title: Salt stressed, replicate #3

status: Public on Aug 05 2009

description:
NS0 mouse myeloma
Gene expression data from NS0 cells cultured in animal-derived protein-free media under salt stress

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Glyco-Gene Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: NS0 cells, 90-h, salt

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

growth_protocol: One-liter spinner flasks were used to culture the NS0 cells in humidified incubators at 37 ˚C and 5 % CO2. An animal-derived protein-free media, HyQ ADCFMab (Hyclone), supplemented with 5 mM glutamine (Hyclone) and LS-250 cholesterol (4 mL per liter media; Hyclone) was used.  A common seed culture was used to inoculate the control and three treatment cultures, which were then cultured in parallel.  Biological triplicates were used for each condition examined.  Milli-Q water was added to the control and treatment cultures to normalize culture volumes and media concentrations (only 1 to 6 mL per liter).

extract_protocol: Cells were harvested by centrifugation at 3000 g for 5 min at 4 ˚C. The supernatant and pellets were saved at –20 ˚C and –80 ˚C, respectively. Total RNA was isolated from the pellet using the RNAqueous-MidiTM kits (Ambion), except the DNase treatment was increased to 2 µl of DNase and 1 hour. The total RNA was further purified using the RNeasy Qaigen kit. RNA concentrations were determined using a Ribogreen RNA quantification kit (Molecular Probes). Ten micrograms of total RNA (1 µg/µl) per sample was sent to the Consortium for Functional Genomics for gene expression analysis on the Glyco-Gene Chip v3 (an Affymetrix DNA microarray platform).

treatment_protocol: The culture conditions were basal media (control), and basal media supplemented with 5 mM NH4Cl, 5 mM NaCl, or 5 mM NH4Cl and 10 mM proline. The ammonium, salt, and proline stock solutions (all 5000 mM) were prepared in Milli-Q water and added to the fresh media prior to the addition of cells.

tag: cell line


title: Gene Expression profiling of M.bovis BCG strain under hypoxia DyeSwap

status: Public on Aug 06 2009

type: RNA

city: Lucknow

first: Ranjana

last: Srivatsava

address: Chattar Manzil Palace

country: India

institute: Central Drug Research Institute

description: Slides were scanned at 5 micron resolution using Agilent scanner.Automated feature extraction was done using Agilent’s Feature Extraction Software.

hyb_protocol: 825ng each of labeled control cRNA was mixed with 825ng of treated labelled cRNA, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer Mycobacterium tuberculosis microarray using sure hyb chambers at 65degC for 17 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Analysis of feature extracted data was done using Agilent’s GeneSpring GX V 7.3.1 software. Pre-processing of the replicate experiment data was done to flag the outliers. Normalization of the data was done using per spot per chip intensity dependant lowess normalization and dye swap experiment was data transformed. Genes with log2 ratio of 1.29 and above in replicate experiments were considered as up regulated and 0.81 and below was considered down regulated. p-value was calculated by GeneSpring GX for each gene on the basis of replicate probes to indicate statistical significance. Biological significance of differentials were analyzed using Genotypics Biointerpreter - Web based tool for biological interpretation of given genelist.

molecule: total RNA

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Mycobacterium bovis BCG hypoxia culture

label_protocol: Total RNA (500ng) of Mycobacterium under hypoxia was labelled with Cy3 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

extract_protocol: Qiagen’s bacterial RNA kit

tag: stress

value: hypoxia

source_name: Mycobacterium bovis BCG Log Phase Culture

label_protocol: Total RNA (500ng) of Mycobacterium under log phase was labelled with Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

value: control


title: Ammonium stressed with proline, replicate #3

city: Clemson

first: Sarah

middle: W

last: Harcum

state: SC

address: 105 Collings Street

department: Bioengineering

country: USA

institute: Clemson University

description:
NS0 mouse myeloma
Gene expression data from NS0 cells cultured in animal-derived protein-free media under ammonia and proline stress

label: biotin

organism: Mus musculus

source_name: NS0 cells, 90-h, ammonium/proline


title: Mouse fetal liver_E14.5_WT_rep5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: One fetal liver was used for each replicate

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Embryonic day 14.5 wild type (WT) mouse fetal liver

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix Amplification One-Cycle Target labeling kit according to manufacturer's protocol.

extract_protocol: Qiagen Rneasy protocol using mini columns; elute RNA with 70 degree water

tag: age

value: Embryonic day 14.5

tag: genotype

value: wild type (WT)

tag: tissue type

value: fetal liver

tag: strain

value: b6, 129 mixed background strain


title: Salt stressed, replicate #1


title: Liver_C57BL6J_M_B1_rep1

city: Chapel Hill

first: Daniel

middle: M

last: Gatti

address: 135 Dauer Dr.

department: Environmental Sciences & Engineering

institute: University of Noth Carolina

hyb_protocol: Equal amounts of Cy3 and Cy5 labeled cRNA (750 ng) from the individual animals and from the pooled control, respectively, were hybridized to an Agilent Mouse Oligo Microarray (~21,000 features, catalogue# G4121) for 17 hours at 65°C. The hybridized microarrays were then washed and scanned using an Agilent G2565BA scanner.

scan_protocol: scanned using the Agilent G2565BA scanner

data_processing: Data were extracted from the scanned image using Agilent Feature Extraction software version 6.1. A total of 122 arrays were run in 8 batches. The samples were semirandomly distributed throughout the batches prior to microarray analysis in order to separate sexes and strains, and to minimize between- and within- batch bias. Technical and biological replicates were run both within each batch and between batches. The microarray data was deposited in the UNC Microarray Database and extracted using Log2 ratios of the mean red channel intensity over the mean green channel intensity. This was followed by LOWESS normalization to remove the intensity dependent dye bias3. Neither the genes nor the arrays were centered. Inter-batch normalization was carried out using a nested ANOVA mixed model with samples within each batch crossed with sex and strain.

source_name: Liver

label_protocol: A balanced design was used to assign samples across 8 microarray batches. Each batch was balanced by sex and strain and contained both inter and intrabatch technical replicates. The randomized batch design of the microarray experiment minimizes the effect of interbatch variance. Further, the pooling of mRNA from multiple mice within strain/sex reduces the effects of individual variation in the measurement of transcript expression. One μg of total RNA from 3 individual mouse liver samples of the same sex and strain was pooled, amplified and labeled with a fluorescent dye (Cy5) and a common reference - pooled mouse tissues (equal amounts of RNA from liver, kidney, lung, brain and spleen) mRNA isolated from the livers of 100 male C57BL6/J mice [see2 for details] - were amplified and labeled with Cy3 using Agilent Technologies (Palo Alto, CA) Low RNA Input Linear Amplification labeling kit following the manufacturer’s protocol. The quantity of the resulting fluorescently labeled cRNA was measured using a Nanodrop ND-100 spectrophometer (Nanodrop Technologies, Wilmington, DE) and its integrity assessed using an Agilent Bioanalyzer.

growth_protocol: Animals and Tissues. BXD1 through BXD42 mice are original RI strains available from the Jackson Laboratory (Bar Harbor, ME). BXD43 through BXD100 lines were generated using ninth or tenth generation Advanced Intercross Line (AIL) progenitors. AILs are generated by breeding two inbred parents (here is C57BL/6J and DBA/2J) and crossing their offspring so as to minimize inbreeding and maximize recombination events at each generation1. Great care was taken to minimize the effects of gene-environment interactions. Mice were maintained under identical conditions with respect to diet, water and housing conditions. Mice were maintained at 20-24°C on a 14/10 hr light/dark cycle in a pathogen-free colony at the University of Tennessee-Memphis. Animals were fed a 5% fat Agway Prolab 3000 rat and mouse chow and given tap water in glass bottles. Mice were raised to between 54 and 177 days (mean 70 days) of age. Liver tissues were collected following sacrifice by cervical dislocation. The whole liver was removed immediately, and placed in five volumes of RNAlater (Ambion, Austin, TX) at 4°C overnight, before removing from RNAlater and storing at -80°C until processing. All animal studies for this project were approved by Animal Care and Use Committee at the University of Tennessee-Memphis.

extract_protocol: RNA Isolation. Total RNA was isolated from liver samples (~30 mg) using the Rneasy mini kit (Qiagen, Valencia, CA) as detailed by the manufacturer. RNA quality and quantity was determined spectrophotometrically from the absorbance at 260 nm and 280 nm. Aliquots of RNA samples were frozen at −80°C until microarray analysis. For each microarray, RNA was pooled from 2-3 mice of the same sex and strain. All strains used one array per sex per strain except for strains 23, 34 and 33. The proportion of males to female is approximately equal.

tag: gender

value: M

tag: batch

tag: tissue

value: Liver

source_name: Pooled Reference

tag: sample

value: pooled RNA from the same batch


title: Gene Expression profiling of M.bovis BCG strain under hypoxia

label_protocol: Total RNA (500ng) of Mycobacterium under hypoxia was labelled with Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

label_protocol: Total RNA (500ng) of Mycobacterium under log phase was labelled with Cy3 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.


title: Salt stressed, replicate #2


title: Liver_DBA2J_F_B1

value: F


title: Liver_C57BL6J_M_B1_rep2


title: Liver_C57BL6J_F_B1


title: Mouse fetal liver_E14.5_WT_rep3


title: Ammonium stressed with proline, replicate #2


title: Liver_BXD1_M_B1


title: Mouse fetal liver_E14.5_WT_rep1


title: Mouse fetal liver_E14.5_WT_rep4


title: Mouse fetal liver_E14.5_WT_rep2


title: Control, replicate #1

description:
NS0 mouse myeloma
Gene expression data from NS0 cells cultured in animal-derived protein-free media

source_name: NS0 cells, 90-h, control


title: Liver_C57BL6J_M_B2_rep1


title: Control, replicate #3


title: Ammonium stressed, replicate #2

description:
NS0 mouse myeloma
Gene expression data from NS0 cells cultured in animal-derived protein-free media under ammonia stress

source_name: NS0 cells, 90-h, ammonium


title: Ammonium stressed with proline, replicate #1


title: Ammonium stressed, replicate #3


title: Ammonium stressed, replicate #1


title: Control, replicate #2


title: Mouse astrocytes exposed to mock virus rep2

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 432 West 58th, Street

department: Medicine

institute: St.Luke's-Roosevelt Hospital Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: CHP files were obtained using the Affymetrix software, MAS5 algorithm.

source_name: Primary mouse astrocytes, mock

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was prepared from cell cultures using the RNAeasy total RNA extraction kit (Qiagen, CA).  RNA quality was assessed by electrophoresis and spectrophotometric analysis.

treatment_protocol: Day-two neonatal mouse astrocytes were exposed to mock virus at m.o.i. of 1 and cultured for 24 hours.

tag: cell type

value: primary astrocytes

value: neonatal day 2

tag: treatment

value: mock virus


title: NKL17

type: genomic

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

description: MspI representation of genomic DNA vs. HpaII representation of genomic DNA.

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. , genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.

molecule: genomic DNA

organism: Homo sapiens

source_name: De novo normal karyotype AML blast cells

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5.

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55).

value: AML blast cells

tag: restriction enzyme

value: MspI

value: HpaII


title: Mouse astrocytes exposed to mock virus rep1


title: Normal_CD34(+)_#11

source_name: Bone marrow CD34+ cells

tag: disease

value: healthy

value: bone marrow

value: CD34+ cells


title: Mouse astrocytes exposed to mock virus rep3


title: NKL19


title: Mouse astrocytes exposed to HIV-1 rep2

description: Mouse astrocytes exposed to HIV-1 rep2

source_name: Primary mouse astrocytes, HIV-1

treatment_protocol: Day-two neonatal mouse astrocytes were exposed to cell-free HIV-1/NL4-3 at m.o.i. of 1 and cultured for 24 hours.


title: NKL24


title: NKL15


title: Mouse astrocytes exposed to HIV-1 rep1

description: Mouse astrocytes exposed to HIV-1 rep1


title: NKL20


title: NKL13


title: Normal_CD34(+)_#10


title: NKL09


title: NKL11


title: NKL18


title: Normal_CD34(-)_#12

source_name: Bone marrow CD34- fraction

value: CD34- cells


title: Normal_CD34(-)_#9


title: Normal_CD34(+)_#12


title: Mouse astrocytes exposed to HIV-1 rep3

description: Mouse astrocytes exposed to HIV-1 rep3


title: Normal_CD34(+)_#9


title: NKL22


title: NKL14


title: Normal_CD34(-)_#10


title: NKL16


title: Normal_CD34(-)_#11


title: NKL08


title: NKL12


title: dmel_dsim_w501_female_bodies_mixed_DNA

city: Gainesville

first: Rob

middle: J

last: Kulathinal

address: 1376 Mowry Road

department: Department of Biology

institute: University of Florida

description: genomic DNA from adult female bodies

hyb_protocol: gDNA samples were hybridized to GeneChip© Drosophila Tiling 1.0R Arrays according to standard manufacturer protocols.

scan_protocol: GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.

data_processing: The Tiling Analysis Software from Affymetrix was used to produce .bar files containing raw intensities, then the bar2txt program from the affy file manipulation tools (http://www.affymetrix.com/Auth/support/developer/downloads/Tools/tiling_util.tgz) was used to convert the .bar files to plain txt.

organism: Drosophila sp. (in: flies)

source_name: adult female bodies

label_protocol: The genomic DNA samples were fragmented and labeled following protocols provided by Michael E. Zwick (Cutler et al. 2001; Nuzhdin et al. 2007). Fragmentation was analyzed using the Bioanalyzer DNA 1000 LabChip© kit and by agarose gel electrophoresis.

growth_protocol: Flies were propagated in bottles at 25°C on dextrose medium.

extract_protocol: The bodies of 60 female flies were homogenized in 180ul of phosphate buffered saline (pH 7.2). Samples were treated with RNase A and incubated for 2 minutes at room temperature. Proteinase K and buffer AL were added and samples were incubated for 10 minutes at 70°C. The resulting lysate was centrifuged for 5 minutes at 20,000g and the supernatant was transferred to a fresh tube. Genomic DNA was then extracted using the Qiagen DNAeasy blood and tissue kit following the manufacturer protocol.

treatment_protocol: Each independent sample was stored at -80°C prior to DNA extractions.

tag: sex

value: female

value: adult

value: adult bodies

value: Dmel/y;cn bw sp and Dsim/w501

tag: sample size

value: 60 flies


title: dmel_dsim_w501_female_heads_mixed_RNA_rep3

description: total RNA from adult female heads

hyb_protocol: cDNA samples were hybridized to GeneChip© Drosophila Tiling 1.0R Arrays according to standard manufacturer protocols.

source_name: adult female heads

label_protocol: For each of the RNA samples the starting material for sample processing was 5 ul of total RNA in DEPC H2O (7 ug total RNA).  cDNA was synthesized using the GeneChip© WT Double-Stranded cDNA Synthesis Kit (Affymetrix, PN 900813) according to GeneChip© WT Double-Stranded target assay procedure A: First strand cDNA synthesis protocol. The resulting samples were then cleaned, fragmented and labeled using the Sample Cleanup Module (Affymetrix, PN 900371) and WT Double stranded DNA Terminal Labeling Kit (Affymetrix, PN 900812) following procedures B through D of the WT target assay protocol.

extract_protocol: Samples were homogenized using a motorized pestle in 1ml of TRIzol® in pre-chilled microcentrifuge tubes. Total RNA was then isolated according to the DGRC© RNA extraction protocol (Bogart and Andrews, 2006).

treatment_protocol: Flies were collected between 3:30-5:30 pm on consecutive days, lightly anesthetized (under CO2) and snap frozen in liquid nitrogen.  The heads were separated and collected in a cold room using a sieve chilled on dry ice (Telonis-Scott et al. 2008).  Each independent sample was stored at -80°C prior to RNA extractions.

value: adult, 5-7 days post-eclosion

value: adult heads

value: 100 flies


title: dmel_dsim_c1674_female_bodies_hybrid_DNA

description: genomic DNA from adult female bodies

value: F1 derived from Dmel/y;cn bw sp x Dsim/C167.4


title: dsim_c1674_female_bodies_DNA

description: genomic DNA from adult female bodies

organism: Drosophila simulans


title: dmel_female_bodies_DNA

description: genomic DNA from adult female bodies

organism: Drosophila melanogaster

value: y;cn bw sp


title: dsim_w501_female_bodies_DNA

description: genomic DNA from adult female bodies


title: Normal_CD34(+)_#8


title: dmel_dsim_w501_female_bodies_hybrid_DNA

description: genomic DNA from adult female bodies

value: F1 derived from Dmel/y;cn bw sp x Dsim/w501


title: Normal_CD34(+)_#3

value: MspI


title: Normal_CD34(+)_#6

value: HpaII


title: MDS#9_CD34+

source_name: Bone marrow CD34+ fraction

value: Male

value: Myelodysplasia

tag: time

value: baseline

value: CD34+ fraction


title: Normal_CD34(+)_#7

value: bone marrow

value: CD34+ cells


title: NKL07

value: AML blast cells


title: Normal_CD34(+)_#5


title: Normal_CD34(+)_#1


title: dmel_dsim_c1674_female_heads_hybrid_RNA_rep3

description: total RNA from adult female heads

value: female


title: MDS#38_CD34+

value: AML with trilineage dysplasia


title: Normal_CD34(+)_#4


title: MDS#5-Day29

value: 5-azacytidine + etinostat

value: Day +29

value: CD34- fraction


title: MDS#9-Day29


title: MDS#8-Day29

value: Female


title: MDS#13_CD34-

value: Myelomonocytic leukemia


title: dmel_dsim_w501_female_heads_hybrid_RNA_rep3

description: total RNA from adult female heads

value: adult, 5-7 days post-eclosion

value: adult heads

value: F1 derived from Dmel/y;cn bw sp x Dsim/w501

value: 100 flies


title: MDS#10-Day29

value: Male

value: Relapsed AML

value: MspI

value: HpaII


title: dsim_w501_female_heads_RNA_rep3

description: total RNA from adult female heads


title: dsim_c1674_female_heads_RNA_rep3

description: total RNA from adult female heads


title: MDS#2-Day29

value: bone marrow


title: dmel_female_heads_RNA_rep3

description: total RNA from adult female heads

value: y;cn bw sp


title: dmel_dsim_w501_female_heads_mixed_RNA_rep2

description: total RNA from adult female heads

value: female

value: Dmel/y;cn bw sp and Dsim/w501


title: dmel_dsim_c1674_female_heads_hybrid_RNA_rep2

description: total RNA from adult female heads

value: F1 derived from Dmel/y;cn bw sp x Dsim/C167.4


title: dmel_dsim_w501_female_heads_hybrid_RNA_rep2

description: total RNA from adult female heads


title: dsim_c1674_female_heads_RNA_rep2

description: total RNA from adult female heads


title: dmel_female_heads_RNA_rep2

description: total RNA from adult female heads


title: dsim_w501_female_heads_RNA_rep2

description: total RNA from adult female heads


title: MDS#6-Day29

value: Myelodysplasia

value: 5-azacytidine + etinostat

value: Day +29


title: MDS#12-Day29

value: CD34- fraction


title: MDS#14-Day15

value: Myelomonocytic leukemia

value: Day +15


title: dmel_dsim_w501_female_heads_mixed_RNA_rep1

description: total RNA from adult female heads

value: adult, 5-7 days post-eclosion

value: adult heads


title: MDS#12-Day15

value: Male


title: MDS#10-Day15

value: Relapsed AML


title: dmel_dsim_c1674_female_heads_hybrid_RNA_rep1

description: total RNA from adult female heads

value: 100 flies


title: dmel_dsim_w501_female_heads_hybrid_RNA_rep1

description: total RNA from adult female heads

value: F1 derived from Dmel/y;cn bw sp x Dsim/w501


title: MDS#11-Day15

value: Female

value: AML with trilineage dysplasia

value: bone marrow

value: MspI

value: HpaII


title: dsim_w501_female_heads_RNA_rep1

description: total RNA from adult female heads

value: female


title: dmel_female_heads_RNA_rep1

description: total RNA from adult female heads

value: y;cn bw sp


title: dsim_c1674_female_heads_RNA_rep1

description: total RNA from adult female heads


title: MDS#6-Day15

value: Myelodysplasia

value: 5-azacytidine + etinostat


title: MDS#2-Day15

value: CD34- fraction


title: MDS#9-Day15

value: Day +15


title: MDS#38

value: baseline


title: MDS#5-Day15


title: MDS#8-Day15


title: MDS#13

value: Myelomonocytic leukemia

value: CD34+ fraction


title: MDS#11


title: MDS#12

value: Male

value: Relapsed AML


title: MDS#10


title: MDS#15


title: MDS#17


title: MDS#24


title: MDS#14


title: 1000 ng total RNA from vesicles 2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: 1000 ng total RNA from vesicles 2

hyb_protocol: Sentrix® Human- 6 Expression BeadChip hybridization, washing and staining were also done as suggested by the manufacturer.

scan_protocol: Arrays were scanned on Illumina BeadStation 500 (Illumina, San Diego, CA, USA).

data_processing: BeadChip array data quality control was performed using Illumina BeadStudio software version 3.0. Transcript average intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor. Average transcript intensities were log2 transformed and normalized by loess method.

source_name: microvesicles (MV) derived from human liver stem cells (HLSC)

label_protocol: cRNA was synthesized using three different quantities of total RNA (0.25 μg, 0.5 μg and 1 μg). cRNA synthesis and labeling was done using Illumina RNA Amplification Kit (Ambion) following the procedure suggested by manufacturer.

growth_protocol: MV were obtained from supernatants of HLSC cultured overnight in α-MEM deprived of FCS. The viability of HLSC at the time of MV collection was >99% as detected by trypan blue exclusion. After centrifugation at 2,000 g for 20 minutes cell-free supernatants were centrifuged at 100,000 g (Beckman Coulter Optima L-90K ultracentrifuge) for 1 hour at 4°C, washed in serum-free medium 199 containing Hepes 25mM (Sigma) and submitted to a second ultracentrifugation in the same conditions (21,23). The protein content of MV preparation was quantified by Bradford method (Bio-Rad, Hercules, CA, USA).

extract_protocol: RNA was extracted from MVs using TRIZOL reagent (Invitrogen) following the procedure suggested by the manufacturer. Total RNA was quantified spectrophotometrically (Nanodrop ND- 1000, Wilmington DE, USA).

tag: total rna quantity


title: 1000 ng total RNA from vesicles

description: 1000 ng total RNA from vesicles

value: microvesicles (MV) derived from human liver stem cells (HLSC)


title: MDS#8

value: Female


title: MDS#5


title: 500 ng total RNA from vesicles

description: 500 ng total RNA from vesicles


title: MDS#9


title: 500 ng total RNA from vesicles 2

description: 500 ng total RNA from vesicles 2


title: MDS#6


title: MDS#2

value: AML with trilineage dysplasia


title: 250 ng total RNA from vesicles

description: 250 ng total RNA from vesicles


title: 250 ng total RNA from vesicles 2

description: 250 ng total RNA from vesicles 2


title: CN - cy5 (18) - repeat 17 - mAdbID:74284

status: Public on Aug 04 2009

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

description: mAdb experiment ID: 74284

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.28 Temperature: 36.25

data_processing:
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

source_name: Pooled Normal Liver - cy3

label_protocol:
Cy3 Sample Labeling Protocol
Other: Two ug of the aminoallyl-UTP modified aRNA product was indirectly labeled with Cy3 fluorescent dye.

extract_protocol:
RNA Easy Mini Kit Extraction
Other: Total RNA isolation together with the DNase digestion was performed with the RNA Easy Mini kit (Qiagen, Valencia, CA) following the manufacturer recommendations. Approximately one ìg of total RNA was reversed transcribed and linearly amplified with the Aminoallyl MessageAmp II kit (Ambion, Austin, TX) according to the included protocol.

tag: Tissue

value: liver

source_name: CN - cy5

label_protocol:
Cy5 Sample Labeling Protocol
Other: Two ug of the aminoallyl-UTP modified aRNA product was indirectly labeled with Cy5 fluorescent dye.

tag: Disease state

value: Regenerative (cirrhotic) nodules


title: LGDN - cy3 (55) - repeat 4 - mAdbID:74520

description: mAdb experiment ID: 74520

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.37 Temperature: 36.71

source_name: Pooled Normal Liver - cy5

source_name: LGDN - cy3

value: Low-grade dysplastic nodules


title: Early HCC - cy5 (68) - repeat 19 - mAdbID:74256

description: mAdb experiment ID: 74256

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.53 Temperature: 41.11

source_name: Early HCC - cy5

value: Early Hepatocellular Carcinoma


title: Early HCC - cy3 (68) - repeat 20 - mAdbID:74257

description: mAdb experiment ID: 74257

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.48 Temperature: 42.47

source_name: Early HCC - cy3


title: LGDN - cy5 (55) - repeat 3 - mAdbID:74522

description: mAdb experiment ID: 74522

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.27 Temperature: 39.99

source_name: LGDN - cy5


title: CN - cy3 (85) - repeat 40 - mAdbID:74517

description: mAdb experiment ID: 74517

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.56 Temperature: 41.27

source_name: CN - cy3


title: CN - cy3 (84) - repeat 38 - mAdbID:74516

description: mAdb experiment ID: 74516

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.54 Temperature: 41


title: HGDN - cy3 (148) - repeat 22 - mAdbID:74252

description: mAdb experiment ID: 74252

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.32 Temperature: 42.02

source_name: HGDN - cy3

value: High-grade dysplastic nodules


title: CN - cy3 (115) - repeat 32 - mAdbID:74286

description: mAdb experiment ID: 74286

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.26 Temperature: 37.49


title: CN - cy5 (215) - repeat 19 - mAdbID:74182

description: mAdb experiment ID: 74182

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.23 Temperature: 34.81


title: CN - cy3 (54) - repeat 24 - mAdbID:74189

description: mAdb experiment ID: 74189

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.52 Temperature: 38.25


title: CN - cy3 (83) - repeat 26 - mAdbID:74194

description: mAdb experiment ID: 74194

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.47 Temperature: 38.96


title: CN - cy5 (83) - repeat 25 - mAdbID:74193

description: mAdb experiment ID: 74193

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.6 Temperature: 36.82


title: Early HCC - cy3 (89) - repeat 12 - mAdbID:73907

description: mAdb experiment ID: 73907

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.52 Temperature: 42.06


title: CN - cy5 (54) - repeat 23 - mAdbID:74188

description: mAdb experiment ID: 74188

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.39 Temperature: 35.95


title: Early HCC - cy3 (156) - repeat 10 - mAdbID:73903

description: mAdb experiment ID: 73903

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.29 Temperature: 40.44


title: HGDN - cy5 (148) - repeat 21 - mAdbID:74251

description: mAdb experiment ID: 74251

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.55 Temperature: 40.36

source_name: HGDN - cy5


title: CN - cy3 (215) - repeat 20 - mAdbID:74183

description: mAdb experiment ID: 74183

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.56 Temperature: 37.58


title: CN - cy3 (38) - repeat 22 - mAdbID:74187

description: mAdb experiment ID: 74187

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.61 Temperature: 37.91


title: Early HCC - cy3 (217) - repeat 6 - mAdbID:73899

description: mAdb experiment ID: 73899

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.63;; 1.56 Temperature: 42.4


title: HGDN - cy5 (36) - repeat 23 - mAdbID:73900

description: mAdb experiment ID: 73900

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.62 Temperature: 35.12


title: Early HCC - cy5 (217) - repeat 5 - mAdbID:73898

description: mAdb experiment ID: 73898

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.36 Temperature: 41.37


title: HGDN - cy3 (36) - repeat 24 - mAdbID:73901

description: mAdb experiment ID: 73901

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.54 Temperature: 40.21


title: Early HCC - cy5 (156) - repeat 9 - mAdbID:73902

description: mAdb experiment ID: 73902

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.55 Temperature: 33.83


title: CN - cy5 (38) - repeat 21 - mAdbID:74186

description: mAdb experiment ID: 74186

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.25 Temperature: 35.48


title: CN - cy3 (216) - repeat 10 - mAdbID:73897

description: mAdb experiment ID: 73897

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.61;; 1.37 Temperature: 42.39


title: Early HCC - cy5 (89) - repeat 11 - mAdbID:73906

description: mAdb experiment ID: 73906

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.55 Temperature: 35.06


title: HGDN - cy3 (153) - repeat 20 - mAdbID:73889

description: mAdb experiment ID: 73889

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.57 Temperature: 40


title: HGDN - cy5 (153) - repeat 19 - mAdbID:73888

description: mAdb experiment ID: 73888

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.51 Temperature: 39.19


title: CN - cy3 (214) - repeat 8 - mAdbID:73893

description: mAdb experiment ID: 73893

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.6;; 1.36 Temperature: 41.81


title: CN - cy5 (146) - repeat 47 - mAdbID:73873

description: mAdb experiment ID: 73873

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.56 Temperature: 37.2


title: CN - cy5 (214) - repeat 7 - mAdbID:73892

description: mAdb experiment ID: 73892

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.64 Temperature: 35.7


title: Early HCC - cy3 (149) - repeat 18 - mAdbID:73881

description: mAdb experiment ID: 73881

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.34 Temperature: 40.21


title: HGDN - cy5 (152) - repeat 17 - mAdbID:73886

description: mAdb experiment ID: 73886

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.59 Temperature: 37.42


title: CN - cy5 (216) - repeat 9 - mAdbID:73896

description: mAdb experiment ID: 73896

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.54 Temperature: 41.24


title: CN - cy3 (145) - repeat 46 - mAdbID:73872

description: mAdb experiment ID: 73872

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.41 Temperature: 38.36


title: Early HCC - cy5 (149) - repeat 17 - mAdbID:73880

description: mAdb experiment ID: 73880

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.59 Temperature: 37.5


title: HGDN - cy3 (150) - repeat 16 - mAdbID:73884

description: mAdb experiment ID: 73884

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.57 Temperature: 39.45


title: HGDN - cy5 (150) - repeat 15 - mAdbID:73882

description: mAdb experiment ID: 73882

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.6 Temperature: 36.55


title: CN - cy3 (146) - repeat 48 - mAdbID:73874

description: mAdb experiment ID: 73874

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.36 Temperature: 39.48


title: CN - cy5 (145) - repeat 45 - mAdbID:73871

description: mAdb experiment ID: 73871

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.56 Temperature: 36.58


title: CN - cy3 (144) - repeat 36 - mAdbID:73878

description: mAdb experiment ID: 73878

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.54 Temperature: 40.93


title: CN - cy3 (143) - repeat 44 - mAdbID:73870

description: mAdb experiment ID: 73870

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.58 Temperature: 37.83


title: HGDN - cy3 (152) - repeat 18 - mAdbID:73887

description: mAdb experiment ID: 73887

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.56 Temperature: 39.62


title: HGDN - cy3 (142) - repeat 8 - mAdbID:73868

description: mAdb experiment ID: 73868

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.37 Temperature: 38.61


title: CN - cy3 (116) - repeat 28 - mAdbID:73859

description: mAdb experiment ID: 73859

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.37 Temperature: 37.05


title: CN - cy3 (138) - repeat 30 - mAdbID:73861

description: mAdb experiment ID: 73861

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.35 Temperature: 37.54


title: Early HCC - cy5 (117) - repeat 7 - mAdbID:73856

description: mAdb experiment ID: 73856

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.41;; 1.49 Temperature: 33.57


title: CN - cy5 (116) - repeat 27 - mAdbID:73858

description: mAdb experiment ID: 73858

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.62 Temperature: 34.11


title: HGDN - cy5 (142) - repeat 7 - mAdbID:73867

description: mAdb experiment ID: 73867

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.43;; 1.44 Temperature: 34.95


title: CN - cy5 (143) - repeat 43 - mAdbID:73869

description: mAdb experiment ID: 73869

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.46 Temperature: 36.11


title: CN - cy5 (144) - repeat 35 - mAdbID:73877

description: mAdb experiment ID: 73877

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.54 Temperature: 36.22


title: Early HCC - cy3 (117) - repeat 8 - mAdbID:73857

description: mAdb experiment ID: 73857

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.42 Temperature: 36.31


title: HGDN - cy5 (101) - repeat 9 - mAdbID:73853

description: mAdb experiment ID: 73853

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.3 Temperature: 40.7


title: Early HCC - cy5 (98) - repeat 13 - mAdbID:73851

description: mAdb experiment ID: 73851

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.3 Temperature: 40.43


title: Early HCC - cy3 (70) - repeat 16 - mAdbID:73824

description: mAdb experiment ID: 73824

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.56 Temperature: 35.55


title: CN - cy5 (84) - repeat 37 - mAdbID:73825

description: mAdb experiment ID: 73825

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.29 Temperature: 38.22


title: Early HCC - cy5 (70) - repeat 15 - mAdbID:73823

description: mAdb experiment ID: 73823

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.58 Temperature: 36.38


title: LGDN - cy5 (86) - repeat 5 - mAdbID:73830

description: mAdb experiment ID: 73830

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.54 Temperature: 39


title: HGDN - cy5 (65) - repeat 13 - mAdbID:73818

description: mAdb experiment ID: 73818

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.54 Temperature: 33.58


title: HGDN - cy3 (101) - repeat 10 - mAdbID:73854

description: mAdb experiment ID: 73854

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.6;; 1.32 Temperature: 42.46


title: HGDN - cy3 (63) - repeat 12 - mAdbID:73817

description: mAdb experiment ID: 73817

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.33 Temperature: 38.84


title: LGDN - cy3 (86) - repeat 6 - mAdbID:73831

description: mAdb experiment ID: 73831

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.56 Temperature: 41.45


title: Early HCC - cy3 (98) - repeat 14 - mAdbID:73852

description: mAdb experiment ID: 73852

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.59;; 1.33 Temperature: 42.34


title: HGDN - cy3 (65) - repeat 14 - mAdbID:73819

description: mAdb experiment ID: 73819

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.35 Temperature: 39.03


title: CN - cy5 (85) - repeat 39 - mAdbID:73828

description: mAdb experiment ID: 73828

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.58 Temperature: 39.28


title: CN - cy3 (53) - repeat 6 - mAdbID:73804

description: mAdb experiment ID: 73804

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.59;; 1.58 Temperature: 41.55


title: CN - cy5 (138) - repeat 29 - mAdbID:73860

description: mAdb experiment ID: 73860

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.62 Temperature: 34.59


title: HGDN - cy5 (63) - repeat 11 - mAdbID:73816

description: mAdb experiment ID: 73816

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.57 Temperature: 32.33


title: CN - cy5 (53) - repeat 5 - mAdbID:73803

description: mAdb experiment ID: 73803

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.62 Temperature: 34.43


title: CN - cy3 (61) - repeat 42 - mAdbID:73815

description: mAdb experiment ID: 73815

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.55 Temperature: 35.11


title: CN - cy5 (115) - repeat 31 - mAdbID:73855

description: mAdb experiment ID: 73855

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.51 Temperature: 31.82


title: HGDN - cy3 (12) - repeat 4 - mAdbID:73198

description: mAdb experiment ID: 73198

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.5 Temperature: 41.76


title: HGDN - cy5 (12) - repeat 3 - mAdbID:73197

description: mAdb experiment ID: 73197

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.63 Temperature: 40.8


title: CN - cy5 (2) - repeat 33 - mAdbID:73195

description: mAdb experiment ID: 73195

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.57 Temperature: 31.98


title: CN - cy3 (2) - repeat 34 - mAdbID:73196

description: mAdb experiment ID: 73196

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.41;; 1.63 Temperature: 35.75


title: CN - cy3 (39) - repeat 14 - mAdbID:73202

description: mAdb experiment ID: 73202

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.62 Temperature: 42.07


title: CN - cy5 (39) - repeat 13 - mAdbID:73201

description: mAdb experiment ID: 73201

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.63 Temperature: 41.24


title: Microarray_13549941

city: Nouzilly

first: Cécile

last: Berri

address: CR INRA

department: PHASE

country: France

institute: INRA

description: Gene expression profile analysis between chickens differing for muscle glycogen content and meat quality.

hyb_protocol: A dye-swap procedure was used by labeling alternatively high GP and low GP individuals with the Alexa 555 green dye and the Alexa 647 red dye (Molecular Probes, Invitrogen). The slides were dynamically hybridized at 42°C for 16h in 30-40 ul of buffer (PRONTO!, CORNING, Life Science) containing 30-50 pmoles of each dye using SlideBooster (Olympus Advalytix, Germany). Microarrays were finally washed with AdvaWash (Olympus Advalytix, Germany).

scan_protocol: Detection of fluorescence signals was made with a laser scanner (GenePix 4000B from Axon Instrument, CA) keeping a constant PMT gain for each channel. The images were then analyzed with GenepixPro 6.0 software (Axon instruments, Inc., Union City, CA).

data_processing: Raw data file for each array containing all measured values were stored in GenePix files compatible with the Anapuce 2.0 package (http://cran.r-project.org/web/packages/anapuce/index.html) developed in R language. This package contains functions for the normalization and the analysis of data. The ratio Alexa 647/Alexa 555 used for analysis was expressed as the log2 of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized on each individual array (ratio centered on zero) according to the hypothesis that the majority of gene expressions do not differ between two samples. The normalization was performed by global loess and block effect correction via the subtraction of the median by block using the Package Anapuce 2.0.

label: Alexa Fluor 647

organism: Gallus gallus

source_name: Lean line, 9wks, female  Glycolytic potential = 94.63  ultimate pH = 5.83

label_protocol: Fifty micrograms of each RNA sample were reverse-transcribed and Alexa fluorescent-labeled using the SuperScriptTM PlusIndirect cDNA Labeling System (Invitrogen, Cergy-Pontoise, France) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from Pectoralis major muscle samples rapidly frozen in liquid nitrogen after death using the Qiagen RNeasy Midi Kit (Qiagen, Courtaboeuf, France).

tag: glycolytic potential

value: low

value: Lean

value: female

tag: age

value: 9 weeks

value: muscle

tag: muscle type

value: Pectoralis major

label: Alexa Fluor 555

source_name: Fat line, 9wks, female  Glycolytic potential = 127.63  ultimate pH = 5.58

value: high

value: Fat


title: CN - cy5 (61) - repeat 41 - mAdbID:73814

description: mAdb experiment ID: 73814

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.57 Temperature: 31.83


title: Microarray_13549511

source_name: Fat line, 9wks, female  Glycolytic potential = 123.29  ultimate pH = 5.66

tag: strain

tag: gender

source_name: Lean line, 9wks, female  Glycolytic potential = 90.87  ultimate pH = 5.78


title: Microarray_13549493

source_name: Fat line, 9wks, female  Glycolytic potential = 115.67  pHu = 5.73

tag: tissue

source_name: Lean line, 9wks, female  Glycolytic potential = 95.72  ultimate pH = 5.78


title: CN - cy3 (1) - repeat 12 - mAdbID:73193

description: mAdb experiment ID: 73193

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.62 Temperature: 41.89


title: empty_vector_rep2

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

institute: SISSA/ISAS (International School for Advanced Studies)

description: no additional information

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: RMA

source_name: MN9D expressing empty vector

label_protocol: A 2μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, treated with DnaseI (Ambion) and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

tag: cell line

value: MN9D dopaminergic neuroblastoma cell line

tag: protocol

value: control


title: hemoglobin_overexpression_rep2

description: no additional information

source_name: MN9D overexpressing alpha- and beta- chains of hemoglobin

value: overexpression of alpha- and beta- Hb chains


title: CN - cy5 (1) - repeat 11 - mAdbID:73192

description: mAdb experiment ID: 73192

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.62 Temperature: 41.65

source_name: Pooled Normal Liver - cy3

source_name: CN - cy5


title: hemoglobin_overexpression_rep3

description: no additional information


title: HGDN - cy3 (28) - repeat 6 - mAdbID:73189

description: mAdb experiment ID: 73189

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.64 Temperature: 34.89

source_name: Pooled Normal Liver - cy5


title: Spleen 72h infected vs. uninfected 8 (2C)

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

description: Gene expression afer challenging with Aeromonas salmonicida

hyb_protocol: 300 ng ug of each Cy3 and Cy5-labelled cRNA (specific activity >8.0 pmol Cy3-Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul adding 1ul 25x Agilent fragmentation buffer and 5 ul 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction 25 ul 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the turbot custom oligo-microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE2-v5_95_Feb07 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities.  Those microarrays having an average coefficient of variation (CV) across Spike-In and non-Spike-In probes below 10% were considered for further analysis. The Spike-Ins comprise 10 in vitro synthesized, 20-fold replicated polyadenylated transcripts, which are premixed at 10 concentration ratios to monitor the system for linearity, sensitivity and accuracy across the intensity range. Secondly, the following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot); iv) features below the limit where the linear relationship between concentration and intensity was lost according to Spike-In information; v) genes which did not show at least 3 quality replicates out of 5 and/or a coefficient of variation (CV) across replicates >10%.

organism: Scophthalmus maximus

source_name: Spleen 72h 8

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5)  labeled cRNA was prepared from 50 ng RNA using the Two-Color Microarray-Based Gene Expression Analysis (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 40 individuals (20-30 g each) obtained from a mixture of heterogeneous genetic families was collected at CETGA (Aquaculture Galician Technological Centre)

extract_protocol: Total RNA was extracted from pooled tissues of control and infected fish using TRIZOL Reagent (Life Technologies) according to manufacturer’s recommendations. All extractions were performed by the same researcher.

value: spleen

tag: infection

value: uninfected control

value: Aeromonas salmonicida infected


title: empty_vector_rep3

description: no additional information


title: hemoglobin_overexpression_rep4

description: no additional information


title: Microarray_13549151

source_name: Fat line, 9wks, female  Glycolytic potential = 136.38  ultimate pH = 5.60

source_name: Lean line, 9wks, female  Glycolytic potential = 82.00  ultimate pH = 5.84


title: HGDN - cy5 (28) - repeat 5 - mAdbID:73188

description: mAdb experiment ID: 73188

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.38 Temperature: 32.2

value: liver


title: Spleen 72h infected vs. uninfected 9 (2C)

source_name: Spleen 72h 9


title: hemoglobin_overexpression_rep1

description: no additional information


title: Spleen 72h infected vs. uninfected 7 (2C)

source_name: Spleen 72h 7


title: Spleen 72h infected vs. uninfected 10 (2C)

source_name: Spleen 72h 10


title: Spleen 72h infected vs. uninfected 6 (2C)

source_name: Spleen 72h 6


title: Microarray_13549157

source_name: Lean line, 9wks, female  Glycolytic potential = 94.32  ultimate pH = 5.80

source_name: Fat line, 9wks, female  Glycolytic potential = 124.10  ultimate pH = 5.69


title: empty_vector_rep1

description: no additional information


title: CN - cy3 (18) - repeat 18 - mAdbID:73185

description: mAdb experiment ID: 73185

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.63 Temperature: 33.56

source_name: CN - cy3

value: Regenerative (cirrhotic) nodules


title: Microarray_13549145

source_name: Lean line, 9wks, female  Glycolytic potential = 95.08  ultimate pH = 6.02

source_name: Fat line, 9wks, female  Glycolytic potential = 116.30  ultimate pH = 5.73


title: Microarray_13549137

source_name: Fat line, 9wks, female  Glycolytic potential = 124.72  ultimate pH = 5.71

source_name: Lean line, 9wks, female  Glycolytic potential = 88.47  ultimate pH = 5.89


title: Ishikawa_Control_48h_rep3

status: Public on Aug 13 2009

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description:
Cells known to possess both estrogen and progesterone receptors.
Ctrl_48h_3

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Ishikawa cell line, control, 48hr

label_protocol: Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).

growth_protocol: Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.

extract_protocol: Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).  Quadruplicate samples were advanced to target preparation and GeneChip processing.

treatment_protocol: Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 1pM (very low, vL), 100pM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Bisphenol A.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at each specific time point: 8 hours, 24 hours, and 48 hours.

value: Ishikawa

tag: cell line derivation

value: 39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.

tag: treatment

value: vehicle control

tag: treatment time

value: 48 hours


title: Spleen 72h infected vs. uninfected 5 (2C)

source_name: Spleen 72h 5


title: Microarray_13549130

source_name: Lean line, 9wks, female  Glycolytic potential = 91.06  ultimate pH = 5.81

value: low

value: Lean

value: female

value: 9 weeks

source_name: Fat line, 9wks, female  Glycolytic potential = 108.88  ultimate pH = 5.61


title: Spleen 72h infected vs. uninfected 3 (2C)

source_name: Spleen 72h 3


title: Spleen 72h infected vs. uninfected 2 (2C)

source_name: Spleen 72h 2


title: CN - cy5 (17) - repeat 15 - mAdbID:73183

description: mAdb experiment ID: 73183

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.55 Temperature: 30.31

source_name: Pooled Normal Liver - cy3

source_name: CN - cy5


title: Spleen 72h infected vs. uninfected 4 (2C)

source_name: Spleen 72h 4


title: HGDN - cy5 (141) - repeat 1 - mAdbID:68133

description: mAdb experiment ID: 68133

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.63 Temperature: 40.8

source_name: HGDN - cy5

value: High-grade dysplastic nodules


title: Microarray_13549508

description: Gene expression profiles analysis between chickens differing in muscle glycogen content and meat quality.

hyb_protocol: A dye-swap procedure was used by alternatively labeling high GP and low GP samples with the Alexa 555 green dye and the Alexa 647 red dye (Molecular Probes, Invitrogen). The slides were dynamically hybridized at 42°C for 16h in 30-40 ul of buffer (PRONTO!, CORNING Life Sciences) containing 30-50 pmoles of each dye using SlideBooster (Olympus Advalytix, Germany). Microarrays were washed with the AdvaWash (Olympus Advalytix, Germany).

scan_protocol: Detection of the fluorescence signals was made with a laser scanner (GenePix 4000B from Axon Instrument, CA) keeping a constant PMT gain for each channel. The images were then analyzed with GenepixPro 6.0 software (Axon instruments, Inc., Union City, CA)

data_processing: Raw data file for each array containing all measured values were stored in GenePix files compatible with the Anapuce 2.0 package (http://cran.r-project.org/web/packages/anapuce/index.html) developed in R language. This package contains functions for the normalization and analysis of data. The ratio Alexa 647/Alexa 555 used for analysis was expressed as the log2 of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized on each individual array (ratio centered on zero) according to the hypothesis that the majority of gene expression values do not differ between two samples. The normalization was performed by global lowess and block effect correction via the subtraction of the median by block using the Package Anapuce 2.0.

source_name: F2FL population, 9wks, female  Glycolytic potential = 122.17  ultimate pH = 5.62

label_protocol: Fifty micrograms of each RNA sample were reverse-transcribed and Alexa fluor-labeled using the SuperScriptTM Plus Indirect cDNA Labeling System (Invitrogen, Cergy-Pontoise, France), according to the manufacturer's instructions.

value: high

value: cross between Fat and Lean

tag: generation

value: muscle

value: Pectoralis major

source_name: F2FL population, 9wks, female  Glycolytic potential = 77.59  ultiamte pH = 5.83


title: Spleen 72h infected 14 (1C)

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul adding 1ul 25x Agilent fragmentation buffer and 5 ul 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction 25 ul 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the turbot custom oligo-microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities.  Those microarrays having an average coefficient of variation (CV) across Spike-In and non-Spike-In probes below 10% were considered for further analysis. The Spike-Ins comprise 10 in vitro synthesized, 20-fold replicated polyadenylated transcripts, which are premixed at 10 concentration ratios to monitor the system for linearity, sensitivity and accuracy across the intensity range. Secondly, the following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot); iv) features below the limit where the linear relationship between concentration and intensity was lost according to Spike-In information; v) genes which did not show at least 3 quality replicates out of 5 and/or a coefficient of variation (CV) across replicates >10%.

source_name: Spleen 72h 14

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Fish were challenged with Aeromonas salmonicida intracelomically with a dose adjusted to LD50. The challenges were performed at the CETGA facilities in quarantine tanks. Fish were sacrificed prior to organ extraction using a lethal dose of MS222 anesthetic. Equal amounts of spleen samples were collected after 3 days of injection both in control and challenged fish for pooling.

value: spleen


title: Spleen 72h infected 15 (1C)

source_name: Spleen 72h 15

value: Aeromonas salmonicida infected


title: Spleen 72h control 7 (1C)

source_name: Spleen 72h control 7

value: uninfected control


title: CN - cy3 (17) - repeat 16 - mAdbID:73184

description: mAdb experiment ID: 73184

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.6 Temperature: 33.17

source_name: Pooled Normal Liver - cy5

value: liver

source_name: CN - cy3

value: Regenerative (cirrhotic) nodules


title: Spleen 72h infected vs. uninfected 1 (2C)

source_name: Spleen 72h 1


title: Microarray_13549490

source_name: F2FL population, 9wks, female  Glycolytic potential = 76.41  ultimate pH = 5.81

source_name: F2FL population, 9wks, female  Glycolytic potential = 127.77  ultimate pH = 5.47


title: Microarray_13549501

source_name: F2FL population, 9wks, female  Glycolytic potential = 76.97  ultimate pH = 5.97

source_name: F2FL population, 9wks, female  Glycolytic potential = 123.28  ultimate pH = 5.62


title: Microarray_13549489

source_name: F2FL population, 9wks, female  Glycolytic potential = 139.81  ultimate pH = 5.56

source_name: F2FL population, 9wks, female  Glycolytic potential = 72.82  ultimate pH = 5.95


title: HGDN - cy3 (141) - repeat 2 - mAdbID:68134

description: mAdb experiment ID: 68134

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.39 Temperature: 42.15

source_name: HGDN - cy3


title: CN - cy5 (139) - repeat 3 - mAdbID:68131

description: mAdb experiment ID: 68131

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.37;; 1.54 Temperature: 41.17

source_name: Pooled Normal Liver - cy3

source_name: CN - cy5


title: Spleen 72h control 6 (1C)

source_name: Spleen 72h control 6


title: Microarray_13549144

source_name: F2FL population, 9wks, female  Glycolytic potential = 129.44  ultimate pH = 5.61

source_name: F2FL population, 9wks, female  Glycolytic potential = 70.08  ultimate pH = 5.88


title: Microarray_13549937

source_name: F2FL population, 9wks, female  Glycolytic potential = 115.50  ultimate pH = 5.45

source_name: F2FL population, 9wks, female  Glycolytic potential = 84.83  ultimate pH = 5.86


title: Microarray_13549131

source_name: F2FL population, 9wks, female  Glycolytic potential = 84.53  ultimate pH = 5.82

source_name: F2FL population, 9wks, female  Glycolytic potential = 116.13  ultimate pH = 5.50


title: Early HCC - cy3 (23) - repeat 2 - mAdbID:68094

description: mAdb experiment ID: 68094

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.59 Temperature: 34.26

source_name: Early HCC - cy3

value: Early Hepatocellular Carcinoma

source_name: Pooled Normal Liver - cy5


title: CN - cy3 (139) - repeat 4 - mAdbID:68132

description: mAdb experiment ID: 68132

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.64 Temperature: 41.58

source_name: CN - cy3


title: CN - cy3 (114) - repeat 2 - mAdbID:68128

description: mAdb experiment ID: 68128

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.35;; 1.64 Temperature: 41.41


title: Spleen 72h infected 13 (1C)

source_name: Spleen 72h 13


title: Early HCC - cy5 (23) - repeat 1 - mAdbID:68093

description: mAdb experiment ID: 68093

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.58 Temperature: 32.86

source_name: Early HCC - cy5


title: LGDN - cy3 (47) - repeat 2 - mAdbID:68090

description: mAdb experiment ID: 68090

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.43;; 1.31 Temperature: 37.82

source_name: LGDN - cy3

value: Low-grade dysplastic nodules


title: Microarray_13549158

source_name: F2FL population, 9wks, female  Glycolytic potential = 83.67  ultimate pH = 5.84

source_name: F2FL population, 9wks, female  Glycolytic potential = 138.62  ultimate pH = 5.59


title: Spleen 72h infected 11 (1C)

source_name: Spleen 72h 11


title: Spleen 72h control 4 (1C)

source_name: Spleen 72h control 4


title: Spleen 72h control 5 (1C)

source_name: Spleen 72h control 5


title: Spleen 72h infected 9 (1C)

source_name: Spleen 72h 9


title: LGDN - cy5 (47) - repeat 1 - mAdbID:68089

description: mAdb experiment ID: 68089

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.29 Temperature: 36.21

source_name: Pooled Normal Liver - cy3

source_name: LGDN - cy5


title: Early HCC - cy5 (147) - repeat 3 - mAdbID:68087

description: mAdb experiment ID: 68087

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.58 Temperature: 35.14


title: Spleen 72h infected 10 (1C)

source_name: Spleen 72h 10


title: chagasic_cardiomyocytes_rep3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Determine the transcriptomic alteration induced by infection with the parasite T. cruzi

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed iterative algorithm, alternating within-array normalization with interarray normalization, until the average corrected ratio differed by <5% from the previous one (Iacobas et al. Physiol Genomics 2005, PMID: 15585606).

label: Alexa Fluor®_647

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: The cultures were maintained at 37°C in a 5% CO2 humidified incubator. Four days after the cardiac myocytes were plated, they displayed spontaneous contractility; they were then infected with trypomastigotes of the myotropic Brazil strain of T. cruzi at a multiplicity of infection of 5:1.  Parasites were maintained and harvested from L6E9 myoblasts.  After 24 hours of incubation, the cultures were washed thoroughly with medium and maintained as described above. At 48 hours after infection the percent parasitism was determined by staining replicate dishes in situ with May-Grunwald-Giemsa. The percent parasitism was approximately 75 % at the time when the cells were harvested for microarray analysis.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Neonatal mice were killed by decapitation, and the hearts were isolated and placed in 60 mm plastic culture dishes containing sterile ice-cold Dulbecco's phosphate-buffered saline (PBS; GIBCO-BRL, Grand Island, NY). After rinsing with PBS to remove the blood, we thoroughly minced the hearts in the dissociation solution [containing 1.25% pancreatin (GIBCO-BRL) and 300 mg of bovine serum albumin (BSA; Sigma, St. Louis, MO) diluted in (in g/100 ml) 8.0 NaCl, 0.2 KCl, 0.05 Na2HPO4, 1.0 NaHCO3, and 2.0 dextrose; pH 7.1-7.2]. The homogenate was then transferred to a 25 ml Ehrlenmeyer flask with 7 ml of the dissociation solution and placed in a water bath (37°C) for 10 min under continuous stirring. The supernatant fraction containing single cells from each digestion period was collected in a conical 15 ml tube and spun at 500 g for 4 min, and the pellet was re-suspended in 3 ml of Dulbecco's modified Eagle's medium (DMEM) [containing 10% fetal bovine serum (GIBCO-BRL) and 1% penicillin/streptomycin (GIBCO-BRL)]. The tube with the dissociated cells was then placed in the incubator (37°C, 5% CO2). This procedure was repeated five to seven times or until the heart tissue was totally dissociated. The cells were pooled and preplated, in 100 mm plastic culture dishes for 1 h, to allow the non muscle cells to attach. Then, the remaining unattached cells, highly enriched in myocytes, were plated (2x105 cells/cm2) into 12.5 cm2 plastic culture flasks (Falcon, USA), placed in the incubator, and allowed to settle for 24 h. After this period, we washed the flasks with DMEM to remove the non-adherent cells and fed the cells with 3 ml of DMEM supplemented with cytosine  -D-arabino-furanoside (12.2 mg/50 ml media; Sigma) to inhibit fibroblast growth.

tag: developmental stage neonatal

value: cardiomyocyte

value: T. cruzi


title: Spleen 72h infected 12 (1C)

source_name: Spleen 72h 12


title: chagasic_cardiomyocytes_rep1

hyb_protocol: The Alexa Fluor®_555-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label_protocol: 20ug total RNA extracted from each culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: chagasic_cardiomyocytes_rep2

hyb_protocol: Alexa Fluor®_555-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: CN - cy5 (114) - repeat 1 - mAdbID:68127

description: mAdb experiment ID: 68127

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.37;; 1.63 Temperature: 40.94

source_name: CN - cy5


title: Spleen 72h control 2 (1C)

source_name: Spleen 72h control 2


title: RR2 + PMNs

city: Copenhagen

first: Morten

last: Alhede

address: Blegdamsvej 3B

department: International Health, Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description: Gene expression in Pseudomonas aeruginosa biofilm exposed to PMNs for 2 hours

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 55C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAO1_deletion_lasRrhlR mutant strain; Pseudomonas Genetic Stock Center

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

growth_protocol: Biofilms were grown at 37 ºC in continuous-culture silicon tubing, as previously described by (Hentzer et al., 2003; Hentzer, 2005), perfused with ABT minimal media supplemented with 0.5 w/v % glucose (AB medium (Clark & Maaløe, 1967)). Media were supplemented with antibiotics where appropriate. Unless otherwise stated, all strains were incubated in growth media at 37 ºC. Due to the need of a large quantity of cells for the transcriptomic analysis the volume of the biofilm flow chambers had to be fairly large. A biofilm flow chamber consisted of a 12 cm long silicon tube (inner diameter: 0.8 cm) with a total volume of 6 ml. The flow chamber was connected to a media reservoir with silica tubing of smaller dimension, with the inclusion of a peristaltic pump creating the liquid flow. Furthermore, a bubble trap was included between the flow cell and the pump and the effluent was collected in a waste flask that was connected via silica tubing to the distal end of the flow cell. 100 µl of wild type or lasRrhlR deletion mutant O/N cultures was diluted in 10 ml fresh medium. Six ml was then injected into each of six channels (3 of each strain). To allow cell attachment the flow into the chamber was halted for one hour, by clamping both the influent and effluent tubes. Sterile ABTG minimal medium were then pumped through the chamber. The medium flow was set to 23 rpm (60 ml hour-1) using a Watson Marlow 205S pump. The relatively high flow rate is maintained to ensure that planktonic bacteria were washed out of the setting.

extract_protocol: RNeasy Mini Kits (QIAGEN)

treatment_protocol: The biofilms were allowed to grow and develop in the biofilm flow chambers for 3 days before challenge with PMNs. Fresh PMNs from human volunteers were isolated and resuspended in RPMI-1640 medium (BIOCHROM AG) as previously described by Bjarnsholt et al. 2005 (Bjarnsholt et al., 2005). Prior to PMN injection the flow was halted. Ten million PMNs were resuspended in 6 ml of RPMI media and injected into the flow chamber. The concentration of PMNs was found by microscopy to be approximately 1 PMN per 1000 bacterial cells. PMNs and biofilm were incubated for 2 hours. The flow chambers were rolled every 15 minutes to ensure that the entire biofilm was exposed to the PMNs. After incubation the fluid inside the chamber was discarded and the attached biofilm cells were loosened by rolling. The cells were then mechanically removed and collected in 6 ml of RNAlater®.

tag: Biofilm + PMNs

tag: Age


title: Spleen 72h infected 8 (1C)

source_name: Spleen 72h 8


title: Spleen 72h infected 7 (1C)

source_name: Spleen 72h 7


title: Spleen 72h control 3 (1C)

source_name: Spleen 72h control 3


title: Spleen 72h infected 6 (1C)

source_name: Spleen 72h 6


title: RR2 Control

tag: Biofilm control


title: Spleen 72h infected 4 (1C)

source_name: Spleen 72h 4


title: RR1 + PMNs


title: Spleen 72h infected 5 (1C)

source_name: Spleen 72h 5


title: Early HCC - cy3 (147) - repeat 4 - mAdbID:68088

description: mAdb experiment ID: 68088

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.58 Temperature: 34.8

source_name: Early HCC - cy3

tag: Tissue

tag: Disease state

source_name: Pooled Normal Liver - cy5


title: RR1 Control


title: chagasic_cardiomyocytes_rep4


title: WT3+PMNs

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas Genetic Stock Center

tag: Biofilm - PMNs


title: Spleen 72h infected 2 (1C)

source_name: Spleen 72h 2


title: control_cardiomyocytes_rep2

hyb_protocol: 20ug total RNA extracted from each culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA). The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-aha-dUTP labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label_protocol: 20 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Alexa Fluor®_555 (Invitrogen, CA)

growth_protocol: The cultures were maintained at 37°C in a 5% CO2 humidified incubator.

tag: strain

value: control


title: Spleen 72h infected 3 (1C)

source_name: Spleen 72h 3


title: control_cardiomyocytes_rep4


title: control_cardiomyocytes_rep3

hyb_protocol: 20ug total RNA extracted from atria of each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA). The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-aha-dUTP labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label_protocol: 20 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Alexa Fluor®_647 (Invitrogen, CA)


title: control_cardiomyocytes_rep1

hyb_protocol: The Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.


title: WT1+PMNs


title: Spleen 72h infected 1 (1C)

source_name: Spleen 72h 1


title: WT2 Control


title: Spleen 72h control 1 (1C)

source_name: Spleen 72h control 1


title: Rightwhale_4hour_Control_biologicalreplicate1

status: Public on Aug 03 2009

city: Charleston

first: Marine

last: Genomics

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

description: Data 'condensed' from 2-3 biological replicates.

hyb_protocol: Cy3 labeled aRNA (approx. 700ng) of each sample with Agilent spike in control was incubated with fragmentation buffer for 30 minutes at 60 ºC and then hybridized to the right whale oligonucleotide microarray (Agilent design # 019375) for 17 hrs at 65ºC.

scan_protocol: Following hybridization, arrays were washed with Agilent gene expression wash buffers I and II for 1 minute each at room temperature and 37°C, respectively, dried with acetonitrile, and scanned using the Agilent Scanner. Data were extracted with Agilent Feature Extraction software version A8.5.1. Data for one biological replicate of cells exposed to 10-8M CdCl2 for 4 hours was not used for statistical analysis due to extremely high spot intensity values believed to be an artifact of over-fragmentation of the RNA. Therefore, we suggest that RNA to be hybridized to the right whale array should be amplified and labeled using Agilent’s Quick Amp Labeling kit to ensure proper RNA fragmentation.

data_processing: Raw data from Feature Extraction software was uploaded to Bioconductor in R language and was background corrected using the normexp model (Ritchie et al., 2007). Next, the data was quantile normalized using the aroma.light package (Bengtsson et al., 2008).  Genes with the 3 replicates having a mean expression less than the mean expression of the K. brevis probes in 10% of the arrays were removed as a control for non-specific binding. Replicates of each probe were averaged. Furthermore, the data was variance stabilized normalization (VSN) transformed using the vsn package (Huber et al., 2002). T-tests with Empirical Bayes correction was used to compare significant differentially expressed genes for each cadmium concentration versus control at each time of exposure (Smyth, 2004). The p-values of the t-test were adjusted using the false discovery rate method (Benjamini and Hochberg, 1995). Significantly regulated genes were given parameters of greater than one log fold change (lfc) and an adjusted p-value <0.001.

organism: Eubalaena glacialis

source_name: Kidney fibroblast cells

label_protocol: RNA (approx. 700ng) of each sample was amino allyl-modified and amplified using Amino Allyl Message AmpTM II aRNA Amplification Kit (Ambion Inc, Austin, TX) and stored at -80ºC. Approximately 3µg of the allyl-modified aRNA was Cy3 dye labeled using Amino Allyl Message AmpTM II aRNA Amplification Kit (Ambion Inc, Austin, TX) and stored at -80ºC.

growth_protocol: E. glacialis kidney fibroblast immortalized cell line was acquired from the Wise Laboratory, University of Southern Maine. Cells were grown and passaged in DMEM/F12 (1:1 Ham 1x) containing L-Glutamine and 15mM HEPES media (Gibco-BRL, Bethesda, MD) with 15% fetal bovine serum (FBS) and antibiotic master mix (10ug/mL Penicillin, 10ug/mL Streptomycin, 25ug/mL Amphotericin B) and incubated at 37°C and 5% CO2.

extract_protocol: After exposure, media was aspirated off and cells of each row were lysed and pooled together with 350µL RLT buffer into a 1.5mL microcentrifuge tube containing 3.5µL β-mercaptoethanol. Total RNA of each sample was extracted using RNeasy Mini Kit (Qiagen, Austin, TX) and stored at -80ºC.

treatment_protocol: Cells were plated (approx. 200,000 cells/well) with 1mL DMEM/F12 15% FBS media into nine 24-well tissue culture plates and allowed to adhere overnight in 37°C and 5% CO2 incubation. Culture medium was aspirated off and cells were washed with 1mL DMEM serum free media to remove excess serum. One row of cells for each plate (6 wells) was exposed to 1mL of DMEM/F12 serum free media (Control), or to 10-6M CdCl2, 10-7M CdCl2, or 10-8M CdCl2 in the same medium. Plates were incubated for exposure times of 1 hour, 4 hours, or 24 hours with three plates/exposure time thereby having three biological replicates for each treatment.

value: Kidney

tag: cell type

value: fibroblasts

tag: agent

tag: time


title: WT2+PMNs


title: WT3 Control


title: Rightwhale_4hour_0.1uMCdCl2_biologicalreplicate1

tag: tissue

tag: dose


title: Rightwhale_4hour_1.0uMCdCl2_biologicalreplicate1


title: Rightwhale_4hour_0.01uMCdCl2_biologicalreplicate1


title: Liver irradiated 1Gy 3h rep11

city: Evry

first: Alexandre

last: Pawlik

address: 2, rue Gaston Crémieux

department: DSV/DRR

institute: CEA

description: totalRNA sample from non-irradiated liver was labeled in Cy3 and hybridized against totalRNA sample from irradiated liver labeled in Cy5.

data_processing: lowess normalization using Genespring 6.0

source_name: Non-Irradiated Liver

tag: Organism Part:Liver

tag: total RNA was isolated using RNeasy kit

source_name: Irradiated Liver

tag: Liver was removed 3 hours after whole body gamma irradiation of a single dose (1Gy)


title: Liver irradiated 1Gy 3h rep15


title: Rightwhale_24hour_Control_biologicalreplicate1


title: Liver irradiated 1Gy 3h rep16

description: totalRNA sample from non-irradiated liver was labeled in Cy5 and hybridized against totalRNA sample from irradiated liver labeled in Cy3.


title: Liver irradiated 1Gy 3h rep10


title: Rightwhale_24hour_1.0uMCdCl2_biologicalreplicate1


title: Liver irradiated 1Gy 3h rep13


title: Liver irradiated 1Gy 3h rep9


title: Liver irradiated 1Gy 3h rep6


title: Liver irradiated 1Gy 3h rep7


title: Liver irradiated 1Gy 3h rep14


title: Rightwhale_24hour_0.1uMCdCl2_biologicalreplicate1


title: Rightwhale_24hour_0.01uMCdCl2_biologicalreplicate1


title: Liver irradiated 1Gy 3h rep5


title: Rightwhale_1hour_0.1uMCdCl2_biologicalreplicate1


title: Rightwhale_1hour_0.01uMCdCl2_biologicalreplicate1


title: Rightwhale_1hour_Control_biologicalreplicate1


title: Rightwhale_1hour_1.0uMCdCl2_biologicalreplicate1


title: Liver irradiated 1Gy 3h rep12


title: A2780 DMSO/BIO treatment 3 rep 1

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

country: United Kingdom

institute: The University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm as per manufacturor's instructions.

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: All data was analysed within Genespring GX version 7.3.1. Data was normalised using a Lowess intensity dependant normalisation.

source_name: A2780 ovarian adenocarcinoma cells, treated with DMSO

label_protocol: 800 ng of total RNA was labelled with Cy3 (DMSO treated cells) or Cy5 (BIO treated cells) using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

growth_protocol: A2780 ovarian adenocarcinoma cells were cultured in RPMI medium containing 10 % Fetal Bovine Serum and 1 % L-glutamine.

extract_protocol: Cells were rinsed in PE, trypsanised and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions.

treatment_protocol: 21 day continual culture in the presence of DMSO or 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO) with replenishment weekly on days 1 and 4.

source_name: A2780 ovarian adenocarcinoma cells, treated with 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO)


title: Liver irradiated 1Gy 3h rep2


title: A2780 DMSO/BIO treatment 3 rep 2

tag: A2780 ovarian adenocarcinoma cells, treated with DMSO

tag: A2780 ovarian adenocarcinoma cells, treated with 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO)


title: A2780 DMSO/BIO treatment 2 rep 2


title: Liver irradiated 1Gy 3h rep8


title: Liver irradiated 1Gy 3h rep1


title: Stat-rpoS-rep2

city: Hamilton

first: Herb

middle: E

last: Schellhorn

state: ON

address: 1280 Main St. W.,

department: Biology

country: Canada

institute: McMaster University

description: no additional information

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GCRMA method

organism: Escherichia coli O157:H7 str. EDL933

source_name: Stationary phase culture of EDL933 rpoS mutants in LB at OD600 of 1.5

label_protocol: Affymetrix protocol

growth_protocol: Cells were grown in Luria Bertani (LB) media at 37C at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at OD600 = 0.3 in exponential phase and at OD600 = 1.5 in stationary phase.

extract_protocol: Acidic Hot Phenol

tag: growth phase

value: Stationary

tag: genotype

value: rpoS


title: Liver irradiated 1Gy 3h rep4


title: Liver irradiated 1Gy 3h rep3


title: IP20D-3-rep3

city: Shanghai

first: Fanyi

last: Zeng

address: 24/1400 West Beijing Road

department: Institute of Medical Genetics

country: China

institute: Shanghai Jiao Tong University

description: Gene expression data from iPS cell line IP20D-3.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: Expression Console (with MAS5.0) was used to quantify microarray signals with default analysis parameters and global scaling to target mean=150.

source_name: Induced pluripotent stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells and iPS cells were cultured on mitomycin C treated MEF cells with DMEM plus 15% FBS or 20% Knockout serum replacement (KOSR), 1000u/ml LIF, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol and 0.1 mM nonessential amino acid (NEAA).

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

treatment_protocol: Cells were collected and pelleted before Trizol was added and stored in -80oC before extraction.

tag: cell line

value: iPS

tag: genetic background


title: A2780 DMSO/BIO treatment 1 rep 1


title: IP20D-3-rep1


title: A2780 DMSO/BIO treatment 1 rep 2


title: IP14D-101-rep3

description: Gene expression data from iPS cell line IP14D-101.


title: IP14D-101-rep2


title: Stat-WT-rep1

description: no additional information

source_name: Stationary phase culture of EDL933 wild type in LB at OD600 of 1.5

value: WT


title: Stat-WT-rep3

description: no additional information


title: Stat-rpoS-rep1

description: no additional information


title: Exp-rpoS-rep1

description: no additional information

source_name: Exponential phase culture of EDL933 rpoS mutants in LB at OD600 of 0.3

value: Exponential


title: IP14D-1-rep1

description: Gene expression data from iPS cell line IP14D-1.


title: IP14D-1-rep3


title: Exp-rpoS-rep2

description: no additional information


title: MEF-rep2

description: Gene expression data from Mouse Embryonic Fibroblast cells that was used to generate iPS cells.

source_name: Mouse embryo fibroblast

value: MEF


title: Exp-WT-rep3

description: no additional information

source_name: Exponential phase culture of EDL933 wild type in LB at OD600 of 0.3


title: IP20D-3-rep2