title: IM9 cells - ch128.1Av - 24h - rep2

description:
Time course experiment
Replicate 2/2
IM9AT24R2

source_name: IM9 cells (sensitive) - ch128.1Av - 24h - rep2

value: IM9 (sensitive)


title: cell line: U266 - ch128.1Av - 1h - rep2

status: Public on Feb 09 2010

type: RNA

city: Los Angeles

first: Manuel

last: Penichet

state: CA

department: Department of Surgery

country: USA

institute: University of California, Los Angeles

description:
Time course experiment
Replicate 2/3
U266AT1R2

hyb_protocol: Illumina HumanRef-8 V2 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data was extracted with Illumina BeadStudio software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: cell line: U266 (tolerant) - ch128.1Av - 1h - rep2

label_protocol: Illumina protocol

growth_protocol: Cells were grown in 24-well plates under tissue culture conditions (37ºC and 5%CO2)

extract_protocol: RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978). Targets were prepared from 200 ng total RNA using Illumina. TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791).

treatment_protocol:
Treatment with ch128.1Av
2x10e5 IM-9 and cell line: U266 (tolerant) were incubated in 24-well plates under tissue culture conditions (37ºC and 5%CO2) with 10 nM ch128.1Av or buffer for 1h, 3h, 9h, and 24h

tag: cell line

value: U266 (tolerant)


title: cell line: U266 - Control - 24h - rep1

description:
Time course experiment
Replicate 1/2
U266CT24R1

source_name: cell line: U266 (tolerant) - Control - 24h - rep1

treatment_protocol:
No treatment
2x10e5 IM-9 and cell line: U266 (tolerant) were incubated in 24-well plates under tissue culture conditions (37ºC and 5%CO2) with 10 nM ch128.1Av or buffer for 1h, 3h, 9h, and 24h


title: IM9 cells - ch128.1Av - 24h - rep1

description:
Time course experiment
Replicate 1/2
IM9AT24R1

source_name: IM9 cells (sensitive) - ch128.1Av - 24h - rep1


title: cell line: U266 - Control - 9h - rep1

description:
Time course experiment
Replicate 1/2
U266CT9R1

source_name: cell line: U266 (tolerant) - Control - 9h - rep1


title: cell line: U266 - Control - 9h - rep2

description:
Time course experiment
Replicate 2/2
U266CT9R2

source_name: cell line: U266 (tolerant) - Control - 9h - rep2


title: cell line: U266 - ch128.1Av - 9h - rep1

description:
Time course experiment
Replicate 1/3
U266AT9R1

source_name: cell line: U266 (tolerant) - ch128.1Av - 9h - rep1


title: cell line: U266 - Control - 1h - rep1

description:
Time course experiment
Replicate 1/2
U266CT1R1

source_name: cell line: U266 (tolerant) - Control - 1h - rep1


title: cell line: U266 - Control - 3h - rep2

description:
Time course experiment
Replicate 2/2
U266CT3R2

source_name: cell line: U266 (tolerant) - Control - 3h - rep2


title: cell line: U266 - Control - 24h - rep2

description:
Time course experiment
Replicate 2/2
U266CT24R2

source_name: cell line: U266 (tolerant) - Control - 24h - rep2


title: cell line: U266 - ch128.1Av - 9h - rep2

description:
Time course experiment
Replicate 2/3
U266AT9R2

source_name: cell line: U266 (tolerant) - ch128.1Av - 9h - rep2


title: Pancreatic islets_DBD_4

city: Madison

first: Jamie

middle: M

last: Sperger

state: WI

address: 1111 Highland Ave.  RM 5168

institute: University of Wisconsin - Madison

description: Biological replicate 4 of 10.

hyb_protocol: After purification, 1.65 ug of cRNA was fragmented and hybridized to the array for 17 hr. at 65 C.  Microarray slides were hybridized overnight, then washed.

scan_protocol: Microarray slides were scanned with Agilent G2565CA Microarray Scanner. Images were analyzed with Feature Extraction 9.5.3 or Feature Extraction 10.1 (Agilent Technologies, CA).

data_processing: Data was processed using the Genesifter software package.  Data were normalized using median normalization.  Pairwise analysis (t-test with cutoff of 0.05 and fold change cutoff of 2) were done to determine the list of differentially expressed genes.

source_name: Pancreatic islets, DBD

label_protocol: Approximately 500 ng of total RNA was amplified and labeled with Cy3 using the Quick Amp Labeling Kit, One Color (Agilent Technologies, CA). This labeling reaction produces 0.25 – 2.0 µg of Cy3-labeled cRNA (anti-sense), by first Converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

growth_protocol: Pancreatic islets were isolated from DCD or DBD donors.

extract_protocol: Islets (2000 – 4000 IEQ) were pelleted by centrifugation, washed in PBS, resuspended in 1 mL Trizol (Invitrogen, Carlsbad, CA) and RNA purified following manufacturer’s instructions.   RNA was further purified using the Qiagen RNeasy Kit (Qiagen, Germantown, MD) including the on-column DNase digestion step.  The concentration of the samples was determined using the NanoDrop® ND-1000 UV-Vis Spectrophotometer. RNA samples were analyzed by the FGC using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples. The RNA was of high quality and all samples passed our QC cutoff.

treatment_protocol: Islets were isolated using a modification of the automated Ricordi method. In brief, Collagenase NB1, Neutral Protease (Serva Electrophoresis, Heidelberg, Germany) and DNase (RocheApplied-Sciences, Inc., Indianapolis, IN) in Hanks’ balanced salt solution were infused manually into the main pancreatic duct. The Ricordi chamber was shaken manually and islets purified by centrifugation on a continuous biocoll gradient (Biochrom AG, Berlin, Germany) in a COBE 2991 cell processor (Lakewood, CO).  For islet equivalent (IEQ) determination, islet samples were stained with dithizone (Sigma-Aldrich) and sized using an eyepiece reticle and inverted microscope.  The calculation of purity was based on the ratio of dithizone positive (islets) compared to dithizone negative (acinar) elements.  Islets were cultured in M1A Media (Mediatech, Herndon, VA) supplemented with reduced glutathione (Sigma-Aldrich) at 25oC in a 5% CO2/95% air incubator.

tag: donation time

value: after brain death

tag: tissue

value: pancreatic islets

tag: cold ischemia time

value: 397 min

tag: gender

value: male

tag: age

tag: bmi


title: Pancreatic islets_DBD_3

description: Biological replicate 3 of 10.

value: 120 min


title: cell line: U266 - ch128.1Av - 3h - rep1

description:
Time course experiment
Replicate 1/2
U266AT3R1

source_name: cell line: U266 (tolerant) - ch128.1Av - 3h - rep1


title: cell line: U266 - Control - 0h - rep2

description:
Time course experiment
Replicate 2/2
U266CT0R2

source_name: cell line: U266 (tolerant) - Control - 0h - rep2


title: cell line: U266 - Control - 0h - rep1

description:
Time course experiment
Replicate 1/2
U266CT0R1

source_name: cell line: U266 (tolerant) - Control - 0h - rep1


title: IM9 cells - ch128.1Av - 3h - rep1

description:
Time course experiment
Replicate 1/3
IM9AT3R1

source_name: IM9 cells (sensitive) - ch128.1Av - 3h - rep1


title: IM9 cells - ch128.1Av - 9h - rep2

description:
Time course experiment
Replicate 2/2
IM9AT9R2

source_name: IM9 cells (sensitive) - ch128.1Av - 9h - rep2


title: IM9 cells - ch128.1Av - 1h - rep1

description:
Time course experiment
Replicate 1/2
IM9AT1R1

source_name: IM9 cells (sensitive) - ch128.1Av - 1h - rep1


title: IM9 cells - Control - 24h - rep1

description:
Time course experiment
Replicate 1/2
IM9CT24R1

source_name: IM9 cells (sensitive) - Control - 24h - rep1


title: IM9 cells - Control - 9h - rep2

description:
Time course experiment
Replicate 2/2
IM9CT9R2

source_name: IM9 cells (sensitive) - Control - 9h - rep2


title: IM9 cells - ch128.1Av - 1h - rep2

description:
Time course experiment
Replicate 2/2
IM9AT1R2

source_name: IM9 cells (sensitive) - ch128.1Av - 1h - rep2


title: IM9 cells - Control - 1h - rep2

description:
Time course experiment
Replicate 2/2
IM9CT1R2

source_name: IM9 cells (sensitive) - Control - 1h - rep2


title: IM9 cells - ch128.1Av - 9h - rep1

description:
Time course experiment
Replicate 1/2
IM9AT9R1

source_name: IM9 cells (sensitive) - ch128.1Av - 9h - rep1


title: IM9 cells - Control - 3h - rep1

description:
Time course experiment
Replicate 1/2
IM9CT3R1

source_name: IM9 cells (sensitive) - Control - 3h - rep1


title: IM9 cells - ch128.1Av - 3h - rep3

description:
Time course experiment
Replicate 3/3
IM9AT3R3

source_name: IM9 cells (sensitive) - ch128.1Av - 3h - rep3


title: IM9 cells - Control - 0h - rep2

description:
Time course experiment
Replicate 2/2
IM9CT0R2

source_name: IM9 cells (sensitive) - Control - 0h - rep2


title: IM9 cells - ch128.1Av - 3h - rep2

description:
Time course experiment
Replicate 2/3
IM9AT3R2

source_name: IM9 cells (sensitive) - ch128.1Av - 3h - rep2


title: IM9 cells - Control - 3h - rep2

description:
Time course experiment
Replicate 2/2
IM9CT3R2

source_name: IM9 cells (sensitive) - Control - 3h - rep2


title: IM9 cells - Control - 24h - rep2

description:
Time course experiment
Replicate 2/2
IM9CT24R2

source_name: IM9 cells (sensitive) - Control - 24h - rep2


title: WGA_384, NCFM, 1 ml (C), 10 ml (T)

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description: The ratio between the average absolute pixel values for the replicated spots of each gene with and without treatment represented the fold change in gene expression.  Confidence intervals and P values on the fold change were also calculated with the use of a two-sample t test. P values of 0.05 or less were considered significant

hyb_protocol: see TIGR Microarray Protocols and Standard Operating Procedures website

scan_protocol: Fluorescence intensities were acquired using a General Scanning ScanArray 4000 Microarray Scanner (Packard Biochip BioScience, Biochip Technologies LLC, Mas.) and processed as TIFF images.

data_processing: Signal intensities were quantified using the QuantArray 3.0 software package (Packard BioScience). The local background was subsequently subtracted from the recorded spot intensities.  Data was median normalized.

organism: Lactobacillus acidophilus

source_name: NCFM_log phase_10 ml

extract_protocol: Azcarate-Peril et al., 2005

tag: Non-concentrated, incubated (1h, 37°C) log phase cultures

source_name: NCFM_log phase_1 ml

tag: 10-fold concentrated, incubated (1h, 37°C) log-phase cultures


title: IM9 cells - Control - 1h - rep1

description:
Time course experiment
Replicate 1/2
IM9CT1R1

source_name: IM9 cells (sensitive) - Control - 1h - rep1


title: IM9 cells - Control - 0h - rep1

description:
Time course experiment
Replicate 1/2
IM9CT0R1

source_name: IM9 cells (sensitive) - Control - 0h - rep1


title: WGA, NCFM, 10 ml (C), 1 ml (T)

label_protocol: see TIGR Microarray Protocols and Standard Operating Procedures website

tag: Non-concentrated, incubated (1h 37°C) log-phase cultures

tag: 10-fold concentrated, incubated (1h 37°C) log-phase cultures


title: WGA_384, NCFM, 1 ml (C), 10 ml (T) - Biological Replicate 2

source_name: NCFM-log phase_10 ml

tag: Non-concentrated, incubated (1h, 37°C) log-phase cultures


title: IM9 cells - Control - 9h - rep1

description:
Time course experiment
Replicate 1/2
IM9CT9R1

source_name: IM9 cells (sensitive) - Control - 9h - rep1


title: WGA, NCFM, 10 ml (C), 1 ml (T)-Biological Replicate 2

tag: Non-concentrated, incubated (1 h, 37°C) log phase cultures.

tag: 10-fold concentrated, incubated (1 h, 37°C) log phase cultures.


title: Prieurianin treated 240 hr

status: Public on Feb 08 2010

city: Toledo

first: Khew-Voon

last: Chin

state: OH

address: 3000 Arlington Avenue

department: Medicine

institute: The University of Toledo College of Medicine

description: Prieurianin treated 240 hr

hyb_protocol: The Mouse OneArray was hybridized using 2X Gex Hybridization Buffer (Agilent) for 17 h at 65oC; then washed in Gene Expression Wash Buffer 1 and 2 (Agilent) per manufacturer's instruction.

scan_protocol: The arrays were scanned with GenePix 4000B array scanner, images of the hybridized arrays were processed BioDiscovery's ImaGene and signal intensities quantified.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

organism: Mus musculus

source_name: Mouse 3T3-L1 Preadipocytes

label_protocol: cDNA were synthesized from the isolated total RNA by reverse transcription followed by second strand synthesis using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion, Austin, TX) with oligo(dT) primer that contain a T7 RNA polymerase promoter sequence, according to the manufacturer’s specification.  In vitro transcription was then performed with the purified cDNA and amino allyl UTP was incorporated during transcription to produce amino allyl modified aRNA that was subsequently coupled to cy5 dye label.

growth_protocol: Mouse 3T3-L1 cells, obtained from ATCC, were cultured at 37oC in 5% CO2.

extract_protocol: Total RNA was isolated using Qiagen's Rneasy column according to manufacturer's specification.

treatment_protocol: Cell were treated with either 0.5% DMASO or 2 µM of prieurianin for the indicated times follows by RNA isolation.

value: 3T3-L1 Preadipocytes


title: Prieurianin treated 48 hr

description: Prieurianin treated 48 hr


title: Prieurianin treated 192 hr

description: Prieurianin treated 192 hr


title: Prieurianin treated 288 hr

description: Prieurianin treated 288 hr


title: Prieurianin treated 144 hr

description: Prieurianin treated 144 hr


title: Prieurianin treated 96 hr

description: Prieurianin treated 96 hr


title: Prieurianin treated 24 hr

description: Prieurianin treated 24 hr


title: Prieurianin treated 9 hr

description: Prieurianin treated 9 hr


title: Prieurianin treated 36 hr

description: Prieurianin treated 36 hr


title: Prieurianin treated 15 hr

description: Prieurianin treated 15 hr


title: Prieurianin treated 12 hr

description: Prieurianin treated 12 hr


title: Prieurianin treated 0.25 hr

description: Prieurianin treated 0.25 hr


title: DMSO treated 288 hr

description: DMSO treated 288 hr


title: Prieurianin treated 0 hr

description: Prieurianin treated 0 hr


title: DMSO treated 24 hr

description: DMSO treated 24 hr


title: DMSO treated 48 hr

description: DMSO treated 48 hr


title: Prieurianin treated 3 hr

description: Prieurianin treated 3 hr


title: DMSO treated 240 hr

description: DMSO treated 240 hr


title: Prieurianin treated 0.5 hr

description: Prieurianin treated 0.5 hr


title: DMSO treated 36 hr

description: DMSO treated 36 hr


title: Prieurianin treated 2 hr

description: Prieurianin treated 2 hr


title: Prieurianin treated 1 hr

description: Prieurianin treated 1 hr


title: DMSO treated 192 hr

description: DMSO treated 192 hr


title: Prieurianin treated 5 hr

description: Prieurianin treated 5 hr


title: DMSO treated 15 hr

description: DMSO treated 15 hr


title: DMSO treated 12 hr

description: DMSO treated 12 hr


title: DMSO treated 0 hr

description: DMSO treated 0 hr


title: DMSO treated 96 hr

description: DMSO treated 96 hr


title: DMSO treated 1 hr

description: DMSO treated 1 hr


title: DMSO treated 3 hr

description: DMSO treated 3 hr


title: DMSO treated 0.5 hr

description: DMSO treated 0.5 hr


title: DMSO treated 2 hr

description: DMSO treated 2 hr


title: DMSO treated 0.25 hr

description: DMSO treated 0.25 hr


title: DMSO treated 5 hr

description: DMSO treated 5 hr


title: DMSO treated 9 hr

description: DMSO treated 9 hr


title: DMSO treated 144 hr

description: DMSO treated 144 hr


title: Untreated Control at 288 hr

description: Untreated Control at 288 hr


title: Untreated Control at 96 hr

description: Untreated Control at 96 hr


title: Untreated Control at 240 hr

description: Untreated Control at 240 hr


title: Untreated Control at 144 hr

description: Untreated Control at 144 hr


title: Untreated Control at 192 hr

description: Untreated Control at 192 hr


title: Untreated Control at 15 hr

description: Untreated Control at 15 hr


title: Untreated Control at 24 hr

description: Untreated Control at 24 hr


title: Untreated Control at 2 hr

description: Untreated Control at 2 hr


title: Untreated Control at 5 hr

description: Untreated Control at 5 hr


title: spnD39_ccnA_IU2841vsIU2678_BHI_rep2

status: Public on Feb 03 2010

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio~1.0). Images were analysed using GenePix Pro 5.0 software (molecular Devices)

data_processing: Data were normalized with BASE (Bioarray Software Environment) using the Lowess normalization method without background subtraction.

organism: Streptococcus pneumoniae

source_name: IU2678, S. pneumoniae bacterial strain D39 ΔciaR::P-ermB CEP::Pnative-ccnA

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight. Low density (OD620 0.05 to 0.1) overnight cultures of 10 to 11 hours were diluted into 30 mL of BHI in 250 mL bottles to a starting OD of 0.001. Separate bottles were used for each time points. The cultures were mixed by gentle swirling only at the time of inoculation and when cultures were removed for RNA preparation. Cultures were grown at 37C and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from growing cultures (OD620~0.1) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520. Because this procedure used Centriplus YM-30 cartridges (Millipore) and RNeasy (Qiagen) columns, RNA species smaller than 200 nt are excluded.

tag: IU2678-- S. pneumoniae bacterial strain D39 with deletion of ciaR, and an ectopic construct in the CEP site. There is no ccnA expression in this strain because ccnA expression is under the control of its native promoter, which is totally dependent on CiaR

source_name: IU2841, S. pneumoniae bacterial strain D39 ΔciaR::P-ermB CEP::Pmal(c)-ccnA

tag: IU2841-- S. pneumoniae bacterial strain D39 with deletion of ciaR, and an ectopic construct in the CEP site. There is ccnA expression in this strain because ccnA expression is under the control of the constitutive promoter, Pmal(c).


title: Untreated Control at 12 hr

description: Untreated Control at 12 hr


title: Untreated Control at 48 hr

description: Untreated Control at 48 hr


title: Untreated Control at 9 hr

description: Untreated Control at 9 hr


title: Untreated Control at 3 hr

description: Untreated Control at 3 hr


title: Untreated Control at 0.25 hr

description: Untreated Control at 0.25 hr


title: Untreated Control at 36 hr

description: Untreated Control at 36 hr


title: Untreated Control at 0.5 hr

description: Untreated Control at 0.5 hr


title: spnD39_ccnA_IU2841vsIU2678_BHI_rep3


title: Untreated Control at 1 hr

description: Untreated Control at 1 hr


title: spnD39_ccnA_IU2841vsIU2678_BHI_rep1

tag: IU2678-- S. pneumoniae bacterial strain D39 with deletion of ciaR, and an ectopic construct in the CEP site.  There is no ccnA expression in this strain because ccnA expression is under the control of its native promoter, which is totally dependent on CiaR

tag: IU2841-- S. pneumoniae bacterial strain D39 with deletion of ciaR, and an ectopic construct in the CEP site.  There is ccnA expression in this strain because ccnA expression is under the control of the constitutive promoter, Pmal(c.


title: Untreated Control at 0 hr

description: Untreated Control at 0 hr

tag: cell line


title: CC+

status: Public on Feb 02 2010

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Gene expression of 7-2_14CCw

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

label_protocol: Affymetrix standard protocol

extract_protocol: Affymetrix standard protocol

treatment_protocol: Control treated with CMP

tag: Control treated with CMP


title: CTLCMP-

description: Gene expression of CTL_CMP-

treatment_protocol: Control treated with No CMP

tag: Control treated with No CMP


title: CMPKO+a

description: Gene expression of CMP_KO+a

treatment_protocol: Stat5 KO treated with CMP

tag: Stat5 KO treated with CMP


title: KOCMP-

description: Gene expression of KO_CMP-

treatment_protocol: Stat5 KO treated with No CMP

tag: Stat5 KO treated with No CMP


title: osteosarcoma biopsy sample OSE09

status: Public on Feb 01 2010

city: Tsukiji

first: Eisuke

last: Kobayashi

state: Chuou-ku Tokyo

department: Chemotherapy Division

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix human genome HG-U133A genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanned on a GeneArray scanner.

data_processing: The data were analyzed and normalized using MAS5 algorithm with the ArrayAssist 5.0 software package (Stratagene, La Jolla, CA).

source_name: The total RNA from osteosarcoma

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

extract_protocol: Total RNA extracted using IsoGen lysis buffer following manufacturer's instructions.

tag: age

tag: gender

tag: subtype

value: osteoblastic

value: Tibia

value: Proximal

tag: chemotherapeutic response

value: poor

tag: development of metastasis

value: No


title: KC+

description: Gene expression of 6-26_2KCw


title: CC-

description: Gene expression of 7-2_13CCwo


title: KOCMP+

description: Gene expression of KO_CMP+


title: osteosarcoma biopsy sample OSE15

value: female

value: telangiectatic

value: Femur

value: Distal

value: good


title: osteosarcoma biopsy sample OSE16

value: Yes


title: CMPKO-

description: Gene expression of CMP_KO-


title: osteosarcoma biopsy sample OSE14

value: Humerus


title: KC-

description: Gene expression of 7-2_9KCwo


title: CMPCTL+

description: Gene expression of CMP_CTL+


title: CTLCMP+

description: Gene expression of CTL_CMP+


title: osteosarcoma biopsy sample OSE08


title: osteosarcoma biopsy sample OSE05

value: chondroblastic


title: osteosarcoma biopsy sample OSE02


title: osteosarcoma biopsy sample OSE01


title: osteosarcoma biopsy sample OSR49

value: Osteoblastic


title: osteosarcoma biopsy sample OSR48

value: male


title: osteosarcoma biopsy sample OSR39


title: osteosarcoma biopsy sample OSR50


title: osteosarcoma biopsy sample OSR45


title: osteosarcoma biopsy sample OSR46

value: Chondroblastic


title: osteosarcoma biopsy sample OSR28


title: osteosarcoma biopsy sample OSR35

value: Fibroblastic


title: L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 1

city: Baltimore

first: Yanqin

last: Yang

address: 600 N. Wolfe Street

institute: The Johns Hopkins University

description: E.coli WT3110

hyb_protocol: Fragmented, biotinylated cDNA was hybridized to E. coli Genome 2.0  GeneChips for 16hours at 45oC and 60rpm.  Washing/staining was performed according to Affymetrix recommended Prokaryotic protocol, in a FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with GCOS 1.4 software.  All probe sets scaling was performed with a target signal value of 500.  No normalization was performed.

organism: Escherichia coli str. K-12 substr. W3110

source_name: L-form colony morphology

label_protocol: 10 ug total RNA was processed according to the Affymetrix recommended protocol for prokaryotic targets.  cDNA was fragmented and endlabeled with biotin.

growth_protocol: 72hr colony growth equiv. to wildtype colony size

extract_protocol: MasterPure RNA purification Kit

treatment_protocol: 10,000U Pencillin G in media

tag: strain

value: L-form


title: wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 2

description: E.coli WT3110

source_name: wildtype colony morphology

growth_protocol: overnight colony growth

value: wildtype


title: wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 3

description: E.coli WT3110


title: wildtype, brain heart infusion agar, rep 2

description: E.coli WT3110


title: L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 3

description: E.coli WT3110


title: L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 2

description: E.coli WT3110


title: osteosarcoma biopsy sample OSR32


title: osteosarcoma biopsy sample OSR47

value: Proximal


title: wildtype, brain heart infusion agar, rep 3

description: E.coli WT3110


title: wildtype, brain heart infusion agar, rep 1

description: E.coli WT3110


title: osteosarcoma biopsy sample OSR25


title: osteosarcoma biopsy sample OSR27


title: wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 1

description: E.coli WT3110


title: osteosarcoma biopsy sample OSR26

value: poor


title: osteosarcoma biopsy sample OSR18

value: Tibia

value: No


title: 12 hpi

status: Public on Jan 08 2010

type: mixed

city: Guelph

first: Dan-Hui

state: Ontario

address: 488 Gordon Street

department: Dept. of Molecular and Cellular Biology

country: Canada

institute: University of Guelph

description: Temporal expression profiles of all 146 ORFs, and their complements, of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) were determined by a modified oligonucleotide based two-channel DNA microarray. Total RNA was isolated at different times post infection from Cf203 insect cells infected with CfMNPV. The cDNA was synthesized, fluorescently labeled with Cy3, and co-hybridized to the microarray chips along with Cy5-labeled CfMNPV viral genomic DNA (vgDNA), which was used as an equimolar reference standard for each gene.

hyb_protocol: The Cy3-labeled cDNA and Cy5-labeled vgDNA samples were combined at a 4 to 1 ratio (w/w) in DIG Easy-Hyb (Roche Applied Science) containing 0.45 mg/ml yeast tRNA, 0.45 mg/ml calf thymus DNA (20 ml in total), denatured at 95°C for 5 min, snap-cooled and co-hybridized to a prehybridized microarray glass slide (15 ml each array area) overnight (16-20 h) at 42°C in a hybridization chamber (Die-Tech).

scan_protocol: The microarray slides were scanned using GenePix 4200A (Axon Instruments Inc.Foster City, CA) with an excitation wavelength of 532 nm (Cy3) and 635 nm (Cy5).

data_processing: The GPR files derived from the GenePix Pro program were imported into GeneSpring GX 7.3.1 (Agilent) for data normalization. The fluorescence intensity for each array probe was expressed as the difference between the average median signal intensity for all spots representing the same probe and the local median background intensity. The relative fluorescence intensities were expressed as GeneSpring normalized log2 ratios of the Cy3-cDNA to Cy5-vgDNA fluorescence levels.

molecule: genomic DNA

organism: Choristoneura fumiferana multiple nucleopolyhedrovirus

source_name: vgDNA, 12 hpi

label_protocol: The vgDNA was labeled with the Cy5 fluorescent dye (Perkin-Elmer) by nick translation (Roche Applied Science). The dye-labeled DNAs were purified using the QIAquick PCR purification kit (Qiagen), precipitated and resuspended in 5-10 ml nuclease-free H2O each. The quantity and quality of the dye-labeled DNAs were determined using ND-1000 spectrophotometer (NanoDrop Technologies Inc.).

extract_protocol: CfMNPV genomic DNA extracted by phenol chloroform

tag: biomaterial

value: CfMNPV viral genomic DNA

source_name: cDNA, 12 hpi

label_protocol: The Cy3 fluorescent dye (Perkin-Elmer) labeled cDNAs were synthesized from 20 mg total RNA using 2 mg oligo dT20VN primer (Sigma) for each sample according to the Direct cDNA Labeling Synthesis Protocol (Qiagen)

extract_protocol: Total RNA was extracted from the cells using the TRIZOL-Invitrogen protocol and further purified using the RNAeasy Qiagen columns

value: Cf203 insect cells infected with CfMNPV


title: 48 hpi

source_name: vgDNA, 48 hpi

source_name: cDNA, 48 hpi


title: 24 hpi

source_name: vgDNA, 24 hpi

source_name: cDNA, 24 hpi


title: 36 hpi

source_name: vgDNA, 36 hpi

source_name: cDNA, 36 hpi


title: osteosarcoma biopsy sample OSR13

value: female

value: Teleangiectatic

value: Femur


title: 9 hpi

source_name: vgDNA, 9 hpi

source_name: cDNA, 9 hpi


title: 18 hpi

source_name: vgDNA, 18 hpi

source_name: cDNA, 18 hpi


title: 72 hpi

source_name: vgDNA, 72 hpi

source_name: cDNA, 72 hpi


title: osteosarcoma biopsy sample OSR20

source_name: The total RNA from osteosarcoma

value: Distal


title: osteosarcoma biopsy sample OSR17

value: Yes


title: 3 hpi

source_name: vgDNA, 3 hpi

source_name: cDNA, 3 hpi


title: Cy3-nodal-overexpressing & Cy5-control

status: Public on Jan 26 2010

city: Kochi

first: Kaoru

last: Mita

address: 2-5-1, Akebono-cho

institute: Kochi University

description: Late gastrulae carrying Ci-FoxD/lacZ transgene were used for the reference sample. Late gastrulae carrying Ci-FoxD/Ci-nodal transgene were used for the Nodal-overexpressing sample.

hyb_protocol: Hybridization and washing protocols were according to the manufacturer’s instructions (Agilent Technologies).

scan_protocol: The microarrays were scanned with a GenePix4000B DNA Microarray Scanner (Axon Instruments, Foster City, CA). The resulting fluorescence intensity for each spot was quantified using GENEPIX PRO 4.0 microarray analysis software (Axon Instruments).

data_processing: Quantified images were exported into text files for statistical analysis. After removing the flagged features and subtracting the background value we took the ratio (Cy5/Cy3) of the intensity signals. The data were not normalized.

organism: Ciona intestinalis

source_name: Nodal-overexpressing LG

label_protocol: Five micrograms of total RNA was labeled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: C. intestinalis was cultivated for a few months in the Uranouchi Inlet near the Usa Marine Biological Institute of Kochi University, Kochi, Japan. Gametes were surgically obtained from the gonoducts of mature adults. Eggs were inseminated with non-self sperm. Dechorionated 1-cell embryos were electroporated with the Ci-FoxD/Ci-nodal transgene. Embryos were raised in seawater at room temperature (18-20˚C) until the late gastrula stage.

extract_protocol: To prepare total RNA from C. intestinalis eggs, the acid guanidine thiocyanate-phenol/chloroform (AGPC) method was used.

tag: developmental stage

value: late gastrula

tag: transgene

value: Ci-FoxD/Ci-nodal

source_name: control LG

label_protocol: Five micrograms of total RNA was labeled with Cy5 using the Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: C. intestinalis was cultivated for a few months in the Uranouchi Inlet near the Usa Marine Biological Institute of Kochi University, Kochi, Japan. Gametes were surgically obtained from the gonoducts of mature adults. Eggs were inseminated with non-self sperm. Dechorionated 1-cell embryos were electroporated with the Ci-FoxD/lacZ transgene. Embryos were raised in seawater at room temperature (18-20˚C) until the late gastrula stage.

value: Ci-FoxD/lacZ


title: 0 hpi

source_name: vgDNA, 0 hpi

source_name: cDNA, 0 hpi


title: osteosarcoma biopsy sample OSR24

value: Osteoblastic

value: good


title: 1 hpi

source_name: vgDNA, 1hpi

source_name: cDNA, 1hpi


title: Cy3-control & Cy5-nodal-overexpressing

growth_protocol: C. intestinalis was cultivated for a few months in the Uranouchi Inlet near the Usa Marine Biological Institute of Kochi University, Kochi, Japan.  Gametes were surgically obtained from the gonoducts of mature adults.  Eggs were inseminated with non-self sperm.  Dechorionated 1-cell embryos were electroporated with the Ci-FoxD/lacZ transgene.  Embryos were raised in seawater at room temperature (18-20˚C) until the late gastrula stage.

growth_protocol: C. intestinalis was cultivated for a few months in the Uranouchi Inlet near the Usa Marine Biological Institute of Kochi University, Kochi, Japan.  Gametes were surgically obtained from the gonoducts of mature adults.  Eggs were inseminated with non-self sperm.  Dechorionated 1-cell embryos were electroporated with the Ci-FoxD/Ci-nodal transgene.  Embryos were raised in seawater at room temperature (18-20˚C) until the late gastrula stage.


title: 6 hpi

source_name: vgDNA, 6 hpi

source_name: cDNA, 6 hpi


title: osteosarcoma biopsy sample OSR07

value: male


title: MO-B.1.13.259 (Cy3)

status: Public on Jan 01 2010

city: Irapuato

first: June

last: Simpson-Williamson

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Plant Genetic Engineering

country: Mexico

institute: Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 ?g/ l tRNA and 0.2 ?g/ l Salmon Sperm DNA) for 14h. After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation at 1600 r.p.m.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis.

data_processing: Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method substract whereas normalization of the signal intensities within slides was carried out using the printtiploess method and the Aquantile normalization (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org).

organism: Zea mays

source_name: total RNA leaves

label_protocol: 30 ?g total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

growth_protocol: Zea mays L. seeds from 85-2, Cajete criollo and Michoacan 21 landraces were surface sterilized with NaOCl (10%) for 30 min and then washed with distilled water before sowing. After washes in distilled water, seeds were germinated and grown in 15 L plastic pots in a substrate of 92.46% sand and 7.44% clay under greenhouse conditions. Temperatures were between 19° C to 32°C and relative humidity was 60±5%.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and a second re-extraction with Plant RNA purification Reagent Concert (Invitrogen) according to the manufacturer's guidelines.

treatment_protocol: 30 day old plants were subjected to a progressive water deficit by leaving them unwatered for 10 days, 17 days (severe stress) and then given a recovery irrigation

tag: treatment

value: Recovery irrigation

tag: biological replicate

tag: landrace

value: Michoacan 21


title: MO-B.1.13.271 (Cy5)

value: 17 days stress


title: MO-B.1.13.260 (Cy3)


title: MO-B.1.13.269 (Cy3)


title: MO-B.1.13.258 (Cy5)


title: MO-B.1.13.272 (Cy5)


title: MO-B.1.13.264 (Cy5)

value: 10 days stress


title: MO-B.1.13.261 (Cy5)


title: MO-B.1.13.273 (Cy3)

value: 0 days stress


title: MO-B.1.13.288 (Cy5)


title: MO-B.1.13.296 (Cy5)

value: Cajete criollo


title: MO-B.1.13.257 (Cy3)


title: MO-B.1.13.297 (Cy3)


title: MO-B.1.13.263 (Cy5)


title: MO-B.1.13.268 (Cy5)


title: MO-B.1.13.267 (Cy3)


title: MO-B.1.13.292 (Cy3)


title: MO-B.1.13.259 (Cy5)


title: MO-B.1.13.265 (Cy5)


title: MO-B.1.13.275 (Cy5)


title: MO-B.1.13.266 (Cy5)


title: MO-B.1.13.274 (Cy3)


title: MO-B.1.13.258 (Cy3)


title: MO-B.1.13.271 (Cy3)


title: MO-B.1.13.296 (Cy3)


title: MO-B.1.13.293 (Cy3)


title: MO-B.1.13.274 (Cy5)


title: MO-B.1.13.261 (Cy3)

value: 85-2 maize


title: MO-B.1.13.260 (Cy5)


title: MO-B.1.13.268 (Cy3)


title: MO-B.1.13.290 (Cy5)


title: MO-B.1.13.288 (Cy3)


title: MO-B.1.13.267 (Cy5)


title: MO-B.1.13.257 (Cy5)


title: MO-B.1.13.263 (Cy3)


title: MO-B.1.13.289 (Cy3)


title: MO-B.1.13.292 (Cy5)


title: MO-B.1.13.264 (Cy3)


title: MO-B.1.13.272 (Cy3)


title: MO-B.1.13.297 (Cy5)


title: MO-B.1.13.273 (Cy5)


title: MO-A.1.13.254 (Cy5)

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 μg/ l tRNA and 0.2 μg/ l Salmon Sperm DNA) for 14h. After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation at 1600 r.p.m.

label_protocol: 30 μg total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

tag: replicate

value: Biological 2


title: MO-B.1.13.275 (Cy3)


title: MO-A.1.13.242 (Cy3)

value: Biological 1


title: MO-B.1.13.266 (Cy3)


title: MO-A.1.13.285 (Cy3)


title: MO-A.1.13.260 (Cy5)


title: MO-A.1.13.277 (Cy5)


title: MO-A.1.13.247 (Cy5)


title: MO-A.1.13.257 (Cy3)


title: MO-B.1.13.290 (Cy3)


title: MO-A.1.13.252 (Cy5)


title: MO-B.1.13.269 (Cy5)


title: MO-A.1.13.262 (Cy5)


title: MO-A.1.13.245 (Cy3)


title: MO-B.1.13.265 (Cy3)


title: MO-A.1.13.272 (Cy3)


title: MO-A.1.13.249 (Cy3)


title: MO-A.1.13.251 (Cy5)


title: MO-B.1.13.289 (Cy5)


title: MO-A.1.13.250 (Cy5)


title: MO-B.1.13.293 (Cy5)


title: MO-A.1.13.274 (Cy3)


title: MO-A.1.13.255 (Cy3)


title: MO-A.1.13.245 (Cy5)


title: MO-A.1.13.253 (Cy5)


title: MO-A.1.13.254 (Cy3)


title: MO-A.1.13.255 (Cy5)


title: MO-A.1.13.280 (Cy3)


title: MO-A.1.13.242 (Cy5)


title: MO-A.1.13.261 (Cy3)


title: MO-A.1.13.285 (Cy5)


title: MO-A.1.13.258 (Cy5)


title: MO-A.1.13.253 (Cy3)


title: MO-A.1.13.261 (Cy5)


title: MO-A.1.13.279 (Cy5)


title: MO-A.1.13.256 (Cy3)


title: MO-A.1.13.250 (Cy3)


title: MO-A.1.13.247 (Cy3)


title: MO-A.1.13.275 (Cy5)


title: MO-A.1.13.251 (Cy3)


title: MO-A.1.13.248 (Cy3)


title: MO-A.1.13.256 (Cy5)


title: CMPCTL-

description: Gene expression of CMP_CTL-


title: MO-A.1.13.249 (Cy5)


title: MO-A.1.13.260 (Cy3)


title: MO-A.1.13.280 (Cy5)


title: MO-A.1.13.252 (Cy3)


title: MO-A.1.13.257 (Cy5)


title: MO-A.1.13.277 (Cy3)


title: MO-A.1.13.279 (Cy3)


title: MO-A.1.13.248 (Cy5)


title: MO-A.1.13.258 (Cy3)


title: MO-A.1.13.272 (Cy5)


title: MO-A.1.13.262 (Cy3)


title: MO-A.1.13.274 (Cy5)


title: MO-A.1.13.275 (Cy3)


status: Public on Dec 31 2009

city: Bellaterra

first: Anna

last: Tomas

state: Barcelona

address: campus UAB

department: Viral infections

country: Spain

institute: CReSA

description: Gene expression data of blood, PCV2 inoculated pig, 29dpi, biological rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Genechip Scanner 3000

data_processing: The data were analyzed with the Data Mining Tool (DMT) from Affymetrix. RMA was used as normalization method.

organism: Sus scrofa

source_name: blood of a PCV2 inoculated pig at day 29

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

growth_protocol: Whole blood samples were collected at 0, 7, 14, 21 and 29 days post-inoculation in EDTA tubes. Samples were immediately lysed with nucleic acid purification lysis solution (Applied Biosystems, Warrington, UK) and frozen at -80ºC until usage

extract_protocol: Total RNA was extracted with the RiboPure kit (Ambion Cat #1924) according to the manufacturer's instructions.

treatment_protocol: Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n=4) and inoculated with 105.2 TCID50 of the Burgos PCV2 isolate (n=4). Pigs were bled at 0, 7, 14, 21, and 29 days post-inoculation.

tag: cell type

value: whole blood

tag: agent

value: PCV2 inoculated


description: Gene expression data of blood, PCV2 inoculated pig, 21dpi, biological rep 2

source_name: blood of a PCV2 inoculated pig at day 21


description: Gene expression data of blood, PCV2 inoculated pig, 29dpi, biological rep 3


description: Gene expression data of blood, PCV2 inoculated pig, 21dpi, biological rep 1


description: Gene expression data of blood, control pig, 21dpi, biological rep 2

source_name: blood of a control pig at day 21

value: Control


description: Gene expression data of blood, control pig, 29dpi, biological rep 3

source_name: blood of a control pig at day 29


description: Gene expression data of blood, control pig, 21dpi, biological rep 1


description: Gene expression data of blood, control pig, 29dpi, biological rep 1


description: Gene expression data of blood, PCV2 inoculated pig, 14dpi, biological rep 1

source_name: blood of a PCV2 inoculated pig at day 14


description: Gene expression data of blood, PCV2 inoculated pig, 29dpi, biological rep 4


description: Gene expression data of blood, PCV2 inoculated pig, 21dpi, biological rep 3


description: Gene expression data of blood, control pig, 29dpi, biological rep 4


description: Gene expression data of blood, PCV2 inoculated pig, 7dpi, biological rep 3

source_name: blood of a PCV2 inoculated pig at day 7


title: High phosphate 4hr-2

city: Seoul

first: Joo Myung

last: Ahn

address: Anam-dong, Seongbuk-gu

department: Life Science and Biotechnology

country: South Korea

institute: Korea University

description: Data with flag value 0 were used for normalization processing.

hyb_protocol: HS400™ Pro hybridization system (TECAN, Switzerland) was used for hybridization, washing, and drying for 17 h at 60 C.

scan_protocol: The fluorescent intensities of each spot were scanned with a Genepix 4000B laser scanner (Axon Instruments, Inc., CA, USA). We scanned each duplicated block in  Agilent-013384 Yeast Oligo Microarray separately. The scanned images were captured and analyzed using GenepixPro 3.0 software (Axon Instruments Inc., CA, USA).

data_processing: The Cy3 and Cy5 intensity values were derived from a median value of the pixel-by-pixel intensity after subtracting the background fluorescence. The Cy5/Cy3 intensity ratios were calculated and normalized with a median value for all the spots. The defective spots were eliminated from the data sets, and excluded as non-specific hybridizations accoding to Acuity 4.0 filter criterion.

organism: Saccharomyces cerevisiae

source_name: Arsenate treated 4hr with normal phosphate condition

label_protocol: Each RNA sample, i.e., the control and chemical treated samples was mixed with polyA and incubated at 65°C for 10 min and immediately cooled on ice. Afterwards, both samples were labeled using fluorescent cyanine 3 (Cy3)-dUTP (for the control) and Cy5-dUTP (for the treated sample) (PerkinElmer Life Science, USA) at 42 °C for 2 hour using Superscript II reverse transcriptase (BD Biosciences, CA, USA) and in presence of dNTPs (10mM of dATP, dCTP, dGTP and 2mM dTTP). The RNA was degraded by adding 0.1M NaOH followed by incubation at 65 °C for 15 min. The reaction mixture containing labeled cDNA was neutralized by adding same volume of 0.1M HCl. Both of the labeled probes were then mixed and purified using a PCR purification kit (QIAGNEN, USA).

growth_protocol: Yeast S. cerivisiae strain S288C  was used in this study. Initially, a single colony was inoculated in YNB medium (without phosphate and sodium chloride) that contained 2% sucrose and different concentration of phosphate (KH2PO4) and pH was adjusted to 5.7. The culture was incubated at 30 C and 250 rpm and cells were allowed to grow until an optical density reaches to 1.0 at 660 nm followed by re-inoculation of 2 ml of this culture into fresh media (98 ml).

extract_protocol: The total RNA was extracted and purified using an RNeasy Mini Kit (QIAGEN, USA)

treatment_protocol: The cultures were allowed to grow until the optical density reached to 0.08 at 660 nm and 200 μl of arsenate (Na2HAsO4•7H2O) stock was added (Final Concentration 2μM). For control, 200 mM sodium chloride (NaCl) was added in place of arsenate for ion balance.

source_name: Control (without treatment)


description: Gene expression data of blood, PCV2 inoculated pig, 14dpi, biological rep 2


description: Gene expression data of blood, control pig, 21dpi, biological rep 3


description: Gene expression data of blood, PCV2 inoculated pig, 14dpi, biological rep 4


description: Gene expression data of blood, PCV2 inoculated pig, 14dpi, biological rep 3


title: High phosphate 8hr-2

source_name: Arsenate treated 8hr with normal phosphate condition


title: High phosphate 8hr-1


title: High phosphate 10hr-1

source_name: Arsenate treated 10hr with normal phosphate condition


description: Gene expression data of blood, PCV2 inoculated pig, 29dpi, biological rep 1


description: Gene expression data of blood, control pig, 14dpi, biological rep 3

source_name: blood of a control pig at day 14


description: Gene expression data of blood, control pig, 14dpi, biological rep 1


description: Gene expression data of blood, control pig, 14dpi, biological rep 2


description: Gene expression data of blood, PCV2 inoculated pig, 7dpi, biological rep 4


description: Gene expression data of blood, PCV2 inoculated pig, 7dpi, biological rep 2


description: Gene expression data of blood, control pig, 14dpi, biological rep 4


title: High phosphate 4hr-1


description: Gene expression data of blood, control pig, 7dpi, biological rep 3

source_name: blood of a control pig at day 7


description: Gene expression data of blood, control pig, 7dpi, biological rep 4


description: Gene expression data of blood, control pig, 21dpi, biological rep 4


description: Gene expression data of blood, control pig, 7dpi, biological rep 1


description: Gene expression data of blood, control pig, 0dpi, biological rep 3

source_name: blood of a control pig at day 0


description: Gene expression data of blood, PCV2 inoculated pig, 0dpi, biological rep 1

source_name: blood of a PCV2 inoculated pig at day 0


description: Gene expression data of blood, PCV2 inoculated pig, 0dpi, biological rep 4


title: Low phosphate 10hr-2

description: Data with flag value 0 were used for normalization processing.

scan_protocol: The fluorescent intensities of each spot were scanned with a Genepix 4000B laser scanner (Axon Instruments, Inc., CA, USA). The scanned images were captured and analyzed using GenepixPro 3.0 software (Axon Instruments Inc., CA, USA).

source_name: Arsenate treated 10hr with limited phosphate


description: Gene expression data of blood, control pig, 0dpi, biological rep 1


title: Low phosphate 10hr-1


title: Low phosphate 4hr-2

source_name: Arsenate treated 4hr with limited phosphate


title: Low phosphate 4hr-1


description: Gene expression data of blood, PCV2 inoculated pig, 0dpi, biological rep 2


description: Gene expression data of blood, control pig, 0dpi, biological rep 2


title: Low phosphate 8hr-2

source_name: Arsenate treated 8hr with limited phosphate


title: Low phosphate 8hr-1


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 5

city: Bonn

first: Michaela

last: Kern

address: Sigmund-Freud-Str. 25

country: Germany

institute: University of Bonn

description: Sufficient amount of high quality RNA was isolated and LSEC transcriptome was assessed using Mouse WG-6 BeadChip microarray.

hyb_protocol: cRNA (1.5 µg) was hybridized to Illumina Mouse WG-6 BeadChip microarrays.

scan_protocol: Illumina Mouse WG-6 BeadChip microarrays were scanned on Illumina BeadStation 500x.

data_processing: BeadStudio raw data were normalized using R (quantile normalization implemented in the affy package). Further statistical and bioinformatic analyses were performed using R language and packages from the Bioconductor project (affy, multtest, hcluster).

source_name: Liver sinusoidal endothelial cells

label_protocol: Biotin labeled cRNA preparation was performed using the Ambion Illumina® TotalPrep™ RNA amplification kit (Ambion Europe, Huntington, Cambridgeshire, UK).

extract_protocol: LSEC were lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: LSEC were infected with MCMV-GFP with a MOI of 0.1 for 6h

value: Liver sinusoidal endothelial cells

value: female

value: 6-8 weeks


description: Gene expression data of blood, control pig, 7dpi, biological rep 2


description: Gene expression data of blood, control pig, 29dpi, biological rep 2


description: Gene expression data of blood, PCV2 inoculated pig, 0dpi, biological rep 3


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 8


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 6


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 4


title: Liver sinusoidal endothelial cells, treated with LPS, sample 3

treatment_protocol: LSEC were stimulated with LPS (100ng/ml) for 6 hours.


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 2


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 7


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 3


description: Gene expression data of blood, control pig, 0dpi, biological rep 4


title: Liver sinusoidal endothelial cells, treated with LPS, sample 4


title: Liver sinusoidal endothelial cells, sample 3


title: Liver sinusoidal endothelial cells, sample 6


title: Liver sinusoidal endothelial cells, treated with LPS, sample 2


title: Liver sinusoidal endothelial cells, sample 5


description: Gene expression data of blood, PCV2 inoculated pig, 7dpi, biological rep 1


title: Liver sinusoidal endothelial cells, sample 2


title: Liver sinusoidal endothelial cells, sample 4


title: Liver sinusoidal endothelial cells, treated with LPS, sample 1


title: DiploidRef-Aug-9 (250K_Sty2_SNP)

status: Public on Dec 22 2009

type: genomic

city: Toronto

first: David

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: Affymetrix CEL files were generated using the Affymetrix Genotyping Analysis Software (GTYPE 4.1). The CEL files and corresponding SNP genotype cell files were imported into dChip, normalized and modeled. Probe intensity data for each array were normalized using the invariant set method, and model-based expression was performed using the perfect-match/mismatch (PM/MM) model to summarize signal intensities for each probe set. (DNA copy number was inferred by comparing the signal intensity of each SNP probe set for each tumor sample against the diploid reference set, with subsequent median smoothing over a window size of 10.)

source_name: Normal brain tissue

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix).

extract_protocol: Standard phenol-chloroform extraction

tag: histology

value: Normal

tag: age (months)


title: Liver sinusoidal endothelial cells, infected with MCMV, sample 1

treatment_protocol: LSEC were infected with MCMV-GFP (MOI=0.1) for 6h.

tag: age


title: DiploidRef-Aug-2 (250K_Sty2_SNP)

tag: gender


title: Liver sinusoidal endothelial cells, sample 1

source_name: Liver sinusoidal endothelial cells, untreated


title: DiploidRef-Aug-7 (250K_Sty2_SNP)

value: male


title: DiploidRef-May-6 (250K_Sty2_SNP)


title: DiploidRef-May-5 (250K_Sty2_SNP)


title: DiploidRef-Aug-4 (250K_Sty2_SNP)


title: DiploidRef-May-9 (250K_Sty2_SNP)


title: DiploidRef-Jan-8 (250K_Sty2_SNP)


title: DiploidRef-Aug-10 (250K_Sty2_SNP)


title: DiploidRef-Aug-6 (250K_Sty2_SNP)


title: DiploidRef-May-3 (250K_Sty2_SNP)


title: DiploidRef-May-10 (250K_Sty2_SNP)


title: DiploidRef-Aug-5 (250K_Sty2_SNP)


title: DiploidRef-May-7 (250K_Sty2_SNP)


title: DiploidRef-May-4 (250K_Sty2_SNP)


title: DiploidRef-Jan-6 (250K_Sty2_SNP)


title: DiploidRef-Jan-5 (250K_Sty2_SNP)


title: DiploidRef-Aug-3 (250K_Sty2_SNP)


title: DiploidRef-Jan-10 (250K_Sty2_SNP)


title: DiploidRef-Aug-8 (250K_Sty2_SNP)


title: DiploidRef-Jan-7 (250K_Sty2_SNP)


title: DiploidRef-May-8 (250K_Sty2_SNP)


title: DiploidRef-May-2 (250K_Sty2_SNP)


title: DiploidRef-Jan-4 (250K_Sty2_SNP)


title: DiploidRef-May-1 (250K_Sty2_SNP)


title: PNET55 (250K_Sty2_SNP)

source_name: Primary primitive neuroectodermal tumour

value: PNET


title: PNET53 (250K_Sty2_SNP)


title: PNET46 (250K_Sty2_SNP)


title: DiploidRef-Jan-9 (250K_Sty2_SNP)


title: PNET48 (250K_Sty2_SNP)


title: PNET47 (250K_Sty2_SNP)


title: PNET51 (250K_Sty2_SNP)


title: DiploidRef-Jan-3 (250K_Sty2_SNP)


title: PNET45 (250K_Sty2_SNP)


title: PNET54_BL

data_processing: Affymetrix CEL files were generated using the Affymetrix Genotyping Analysis Software (GTYPE 4.1). The CEL files and corresponding SNP genotype cell files were imported into dChip, normalized and modeled. Probe intensity data for each array were normalized using the invariant set method, and model-based expression was performed using the perfect-match/mismatch (PM/MM) model to summarize signal intensities for each probe set.

source_name: Peripheral blood lymphocyte


title: PNET44 (250K_Sty2_SNP)


title: PNET43 (250K_Sty2_SNP)


title: PNET41 (250K_Sty2_SNP)


title: PNET40 (250K_Sty2_SNP)


title: PNET42 (250K_Sty2_SNP)


title: PNET39 (250K_Sty2_SNP)

value: PNET with ependymoblastic differentation


title: PNET54

value: PNET/ependymoblastoma


title: DiploidRef-May-10 (250K_Nsp_SNP)

description: no additional information

data_processing: Affymetrix CEL files were generated using the Affymetrix Genotyping Analysis Software (GTYPE 4.1). The CEL files and corresponding SNP genotype cell files were imported into dChip, normalized and modeled. Probe intensity data for each array were normalized using the invariant set method, and model-based expression was performed using the perfect-match/mismatch (PM/MM) model to summarize signal intensities for each probe set. (DNA copy number was inferred by comparing the signal intensity of each SNP probe set for each tumor sample against a diploid reference set of 39 samples, with subsequent median smoothing over a window size of 10.)


title: PNET34 (250K_Sty2_SNP)


title: DiploidRef-May-8 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-2 (250K_Sty2_SNP)


title: DiploidRef-May-6 (250K_Nsp_SNP)

description: no additional information


title: PNET31 (250K_Sty2_SNP)


title: PNET32 (250K_Sty2_SNP)


title: DiploidRef-May-3 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-May-7 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-May-9 (250K_Nsp_SNP)

description: no additional information


title: PNET24 (250K_Sty2_SNP)


title: PNET30 (250K_Sty2_SNP)


title: PNET20 (250K_Sty2_SNP)


title: PNET28 (250K_Sty2_SNP)


title: PNET35 (250K_Sty2_SNP)


title: DiploidRef-May-4 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-May-5 (250K_Nsp_SNP)

description: no additional information


title: PNET22 (250K_Sty2_SNP)


title: PNET19 (250K_Sty2_SNP)


title: DiploidRef-May-2 (250K_Nsp_SNP)

description: no additional information


title: PNET15 (250K_Sty2_SNP)

value: PNET/medulloepithelioma


title: PNET14 (250K_Sty2_SNP)


title: PNET18 (250K_Sty2_SNP)


title: PNET25 (250K_Sty2_SNP)


title: PNET11 (250K_Sty2_SNP)


title: DiploidRef-Jan-9 (250K_Nsp_SNP)

description: no additional information


title: PNET17 (250K_Sty2_SNP)


title: PNET10 (250K_Sty2_SNP)


title: PNET13 (250K_Sty2_SNP)


title: PNET3 (250K_Sty2_SNP)

value: PNET with ependymal differentation


title: PNET7 (250K_Sty2_SNP)


title: PNET4 (250K_Sty2_SNP)


title: PNET5 (250K_Sty2_SNP)


title: DiploidRef-Jan-7 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-2 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-6 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-4 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-5 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-3 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-6 (250K_Nsp_SNP)

description: no additional information


title: PNET9 (250K_Sty2_SNP)


title: PNET8 (250K_Sty2_SNP)


title: DiploidRef-Jan-1 (250K_Nsp_SNP)

description: no additional information


title: PNET2 (250K_Sty2_SNP)


title: DiploidRef-Jan-10 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-4 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-8 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-1 (250K_Nsp_SNP)

description: no additional information


title: PNET47 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-3 (250K_Nsp_SNP)

description: no additional information


title: PNET6 (250K_Sty2_SNP)


title: PNET53 (250K_Nsp_SNP)

description: no additional information


title: PNET55 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-2 (250K_Nsp_SNP)

description: no additional information


title: PNET51 (250K_Nsp_SNP)

description: no additional information


title: PNET48 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-May-1 (250K_Nsp_SNP)

description: no additional information


title: PNET44 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Jan-8 (250K_Nsp_SNP)

description: no additional information


title: PNET42 (250K_Nsp_SNP)

description: no additional information


title: PNET39 (250K_Nsp_SNP)

description: no additional information


title: PNET40 (250K_Nsp_SNP)

description: no additional information


title: PNET43 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-7 (250K_Nsp_SNP)

description: no additional information


title: PNET46 (250K_Nsp_SNP)

description: no additional information


title: PNET34 (250K_Nsp_SNP)

description: no additional information


title: PNET22 (250K_Nsp_SNP)

description: no additional information


title: PNET24 (250K_Nsp_SNP)

description: no additional information


title: PNET31 (250K_Nsp_SNP)

description: no additional information


title: PNET41 (250K_Nsp_SNP)

description: no additional information


title: PNET35 (250K_Nsp_SNP)

description: no additional information


title: PNET20 (250K_Nsp_SNP)

description: no additional information


title: PNET19 (250K_Nsp_SNP)

description: no additional information


title: DiploidRef-Aug-5 (250K_Nsp_SNP)

description: no additional information


title: PNET25 (250K_Nsp_SNP)

description: no additional information


title: PNET30 (250K_Nsp_SNP)

description: no additional information


title: PNET32 (250K_Nsp_SNP)

description: no additional information


title: PNET28 (250K_Nsp_SNP)

description: no additional information


title: PNET18 (250K_Nsp_SNP)

description: no additional information


title: Bubble cell-array gene expression for C2C12 cells Ex2R (Technical replicate)

status: Public on Dec 10 2009

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Scans images were quantified with ScanArray Express (PerkinElmer) software using the fixed circle method.

hyb_protocol: Ranges along 200 and 160 pico-moles and 2.5 and 1.8 µg of aRNA labeled with Cy3 and Cy5 were co-precipitated with the ammonium acetate and ethanol. Pellet was resuspended in 110 µl with the hybridization solution composed by SSC 5X, SDS 0.1%, Formamide 25% and salmon sperm purified DNA 100 ng/µl and carried out in an automatic hybridization station (ArrayBooster, Advalytix) at 48° C for 24 hours in the competitive hybridization. Microarray slides, before hybridization, have been blocked with the pre-hybridization solution (SSC 5X, SDS 0.1%, salmon sperm purified DNA 100 ng/ul and Denhardt's solution 5X) for 8 hours at 48° C. After the hybridization slides were washed at room temperature with 1X SSC 0.2% SDS for 4 minutes one time; 0.1X SSC 0.2% SDS for 4 minutes one time; 0.2X SSC for 3 minutes two times each with new solution and 0.1X SSC for 3 minutes one time. Slides were dried centrifuging 1 minute at 800 X g at 20° C.

scan_protocol: After stringent washings, fluorescence left in the microarray slides were read with the ScanArray LITE confocal laser scanner (PerkinElmer) with 5 µm resolution.

data_processing:
Fluorescence intensity was determined with the ScanArray Express software (PerkinElmer) using fixed circle method and median spot intensity background subtracted was normalized in the MIDAW tool using sequentially global mean normalization and local mean normalization (LOWESS) methods. Lowess normalization was performed without distinguishing between different sub-arrays.
Normalized log2(C2C12state_ch2/C2C12controls_ch1) values were filtered according to the median of the value calculated in the empty array position for the average of the Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD values.  Ch1% or Ch2% > BKG + 1 SD value is the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity. Processing for data filtering is here summarized:
1.	calculate average for Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD for each gene;
2.	calculate median of the average calculated in point 1 for the empty position (see "Experiment filtering details" in Series data table);
3.	exclude normalized gene expression values presenting average calculated in point 1 under median calculated in point 2 for each experiment;
4.	generated expression matrix was loaded in to TIGR MeV software to identify clustering and differentially expressed genes by KMC analysis.

source_name: C2C12 cells cultured in bubble cell-array for 1 day in a confluence state in proliferative medium in dynamic way

label_protocol:
CyDye Post-Labeling Reactive Dye Packs (Amersham, GE Healthcare). Label was performed using Cy3 and Cy5 fluors to label amine-modified nucleic acids prepared via the post-labeling (aminoallyl) route.
Details: Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer. All RNAs utilized in this study presented RIN at least 9.
400 ng of total RNA for each studied cell condition was linearly amplified with the MessageAmp™ aRNA amplification kit (Ambion). 3ug of the amplified RNA (aRNA) have been dried for 12 hours using a Heto Lyolab 3000 freeze-dryer (Heto-Holten A/S) and coupled with Cy3 and Cy5 post-labeling dye (Amersham, GE Healthcare). Coupling was performed for 1 hour at room temperature. Unincorporated dyes were eliminated using MEGAclear™ Kit (Ambion). Labeled aRNA was eluted in ultraPURE™ distilled water DNase, RNase Free (Gibco) and quantized in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
CyDye Post-Labeling Reactive Dye Packs (Amersham, GE Healthcare). Label was performed using Cy3 and Cy5 fluors to label amine-modified nucleic acids prepared via the post-labeling (aminoallyl) route.

growth_protocol: The desired number of cells was resuspended in 150 μL of supplemented DMEM culture medium and seeded depositing the suspension over each circular gel film. The cellular concentration of the suspension varied depending on the desired degree of confluence of the microarray spots. The combination of the hydrophilicity of the hydrogel and the hydrophobicity of the glass surface allowed confining the fluid over the polymeric film forming bubbles in each slide. After 2 hours of incubation, unattached cells were removed through repeated washing carried out adding and immediately removing a 150 μL aliquot of DMEM. Cellular microarrays were then maintained in dynamic or static culture.

extract_protocol:
Total RNA was extracted with TRIzol method (Invitrogen). The procedure was:
1. Dispensation of 100 µl onto the cultured bubble cell-array;
2. Incubation, at room temperature, for 1 minute;
3. Recover TRIzol solution and desegregated gel and put the solution in a final volume of 1 ml of TRIzol;
4. Incubation, at room temperature, for 15 minutes;
5. Addition of 0.2ml/1ml Trizol and shake for 1 minute;
6. Leave in ice for 15 minutes and then centrifuge at 4º C for 20 minutes at 14,000 X g;
7. Transfer the supernatant to 1.5 ml microfuge non-stick tubes and add an equal volume of isopropanol to precipitate the RNA;
8. Incubate at -20º C for one hour and centrifuge at 4º C for 20 minutes at 14,000 X g;
9. Discard the supernatant and wash with ethanol 75% three times centrifuging every time for 15 minutes at 4º C at 14,000 X g;
10. Pellet was resuspended in ultraPURE™ distilled water DNase, RNase Free (Gibco).

treatment_protocol: C2C12 cells were cultured onto a protein microarray in proliferative and differentiative medium. Protein microarray was constructed onto a polyacrylamide gel surface permitting the formation of a bubble medium of 150 µl. Medium was changed in continuum during time using a dynamic culture system included the bioreactor, a gas exchanger unit and a syringe pump (PHD, Harvard Apparatus, Holliston, MA). Total RNA was extracted with TRIzol (Invitrogen).

tag: 24H confluence cells in proliferative medium (reference)

source_name: C2C12 cells cultured in bubble cell-array changing medium during time

tag: Cells are cultured in time dependent proliferative and differentiative medium (24H differentiative medium)


title: Bubble cell-array gene expression for C2C12 cells EX3R (Technical replicate)

label_protocol:
Details: Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer. All RNAs utilized in this study presented RIN at least 9.
400 ng of total RNA for each studied cell condition was linearly amplified with the MessageAmp™ aRNA amplification kit (Ambion). 3ug of the amplified RNA (aRNA) have been dried for 12 hours using a Heto Lyolab 3000 freeze-dryer (Heto-Holten A/S) and coupled with Cy3 and Cy5 post-labeling dye (Amersham, GE Healthcare). Coupling was performed for 1 hour at room temperature. Unincorporated dyes were eliminated using MEGAclear™ Kit (Ambion). Labeled aRNA was eluted in ultraPURE™ distilled water DNase, RNase Free (Gibco) and quantized in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

tag: Cells are cultured in time dependent proliferative and differentiative medium (60H differentiative medium)


title: Bubble cell-array gene expression for C2C12 cells Ex3


title: PNET11 (250K_Nsp_SNP)

description: no additional information


title: Bubble cell-array gene expression for C2C12 cells-EX1

source_name: C2C12 cells cultured in bubble cell-array in a confluence state for 1 day in proliferative medium in dynamic way

tag: Cells are cultured in time dependent proliferative and differentiative medium (6H proliferative medium)


title: Bubble cell-array gene expression for C2C12 cells Ex.2


title: Bubble cell-array gene expression for C2C12 cells-Ex1R (Technical replicate)


title: PNET15 (250K_Nsp_SNP)

description: no additional information


title: PNET3 (250K_Nsp_SNP)

description: no additional information


title: PNET2 (250K_Nsp_SNP)

description: no additional information


title: PNET45 (250K_Nsp_SNP)

description: no additional information


title: PNET6 (250K_Nsp_SNP)

description: no additional information


title: PNET17 (250K_Nsp_SNP)

description: no additional information


title: PNET10 (250K_Nsp_SNP)

description: no additional information


title: PNET4 (250K_Nsp_SNP)

description: no additional information


title: PNET13 (250K_Nsp_SNP)

description: no additional information


title: PNET9 (250K_Nsp_SNP)

description: no additional information


title: COG.T.ALL.39

status: Public on Dec 01 2009

city: Houston

first: Alexei

last: Protopopov

state: TX

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

hyb_protocol: Agilent Oligo aCGH Hybridization Kit (p/n 5188-5220) and Agilent Oligo aCGH Wash Buffers (p/n 5188-5226) were used according to manufacturer protocols.

scan_protocol: Agilent G2565BA Scanner was used according to manufacturer protocol. Data extraction has been performed with Agilent G2567AA Feature Extraction Software v9.1.

data_processing: Feature extraction data was obtained using Agilent G2567AA Feature Extraction Software, normalized using LOcally-WEighted regression Scatterplot Smoother

source_name: T-ALL

label_protocol: Random primers and the exo-Klenow fragment -based ENZO CGH Labeling Kit (ENZO LIfe Sciences p/n ENZ-42671) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Protopopov A, Feng B, Chin L. Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH). Methods Mol Biol.2008;439:87-100.

extract_protocol: QIAGEN DNeasy

value: Male

tag: treatment regimen

source_name: male DNA

extract_protocol: male DNA G147A (Promega, Madison, WI)

tag: male DNA G147A (Promega, Madison, WI)


title: PNET7 (250K_Nsp_SNP)

description: no additional information


title: PNET8 (250K_Nsp_SNP)

description: no additional information


title: PNET5 (250K_Nsp_SNP)

description: no additional information


title: COG.T.ALL.40


title: COG.T.ALL.42


title: COG.T.ALL.35

value: Female


title: COG.T.ALL.27


title: COG.T.ALL.34


title: COG.T.ALL.41


title: PNET14 (250K_Nsp_SNP)

description: no additional information


title: COG.T.ALL.25


title: COG.T.ALL.29


title: COG.T.ALL.32


title: COG.T.ALL.20


title: COG.T.ALL.26


title: COG.T.ALL.23


title: COG.T.ALL.19


title: COG.T.ALL.28


title: COG.T.ALL.31


title: COG.T.ALL.38


title: COG.T.ALL.22


title: COG.T.ALL.17


title: COG.T.ALL.21


title: COG.T.ALL.24


title: COG.T.ALL.11


title: COG.T.ALL.13


title: COG.T.ALL.30


title: COG.T.ALL.16


title: COG.T.ALL.33


title: COG.T.ALL.18


title: COG.T.ALL.15


title: COG.T.ALL.8


title: COG.T.ALL.12


title: COG.T.ALL.10


title: 24Hrs C3

city: Cincinnati

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: In air control

hyb_protocol: based on Affymetrix protocols

scan_protocol: based on Affymetrix protocols

data_processing: RMA signal intensity calculation

source_name: 7-8 wk isolated type II cells

label_protocol: based on Affymetrix protocols

extract_protocol: GITC

value: isolated alveolar type II cells

tag: genotype

value: CEBP/a(flx/flx) littermates lacking either rtTA or Cre-genes


title: 24Hrs KO2

description: In air knockout

value: CCSP/rtTA/CEBPa(flx/flx)


title: COG.T.ALL.4


title: COG.T.ALL.7


title: 24Hrs C2

description: In air control


title: COG.T.ALL.3


title: COG.T.ALL.14


title: 2Hrs KO4

description: In air knockout


title: 24Hrs KO4

description: In air knockout


title: 2Hrs KO3

description: In air knockout


title: 24Hrs KO1

description: In air knockout


title: 2Hrs C2

description: In air control


title: COG.T.ALL.2

value: COG 940


title: Day0 C3

description: In air control


title: COG.T.ALL.9


title: Day0 KO3

description: In air knockout


title: 24Hrs C1

description: In air control


title: Day0 C2

description: In air control


title: Day0 KO2

description: In air knockout


title: COG.T.ALL.6


title: COG.T.ALL.5


title: 2Hrs KO2

description: In air knockout


title: COG.T.ALL.1


title: H3K9me3 Yaswen3C RenLab ENCODE PCR tiling array replicate 1 llee_enc_105_H3K9me3_3C_060408.gpr

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: GenePix

scan_protocol: GenePix

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from Yaswen3C cells using H3K9me3 antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: GenePix

source_name: Input DNA from Yaswen3C cells

tag: Input DNA from Yaswen3C cells


title: H3K9me3 Yaswen3A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K9me3_Yaswen3A_031608.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3A cells using H3K9me3 antibody

source_name: Input DNA from Yaswen3A cells

tag: Input DNA from Yaswen3A cells


title: H3K9me3 Yaswen2C RenLab ENCODE PCR tiling array replicate 1 llee_enc_104_H3K9me3_2C_060408.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2C cells using H3K9me3 antibody

source_name: Input DNA from Yaswen2C cells

tag: Input DNA from Yaswen2C cells


title: H3K4me3 Yaswen3A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen3A_031108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3A cells using H3K4me3 antibody


title: H3K9me3 Yaswen1A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K9me3_Yaswen1A_031608.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1A cells using H3K9me3 antibody

source_name: Input DNA from Yaswen1A cells

tag: Input DNA from Yaswen1A cells


title: H3K4me3 Yaswen3B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen3B_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3B cells using H3K4me3 antibody

source_name: Input DNA from Yaswen3B cells

tag: Input DNA from Yaswen3B cells


title: H3K4me3 Yaswen2B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen2B_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2B cells using H3K4me3 antibody

source_name: Input DNA from Yaswen2B cells

tag: Input DNA from Yaswen2B cells


title: Day0 C1

description: In air control

tag: cell type


title: H3K4me3 Yaswen2A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen2A_031108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2A cells using H3K4me3 antibody

source_name: Input DNA from Yaswen2A cells

tag: Input DNA from Yaswen2A cells


title: H3K9me3 Yaswen1C RenLab ENCODE PCR tiling array replicate 1 llee_enc_103_H3K9me3_1C_060408.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1C cells using H3K9me3 antibody

source_name: Input DNA from Yaswen1C cells

tag: Input DNA from Yaswen1C cells


title: 2Hrs C3

description: In air control

source_name: 7-8 wk isolated type II cells


title: H3K9me3 Yaswen1B RenLab ENCODE PCR tiling array replicate 1 llee_enc_100_H3K9me3_1B_060408.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1B cells using H3K9me3 antibody

source_name: Input DNA from Yaswen1B cells

tag: Input DNA from Yaswen1B cells


title: H3K4me3 Yaswen2C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen2C_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2C cells using H3K4me3 antibody


title: H3K9me3 Yaswen3B RenLab ENCODE PCR tiling array replicate 1 llee_enc_102_H3K9me3_3B_060408.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3B cells using H3K9me3 antibody


title: H3K27me3 Yaswen1C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen1C_050808.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1C cells using H3K27me3 antibody


title: H3K4me3 Yaswen3C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen3C_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3C cells using H3K4me3 antibody

source_name: Input DNA from Yaswen3C cells


title: H3K9me3 Yaswen2A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K9me3_Yaswen2A_031608.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2A cells using H3K9me3 antibody


title: H3K27me3 Yaswen3C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen3C_050808.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3C cells using H3K27me3 antibody


title: Day0 KO1

description: In air knockout


title: H3K27me3 Yaswen3A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen3A_031108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3A cells using H3K27me3 antibody

source_name: Input DNA from Yaswen3A cells


title: H3K4me3 Yaswen1C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen1C_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1C cells using H3K4me3 antibody


title: H3K27me3 Yaswen2B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen2B_050108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2B cells using H3K27me3 antibody

source_name: Input DNA from Yaswen2B cells


title: H3K27me3 Yaswen2A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen2A_031108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2A cells using H3K27me3 antibody

source_name: Input DNA from Yaswen2A cells


title: H3K27me3 Yaswen3B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen3B_050108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen3B cells using H3K27me3 antibody

source_name: Input DNA from Yaswen3B cells


title: H3K4me3 Yaswen1A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen1A_031608.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1A cells using H3K4me3 antibody

source_name: Input DNA from Yaswen1A cells


title: 2Hrs C1

description: In air control

source_name: 7-8 wk isolated type II cells


title: H3K27me3 Yaswen1B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen1B_050108.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1B cells using H3K27me3 antibody

source_name: Input DNA from Yaswen1B cells


title: H3K27me3 Yaswen2C RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen2C_050808.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2C cells using H3K27me3 antibody

source_name: Input DNA from Yaswen2C cells


title: H3K9me3 Yaswen2B RenLab ENCODE PCR tiling array replicate 1 llee_enc_101_H3K9me3_2B_060408.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen2B cells using H3K9me3 antibody


title: Liver, Dor 2007 and 2008

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description:
D07-08|Liver, Dor 2007|GSM366240_1185d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 7|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2007|GSM366240_1185u.gpr|Fish 7|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2007|GSM366240_1186d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 9|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2007|GSM366240_1186u.gpr|Fish 9|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2007|GSM366240_1188d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 12|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2007|GSM366240_1188u.gpr|Fish 12|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2007|GSM366240_1202d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 14|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2007|GSM366240_1202u.gpr|Fish 14|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_1175u.gpr|Reference RNA|No reproductive activity|Cy3|Fish 89|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_0651u.gpr|Fish 89|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_0652d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 90|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_1174u.gpr|Fish 90|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_0653d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 91|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_0653u.gpr|Fish 91|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_1206d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 92|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_1174d.gpr|Fish 92|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_1175d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 93|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_1207u.gpr|Fish 93|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_1208d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 95|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_1208u.gpr|Fish 95|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
D07-08|Liver, Dor 2008|GSM366240_1209d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 96|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
D07-08|Liver, Dor 2008|GSM366240_1209u.gpr|Fish 96|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|

hyb_protocol: Microarray slides were hybridized according to Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A., Tom M., 2007.  Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the molt cycle. Insect Mol. Biol. 16, 661–674.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Axon), which provided also weight index of the quality for each hybridized spot

data_processing: Data analysis was conducted under the R/BioConductor environment (Gentleman et al., 2005). Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each unique spot across a binary comparison was carried out using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, 2004). GENEPIX quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using global Loess method. No background correction was applied. Only spots with fluorescent value > 800 (out of 65536) in at least one of the dyes were included in the analysis. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to the statistical p-value, derived from a moderated t-statistic after multiple testing correction according to Benjamini and Hochberg (1995).

label: Cy3, Cy5

molecule: polyA RNA

organism: Lithognathus mormyrus

source_name: Reference RNA

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5, according to Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A., Tom M., 2007.  Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the molt cycle. Insect Mol. Biol. 16, 661–674.

growth_protocol: Fish were sampled at sea and kept alive for 2-3 hours in 700 liter clean seawater flow-through tanks under ambient temperature regime before their sacrifice.

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions

treatment_protocol: Fish were not experimentally treated.

tag: No reproductive activity

source_name: Liver, Dor 2007 and 2008


title: Liver, Haifa 2008

description:
H08|Liver, Haifa 2008|GSM366242_1210d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 52|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_1177u.gpr|Fish 52|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0654d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 55|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0654u.gpr|Fish 55|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0655d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 56|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0655u.gpr|Fish 56|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0656d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 58|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0656u.gpr|Fish 58|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0657d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 60|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0657u.gpr|Fish 60|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0644d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 62|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0644u.gpr|Fish 62|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_1177d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 68|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0646u.gpr|Fish 68|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_0647d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 69|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_0647u.gpr|Fish 69|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H08|Liver, Haifa 2008|GSM366242_1211d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 71|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H08|Liver, Haifa 2008|GSM366242_1211u.gpr|Fish 71|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|

label: Cy3, Cy7

source_name: Liver, Haifa 2008


title: Liver, Haifa 2007

description:
H07|Liver, Haifa 2007|GSM366241_1190d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 36|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1190u.gpr|Fish 36|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_1191d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 37|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1178u.gpr|Fish 37|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_1193d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 41|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1193u.gpr|Fish 41|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_1194d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 43|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1194u.gpr|Fish 43|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_1204d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 44|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1204u.gpr|Fish 44|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_1205d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 45|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1205u.gpr|Fish 45|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_0663d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 46|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1173d.gpr|Fish 46|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_0664d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 47|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_0664u.gpr|Fish 47|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|
H07|Liver, Haifa 2007|GSM366241_0665d.gpr|Reference RNA|No reproductive activity|Cy3|Fish 49|No reproductive activity|Cy5|This array and the following one are dye-swapped duplicates
H07|Liver, Haifa 2007|GSM366241_1178d.gpr|Fish 49|No reproductive activity|Cy3|Reference RNA|No reproductive activity|Cy5|

source_name: Liver, Haifa 2007


title: 226_7

status: Public on Nov 30 2009

city: Lausanne

first: Alexandre

last: Reymond

address: Genopode building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor affy and affyPLM packages (Gautier et al., 2004).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: C57BL/6-Tyr c-Brd, hippocampus, individual 226

label_protocol: Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used.

extract_protocol: Mice were sacrificed by cervical dislocation. RNA from whole brain, testis, kidney, heart, liver and lung was isolated with TRIzol (Invitrogen) and purified on Qiagen RNeasy Mini columns (Qiagen), according to manufacturers' instructions.

tag: Strain

value: C57BL/6-Tyr c-Brd, Genotype:+/+, Gender:male, Age:11-14 weeks of age, Tissue:hippocampus


title: Rat_prefrontal_cortex-rep9-expt1

status: Public on Nov 24 2009

first: Paul

middle: C

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: experiment 1

hyb_protocol: Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).

scan_protocol: Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).

data_processing: Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).

organism: Rattus norvegicus

source_name: Rat Prefrontal cortex, individual #9

label_protocol: Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).

growth_protocol: Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI.  Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.

extract_protocol: Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.

treatment_protocol: No treatments applied

tag: gender

tag: strain

value: Lewis

tag: tissue

value: prefrontal cortex

tag: weight

tag: light cycle

tag: startle

tag: plus maze

tag: sugar feeding


title: Rat_prefrontal_cortex-rep8-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #8


title: 339_9

source_name: Dp(11)17/+, hippocampus, individual 339

value: C57BL/6-Tyr c-Brd, Genotype:Dp(11)17/+, Gender:male, Age:11-14 weeks of age, Tissue:hippocampus