and purified using the Qiagen Rneasy kit.

treatment_protocol: Two volumes of RNAprotect was added to each strain, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.

tag: strain

value: PEL mutant

tag: growth phase

value: stationary phase


title: Breast_tumor_T048

tag: tissue


title: Breast_tumor_T058


title: Breast_tumor_T057


title: Breast_tumor_T084


title: Breast_tumor_T041


title: Breast_tumor_T051


title: Breast_tumor_T046


title: Breast_tumor_T036


title: Breast_tumor_T040


title: Breast_tumor_T044


title: Breast_tumor_T037


title: Breast_tumor_T032


title: Breast_tumor_T027


title: Breast_tumor_T016


title: Breast_tumor_T022


title: Breast_tumor_T210


title: Breast_tumor_T031


title: Breast_tumor_T030


title: Breast_tumor_T038


title: Breast_tumor_T023


title: Breast_tumor_T010


title: Breast_tumor_T214


title: Breast_tumor_T025


title: Breast_tumor_T012


title: Breast_tumor_T013


title: Breast_tumor_T019


title: Breast_tumor_T006


title: Breast_tumor_T007


title: Breast_tumor_T003


title: Breast_tumor_T001


title: Breast_tumor_T017


title: Breast_tumor_T005


title: control vs. glutamine alone_rep 4

city: Salt Lake City

first: Mohan

middle: Rao

last: Kaadige

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: no additional information

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution using the Extended Dynamic Range scanning protocol. Images were processed using Agilent Feature Extraction software version 9.5.1.1.

data_processing: LOWESS normalized log ratios reported by the Agilent platform were converted to log base 2.

source_name: BxPC-3 pancreatic cancer cells

label_protocol: The Agilent Two-Color Low RNA Input Linear Amplification Kit is used to generate fluorescently labeled cRNA for two-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 500 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.  Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: BxPC-3 cells were plated in quadruplicate and starved overnight in glucose and glutamine free media. For glucose and/or glutamine induction, cells were incubated for 6hrs in media containing glucose (25mM) or glutamine (2mM) or glucose plus glutamine (25mM and 2mM).

extract_protocol: Total RNA was isolated using RNAeasy minikit from qiagen

tag: growth condition

value: Glucose and glutamine depleted (control)

value: Glutamine alone


title: control vs. glutamine alone_rep 1

description: no additional information


title: control vs. glucose plus glutamine_rep 4

description: no additional information

value: Glucose plus Glutamine


title: control vs. glucose alone_rep 3

description: no additional information

value: Glucose alone


title: control vs. glucose alone_rep 2

description: no additional information


title: control vs. glutamine alone_rep 3

description: no additional information


title: control vs. glucose plus glutamine_rep 3

description: no additional information


title: MCF7 vector control, rep2

city: Gainesville

first: Vita

last: Golubovskaya

state: FL

address: 1376 Mowry Road

department: Surgery

institute: university of florida, Shands Cancer Center

description: Gene expression data from MCF7 vector control

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Plus 2 arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized with RMA algorithm

source_name: human breast cancer cell line, MCF-7, vector control

label_protocol: Biotiylated cRNA was prepared according to the manufacturer's protocol using the MessageAmpII-Biotin Enhanced Amplification system (Ambion) from 1ug total RNA

growth_protocol: Cell lines were cultivated according ATCC protocol, stable cell lines hyg-resistant

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


title: control vs. glutamine alone_rep 2

description: no additional information


title: control vs. glucose plus glutamine_rep 1

description: no additional information


title: Differential expression in high and low MIC strains_rep1

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description: No ethanol treatment for High MIC uninduced-Low MIC Uniduced samples.

hyb_protocol: Labelled cDNA hybridised in slides placed in  water bath for 16 h at 42 °C. Arrays then washed in 1x SSC (+0.02 % SDS)at room temperature for 2 and 5 min,  in  0.1x SSC+0.1%SDS for 5 min,  and then in 0.1x SSC for 10 min 2 times prior to drying and scanning.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 4.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html. Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Staphylococcus aureus Gene Sorter (SAGS). Several controls were employed to minimize the technical and biological variations and to ensure that the data obtained were of good quality. First, each ORF was present in triplicate on the array. Second, each RNA preparation was used to make probes for at least two separate arrays for which the incorporated dye was reversed.

organism: Staphylococcus aureus

source_name: S. aureus strain not stressed with alcohol

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Overnight grown S. aureus LP9 and S. aureus MM66 was inoculated in MHB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 625 nm until OD= ~0.5.

extract_protocol: Bacterial cultures flushed directly into QIAGEN RNAprotect before total RNA isolation using QIAGEN RNEasy Midi kit with on column DNAse digestion.


title: Differential expression in high and low MIC strains_rep2

treatment_protocol: No ethanol treatment for High MIC uninduced-Low MIC Uniduced samples.


title: control vs. glucose alone_rep 4

description: no additional information


title: control vs. glucose plus glutamine_rep 2

description: no additional information


title: MCF7 siRNA control

description: Gene expression data from MCF7 siRNA control

source_name: human breast cancer cell line, MCF-7, siRNA control

treatment_protocol: siRNA control

tag: MCF7 siRNA control


title: control vs. glucose alone_rep 1

description: no additional information


title: FAKsiRNA, rep4

description: Gene expression data from FAKsiRNA

source_name: human breast cancer cell line, MCF-7, FAKsiRNA

treatment_protocol: FAKsiRNA stable cell lines, hygromycin-resistant


title: MCF7 vector control

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip U133_plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized with RMA algorithm.

source_name: human breast cancer cell line, MCF-7-Vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: FAKsiRNA, rep2

description: Gene expression data from FAKsiRNA


title: MM66_low MiC strain_susceptibilities to the Biocide Ethanol_rep2

description: Analysis used MM66 uninduced RNA as control samples for comparison to the experimental samples taken from MM66 induced with 10% ethanol for 15 min. Raw files d.txt and h.txt are the second replicate of dye swap.

source_name: S. aureus strain stressed with alcohol

growth_protocol: Overnight grown S. aureus MM66 was inoculated in MHB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 625 nm until OD= ~0.5.

treatment_protocol: Based on previous minimum inhibitory concentration studies a 10% final ethanol concentration was added for 15 min of challenge.

tag: stress

value: ethanol

value: control


title: FAKsiRNA, rep3

description: Gene expression data from FAKsiRNA


title: Lp9_high MiC strain_susceptibilities to the Biocide Ethanol_rep2

description: Analysis used Lp-9 uninduced RNA as control samples for comparison to the experimental samples taken from Lp-9 induced with 10% ethanol for 15 min. Raw files b.txt and f.txt are the second replicate of dye swap.

growth_protocol: Overnight grown S. aureus LP9 was inoculated in MHB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 625 nm until OD= ~0.5.

treatment_protocol: Based on previous minimum inhibitory concentration studies a 10% final ethanol concentration was added for 15 min of challenge for both S. aureus Lp9


title: MM66_low MiC strain_susceptibilities to the Biocide Ethanol_rep1

description: Analysis used MM66 uninduced RNA as control samples for comparison to the experimental samples taken from MM66 induced with 10% ethanol for 15 min. Raw files c.txt and g.txt are the first replicate of dye swap


title: Lp9_high MiC strain_susceptibilities to the Biocide Ethanol_rep1

description: Analysis used Lp-9 uninduced RNA as control samples for comparison to the experimental samples taken from Lp-9 induced with 10% ethanol for 15 min. Raw files a.txt and e.txt are the first replicate of dye swap.

treatment_protocol: Based on previous minimum inhibitory concentration studies a 10% final ethanol concentration was added for 15 min of challenge for both S. aureus LP9


title: MCF7

description: Gene expression data from MCF7

source_name: human breast cancer cell line, MCF-7


title: ALL cells from pediatric diagnostic bone marrow 43

status: Public on Aug 16 2009

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0219-ALL-v5-U133A

hyb_protocol: Following fragmentation, 15ugs of cRNA were hybridized for 16hr at 45C on the Human Genome U133A GeneChip Array. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Leukemic blasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Leukemic blast cells were enriched from bone marrow aspirates by centrifugation on a Ficoll gradient.

extract_protocol: TriReagent extraction of total RNA was performed according to the manufacturer's instructions (MRC).

tag: disease status

value: acute lymphoblastic leukemia

tag: developmental stage

value: pediatric

value: diagnostic bone marrow

tag: cell type

value: leukemic blast cells


title: ALL cells from pediatric diagnostic bone marrow 38

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0130-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 42

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0196-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 37

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0128-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 39

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0135-ALL-v5-U133A


title: FAKsiRNA, rep1

description: Gene expression data from FAKsiRNA


title: ALL cells from pediatric diagnostic bone marrow 44

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0228-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 40

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0151-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 35

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0121-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 41

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0167-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 36

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0125-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 34

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0120-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 33

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0117-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 32

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0111-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 28

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0076-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 30

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0097-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 31

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0110-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 29

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0077-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 23

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0039-ALL-v5-U133A


title: ALL cells from pediatric diagnostic bone marrow 27

description:
Gene expression data from human acute lymphoblastic leukemia cells
JD0070-ALL-NA-v5-U133A