title: HLHS, biological rep 6

city: Miami

first: Marco

last: Ricci

state: FL

address: 1611 NW 12th Ave, Holtz Center 3072

department: Pediatric Cardiac Surgery

institute: Jackson Memorial Hospital

description: Gene expression data from affected HLHS ventricle

hyb_protocol: Microarrays were hybridized 17 hours at 45oC in the Affymetrix Hybridization Oven 645 according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned with the Affymetrix Scanner 3000 7G.

data_processing: Image analysis was carried out using the Affymetrix Command Console Software (AGCC). Resulting CEL files were imported into Partek software (Partek, Inc., St. Louis, MO, USA) using median polish probe set summarization, GCRMA background correction, and quantile normalization. Transcript expression levels were calculated using the well-established “core” set. The analysis of variance (ANOVA) model including only three sample goups (RV, LV, and HLHS) was built, and fold change from the contrasts were calculated.

source_name: Hypoplastic left heart syndrome ventricle

label_protocol: RNA samples were amplified and labeled using NuGEN Ovation Pico WTA system, WT-Ovation Exon module and Encore Biotin Module (NuGEN, San Carlos, CA, USA). Briefly 20 to 50 ng of total RNA was subjected to the synthesis of first strand cDNA using a unique DNA/RNA chimeric primer mix and reverse transcriptase. After generating of DNA/RNA heteroduplex double strand cDNA it was subjected to SPIA amplification, which uses SPIA DNA/RNA chimeric primer, DNA polymerase and RNase H in a homogeneous isothermal assay. Resulting cDNA was used to generate sense transcript cDNA suitable for fragmentation and labeling as target for Affymetrix Human Exon 1.0 ST arrays.

extract_protocol: RNA was extracted from HLHS-RV, control-LV and control-RV using TRIzol reagent (Invitrogen, Carlsbad, CA) or Qiagen RNeasy Mini Kit according to the manufacturer’s instructions

tag: tissue

value: Heart

tag: tissue subtype

value: HLHS ventricle

tag: developmental stage

value: neonatal

tag: disease status

value: HLHS (hypoplastic left heart syndrome)


title: Septum_animal N63_0.2 mL sarin_no seize_no drugs_24hr

status: Public on Dec 31 2011

type: RNA

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

country: USA

institute: U.S. Army Medical Research Institute of Chemical Defense

description: Gene expression data from Septum of animal N63_0.2 mL sarin_no seize_no drugs_24hr

hyb_protocol: Spike controls were added to 15 µg fragmented cRNA before hybridization (36h) using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

scan_protocol: After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.

data_processing: Raw signal intensities were imported into Partek Genomics Solutions v6.3 (Partek, St. Louis, MO) and normalized using the robust multi-array averaging (RMA) algorithm (Irizarry et al., 2003)

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Total RNA was processed for hybridization to GeneChip® Rat Genome 230 2.0 oligonucleotide arrays (Affymetrix, Inc., Santa Clara, CA) using the BioArray Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Inc., Farmingdale, NY) as previously described [20].  In brief, 1 µg of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer.  After second strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP for cRNA amplification.

extract_protocol: Tissues were homogenized in RNeasy lysis buffer (QIAGEN, Valencia, CA) for three seconds at 5,000 rpm and ramped to 17,000 rpm for 30 sec using an Omni Programmable Digital Homogenizer (Omni International, Kennesaw, GA).  Each homogenate was subsequently centrifuged for 10 min at 16,110 x g at room temperature, and the supernatant was transferred to a new microcentrifuge tube.  Total RNA was then extracted and DNase I-treated using the RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol.  The quantity and quality of the RNA was determined with a NanoDrop ND-1000 UV-vis spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent bioanalyzer (Agilent Technologies, Santa Clara, CA) throughout sample processing.

treatment_protocol: Male Sprague-Dawley rats (350-500 g) were obtained from Charles River Laboratories (Wilmington, MA).  They were housed in a temperature-controlled room with a 12-h light/12-h dark cycle and given food and water ad libitum.  The research for this study was conducted at the United States Army Medical Research Institute of Chemical Defense (USAMRICD; Aberdeen Proving Ground, MD), which is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care, International.  All of the animal procedures were approved by the Institute Animal Care and Use Committee at USAMRICD and conducted in accordance with the principles stated in the Guide for the Care and Use of Laboratory Animals (National Research Council, 1996) and the Animal Welfare Act of 1966 (P.L. 89-544), as amended.    PhysioTel® F40-EET transmitters (Data Sciences International, St. Paul, MN) were surgically implanted into the animals to record bi-hemispheric cortical electroencephalogram (EEG) activity, body temperature, and gross motor activity throughout the study.  After a two-week recovery period, the animals were challenged with 1 x LD50 sarin (108 µg/kg, sc) that was obtained and diluted in sterile saline at USAMRICD.  One minute after seizure onset, animals were treated with atropine sulfate (2 mg/kg; Sigma-Aldrich, St. Louis, MO) and 2-pyridine aldoxime methylchloride (2-PAM; 25 mg/kg; Sigma-Aldrich), both administered in a single injection (im).  Thirty minutes later, animals were given the anticonvulsant diazepam (10 mg/kg, sc; TW Medical Veterinary Supply, Austin, TX).  Control animals received an equivalent volume of vehicle (saline), atropine sulfate, 2-PAM, and diazepam at time points corresponding to the injections administered to sarin-exposed animals.  Drug treatments were not given to sarin-exposed non-seizure animals or their matched controls.  Naïve animals received no injections.  Animals were euthanized by decapitation at 0.25, 1, 3, 6, and 24 h after seizure onset.  Each tissue was immediately snap-frozen in liquid nitrogen and stored at -80°C until use.

tag: animal number

value: Septum

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: HLHS, biological rep 2

organism: Homo sapiens

tag: tissue


title: 14 day old bHR strain rat hippocampus, biological replicate 3

city: Birmingham

first: Sarah

middle: Megan

last: Clinton

state: Alabama

address: 1720 7th Avenue South, SC 745

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama-Birmigham

description:
P14_HR_HPC_H03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: To account for recent advances in annotation and accuracy of rat genome bioinformatics, GeneChip data were interpreted using a custom cdf (filename RUG34A_Rn_UG), which groups individual probes from the GeneChip into newly defined probe sets based on a very recent version of UniGene (build updated 6th July 2010). Data were analyzed by RMA in Bioconductor.

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 14 days after birth

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

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

value: Selectively bred High Responder (derived from an original Sprague Dawley)

value: Hippocampus

tag: age

value: 14 days after birth


title: Septum_animal N60_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N60_0.2 mL sarin_no seize_no drugs_3hr


title: 14 day old bHR strain rat hippocampus, biological replicate 4

description:
P14_HR_HPC_H04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth


title: melanoma patient 2 sample 8

city: Granada

first: Rafael

last: Carretero

address: Avenida del Hospicio

country: Spain

institute: Universidad de Granada

hyb_protocol: 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction.

source_name: melanoma metastasis 8

label_protocol: 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion).

extract_protocol: Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions

value: melanoma

tag: treatment protocol

value: M-VAX

tag: status

value: regressing

tag: patient

source_name: Total RNA from pooled PBMC

value: Blood

tag: preservation

value: cryopreservation

tag: reference

value: Total RNA from pooled PBMC


title: 14 day old bHR strain rat hippocampus, biological replicate 2

description:
P14_HR_HPC_H02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth


title: melanoma patient 2 sample 7

source_name: melanoma metastasis 7


title: Septum_animal N59_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N59_0.2 mL sarin_no seize_no drugs_6hr

tag: animal number

tag: agent

tag: amount administered

tag: agent dose


title: HLHS, biological rep 4

value: Heart

tag: tissue subtype

tag: developmental stage

tag: disease status


title: Septum_animal N61_0.21 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Septum of animal N61_0.21 mL sarin_no seize_no drugs_1hr

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: melanoma patient 2 sample 5

source_name: melanoma metastasis 5

tag: tissue

tag: treatment protocol

value: interferon

tag: status

value: progressing

tag: patient


title: HLHS, biological rep 5

value: HLHS ventricle

value: neonatal

value: HLHS (hypoplastic left heart syndrome)


title: HLHS, biological rep 3


title: HLHS, biological rep 1


title: melanoma patient 2 sample 6

source_name: melanoma metastasis 6

tag: preservation

tag: reference


title: melanoma patient 2 sample 4

source_name: melanoma metastasis 4


title: Control RV, biological rep 5

description: Gene expression data from control right ventricle

source_name: Control right ventricle

value: Right ventricle

value: normal control


title: Control RV, biological rep 4


title: 14 day old bHR strain rat hippocampus, biological replicate 1

description:
P14_HR_HPC_H01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 14 days after birth

value: Selectively bred High Responder (derived from an original Sprague Dawley)

tag: age


title: 7 day old bHR strain rat hippocampus, biological replicate 6

description:
P7_HR_HPC_H06
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

source_name: Selectively-bred High responder rat strain derived from Sprague Dawley stock, 7 days after birth

value: Hippocampus

value: 7 days after birth


title: Septum_animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

description: Gene expression data from Septum of animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

tag: animal number

value: Septum

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

value: Sprague-Dawley

value: Y

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: 7 day old bHR strain rat hippocampus, biological replicate 5

description:
P7_HR_HPC_H05
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

tag: strain


title: Control RV, biological rep 3

tag: tissue subtype

tag: developmental stage

tag: disease status


title: 7 day old bHR strain rat hippocampus, biological replicate 2

description:
P7_HR_HPC_H02
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

tag: tissue


title: 7 day old bHR strain rat hippocampus, biological replicate 4

description:
P7_HR_HPC_H04
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth


title: Septum_animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

description: Gene expression data from Septum of animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: Septum_animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

description: Gene expression data from Septum of animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

tag: animal number

tag: agent

tag: amount administered


title: 7 day old bHR strain rat hippocampus, biological replicate 1

description:
P7_HR_HPC_H01
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

tag: age


title: Control RV, biological rep 2


title: melanoma patient 2 sample 2

source_name: melanoma metastasis 2

value: melanoma

tag: treatment protocol

tag: status

value: regressing

tag: patient

value: Blood

tag: preservation

value: cryopreservation

tag: reference


title: Septum_animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

tag: agent dose

tag: strain

value: N

tag: presence of seizure

tag: animal weight (g)


title: 7 day old bHR strain rat hippocampus, biological replicate 3

description:
P7_HR_HPC_H03
Gene expression data from hippocampus of selectively-bred sprague dawley rats (High Reponder strain), 7 days after birth

tag: tissue


title: Septum_animal N54_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Septum of animal N54_0.2 mL saline_no seize_drugs_6hr

value: Saline

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected


title: genomic DNA from colon cancer cell line_SW48

type: genomic

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

country: South Korea

institute: KRIBB

description: tumor colon sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

molecule: genomic DNA

source_name: Stomach

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: cell line

value: colon tissue

tag: disease state

value: tumor


title: melanoma patient 2 sample 1

source_name: melanoma metastasis 1

value: interferon

value: Total RNA from pooled PBMC


title: RQ_rep2

city: Frederick

first: Suhwan

last: Chang

address: PO Box B, NCI-Frederick

institute: National Cancer Institute

description: Biological replicate 2 of 2. RQ mutant embryoid body

hyb_protocol: The labeled RNA was subsequently used for hybridization onto the microarrays without purification.

scan_protocol: Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: [control] mouse embryoid body with wild type human BRCA1

label_protocol: The 3´-end of the total RNA was enzymatically labeled with the Hy3 and/or Hy5 fluorescent dye (Exiqon) by incubating with T4 RNA ligase at 0oC for 1 hour followed by an enzyme inactivation at 65oC for 15 minutes.

growth_protocol: To generate embryoid bodies, ES cells were trypsinized and the feeder cells were removed by incubating the cells on gelatinized plate for one hour. The ES cells in supernatant were counted and diluted to 5X104 cells/ml. The cell suspension was culture in Petri dish, in DMEM-10 media. The media was changed on day 3 and later it was changed every other day.

extract_protocol: The total RNA from the embryoid body of WT, R1699Q and M1652I at day 7 was labeled using the miRCURY ™ miRNA Array Labeling kit

treatment_protocol: embryoid bodies were collected on day 7.

tag: cell type

value: embryoid body

value: 129S7/SvEv Brd-Hprt b-m2

source_name: mouse embryoid body with R1699Q mutated human BRCA1


title: Septum_animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Septum of animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

tag: animal number

tag: agent

tag: amount administered

tag: date sacrificed

tag: time sacrificed


title: Septum_animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

description: Gene expression data from Septum of animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

tag: agent dose

tag: seizure time

tag: seizure latency


title: genomic DNA from colon cancer cell line_HT29

description: tumor colon sample


title: Control RV, biological rep 1

value: Heart

tag: tissue subtype

value: Right ventricle

tag: developmental stage

value: neonatal

tag: disease status

value: normal control


title: melanoma patient 2 sample 3

source_name: melanoma metastasis 3

tag: tissue

tag: treatment protocol

tag: status

tag: patient

tag: preservation

tag: reference


title: genomic DNA from colon cancer cell line_HCT116

description: tumor colon sample

tag: cell line

tag: disease state


title: Septum_animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

description: Gene expression data from Septum of animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

tag: animal number

value: Septum

tag: agent

value: Sarin

tag: amount administered

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: presence of seizure

tag: animal weight (g)


title: genomic DNA from colon cancer cell line_SW480

description: tumor colon sample

tag: tissue


title: Septum_animal N47_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Septum of animal N47_0.2 mL saline_no seize_drugs_1hr

tag: agent dose

tag: date sacrificed

tag: time sacrificed


title: Control LV, biological rep 3

description: Gene expression data from control left ventricle

source_name: Control left ventricle

tag: tissue subtype

value: Left ventricle

tag: developmental stage

tag: disease status


title: Control LV, biological rep 2


title: Control LV, biological rep 4


title: RQ_rep1

description: Biological replicate 1 of 2. RQ mutant embryoid body

tag: cell type


title: Control LV, biological rep 5


title: MI_rep2

description: Biological replicate 2 of 2. MI mutant embryoid body

source_name: mouse embryoid body with M1652I mutated human BRCA1


title: MI_rep1

description: Biological replicate 1 of 2. MI mutant embryoid body


title: WT_rep2

description: Biological replicate 2 of 2. WT embryoid body

source_name: mouse embryoid body with wild type human BRCA1


title: P306M

city: Sao Paulo

first: Vinicius

last: Maracaja-Coutinho

state: Sao Paulo

address: Av. Prof. Lineu Prestes 748, sala 1200

department: Departamento de Bioquimica, Instituto de Quimica

country: Brazil

institute: Universidade de Sao Paulo

description: One microgram of total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen) and the Rneasy Mini Kit (QIAGEN). RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the first-strand synthesis. DNA polymerase and TS (template switch) primer  were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Second round of amplification were done with 1µg of cRNA. This cRNA was reverse transcribed using random hexamer oligo to primer the first strand synthesis. The following steps were the same as previously reported to obtain the purified cDNA double strand. To generate the 2º round of cRNA, we performed a in vitro transcription in the presence of 5-(3-amino-allyl)-UTP combined with a mix comprised by rNTPs (A, C, G, U). Five micrograms of cRNAs were labeled with Cy5-esther according to label protocol. Array platform was hybridized with the fragmented labeled cRNA for 16 h at 42 °C. Slides hybridized were processed using Generation III Array Scanner and the Array Scanner control software (Molecular Dynamics).

hyb_protocol: Labeled targets were resuspended in 1X buffer hybridization comprised by 100µl of Formamide 100%, 50µl of RPK032 4X Microarray Hybridization Buffer (Amershan Pharmacia Bioscience), 1µl of RefOligo (100pmol/µl),  5µg of competing sequences and treated-DEPC water in a volume to complete 200µl of total volume counting the labeled target volume. The hybridization mixture was denatured at 92ºC for 2minutes and cooled on ice for 2 minutes, and then it was centrifuged at 13000rpm for 5 minutes.

scan_protocol: Images were obtained using a laser Generation III Array Scanner and the Array Scanner control software (Molecular Dynamics). Slides were scanned with scanning resolution of 10µm pixel, excitation wavelength of 633nm (for cy5-labeled targets), emission filter 675nm and PMT voltage of 600 Volts.

data_processing:
Raw images were analyzed using ArrayVision software (Version 8.0, Imaging Research Inc.) and consisted in images in gray scale,  corresponding to Cy5 channel. The procession analysis is required to extract the numerical data. It involves an array template (or grid) automatically aligned to locate the position of each spot in the array, and if required a subsequently manual adjustment to obtain the best possible alignment. After estimating spot location on the array, measurement the spot intensity is made as well as the background intensity based on the area outside of the spot.
To remove artifacts signal from our analyses, we employed the Artifact-Removed densities values (ARM) calculated for each spot by ArrayVision. The ARM is calculated through MTM Density (Median-based trimmed Mean Density Value), which represents the average of all pixels remaining in the spot, after removing pixels with density values that exceed four median absolute deviations (MADs) from the median. This procedure removes the influence of image artifacts (e.g. dust particles) on the density estimation. The ARM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels).
Since each microarray platform contains two replicates of each spotted cDNA, a total of four replicates measurements were obtained for each spot in each patient. The raw data of each spot was compared to the median of all spots in the array platform to filter low values intensities. Only spots that presented value above or equal to the median were considered to further analysis. Replicas that presented median equal to 0 were discarded. To calculate the average of the spot among the patient sample replicas, first we normalized all the spots values considered in previous filtering using QUANTIL method to remove systematic biases, in order to compare across array. Thus we calculated the average value only for spots that presented at least 3 replicas measurements for 4 validated replicas or 2 replicas measurements for 3 or 2 validated replicas. To be considered as expressed transcript, each spot value had to be presented in 75% of samples in at least one histological group. As we were working with different batches of spot cDNA platform production, we performed a batch adjustment using the algorithm ComBat, in order to remove non biological bias.

label: Cy5 (Amersham)

source_name: Biopsy (ganglion)

label_protocol:
All the steps in this part were performed protected from light. Labeled targets were generated from 5µg of cRNA from 2º round of amplification modified with 5-(3-amino-allyl)-UTP. The sample were resuspended in 4.5µl of coupling buffer (0.1M carbonate buffer pH 8.5-9.0) combined with 4µl of mono-reactive Cy5-esters (Amersham) and 2.5µl of treated-DEPC water. The reaction was incubated at room temperature for 1 hour.
To stop coupling reaction 6µl of Hydroxylamine 4M was added and incubated at room temperature for 15 minutes. Labeled targets were purified using RNeasy Mini kit spin columns (QIAGEN) following manufacturer’s instructions. Incorporation of mono-reactive Cy5-esters was verified by NanoDrop spectrophotometer (Thermo Scientific) measuring OD 260 and 650nm. The total volume of labeled targets was concentrated to approximately 10µl using Microcon YM-30 (Millipore) following manufacturer’s instruction.

extract_protocol: Total RNA was extracted from pancreatic tissue samples (50-100mg tissue) using Trizol (Invitrogen) according to manufacturer’s recommendations. Aliquots of RNA were cleaned up in RNeasy Mini Kit spin columns (QIAGEN) including DNAse I RNAse free (QIAGEN) digestion step for removal of genomic DNA. Total RNA integrity was measured by the relative abundance of 28S/18S ribosomal subunits and verified through micro fluid capillary electrophoresis (Agilent Bioanalyzer 2100).

value: pancreatic metastatic tumor (ganglion)


title: genomic DNA from colon cancer cell line_AMC5

description: tumor colon sample

tag: cell line

tag: disease state


title: WT_rep1

description: Biological replicate 1 of 2. WT embryoid body

tag: strain


title: P305M

source_name: Biopsy (liver tissue)

value: pancreatic metastatic tumor (liver)


title: Septum_animal N46_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N46_0.2 mL sarin_no seize_no drugs_3hr

tag: animal number

tag: agent

tag: amount administered

tag: atropine, 2-pam, diazepam

value: N


title: P304M


title: genomic DNA from colon cancer cell line_WiDr

description: tumor colon sample

value: WiDr

value: colon tissue

value: tumor


title: Septum_animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

description: Gene expression data from Septum of animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

tag: time point (hr)

tag: date injected

tag: time injected

tag: presence of seizure

tag: seizure time

tag: seizure latency


title: P302M

tag: tissue


title: Septum_animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

description: Gene expression data from Septum of animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

tag: agent dose

tag: date sacrificed

tag: time sacrificed

tag: animal weight (g)


title: genomic DNA from colon cancer cell line_DLD1

description: tumor colon sample

tag: cell line

tag: disease state


title: P218T

source_name: Pancreatic tissue surgery dissection

value: pancreatic primary tumor


title: P303M

source_name: Biopsy (peritoneum tissue)

value: pancreatic metastatic tumor (peritoneum)


title: Septum_animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Septum of animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

tag: animal number

tag: strain


title: genomic DNA from colon cancer cell line_KM12C

description: tumor colon sample


title: Control LV, biological rep 1

value: Heart

tag: tissue subtype

tag: developmental stage

tag: disease status


title: P217T


title: Septum_animal N44_0.21 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Septum of animal N44_0.21 mL sarin_no seize_no drugs_6hr

tag: agent

tag: amount administered

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: P214M

tag: tissue


title: genomic DNA from colon cancer cell line_LoVo

description: tumor colon sample

value: LoVo


title: genomic DNA from colon cancer cell line_CaCo2

description: tumor colon sample


title: Septum_animal N75_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Septum of animal N75_0.2 mL sarin_no seize_no drugs_3hr

tag: agent dose

tag: time injected

tag: presence of seizure


title: Septum_animal N38_0.2 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Septum of animal N38_0.2 mL sarin_no seize_no drugs_24hr

tag: date sacrificed

tag: time sacrificed

tag: animal weight (g)


title: P216T


title: P212T


title: P211T


title: Septum_animal N40_0.21 mL saline_no seize_drugs_3hr

description: Gene expression data from Septum of animal N40_0.21 mL saline_no seize_drugs_3hr

tag: animal number

value: Saline


title: genomic DNA from colon cancer cell line_HCT15

description: tumor colon sample

tag: cell line

tag: disease state


title: Septum_animal N37_0.19 mL saline_no seize_drugs_3hr

description: Gene expression data from Septum of animal N37_0.19 mL saline_no seize_drugs_3hr

tag: strain


title: Septum_animal N41_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Septum of animal N41_0.2 mL saline_no seize_drugs_24hr


title: genomic DNA from colon cancer tissue_CRC2126T

description: tumor colon sample

source_name: Colon

tag: gender

value: Male

value: Colon cancer tissue


title: genomic DNA from colon cancer cell line_RKO

description: tumor colon sample

value: RKO


title: Septum_animal N35_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Septum of animal N35_0.2 mL saline_no seize_drugs_6hr

value: Septum

tag: agent

value: Sprague-Dawley


title: P209T


title: P208T


title: Septum_animal N36_0.2 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Septum of animal N36_0.2 mL saline_no seize_drugs_0.25hr

tag: amount administered

value: Y


title: genomic DNA from colon cancer tissue_CRC2125T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2126N

description: normal colon sample

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2125N

description: normal colon sample


title: Septum_animal N33_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Septum of animal N33_0.2 mL saline_no seize_drugs_1hr

tag: atropine, 2-pam, diazepam


title: Amygdala_animal N259_naive_no agent_0hr

description: Gene expression data from Amygdala of animal N259_naive_no agent_0hr

source_name: Amygdala_animal N259_naive_no agent_0hr

value: Amygdala

value: Naive

tag: time point (hr)


title: Septum_animal N34_0.22 mL saline_no seize_drugs_3hr

description: Gene expression data from Septum of animal N34_0.22 mL saline_no seize_drugs_3hr

tag: date injected

value: N


title: P206T

description: One microgram of total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen) and the Rneasy Mini Kit (QIAGEN). RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the first-strand synthesis. DNA polymerase and TS (template switch) primer  were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Second round of amplification were done with 1µg of cRNA. This cRNA was reverse transcribed using random hexamer oligo to primer the first strand synthesis. The following steps were the same as previously reported to obtain the purified cDNA double strand. To generate the 2º round of cRNA, we performed a in vitro transcription in the presence of 5-(3-amino-allyl)-UTP combined with a mix comprised by rNTPs (A, C, G, U). Five micrograms of cRNAs were labeled with Cy5-esther according to label protocol. Array platform was hybridized with the fragmented labeled cRNA for 16 h at 42 °C. Slides hybridized were processed using Generation III Array Scanner and the Array Scanner control software (Molecular Dynamics).

tag: tissue


title: P207T


title: P210T


title: genomic DNA from colon cancer tissue_CRC2122T

description: tumor colon sample

value: Female


title: Amygdala_animal N258_naive_no agent_0hr

description: Gene expression data from Amygdala of animal N258_naive_no agent_0hr

source_name: Amygdala_animal N258_naive_no agent_0hr


title: genomic DNA from colon cancer tissue_CRC2123T

description: tumor colon sample

value: tumor


title: genomic DNA from colon cancer adjacent normal tissue_CRC2123N

description: normal colon sample


title: P205T

value: pancreatic primary tumor


title: Amygdala_animal N260_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N260_0.21 mL saline_no seize_no drugs_0.25hr

tag: agent dose


title: genomic DNA from colon cancer tissue_CRC2121T

description: tumor colon sample


title: Amygdala_animal N257_naive_no agent_0hr

description: Gene expression data from Amygdala of animal N257_naive_no agent_0hr

source_name: Amygdala_animal N257_naive_no agent_0hr


title: genomic DNA from colon cancer adjacent normal tissue_CRC2122N

description: normal colon sample


title: P202T


title: P203T


title: P204T


title: wild type (ProβCG:GUS) (biological rep3)

city: London

first: Xurong

last: Tang

address: 1391 Sandford Street

country: Canada

institute: Agriculture and Agri-Food Canada

description:
wt-rep3
WT 3-YF051031ATH09
βCGpro:GUS transgenic line on Col-0

hyb_protocol: Labelling, hybridization, and detection were performed in McGill University and Genome Quebec Innovation Centre  (http://genomequebec.mcgill.ca).

data_processing:
MAS 5.0 raw data were generated by FLEXARRAY provided by McGill University and Genome Quebec Innovation Centre.
The raw MAS 5.0 data files obtained from scanned array images are then imported into GeneSpring 7.3.1 (Silicon Genetics). Only genes with Present (P) calls were included in the analysis. Raw signals of each gene were normalized with the median of all measurements on the chip. The average normalized value of the signal intensity for each gene in three replicate hybridization experiments was adopted as the expression value of the gene. The normalized values were used to identify the differentially regulated genes by calculating the log2 ratios, where the normalized mean intensity values of sdg8 were divided by respective values from ProβCG:GUS. Fold changes of differentially regulated genes in sdg8 compared with ProβCG:GUS were calculated from these ratios.For multiple comparisons among slides, a false discovery rate (FDR) multiple testing correction (Benjamini and Hochberg, 1995) was applied to generate adjusted p-values in GeneSpring 7.3.1 Using a FDR at 5% (p-value=0.05), we selected only the statistically significant genes that were regarded as differentially regulated only if their fold-change was ≥ 2.0 for up- and ≤ -2.0 fold for downregulated.

organism: Arabidopsis thaliana

source_name: leaves at 14 day old

growth_protocol: All plants were grown under 16-h-light (22°C)/8-h-dark (20°C) cycles, either grown on soil or on plates with MS media containing 1.5% sucrose and 0.8% agar with appropriate selection markers. All seeds were vernalized at 4oC for 3 days before placement in a growth environment.

extract_protocol: Total RNA was isolated in three biological replicates from leaves of two-week-old wild type (ProβCG:GUS) and two biological replicates from mutants (essp4/sdg8-5, sdg8-2) seedlings grown on MS agar plates (1.5% sucrose) using the RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Leaves were harvested at 14 days after placing on growth conditions and ground on liquid nitrogen.

tag: ecotype

value: Col-0 backgroud

tag: genotype/variation

value: wild type

value: leaf


title: wild type (ProβCG:GUS) (biological rep2)

description:
wt-rep2
WT 2-YF051031ATH08
βCGpro:GUS transgenic line on Col-0

scan_protocol: Labelling, hybridization, and detection were performed in McGill University and Genome Quebec Innovation Centre  (http://genomequebec.mcgill.ca).


title: Amygdala_animal N256_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N256_0.2 mL saline_no seize_no drugs_24hr

value: Saline

tag: time injected

tag: date sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2121N

description: normal colon sample


title: Amygdala_animal N254_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N254_0.2 mL saline_no seize_no drugs_24hr

tag: animal number

tag: time sacrificed

tag: animal weight (g)


title: genomic DNA from colon cancer tissue_CRC2120T

description: tumor colon sample

tag: disease state


title: P107PC

value: chronic pancreatitis


title: genomic DNA from colon cancer tissue_CRC2119T

description: tumor colon sample

tag: gender

value: Colon cancer tissue


title: P201T


title: wild type (ProβCG:GUS) (biological rep1)

description:
wt-rep1
WT 1-YF051031ATH07
βCGpro:GUS transgenic line on Col-0

label_protocol: Labelling, hybridization, and detection were performed in McGill University and Genome Quebec Innovation Centre (http://genomequebec.mcgill.ca).


title: P108PC


title: genomic DNA from colon cancer adjacent normal tissue_CRC2120N

description: normal colon sample


title: Amygdala_animal N249_0.21 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N249_0.21 mL saline_no seize_no drugs_0.25hr

tag: agent

tag: strain


title: Amygdala_animal N250_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N250_0.21 mL saline_no seize_no drugs_3hr

tag: amount administered

tag: atropine, 2-pam, diazepam


title: essp4/sdg8-5 (biological rep1)

description:
sdg8-5-rep1
sdg8-5-IG070405ATH01
mutants on βCGpro:GUS transgenic background

value: essp4/sdg8-5 mutant


title: Amygdala_animal N251_0.21 mL saline_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N251_0.21 mL saline_no seize_no drugs_1hr

tag: time point (hr)

tag: date injected


title: sdg8-2 (biological rep2)

description:
sdg8-2-rep2
sdg8-2-IG070405ATH04
T-DNA null knockout line on Col-0

value: sdg8-2 mutant

tag: tissue


title: essp4/sdg8-5 (biological rep2)

description:
sdg8-5-rep2
sdg8-5-IG070405ATH02
mutants on βCGpro:GUS transgenic background

tag: ecotype


title: genomic DNA from colon cancer adjacent normal tissue_CRC2119N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2118T

description: tumor colon sample


title: Amygdala_animal N252_0.2 mL saline_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N252_0.2 mL saline_no seize_no drugs_24hr

tag: agent dose

value: Sprague-Dawley


title: genomic DNA from colon cancer adjacent normal tissue_CRC2118N

description: normal colon sample


title: sdg8-2 (biological rep1)

description:
sdg8-2-rep1
sdg8-2-IG070405ATH03
T-DNA null knockout line on Col-0

tag: genotype/variation


title: P106PC

description: One microgram of total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen) and the Rneasy Mini Kit (QIAGEN). RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the first-strand synthesis. DNA polymerase and TS (template switch) primer  were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Second round of amplification were done with 1µg of cRNA. This cRNA was reverse transcribed using random hexamer oligo to primer the first strand synthesis. The following steps were the same as previously reported to obtain the purified cDNA double strand. To generate the 2º round of cRNA, we performed a in vitro transcription in the presence of 5-(3-amino-allyl)-UTP combined with a mix comprised by rNTPs (A, C, G, U). Five micrograms of cRNAs were labeled with Cy5-esther according to label protocol. Array platform was hybridized with the fragmented labeled cRNA for 16 h at 42 °C. Slides hybridized were processed using Generation III Array Scanner and the Array Scanner control software (Molecular Dynamics).


title: P104PC


title: P102PC


title: Amygdala_animal N246_0.18 mL saline_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N246_0.18 mL saline_no seize_no drugs_6hr

tag: time injected

tag: date sacrificed


title: Amygdala_animal N245_0.2 mL saline_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N245_0.2 mL saline_no seize_no drugs_3hr

tag: animal number

tag: presence of seizure


title: genomic DNA from colon cancer tissue_CRC2117T

description: tumor colon sample

value: Male


title: Amygdala_animal N247_0.2 mL saline_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N247_0.2 mL saline_no seize_no drugs_0.25hr

tag: time sacrificed

tag: animal weight (g)


title: P103PC


title: genomic DNA from colon cancer adjacent normal tissue_CRC2117N

description: normal colon sample

tag: gender

tag: disease state

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2116N

description: normal colon sample


title: P09N

value: pancreatic non-tumor


title: genomic DNA from colon cancer tissue_CRC2115T

description: tumor colon sample


title: P08N


title: P105PC


title: P101PC


title: Amygdala_animal N244_0.18 mL saline_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N244_0.18 mL saline_no seize_no drugs_1hr

value: Amygdala

tag: agent

tag: strain


title: Amygdala_animal N248_0.2 mL saline_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N248_0.2 mL saline_no seize_no drugs_1hr

tag: amount administered

tag: atropine, 2-pam, diazepam

value: N


title: genomic DNA from colon cancer tissue_CRC2116T

description: tumor colon sample


title: Amygdala_animal N243_0.21 mL saline_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N243_0.21 mL saline_no seize_no drugs_3hr

tag: time point (hr)

tag: date injected


title: genomic DNA from colon cancer tissue_CRC2114T

description: tumor colon sample

tag: tissue


title: Amygdala_animal N241_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N241_0.2 mL saline_no seize_no drugs_6hr

tag: agent dose


title: genomic DNA from colon cancer adjacent normal tissue_CRC2115N

description: normal colon sample


title: Amygdala_animal N174_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Amygdala of animal N174_0.21 mL saline_no seize_drugs_0.25hr

value: Y


title: genomic DNA from colon cancer tissue_CRC2113T

description: tumor colon sample

value: tumor


title: genomic DNA from colon cancer adjacent normal tissue_CRC2114N

description: normal colon sample


title: P05N


title: Amygdala_animal N242_0.2 mL saline_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N242_0.2 mL saline_no seize_no drugs_6hr


title: P06N


title: genomic DNA from colon cancer adjacent normal tissue_CRC2113N

description: normal colon sample


title: Amygdala_animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

description: Gene expression data from Amygdala of animal N173_0.22 mL sarin_seize (10 min latency)_drugs_24hr

value: Sarin

tag: seizure time

tag: seizure latency


title: Amygdala_animal N172_0.21 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N172_0.21 mL sarin_no seize_no drugs_24hr

tag: time injected

tag: date sacrificed


title: P07N


title: P04N


title: P03N


title: genomic DNA from colon cancer tissue_CRC2112T

description: tumor colon sample

value: Female


title: Amygdala_animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr

description: Gene expression data from Amygdala of animal N170_0.21 mL sarin_seize (5 min latency)_drugs_24hr

tag: animal number

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2112N

description: normal colon sample


title: PES2

city: Seoul

first: Jinkyu

last: Park

address: Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

institute: Seoul National University

description:
PES2(080731)
Gene expression data from embryonic stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Porcine genome  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Sus scrofa

source_name: porcine embryonic stem cells.

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

growth_protocol: Porcine embryonic stem cells were routinely passaged via the pulled glass pipette method every 5-7 days.

extract_protocol: Total RNA from individual samples was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Porcine embryonic stem cells were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) in pESC medium(DMEM/F10/15% FBS)

tag: cell type

value: embryonic stem cells


title: Amygdala_animal N82_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Amygdala of animal N82_0.2 mL saline_no seize_drugs_1hr

tag: time sacrificed

tag: animal weight (g)


title: genomic DNA from colon cancer tissue_CRC2109T

description: tumor colon sample

tag: gender

tag: disease state


title: P02N


title: genomic DNA from colon cancer tissue_CRC2111T

description: tumor colon sample


title: PES5

description:
PES5(080731)
Gene expression data from embryonic stem cells


title: PES6

description:
PES6(080731)
Gene expression data from embryonic stem cells


title: Amygdala_animal N79_0.22 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N79_0.22 mL sarin_no seize_no drugs_1hr

tag: agent

tag: amount administered

tag: strain


title: genomic DNA from colon cancer adjacent normal tissue_CRC2111N

description: normal colon sample


title: Amygdala_animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: Amygdala_animal N78_0.23 mL saline_no seize_drugs_6hr

description: Gene expression data from Amygdala of animal N78_0.23 mL saline_no seize_drugs_6hr

tag: tissue

tag: agent dose


title: P01N

description: One microgram of total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen) and the Rneasy Mini Kit (QIAGEN). RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the first-strand synthesis. DNA polymerase and TS (template switch) primer  were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Second round of amplification were done with 1µg of cRNA. This cRNA was reverse transcribed using random hexamer oligo to primer the first strand synthesis. The following steps were the same as previously reported to obtain the purified cDNA double strand. To generate the 2º round of cRNA, we performed a in vitro transcription in the presence of 5-(3-amino-allyl)-UTP combined with a mix comprised by rNTPs (A, C, G, U). Five micrograms of cRNAs were labeled with Cy5-esther according to label protocol. Array platform was hybridized with the fragmented labeled cRNA for 16 h at 42 °C. Slides hybridized were processed using Generation III Array Scanner and the Array Scanner control software (Molecular Dynamics).


title: Amygdala_animal N81_0.24 mL saline_no seize_drugs_1hr

description: Gene expression data from Amygdala of animal N81_0.24 mL saline_no seize_drugs_1hr

tag: time injected


title: genomic DNA from colon cancer tissue_CRC2110T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2110N

description: normal colon sample


title: Amygdala_animal N77_0.21 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Amygdala of animal N77_0.21 mL saline_no seize_drugs_0.25hr

tag: date sacrificed


title: Amygdala_animal N76_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Amygdala of animal N76_0.2 mL saline_no seize_drugs_24hr

tag: animal number


title: genomic DNA from colon cancer tissue_CRC2108T

description: tumor colon sample


title: Amygdala_animal N75_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N75_0.2 mL sarin_no seize_no drugs_3hr

tag: presence of seizure


title: HeDiPig29

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description:
1103 SZ Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 by PLIER algorithm.

source_name: teat tissue taken at slaughter, mean end weight of 110 kg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: teat, mesenchymal tissue

tag: teat phenotype

value: inverted teat

tag: teat affection status

value: affected animal

tag: breed

value: Pietrain x (Large White x  German Landrace)


title: HeDiPig30

description:
1109 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: normal teat

value: non-affected animal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2109N

description: normal colon sample

tag: gender

value: Colon cancer tissue


title: Amygdala_animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Amygdala of animal N74_0.22 mL sarin_seize (8 min latency)_drugs_3hr

value: Sprague-Dawley

tag: time sacrificed

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: HeDiPig28

description:
1103 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: genomic DNA from colon cancer adjacent normal tissue_CRC2108N

description: normal colon sample

value: Male

tag: disease state

value: normal


title: genomic DNA from colon cancer tissue_CRC2107T

description: tumor colon sample


title: HeDiPig27

description:
1059 SZ Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: Large White x German Landrace


title: Amygdala_animal N73_0.2 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N73_0.2 mL sarin_no seize_no drugs_1hr

value: Amygdala

tag: agent

tag: amount administered

tag: strain

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)


title: Amygdala_animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

description: Gene expression data from Amygdala of animal N70_0.21 mL sarin_seize (12 min latency)_drugs_0.25hr

tag: tissue

tag: agent dose

value: Y

tag: date injected

tag: time injected

tag: date sacrificed


title: HeDiPig22

description:
1037 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: teat phenotype

tag: teat affection status

tag: breed


title: Amygdala_animal N71_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N71_0.2 mL sarin_no seize_no drugs_6hr

tag: animal number

value: Sarin

tag: time sacrificed

tag: presence of seizure


title: HeDiPig24

description:
1040 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: genomic DNA from colon cancer adjacent normal tissue_CRC2103N

description: normal colon sample

tag: gender

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2102T

description: tumor colon sample

value: tumor


title: Amygdala_animal N69_0.23 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N69_0.23 mL sarin_no seize_no drugs_24hr

tag: agent

tag: amount administered

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2101N

description: normal colon sample


title: Amygdala_animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

description: Gene expression data from Amygdala of animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: seizure time

tag: seizure latency


title: genomic DNA from colon cancer adjacent normal tissue_CRC2107N

description: normal colon sample

tag: tissue


title: Amygdala_animal N68_0.22 mL saline_no seize_drugs_24hr

description: Gene expression data from Amygdala of animal N68_0.22 mL saline_no seize_drugs_24hr

value: Saline

tag: agent dose

tag: date injected

tag: time injected

tag: date sacrificed


title: HeDiPig26

description:
1059 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: teat, mesenchymal tissue

tag: teat phenotype

tag: teat affection status

tag: breed


title: HeDiPig21

description:
964 SZ Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: inverted teat


title: genomic DNA from colon cancer tissue_CRC2103T

description: tumor colon sample

tag: gender

tag: disease state


title: HeDiPig25

description:
1058 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: Amygdala_animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

description: Gene expression data from Amygdala of animal N65_0.21 mL sarin_seize (16 min latency)_drugs_24hr

tag: animal number

tag: agent

tag: amount administered

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2102N

description: normal colon sample


title: Amygdala_animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

description: Gene expression data from Amygdala of animal N66_0.23 mL sarin_seize (11 min latency)_drugs_3hr

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: seizure time

tag: animal weight (g)


title: HeDiPig23

description:
1037 SZ Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: tissue

value: affected animal


title: genomic DNA from colon cancer tissue_CRC2100T

description: tumor colon sample

value: Female


title: Amygdala_animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

description: Gene expression data from Amygdala of animal N67_0.2 mL sarin_seize (9 min latency)_drugs_1hr

tag: agent dose

tag: date injected

tag: time injected

tag: date sacrificed

tag: seizure latency


title: HeDiPig20

description:
964 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: teat phenotype

value: normal teat

tag: teat affection status

tag: breed


title: Amygdala_animal N63_0.2 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N63_0.2 mL sarin_no seize_no drugs_24hr

tag: animal number

tag: agent

tag: amount administered


title: genomic DNA from colon cancer tissue_CRC2099T

description: tumor colon sample

tag: gender

tag: disease state


title: HeDiPig18

description:
963 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: German Landrace


title: HeDiPig17

description:
957 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: non-affected animal


title: genomic DNA from colon cancer tissue_CRC2101T

description: tumor colon sample

value: Colon cancer tissue


title: genomic DNA from colon cancer adjacent normal tissue_CRC2100N

description: normal colon sample


title: HeDiPig19

description:
963 SZ Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: Amygdala_animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

description: Gene expression data from Amygdala of animal N62_0.21 mL sarin_seize (13.5 min latency)_drugs_6hr

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: time sacrificed

tag: presence of seizure


title: HeDiPig15

description:
1109 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: tissue

value: teat, epithelial tissue

value: Pietrain x (Large White x  German Landrace)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2099N

description: normal colon sample

value: normal


title: HeDiPig14

description:
1103 SZ Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: genomic DNA from colon cancer adjacent normal tissue_CRC2098N

description: normal colon sample

value: Male


title: Amygdala_animal N59_0.2 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N59_0.2 mL sarin_no seize_no drugs_6hr

value: Amygdala

tag: agent dose

value: N

tag: date injected

tag: time injected

tag: animal weight (g)


title: HeDiPig11

description:
1059 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: teat phenotype

tag: teat affection status

value: Large White x German Landrace


title: genomic DNA from colon cancer adjacent normal tissue_CRC2097N

description: normal colon sample


title: Amygdala_animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

description: Gene expression data from Amygdala of animal N57_0.21 mL sarin_seize (25 in latency)_drugs_3hr

tag: animal number

value: Sarin

value: Y

tag: date sacrificed

tag: seizure time

tag: seizure latency


title: HeDiPig16

description:
950 Me.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: teat, mesenchymal tissue

tag: breed


title: genomic DNA from colon cancer tissue_CRC2097T

description: tumor colon sample

tag: gender

tag: disease state

value: tumor


title: genomic DNA from colon cancer tissue_CRC2096T

description: tumor colon sample

value: Female


title: Amygdala_animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

tag: agent

tag: amount administered

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: Amygdala_animal N60_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N60_0.2 mL sarin_no seize_no drugs_3hr

tag: tissue

tag: agent dose

tag: date injected

tag: time sacrificed

tag: presence of seizure


title: HeDiPig13

description:
1103 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: teat phenotype

value: normal teat

tag: teat affection status

value: affected animal


title: Amygdala_animal N61_0.21 mL sarin_no seize_no drugs_1hr

description: Gene expression data from Amygdala of animal N61_0.21 mL sarin_no seize_no drugs_1hr

tag: animal number

tag: time injected

tag: date sacrificed

tag: animal weight (g)


title: HeDiPig12

description:
1059 SZ Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: inverted teat

tag: breed


title: genomic DNA from colon cancer adjacent normal tissue_CRC2096N

description: normal colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: Amygdala_animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

description: Gene expression data from Amygdala of animal N56_0.22 mL sarin_seize (4 min latency)_drugs_0.25hr

tag: agent

tag: amount administered

tag: strain

value: Sprague-Dawley

tag: seizure time

tag: seizure latency


title: Amygdala_animal N54_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Amygdala of animal N54_0.2 mL saline_no seize_drugs_6hr

tag: tissue

value: Saline

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: Amygdala_animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

description: Gene expression data from Amygdala of animal N55_0.22 mL sarin_seize (10 min latency)_drugs_0.25hr

tag: animal number

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer tissue_CRC2095T

description: tumor colon sample


title: Amygdala_animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

description: Gene expression data from Amygdala of animal N52_0.22 mL sarin_seize (9 min latency)_drugs_24hr

tag: time injected

tag: date sacrificed

tag: animal weight (g)


title: HeDiPig9

description:
1040 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: teat, epithelial tissue

tag: teat phenotype

tag: teat affection status

value: non-affected animal

tag: breed


title: genomic DNA from colon cancer adjacent normal tissue_CRC2095N

description: normal colon sample

tag: gender

tag: disease state

value: normal


title: HeDiPig7

description:
1037 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: HeDiPig8

description:
1037 SZ Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: genomic DNA from colon cancer tissue_CRC2094T

description: tumor colon sample

value: Male


title: HeDiPig10

description:
1058 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: Amygdala_animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

description: Gene expression data from Amygdala of animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

value: Amygdala

tag: agent

tag: amount administered

tag: strain

value: N


title: genomic DNA from colon cancer tissue_CRC2098T

description: tumor colon sample

tag: tissue


title: HeDiPig6

description:
964 SZ Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: Large White x German Landrace


title: Amygdala_animal N47_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Amygdala of animal N47_0.2 mL saline_no seize_drugs_1hr

tag: agent dose

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2093N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2092T

description: tumor colon sample


title: Amygdala_animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

description: Gene expression data from Amygdala of animal N48_0.18 mL sarin_seize (11 min latency)_drugs_1hr

tag: animal number

value: Sarin

tag: date injected

tag: time sacrificed

tag: seizure time

tag: seizure latency


title: genomic DNA from colon cancer adjacent normal tissue_CRC2094N

description: normal colon sample


title: young adult_24hr MWCNT exposure_rep1

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-24h_MWCNT

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.

data_processing: Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console 1.1. To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out.

organism: Caenorhabditis elegans

source_name: mRNA isolated from wildtype young adult, MWCNT, 24 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual Affymetrix, P/N 702646 Rev. 1).

growth_protocol: C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli. Young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce age-synchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.

extract_protocol: The total RNA was prepared from the exposed and control worms according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, an experimental concentration of MWCNT (1mg/L) was prepared in k-media (0.032 M KCl and 0.051M NaCl). Worms were incubated with 1mg/L MWCNT at 20°C for 4 or 24 hr.

tag: genotype

value: wildtype

value: hemaphrodite

tag: developmental stage

value: young adult

tag: treatment

value: multiwall carbon nanotube (MWCNT)

tag: treatment time

value: 24 hours


title: HeDiPig5

description:
964 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: teat phenotype

value: normal teat

tag: teat affection status

value: affected animal

tag: breed


title: HeDiPig4

description:
963 SZ Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: inverted teat

value: German Landrace


title: Amygdala_animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

description: Gene expression data from Amygdala of animal N45_0.2 mL sarin_seize (8 min latency)_drugs_1hr

tag: agent

tag: amount administered

tag: strain

value: Sprague-Dawley

tag: time injected

tag: date sacrificed

tag: presence of seizure

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2092N

description: normal colon sample

tag: gender

tag: tissue

value: Colon cancer tissue

tag: disease state

value: normal


title: Amygdala_animal N44_0.21 mL sarin_no seize_no drugs_6hr

description: Gene expression data from Amygdala of animal N44_0.21 mL sarin_no seize_no drugs_6hr

tag: animal number

value: Amygdala

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time sacrificed


title: young adult_4hr MWCNT exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-4h_MWCNT

source_name: mRNA isolated from wildtype young adult, MWCNT, 4 hr

tag: genotype

tag: developmental stage

tag: treatment

tag: treatment time

value: 4 hours


title: HeDiPig1

description:
950 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

value: teat, epithelial tissue

tag: teat phenotype

tag: teat affection status

value: non-affected animal

tag: breed

value: Large White x German Landrace


title: Amygdala_animal N46_0.2 mL sarin_no seize_no drugs_3hr

description: Gene expression data from Amygdala of animal N46_0.2 mL sarin_no seize_no drugs_3hr

tag: agent

value: Sarin

tag: amount administered

tag: strain

value: N

tag: time injected

tag: date sacrificed

tag: presence of seizure

tag: animal weight (g)


title: HeDiPig3

description:
963 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats

tag: tissue


title: genomic DNA from colon cancer tissue_CRC2091T

description: tumor colon sample

tag: gender

value: Male

tag: disease state

value: tumor


title: HeDiPig2

description:
957 Epi.CEL
Gene expression data from teat tissue of peripubertal pigs of commercial dam lines
'characteristics' descriptions:
phenotype of the teat: classification to either inverted or normal according to examination by adspection and palpation
affection status of the animals: classification to group of animals with or without inverted teats


title: Amygdala_animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

description: Gene expression data from Amygdala of animal N42_0.2 mL sarin_seize (8 min latency)_drugs_3hr

tag: animal number

tag: agent dose

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time sacrificed

tag: seizure time

tag: seizure latency


title: Amygdala_animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

description: Gene expression data from Amygdala of animal N43_0.21 mL sarin_seize (9 min latency)_drugs_6hr

tag: agent

tag: amount administered


title: young adult_24hr BTF mix exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-BTF mix

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: mRNA isolated from wildtype young adult, BTF mix

growth_protocol: C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli and young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce age-synchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.

treatment_protocol: From stock solutions, experimental concentrations of benzene, toluene, formaldehyde and BTF mix were prepared in k-media (0.032 M KCl and 0.051M NaCl; 28). For toxicity tests, worms were incubated at 20°C for 24 hr without a food source and then subjected to each type of analysis.

tag: genotype

value: wildtype

value: hemaphrodite

tag: developmental stage

value: young adult

tag: treatment

value: benzene, toluene, formaldehyde

tag: treatment time

value: 24 hours


title: genomic DNA from colon cancer adjacent normal tissue_CRC2091N

description: normal colon sample

tag: tissue

value: Colon cancer tissue


title: young adult_24hr Formaldehyde exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-Formaldehyde

source_name: mRNA isolated from wildtype young adult, formaldehyde

tag: gender

value: formaldehyde


title: genomic DNA from colon cancer tissue_CRC2090T

description: tumor colon sample

tag: disease state


title: young adult_24hr Toluene exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-Toluene

source_name: mRNA isolated from wildtype young adult, toluene

value: toluene


title: young adult_0h MWCNT exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-0h_MWCNT

source_name: mRNA isolated from wildtype young adult, MWCNT, 0 hr

tag: strain

value: 0 hours


title: young adult_24hr Benzene exposure_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-Benzene

source_name: mRNA isolated from wildtype young adult, benzene

value: benzene


title: shallow_yorkshire_20_wk_s59

city: Ames

first: Oliver

last: Couture

state: IA

address: 2255 Kildee

institute: Iowa State University

hyb_protocol: Labeled targets were hybridized to the Affymetrix Porcine GeneChip® for 16–18 hours at 45 °C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip® Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file; except that we did not monitor the Affymetrix 3'5' ratios since there are no recommended values for amplified porcine tissues.

data_processing: MAS 5.0

source_name: shallow, yorkshire, 20 wk

label_protocol: Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Following laser capture microdissection, the cap was incubated in 50 μl PicoPureTM RNA extraction buffer (Molecular Devices Corporation, Sunnyvale, CA) at 42°C for 30 minutes. After DNase (Qiagen, Valencia, CA) treatment, total RNA was eluted in 12 μl of Elution Buffer. RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA), the Agilent RNA 6000 Pico chip, and Eukaryote Total RNA Pico by evaluating the features of the electropherogram and the RNA integrity numbers. 28S and 18S rRNA bands were expected and the intensity of the 28S bands was expected to be higher than the intensity of the 18S. The RNA Integrity Numbers (RIN) were expected to be greater than 6.0. Samples that failed these criteria were repeated.  The LCM RNA and 500 pg control RNA were amplified using the RiboAmpTM HS kit (Molecular Devices Corporation, Sunnyvale, CA). RNA was reverse transcribed and double-stranded cDNAs synthesized and purified.  The first-round cDNA was transcribed using T7 RNA polymerase. The resulting RNA was purified and used in the second round of amplification. The quality and quantity of amplified RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). The required A260/280 ratio was in the range 1.8-2.1. Samples that failed these criteria were repeated.

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #60. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time

value: 20 wk

tag: breed

value: yorkshire

tag: depth

value: shallow


title: deep_yorkshire_20_wk_s60

source_name: deep, yorkshire, 20 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #59. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: deep


title: Amygdala_animal N41_0.2 mL saline_no seize_drugs_24hr

description: Gene expression data from Amygdala of animal N41_0.2 mL saline_no seize_drugs_24hr

tag: animal number

value: Amygdala

value: Saline

tag: agent dose

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: presence of seizure

value: N

tag: animal weight (g)


title: Amygdala_animal N40_0.21 mL saline_no seize_drugs_3hr

description: Gene expression data from Amygdala of animal N40_0.21 mL saline_no seize_drugs_3hr

tag: agent

tag: amount administered

value: Y

tag: time sacrificed


title: Amygdala_animal N37_0.19 mL saline_no seize_drugs_3hr

description: Gene expression data from Amygdala of animal N37_0.19 mL saline_no seize_drugs_3hr

tag: tissue


title: genomic DNA from colon cancer adjacent normal tissue_CRC2089N

description: normal colon sample

tag: gender

value: Male

tag: disease state

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2090N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2093T

description: tumor colon sample

value: Female

value: tumor


title: genomic DNA from colon cancer tissue_CRC2089T

description: tumor colon sample

value: Colon cancer tissue


title: deep_yorkshire_20_wk_s58

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #57. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time

tag: breed


title: Amygdala_animal N38_0.2 mL sarin_no seize_no drugs_24hr

description: Gene expression data from Amygdala of animal N38_0.2 mL sarin_no seize_no drugs_24hr

tag: animal number

value: Sarin

tag: strain


title: genomic DNA from colon cancer adjacent normal tissue_CRC2088N

description: normal colon sample


title: Slide#18_12980426

city: Beaumont

first: Jeff

last: Wilkinson

state: tx

address: 635 Parson

hyb_protocol: Hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540 ( described (Price et al., 2005 Fungal Genet. Biol.  42:506-518.)

scan_protocol: Hybridized slides were scanned using a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) and the independent TIFF images from each channel were analyzed using TIGR Spotfinder (http://www.tm4.org/spotfinder.html) software program. When the slides were printed the columns were slightly off.  So when we scanned the arrays we had to do each one twice and then merge the data when we were handling the statistics. Because of this the raw files (.tav) and the processed files are split into two files for each slide (cols 1-13 and 14-24).

data_processing: The hybridized slides were scanned and analyzed for statistically significant different expression levels as previously described (Chang, P.K., Wilkinson, J.R., Horn, B.W., Yu, J., Bhatnagar, D., Cleveland, T.E. Genes differentially expressed by Aspergillus flavus strains after loss of aflatoxin production by serial transfers. Appl Microbiol Biotechnol. 2007, 77, 917-925). Processed data is linked as supplementary file to GSE30756.

organism: Aspergillus parasiticus

source_name: SerTrans 16hr rep6

label_protocol: RNA was converted to cDNA and labeled using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540 ( described (Price et al., 2005 Fungal Genet. Biol.  42:506-518.)

growth_protocol: For wild-type A. parasiticus (WT), an A. parasiticus 5-AC mutant, and an A. parasiticus serial transfer mutant (serial transfer), fresh conidia were inoculated into 200 ml A&M liquid medium (105 spores/ml) and incubated at 29°C with constant shaking (150 rpm).  Mycelia were collected from clones after 16 and 24 hours from cultures.  A total of six replicates were performed for each condition, with each replicate consisting of a total of 4 separate cultures.  The four cultures were combined and 20 ml of the resultant supernatant was isolated for aflatoxin determination.  The combined mycelia was flash frozen in liquid nitrogen in a pre-chilled mortar and pestle and ground to a fine powder before storage at -80°C

extract_protocol: Mycelia were collected from clones after 16 and 24 hours from cultures.  A total of six replicates were performed for each condition, with each replicate consisting of a total of 4 separate cultures.  The four cultures were combined and 20 ml of the resultant supernatant was isolated for aflatoxin determination.  The combined mycelia was flash frozen in liquid nitrogen in a pre-chilled mortar and pestle and ground to a fine powder before storage at -80°C. RNA was isolated from 100 mg ground mycelia by suspending in 1 ml of Puresol (Biorad). After treatment with RNase-free DNaseI (Aurum Total RNA fatty and fibrous tissue kit, Biorad), the resulting RNA was converted to cDNA and labeled as previously described (Price et al., 2005).

treatment_protocol: A. parasiticus SRRC 143 (or SU-1); ATCC # 56775) was used as the wild-type strain. Non-aflatoxigenic A. parasiticus clones derived from SU-1 were  prepared by serial mycelial transfer as previously described [Kale et al. 1996] or by 5-AC treatment (1 mM in A&M medium for 36 h) as described for A. nidulans  [Tamame et al., 1983].

value: mycelia

source_name: 5-AC 16hr rep6


title: Amygdala_animal N36_0.2 mL saline_no seize_drugs_0.25hr

description: Gene expression data from Amygdala of animal N36_0.2 mL saline_no seize_drugs_0.25hr

tag: agent dose

tag: atropine, 2-pam, diazepam


title: young adult_not exposed_rep1

description:
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-Control

source_name: mRNA isolated from wildtype young adult, not exposed

tag: genotype

value: wildtype

value: hemaphrodite

tag: developmental stage

value: young adult

tag: treatment


title: Amygdala_animal N35_0.2 mL saline_no seize_drugs_6hr

description: Gene expression data from Amygdala of animal N35_0.2 mL saline_no seize_drugs_6hr

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: presence of seizure


title: shallow_yorkshire_20_wk_s55

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #56. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: 20 wk

value: yorkshire

tag: depth

value: shallow


description:
Gene expression data from Danio rerio young adults.
Zebrafish-Formaldehyde

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Danio rerio

growth_protocol: Wild-type zebrafish (Danio rerio) were maintained on a 14/10 h light-dark cycle at 28°C and fed twice daily.

extract_protocol: The total RNA was prepared from the exposed and control zebrafish according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentrations of benzene, toluene, formaldehyde and a BTF mix were prepared in DMSO. For toxicity tests, fish were incubated at 28°C for 24 hr without a food source and then subjected to each type of analysis.

tag: line

value: AB

tag: gender

value: formaldehyde

tag: treatment time

value: 24 hours


title: genomic DNA from colon cancer tissue_CRC2088T

description: tumor colon sample

source_name: Colon

tag: tissue

tag: disease state


title: deep_yorkshire_12_wk_s54

source_name: deep, yorkshire, 12 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #53. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: breed

tag: time

value: 12 wk

value: deep


title: young adult_24hr Benzene exposure_rep1

description:
Gene expression data from Danio rerio young adults.
Zebrafish-Benzene

value: benzene


title: young adult_DMSO exposed_rep1

description:
Gene expression data from Danio rerio young adults.
Zebrafish-Control

source_name: mRNA isolated from wildtype young adult, DMSO

value: DMSO


title: deep_yorkshire_20_wk_s56

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #55. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Amygdala_animal N34_0.22 mL saline_no seize_drugs_3hr

description: Gene expression data from Amygdala of animal N34_0.22 mL saline_no seize_drugs_3hr

tag: animal number

value: Amygdala

tag: agent

value: Saline

tag: amount administered

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: Y

tag: time sacrificed

value: N

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2087N

description: normal colon sample

value: Male

value: Colon cancer tissue

value: normal


title: Amygdala_animal N33_0.2 mL saline_no seize_drugs_1hr

description: Gene expression data from Amygdala of animal N33_0.2 mL saline_no seize_drugs_1hr

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: presence of seizure


title: young adult_24hr Toluene exposure_rep1

description:
Gene expression data from Danio rerio young adults.
Zebrafish-Toluene

tag: line

tag: genotype

value: wildtype

tag: gender

value: hemaphrodite

tag: developmental stage

value: young adult

tag: treatment

value: toluene

tag: treatment time