title: Hepa1c1c7_DMSO_4h_2


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

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 Hippocampus of animal N72_0.21 mL sarin_seize (7 min latency)_drugs_6hr

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

tag: tissue

value: Hippocampus

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: genomic DNA from colon cancer tissue_CRC2059T

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

organism: Homo sapiens

source_name: Colon

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: gender

value: Female

value: Colon cancer tissue

tag: disease state

value: tumor


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

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

tag: animal number

tag: tissue


title: ovary follicles of Chinese Erhualian sows, biological rep2

city: Wuhan

first: Fenge

last: Li

state: Hubei

address: Shizishan Street

country: China

institute: Huazhong Agricultural University

hyb_protocol: Labeled cRNA was fractionated and hybridized with the GeneChip Porcine Genome Array according to the standard procedures provided by the manufacturer. Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix) using the standard fluidics protocol.

scan_protocol: The probe arrays were scanned using the Affymetrix ® GeneChip® Scanner 3000.

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1). Natural logarithms were then taken on quantile normalization（GeneSpring 7.31. Identification of DE genes was conducted using SAS (Ver.8.1, T-test). The p value cutoff for DE genes was set at 0.05.

organism: Sus scrofa

source_name: preovulaory ovarian follicles of Chinese Erhualian sows stimulated by PSMG-hCG

label_protocol: Biotinylated cRNA were prepared  from 5 ug total RN Aaccording to according to Technical Manual of GeneChip® Expression Analysis.

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

treatment_protocol: Three multiparous Erhualian cyclic sows from Jiangsu Changshu Xuqin Corp. and 3 multiparous Large White cyclic sows from Jinpin farm of Huazhong Agricultural University that exhibit normal estrous cycles were selected and treated with 1000IU PMSG, the LH peak was stimulated by administration with 500IU hCG at 80h after PSMG, and 30-38h after hCG sows were killed and the ovaries at the preovulatory phase were removed immediately and kept in ice-cold physiological saline (0.9% wt/vol NaCl) during dissection of follicles.

value: Ovarian follicles

tag: breed

value: Chinese Erhualian


title: Hepa1c1c7_50nMBaP_4h_2

city: Dresden

first: Jacob

last: Michaelson

address: Tatzberg 47/49

country: Germany

institute: BIOTEC, TU Dresden

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials following the manufacture's recommendations. Heat cocktails at 99° for 5 minutes then cooled to 45° for 5 minutes centrifuge at max speed for 1 minute . Transfer 200μl of hyb solution to each array, then tape holes. Hybridize 17 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA normalized using the moex10stv1mmensecdf_12.1.0 package from the University of Michigan. Exon expression values were summarized to the gene level by taking the median of the exons mapping to a gene (using BioMart mappings from Ensembl Exon to Ensembl Gene Ids). Ense to Ensg mappings (mm9) were downloaded from biomart.org via the biomaRt package.

organism: Mus musculus

source_name: murine hepatoma cells treated for 4h with 50nM benzo(a)pyrene

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were seeded at a density of 10 000 cells/cm2 and medium was changed 24h after. Treatment was started 48h after seeding for all conditions.

extract_protocol: For total RNA extraction cells were lysed in Trizol and RNA extracted with chloroform followed by Rneasy® purification (Qiagen). Samples were then treated with the RiboMinus™ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Hepa 1c1c7 cells were treated with either 50nM or 5uM of benzo(a)pyrene for different time points (2,4,12 and 24h). Matched vehicel controls (0.05% DMSO) were prepared in addition. Three biological replicated were generated for each treatment and time point.

tag: cell line

value: Hepa 1c1c7

tag: cell type

value: hepatoma

tag: concentration of chemical

tag: time of exposure


title: Hepa1c1c7_5uMBaP_4h_2

source_name: murine hepatoma cells treated for 4h with 5µM benzo(a)pyrene

value: 5 µM


title: Hippocampus_animal N71_0.2 mL sarin_no seize_no drugs_6hr

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

tag: agent

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)

tag: date injected


title: Hepa1c1c7_DMSO_2h_2

source_name: murine hepatoma cells treated for 2h with Vehicle

value: Vehicle


title: shallow_duroc_1_wk_s1

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, duroc, 1 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 #2. 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: duroc

tag: depth

value: shallow

tag: time

value: 1 wk


title: ovary follicles of Large White sows, biological rep3

source_name: preovulaory ovarian follicles of Large White sows stimulated by PSMG-hCG

value: Large White


title: genomic DNA from colon cancer adjacent normal tissue_CRC2059N

description: normal colon sample

tag: gender

tag: disease state

value: normal


title: genomic DNA from colon cancer tissue_CRC2057T

description: tumor colon sample

value: Male

tag: tissue


title: ovary follicles of Chinese Erhualian sows, biological rep3

tag: breed


title: Hepa1c1c7_DMSO_24h_1

source_name: murine hepatoma cells treated for 24h with Vehicle

tag: cell line


title: Hepa1c1c7_5uMBaP_2h_2

source_name: murine hepatoma cells treated for 2h with 5µM benzo(a)pyrene

tag: cell type


title: Hepa1c1c7_50nMBaP_2h_2

source_name: murine hepatoma cells treated for 2h with 50nM benzo(a)pyrene

tag: concentration of chemical


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

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

tag: animal number

value: Hippocampus

value: Sarin

value: Sprague-Dawley

value: Y

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: Hippocampus_animal N68_0.22 mL saline_no seize_drugs_24hr

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

tag: agent

value: Saline

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: ovary follicles of Chinese Erhualian sows, biological rep1

tag: tissue

value: Ovarian follicles

tag: breed

value: Chinese Erhualian


title: Hippocampus_animal N69_0.23 mL sarin_no seize_no drugs_24hr

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

tag: animal number


title: ovary follicles of Large White sows, biological rep2


title: genomic DNA from colon cancer tissue_CRC2056T

description: tumor colon sample

tag: gender

value: Colon cancer tissue

tag: disease state

value: tumor


title: genomic DNA from colon cancer adjacent normal tissue_CRC2058N

description: normal colon sample

value: Female


title: Hepa1c1c7_DMSO_12h_2

source_name: murine hepatoma cells treated for 12h with Vehicle

tag: cell line

value: Hepa 1c1c7

tag: cell type

value: hepatoma

tag: concentration of chemical

value: Vehicle

tag: time of exposure


title: genomic DNA from colon cancer tissue_CRC2058T

description: tumor colon sample


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

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

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: Hepa1c1c7_50nMBaP_24h_1

source_name: murine hepatoma cells treated for 24h with 50nM benzo(a)pyrene


title: ovary follicles of Large White sows, biological rep1


title: Hepa1c1c7_5uMBaP_24h_1

source_name: murine hepatoma cells treated for 24h with 5µM benzo(a)pyrene

value: 5 µM


title: Hepa1c1c7_DMSO_12h_1


title: (767)Morphology:Brachial artery of pig#9995

city: West Lafayette

first: Martin

last: Bahls

address: 800 W Stadium Ave

institute: Purdue University

description: Brachial artery of pig#9995

hyb_protocol: Following fragmentation, 6.5 microg 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 Affymetrix GeneChip Scanner 3000 (affymetrix).

data_processing: Default GCOS 1.4 raw probe intensities were analyzed using the mas5 module of the affy 1.0 package for R version 2.3.1. The probesets that were present according to MAS5calls and normalized, background corrected, and summarized using the RMA function in Bionconductor.

label: Biotin

source_name: Brachial artery of pig#9995

label_protocol: Biotinylated cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Pigs were on a normal diet

extract_protocol: RNA was isolated using Macherey Nagel Nucleo Spin II for the piglets and CsCl ultracentrifugation followed by MN Nucleospin II for the one and two year olds.

tag: artery

value: Brachial artery

tag: pig id

value: blood, whole

tag: age

value: 2 year


title: Hepa1c1c7_50nMBaP_12h_1

source_name: murine hepatoma cells treated for 12h with 50nM benzo(a)pyrene


title: genomic DNA from colon cancer tissue_CRC2055T

description: tumor colon sample

value: Male

tag: tissue


title: (770)Morphology:Femoral artery of pig#9994

description: Femoral artery of pig#9994

source_name: Femoral artery of pig#9994

value: Femoral artery


title: genomic DNA from colon cancer adjacent normal tissue_CRC2057N

description: normal colon sample

tag: gender

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2055N

description: normal colon sample

tag: disease state


title: Hepa1c1c7_5uMBaP_12h_1

source_name: murine hepatoma cells treated for 12h with 5µM benzo(a)pyrene

tag: cell line


title: Hippocampus_animal N61_0.21 mL sarin_no seize_no drugs_1hr

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

tag: animal number

value: Hippocampus

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


title: (769)Morphology:Brachial artery of pig#9994

description: Brachial artery of pig#9994

source_name: Brachial artery of pig#9994

tag: cell type


title: Hippocampus_animal N60_0.2 mL sarin_no seize_no drugs_3hr

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

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: (758)Morphology:Femoral artery of pig#9175

description: Femoral artery of pig#9175

source_name: Femoral artery of pig#9175

tag: artery

tag: pig id

tag: age

value: 1 year


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

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

tag: animal number

tag: tissue

value: Y

tag: seizure time

tag: seizure latency


title: genomic DNA from colon cancer tissue_CRC2054T

description: tumor colon sample

source_name: Colon

tag: gender

value: Female

value: Colon cancer tissue

tag: disease state

value: tumor


title: genomic DNA from colon cancer adjacent normal tissue_CRC2056N

description: normal colon sample


title: Hippocampus_animal N59_0.2 mL sarin_no seize_no drugs_6hr

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

tag: agent

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: (756)Morphology:Brachial artery of pig#9175

description: Brachial artery of pig#9175

source_name: Brachial artery of pig#9175

tag: cell type


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

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

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: Hepa1c1c7_DMSO_4h_1

source_name: murine hepatoma cells treated for 4h with Vehicle

tag: cell line

value: Hepa 1c1c7

value: hepatoma

tag: concentration of chemical

value: Vehicle

tag: time of exposure


title: Hippocampus_animal N63_0.2 mL sarin_no seize_no drugs_24hr

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

tag: animal number

tag: tissue


title: (774)Morphology:Femoral artery of pig#9487

description: Femoral artery of pig#9487

source_name: Femoral artery of pig#9487

tag: artery

tag: pig id

value: blood, whole

tag: age

value: 1 week


title: genomic DNA from colon cancer tissue_CRC2053T

description: tumor colon sample

tag: gender

tag: disease state


title: Hepa1c1c7_50nMBaP_4h_1

source_name: murine hepatoma cells treated for 4h with 50nM benzo(a)pyrene

tag: cell type


title: (772)Morphology:Femoral artery of pig#9997

description: Femoral artery of pig#9997

source_name: Femoral artery of pig#9997

value: 2 year


title: Hepa1c1c7_5uMBaP_4h_1

source_name: murine hepatoma cells treated for 4h with 5µM benzo(a)pyrene

value: 5 µM


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

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

tag: agent

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: genomic DNA from colon cancer adjacent normal tissue_CRC2054N

description: normal colon sample

value: normal


title: Hepa1c1c7_DMSO_2h_1

source_name: murine hepatoma cells treated for 2h with Vehicle

tag: cell line

tag: concentration of chemical


title: genomic DNA from colon cancer adjacent normal tissue_CRC2053N

description: normal colon sample


title: Hepa1c1c7_50nMBaP_2h_1

source_name: murine hepatoma cells treated for 2h with 50nM benzo(a)pyrene

tag: time of exposure


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

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

tag: animal number

tag: tissue

value: Hippocampus

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: (755)Morphology:Brachial artery of pig#9176

description: Brachial artery of pig#9176

source_name: Brachial artery of pig#9176

tag: artery

value: Brachial artery

tag: pig id

tag: cell type

tag: age


title: Hepa1c1c7_5uMBaP_2h_1

source_name: murine hepatoma cells treated for 2h with 5µM benzo(a)pyrene


title: genomic DNA from colon cancer tissue_CRC2051T

description: tumor colon sample

tag: gender

value: Male

tag: disease state


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

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

tag: agent

value: Sarin

tag: amount administered

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: genomic DNA from colon cancer tissue_CRC2052T

description: tumor colon sample

tag: tissue


title: (768)Morphology:Femoral artery of pig#9995

description: Femoral artery of pig#9995

source_name: Femoral artery of pig#9995

value: Femoral artery


title: (748)Morphology:Brachial artery of pig#9188

description: Brachial artery of pig#9188

source_name: Brachial artery of pig#9188

value: 1 year


title: (761)Morphology:Brachial artery of pig#9192

description: Brachial artery of pig#9192

source_name: Brachial artery of pig#9192


title: (747)Morphology:Femoral artery of pig#9483

description: Femoral artery of pig#9483

source_name: Femoral artery of pig#9483


title: genomic DNA from colon cancer adjacent normal tissue_CRC2051N

description: normal colon sample

value: Colon cancer tissue


title: (750)Morphology:Femoral artery of pig#9485

description: Femoral artery of pig#9485

source_name: Femoral artery of pig#9485


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

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

tag: animal number

value: Y

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time


title: (765)Morphology:Brachial artery of pig#9007

description: Brachial artery of pig#9007

source_name: Brachial artery of pig#9007

tag: artery

tag: pig id

tag: cell type

tag: age


title: (757)Morphology:Femoral artery of pig#9176

description: Femoral artery of pig#9176

source_name: Femoral artery of pig#9176


title: Hippocampus_animal N54_0.2 mL saline_no seize_drugs_6hr

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

tag: agent

value: Saline

tag: amount administered

value: N

tag: animal weight (g)


title: (762)Morphology:Femoral artery of pig#9192

description: Femoral artery of pig#9192

source_name: Femoral artery of pig#9192


title: genomic DNA from colon cancer adjacent normal tissue_CRC2050N

description: normal colon sample

source_name: Colon

tag: gender

value: Female

tag: disease state


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

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

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: seizure latency


title: genomic DNA from colon cancer tissue_CRC2049T

description: tumor colon sample

tag: tissue

value: tumor


title: genomic DNA from colon cancer tissue_CRC2050T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2052N

description: normal colon sample


title: Hippocampus_animal N47_0.2 mL saline_no seize_drugs_1hr

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

tag: animal number

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


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

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

tag: agent

tag: seizure time


title: (759)Morphology:Brachial artery of pig#9237

description: Brachial artery of pig#9237

source_name: Brachial artery of pig#9237

tag: artery

tag: pig id

tag: cell type

value: blood, whole

tag: age


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

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

tag: amount administered

tag: agent dose

tag: strain

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2049N

description: normal colon sample

tag: gender

tag: disease state


title: Swiss Agouti_4_RA

city: Münster

first: Peter

middle: Christian

last: Kahr

address: Grevener Straße 1

institute: University Hospital Münster

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring GX 11.5.1

source_name: right atrium

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy micro fibrous tissue kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Swiss Agouti

value: 12 months

tag: tissue

value: Right atrium


title: genomic DNA from colon cancer adjacent normal tissue_CRC2048N

description: normal colon sample

value: normal


title: Swiss Agouti_1_RA

description: replicate 1


title: (764)Morphology:Femoral artery of pig#9006

description: Femoral artery of pig#9006

source_name: Femoral artery of pig#9006

value: 2 year


title: Hippocampus_animal N44_0.21 mL sarin_no seize_no drugs_6hr

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

tag: animal number

value: Hippocampus

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected


title: Swiss Agouti_3_RA

description: replicate 3


title: genomic DNA from colon cancer tissue_CRC2048T

description: tumor colon sample

value: Male


title: Swiss Agouti_2_RA

description: replicate 2


title: genomic DNA from colon cancer adjacent normal tissue_CRC2047N

description: normal colon sample


title: Hippocampus_animal N46_0.2 mL sarin_no seize_no drugs_3hr

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

tag: agent

value: Sarin

value: Sprague-Dawley

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer tissue_CRC2047T

description: tumor colon sample


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

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

tag: seizure time

tag: seizure latency


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

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

tag: amount administered

tag: agent dose


title: (771)Morphology:Brachial artery of pig#9997

description: Brachial artery of pig#9997

source_name: Brachial artery of pig#9997

tag: artery

value: Brachial artery

tag: pig id

tag: cell type

tag: age


title: (751)Morphology:Femoral artery of pig#9188

description: Femoral artery of pig#9188

source_name: Femoral artery of pig#9188

value: Femoral artery

value: 1 year


title: Swiss Agouti_4_LA

description: replicate 4

source_name: left atrium

tag: strain

tag: tissue

value: Left atrium


title: genomic DNA from colon cancer adjacent normal tissue_CRC2046N

description: normal colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: Swiss Agouti_2_LA

description: replicate 2


title: genomic DNA from colon cancer tissue_CRC2046T

description: tumor colon sample


title: (763)Morphology:Brachial artery of pig#9006

description: Brachial artery of pig#9006

source_name: Brachial artery of pig#9006


title: (752)Morphology:Brachial artery of pig#9193

description: Brachial artery of pig#9193

source_name: Brachial artery of pig#9193


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

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

tag: animal number

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: animal weight (g)


title: Hippocampus_animal N41_0.2 mL saline_no seize_drugs_24hr

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

tag: agent

value: Saline

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

value: N


title: Swiss Agouti_1_LA

description: replicate 1

value: Swiss Agouti


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

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

tag: amount administered

tag: agent dose

tag: seizure time

tag: seizure latency


title: (753)Morphology:Femoral artery of pig#9193

description: Femoral artery of pig#9193

source_name: Femoral artery of pig#9193

tag: artery

tag: pig id

tag: cell type

value: blood, whole

tag: age


title: genomic DNA from colon cancer tissue_CRC2045T

description: tumor colon sample

tag: gender

tag: tissue

tag: disease state

value: tumor


title: Swiss Agouti_3_LA

description: replicate 3

tag: strain

value: 12 months


title: (745)Morphology:Brachial artery of pig#9481

description: Brachial artery of pig#9481

source_name: Brachial artery of pig#9481

value: 1 week


title: Hippocampus_animal N40_0.21 mL saline_no seize_drugs_3hr

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

tag: animal number

value: Hippocampus

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: animal weight (g)


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

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

tag: agent

tag: amount administered

tag: agent dose

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: Hippocampus_animal N35_0.2 mL saline_no seize_drugs_6hr

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


title: (766)Morphology:Femoral artery of pig#9007

description: Femoral artery of pig#9007

source_name: Femoral artery of pig#9007

tag: artery

tag: pig id

tag: cell type

tag: age

value: 2 year


title: genomic DNA from colon cancer adjacent normal tissue_CRC2045N

description: normal colon sample

tag: gender

value: Male

tag: tissue

tag: disease state

value: normal


title: (760)Morphology:Femoral artery of pig#9237

description: Femoral artery of pig#9237

source_name: Femoral artery of pig#9237


title: (773)Morphology:Brachial artery of pig#9487

description: Brachial artery of pig#9487

source_name: Brachial artery of pig#9487

value: Brachial artery


title: genomic DNA from colon cancer tissue_CRC2044T

description: tumor colon sample

value: Female


title: MF1_4_LA

description: replicate 4

tag: strain


title: Hippocampus_animal N38_0.2 mL sarin_no seize_no drugs_24hr

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

tag: animal number

value: Sarin

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: (754)Morphology:Femoral artery of pig#9481

description: Femoral artery of pig#9481

source_name: Femoral artery of pig#9481

value: Femoral artery


title: genomic DNA from colon cancer tissue_CRC2043T

description: tumor colon sample

value: Colon cancer tissue


title: MF1_1_RA

description: replicate 1

value: Right atrium


title: MF1_4_RA

description: replicate 4


title: Hippocampus_animal N33_0.2 mL saline_no seize_drugs_1hr

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

tag: agent

value: Saline

tag: amount administered

value: Y

tag: time injected

value: N

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2043N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2042T

description: tumor colon sample

value: tumor


title: MF1_2_RA

description: replicate 2

value: 12 months


title: MF1_1_LA

description: replicate 1

value: Left atrium


title: genomic DNA from colon cancer adjacent normal tissue_CRC2044N

description: normal colon sample


title: MF1_3_RA

description: replicate 3


title: Hippocampus_animal N37_0.19 mL saline_no seize_drugs_3hr

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

value: Hippocampus

tag: agent dose

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: (746)Morphology:Brachial artery of pig#9483

description: Brachial artery of pig#9483

source_name: Brachial artery of pig#9483

tag: artery

tag: pig id

tag: cell type

value: blood, whole

tag: age

value: 1 week


title: Hippocampus_animal N34_0.22 mL saline_no seize_drugs_3hr

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

tag: tissue

tag: strain


title: MF1_2_LA

description: replicate 2


title: (749)Morphology:Brachial artery of pig#9485

description: Brachial artery of pig#9485

source_name: Brachial artery of pig#9485


title: Piriform Cortex_animal N260_0.21 mL saline_no seize_no drugs_0.25hr

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

tag: animal number

value: Piriform Cortex

tag: atropine, 2-pam, diazepam


title: CRPC-Xeno3

city: Arlington

first: Heng

last: Huang

state: TX

address: 500 UTA Blvd.

department: Computer Science and Engineering

institute: University of Texas at Arlington

hyb_protocol: Agilent FFPE version 5.0

scan_protocol: Agilent Technologies Scanner G2505B US23502362

data_processing: Agilent Feature Extraction Protocol 9.1.3.1, the raw data was Lowess normalized by the Agilent software

label_protocol: Agilent FFPE version 5.0 - ULS

extract_protocol:
mix well, spin down. Incubate for 30 min at 60C. Then add 55ul of 2x hyb buffer and hyb. for 17 hours at 65C.
RNA was isolated using the mirVana total RNA protocol (part #AM1560, Ambion, Austin, TX). RNA integrity was verified using a 2100 Bioanalyzer (part #G2938A) with nano chips (parts #5067-15101 and #G4411B; Agilent Technologies, Alto, CA).

tag: subject

source_name: Control Subject (mixed)

value: Control Subject (mixed)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2042N

description: normal colon sample

source_name: Colon

tag: gender

value: Female

tag: disease state

value: normal


title: MF1_3_LA

description: replicate 3


title: Piriform Cortex_animal N259_naive_no agent_0hr

description: Gene expression data from Piriform Cortex of animal N259_naive_no agent_0hr

tag: agent

value: Naive

tag: time point (hr)


title: Piriform Cortex_animal N254_0.2 mL saline_no seize_no drugs_24hr

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

tag: amount administered

tag: agent dose

value: Sprague-Dawley

tag: date injected

tag: time injected

tag: animal weight (g)


title: Piriform Cortex_animal N257_naive_no agent_0hr

description: Gene expression data from Piriform Cortex of animal N257_naive_no agent_0hr

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2041N

description: normal colon sample

value: Male

tag: tissue

value: Colon cancer tissue


title: CRPC8

source_name: Prostate Cancer

value: Prostate Cancer

tag: cancer treatment

value: Pt Dxed in 1995; RP, XRT hormone Tx chemoTx;  HRPC by 2003

source_name: Prostate Cancer (small cell)

value: Prostate Cancer (small cell)

value: Pt Dxed in 1990; XRT, hormone Tx, chemoTx; HRPC by 1995


title: genomic DNA from colon cancer tissue_CRC2039T

description: tumor colon sample

value: tumor


title: Piriform Cortex_animal N258_naive_no agent_0hr

description: Gene expression data from Piriform Cortex of animal N258_naive_no agent_0hr

tag: animal number

value: N


title: Piriform Cortex_animal N250_0.21 mL saline_no seize_no drugs_3hr

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

value: Saline

tag: strain

tag: atropine, 2-pam, diazepam


title: Piriform Cortex_animal N251_0.21 mL saline_no seize_no drugs_1hr

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


title: genomic DNA from colon cancer tissue_CRC2040T

description: tumor colon sample

tag: gender


title: genomic DNA from colon cancer adjacent normal tissue_CRC2039N

description: normal colon sample

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2041T

description: tumor colon sample


title: CRPC-Xeno1

tag: subject

source_name: Prostate Cancer (xeno parent 130)

value: Prostate Cancer (xeno parent 130)

value: Pt Dxed in 1992; XRT(brachy), hormone Tx, chemoTx, PC-SPES; HRPC by 2000


title: CRPC-Xeno2

source_name: Xenograph 149

value: Xenograph 149


title: CRPC5

source_name: Prostate Cancer (xeno parent 149)

value: Prostate Cancer (xeno parent 149)

value: Pt Dxed in 2002; RP, XRT, hormone Tx, chemoTx; HRPC by 2/2006

source_name: Prostate Cancer (xeno parent 169, small cell)

value: Pt with primary small cell CA in 06/2007; PSA 0.9; Txed with chemoTx and hormonal Tx


title: CRPC6

source_name: Prostate Cancer (xeno parent 170)

value: Prostate Cancer (xeno parent 170)

value: Pt Dxed in 2007; hormone Tx, chemoTx; HRPC by 1/2009

source_name: Prostate Cancer (xeno parent 174)

value: Prostate Cancer (xeno parent 174)

value: Pt Dxed in 2009, hormone Tx, chemoTx; HRPC


title: genomic DNA from colon cancer tissue_CRC2037T

description: tumor colon sample

value: Female

value: Colon cancer tissue


title: CRPC4

value: Prostate Cancer

value: Pt Dxed in 2007; hormone Tx; chemoTx; HRPC by 2008

value: Pt Dxed in 2002; hormone Tx, chemoTx;  HRPC by 5/2007


title: Piriform Cortex_animal N256_0.2 mL saline_no seize_no drugs_24hr

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

value: Piriform Cortex

tag: agent

value: Sprague-Dawley

value: N

tag: time point (hr)


title: CRPC7

value: Pt Dxed in 1990; XRT hormone Tx, vaccine Tx; HRPC by 1999

value: Pt Dxed in 1999 (Bx is HS); hormone Tx, vaccine Tx, chemoTx; HRPC by 09/2003


title: CRPC-Scell

value: Prostate Cancer (small cell)

value: Pt Dxed in 2002; XRT hormone Tx; small cell de-differentiation by 2006; HRPC by 2006

value: Pt Dxed in 1992; XRT hormonal Tx; already HRPC by 2002


title: genomic DNA from colon cancer tissue_CRC2038T

description: tumor colon sample

value: Male

value: tumor


title: CRPC3

source_name: Prostate Cancer (xeno parent 157)

value: Prostate Cancer (xeno parent 157)

value: Pt Dxed in 2002; hormone Tx; chemoTx; already HRPC by 2007

value: Pt Dxed in 2002 (Bx is HS); chemoTx; hormone Tx ; HRPC by 2006


title: genomic DNA from colon cancer adjacent normal tissue_CRC2040N

description: normal colon sample

value: Colon cancer tissue

value: normal


title: Piriform Cortex_animal N252_0.2 mL saline_no seize_no drugs_24hr

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

value: Saline

tag: amount administered

tag: agent dose


title: Piriform Cortex_animal N249_0.21 mL saline_no seize_no drugs_0.25hr

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

tag: date injected

tag: time injected


title: Piriform Cortex_animal N248_0.2 mL saline_no seize_no drugs_1hr

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

tag: date sacrificed

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2038N

description: normal colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2037N

description: normal colon sample

value: Female


title: Piriform Cortex_animal N247_0.2 mL saline_no seize_no drugs_0.25hr

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

value: Piriform Cortex

tag: time sacrificed

tag: presence of seizure


title: CRPC2

source_name: Prostate Cancer (xeno parent 126)

value: Prostate Cancer (xeno parent 126)

tag: cancer treatment

value: Pt Dxed in 1998; hormone Tx; PC-SPES; HRPC by 2002

source_name: Prostate Cancer (xeno parent 127)

value: Prostate Cancer (xeno parent 127)

value: RP in 1995 for ductal PCa; XRT, hormone Tx, chemoTx; HRPC by 2003


title: CRPC1

source_name: Prostate Cancer (xeno parent 124)

value: Prostate Cancer (xeno parent 124)

value: Pt Dxed in 2001; hormone Tx; chemo Tx 2002; HRPC by 2002

value: Prostate Cancer


title: Piriform Cortex_animal N242_0.2 mL saline_no seize_no drugs_6hr

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

tag: animal number

tag: tissue

value: Sprague-Dawley

value: N


title: genomic DNA from colon cancer adjacent normal tissue_CRC2036N

description: normal colon sample

value: Male


title: In_vitro_bac_rep3

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Biological replicate 3

hyb_protocol: Standard Agilent One-colour Microarray hybridization protocol

scan_protocol: Arrays were scanned with the Agilent Technologies Scanner model G2505B according to Agilent One-colour microarray scanning protocol.

data_processing: Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction Software version 9.5.3.1. Processed signals from Feature Extraction were used as spot intensities for analysis and gIsWellAboveBG is used to flag non-significant features with background-subtracted signal is lower than 2.6 times the background standard deviation of that feature. Arrays were then median normalized with BRB-ArrayTools (http://linus.nci.nih.gov).

organism: Burkholderia pseudomallei

source_name: In vitro bacteria

label_protocol: Prior to labelling, bacteria total RNA were polyadenylated based on the PAP method using A-plusTM Poly(A) Polymerase Tailing kit (Epicentre). 500 ng of polyadenylated RNA was reverse transcribed to cRNA and labelled with Agilent’s Low RNA Input Linear Amplification kit according to the manufacturer's instruction.

growth_protocol: Prior to infection, overnight bacteria cultures were diluted to 1:50 in LB broth and grown to mid-logarithmic phase (OD600 = 0.4-0.6) at 37°C, 250 rpm for 3 h. Human macrophage U937 cells were then infected at MOI of 10:1 and intracellular bacteria were harvested at selected time post-infection. For control, bacteria were grown at stationary in complete RPMI medium under 5% CO2 till mid-logarithmic phase before RNA extraction.

extract_protocol: Bacterial RNA was prepared using the Qiagen’s RNeasy Mini Kit and on-column DNase I digestion was performed. Total RNA obtained was purified further by ethanol/ammonium acetate precipitation. Quality control was performed with Agilent 2100 Bioanalyser.

treatment_protocol: Infected macrophage cells were lysed with 1% saponin in PBS at 37°C for 5 min and cells lysate were subjected to centrifugation. Bacterial pellet collected were snap-frozen in liquid nitrogen and kept at -80°C till extraction. Similar treatments were also done for control bacteria.

tag: clinical isolate


title: In_vitro_bac_rep1

description: Biological replicate 1


title: In_vitro_bac_rep2

description: Biological replicate 2


title: Intracell_bac_6hpi_rep3

description: Biological replicate 3

source_name: Intracellular bacteria 6h


title: Intracell_bac_6hpi_rep2

description: Biological replicate 2


title: genomic DNA from colon cancer tissue_CRC2034T

description: tumor colon sample

tag: gender

value: tumor


title: Piriform Cortex_animal N243_0.21 mL saline_no seize_no drugs_3hr

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

tag: strain

tag: atropine, 2-pam, diazepam


title: genomic DNA from colon cancer tissue_CRC2036T

description: tumor colon sample

tag: disease state


title: Control3

source_name: Control Subject

tag: subject

value: Control Subject

source_name: Xenograph 79

value: Xenograph 79


title: genomic DNA from colon cancer adjacent normal tissue_CRC2034N

description: normal colon sample

source_name: Colon

value: Colon cancer tissue

value: normal


title: Piriform Cortex_animal N244_0.18 mL saline_no seize_no drugs_1hr

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

tag: agent

value: Saline

tag: amount administered

tag: time point (hr)


title: genomic DNA from colon cancer tissue_CRC2033T

description: tumor colon sample

value: Female


title: Piriform Cortex_animal N246_0.18 mL saline_no seize_no drugs_6hr

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

value: Piriform Cortex

tag: agent dose

tag: date injected

tag: time injected


title: Control4

source_name: Xenograph 117

value: Xenograph 117


title: genomic DNA from colon cancer adjacent normal tissue_CRC2035N

description: normal colon sample


title: Control2

source_name: Prostate Cancer (xeno parent 79)

value: Prostate Cancer (xeno parent 79)

value: Pt Dxed in 1992; XRT, hormone Tx; chemoTx (1999);1998 Bx is HRPC but chemonaive; HRPC by 1998


title: Piriform Cortex_animal N245_0.2 mL saline_no seize_no drugs_3hr

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

tag: date sacrificed

tag: time sacrificed

tag: animal weight (g)


title: Intracell_bac_6hpi_rep1

description: Biological replicate 1


title: genomic DNA from colon cancer adjacent normal tissue_CRC2033N

description: normal colon sample


title: Piriform Cortex_animal N174_0.21 mL saline_no seize_drugs_0.25hr

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

tag: animal number

value: Y

tag: presence of seizure


title: Control1

source_name: Prostate Cancer (xeno parent 117)

value: Prostate Cancer (xeno parent 117)

tag: cancer treatment

value: Pt Dxed in 1998; 1998 Bx is hormone sensitive(HS); hormone Tx, chemo Tx, dendritic cell, vaccine Tx; HRPC by 2000


title: genomic DNA from colon cancer tissue_CRC2035T

description: tumor colon sample

tag: gender

tag: tissue


title: UNC980090A_DCISN

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Agilent Custom array of UNC980090A_DCISN

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

extract_protocol: Qiagen RNeasy Mini Kit.

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: negative

tag: age at diagnosis (year)

tag: menopause status

value: unknown

tag: histopathology

value: DCIS only

tag: breast cancer subtype (pam50)

tag: er status

value: positive

tag: hormone treated

value: yes

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: UNC990357A_DCISN

description: Agilent Custom array of UNC990357A_DCISN

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

value: no


title: Piriform Cortex_animal N241_0.2 mL saline_no seize_no drugs_6hr

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

tag: animal number

tag: agent

value: Saline

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: Intracell_bac_4hpi_rep3

description: Biological replicate 3

source_name: Intracellular bacteria 4h

tag: clinical isolate


title: Intracell_bac_2hpi_rep2

description: Biological replicate 2

source_name: Intracellular bacteria 2h


title: Intracell_bac_4hpi_rep2

description: Biological replicate 2


title: genomic DNA from colon cancer adjacent normal tissue_CRC2032N

description: normal colon sample

tag: gender

value: Female

tag: tissue

value: Colon cancer tissue

tag: disease state

value: normal


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

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

tag: animal number

value: Piriform Cortex

value: Sarin

value: Y

tag: seizure time

tag: seizure latency


title: genomic DNA from colon cancer tissue_CRC2028T

description: tumor colon sample

value: tumor


title: Intracell_bac_2hpi_rep1

description: Biological replicate 1


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

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

tag: agent

tag: amount administered

tag: agent dose


title: Intracell_bac_1hpi_rep3

description: Biological replicate 3

source_name: Intracellular bacteria 1h


title: genomic DNA from colon cancer tissue_CRC2029T

description: tumor colon sample


title: Intracell_bac_2hpi_rep3

description: Biological replicate 3


title: genomic DNA from colon cancer adjacent normal tissue_CRC2030N

description: normal colon sample

value: Male


title: Piriform Cortex_animal N82_0.2 mL saline_no seize_drugs_1hr

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

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2029N

description: normal colon sample


title: Intracell_bac_4hpi_rep1

description: Biological replicate 1


title: Piriform Cortex_animal N80_0.22 mL sarin_no seize_no drugs_0.25hr

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

tag: date injected

tag: time injected

tag: date sacrificed


title: Piriform Cortex_animal N81_0.24 mL saline_no seize_drugs_1hr

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

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: Piriform Cortex_animal N172_0.21 mL sarin_no seize_no drugs_24hr

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

tag: tissue


title: UNC067083A

description: Agilent Custom array of UNC067083A

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: negative

tag: age at diagnosis (year)

tag: menopause status

tag: histopathology

value: Invasive

tag: breast cancer subtype (pam50)

tag: er status

tag: hormone treated

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: UNC081248A_DCISN

description: Agilent Custom array of UNC081248A_DCISN

value: positive

value: Pre

value: DCIS only

value: unknown

value: yes


title: genomic DNA from colon cancer tissue_CRC2030T

description: tumor colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2032T

description: tumor colon sample

value: Female

tag: tissue


title: UNC061566A_DCISN

description: Agilent Custom array of UNC061566A_DCISN

tag: sample type

tag: composition

value: no


title: UNC060652A_DCISN

description: Agilent Catalog 4by44k whole genome array of UNC060652A_DCISN

tag: patient id

tag: active or "inactive"

value: Post


title: UNC081320A_DCISN

description: Agilent Custom array of UNC081320A_DCISN

tag: age at diagnosis (year)

tag: menopause status


title: Piriform Cortex_animal N78_0.23 mL saline_no seize_drugs_6hr

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

tag: animal number

value: Piriform Cortex

tag: agent

value: Saline

tag: amount administered

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

value: N

tag: animal weight (g)


title: Piriform Cortex_animal N79_0.22 mL sarin_no seize_no drugs_1hr

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

tag: tissue

value: Sarin


title: B[a]P_Test Centre3_BioRep3_TechRepNA

city: Sharnbrook

first: Yeyejide

middle: A

last: Adeleye

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

hyb_protocol: Hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol (v5.7 March 2008). 1.65 micrograms of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/microgram cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F, Part No. G4112-60520; Batch No. 0006045630) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).              Microarray slides were scanned at 5 uM resolution using an extended dynamic range (XDR) scan at 10% and 100% PMT gain on an Agilent scanner (model G2505B at TC1; G2565CA at TC2 and TC3) .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-_105_Dec08 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 mg RNA using the One-Color QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Quiagen, Germantown, MD, USA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Montchanin, U.S.A).

growth_protocol: HepG2 cells (HB8065 #58210525) were purchased independently from ATCC (LGC standards, UK) by all three Test Centres (TCs) and a master and working cell bank was prepared at each TC. HepG2 cells were cultured in EMEM (ATCC 30-2003#3000715) and 10% FCS (PAA A15-151#A15108-0088). After recovery from liquid nitrogen cells were split three times before being used in the experiments (passage number 81).

extract_protocol: HepG2 cells were lysed with Trizol reagent (Invitrogen, Paisley, U.K.) and RNA extracted using RNeasy columns (Quiagen, Germantown, MD, USA) according to the manufacturer’s instructions. The RNA pellet was dissolved in nuclease-free water and subjected to clean-up using RNeasy columns (Quiagen, Germantown, MD, USA) with on-column DNase treatment for the removal of genomic DNA.   RNA quality and integrity were assessed using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, U.S.A) and 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) respectively.  Samples with ratios of absorbance at 280/260 nm between 1.8 and 2.0 and at 280/230 nm between 2.0 and 2.2, and with RNA integrity number (RIN) of  ≥ 9 were judged to be of acceptable quality and integrity to be used for microarray labelling.

treatment_protocol: HepG2 cells were seeded in triplicate at a density of 1×106 cells/well in 6 well plates. After 24 hours cells were exposed to 0 and 3 µM B[a]P (0.5% DMSO) for 24 hours. B[a]P was purchased from Sigma (B1760#077k1502). A 20 mM stock solution was prepared in Dimethyl Sulfoxide (DMSO) at one Test Centre. Stock solutions were prepared in DMSO at 0 µM, 60 µM, 600 µM and 6 mM B[a]P and subsequently shipped on dry ice to the other Test Centres for their experiments in order to minimise the number of potential variables in the study.

tag: cell line

tag: test centre

tag: treatment

value: B[a]P

tag: biological replicate

tag: technical replicate


title: Intracell_bac_1hpi_rep1

description: Biological replicate 1

tag: clinical isolate


title: Intracell_bac_1hpi_rep2

description: Biological replicate 2


title: B[a]P_Test Centre3_BioRep2_TechRepC

value: C


title: B[a]P_Test Centre3_BioRep2_TechRepB

value: B


title: DMH_Rep3

city: Shanghai

first: Jing-Yuan

last: Fang

state: Shanghai

address: 145 Middle Shandong Rd

department: Division of Gastroenterology

institute: Shanghai Jiao-Tong University School of Medicine Ren-Ji Hospital

description: Gene expression in mice of DMH group

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole  Genome Oligo Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization). The positive effect of this median normalization is illustrated in Box-plot, and genes marked present in all samples were chosen for data analysis. Differentially expressed genes were identified through Fold-change and T-test p-value screening.

source_name: Normal colonic mucosa,DMH group ,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs of the normal colonic mucosa are harvested using TRIzol(Invitrogen) and the Rneasy kit(Qiagen) according to manufacturer's instructions.

treatment_protocol: The mice of DMH group were received normal drink water normal diet and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks,the mice of Butyrate group were received drink water with 1.5% Butyrate and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks.

value: ICR

value: normal colonic mucosa

tag: tumor status

value: control

tag: agent

value: DMH


title: B[a]P_Test Centre3_BioRep1_TechRepNA


title: Piriform Cortex_animal N77_0.21 mL saline_no seize_drugs_0.25hr

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

tag: animal number

tag: amount administered

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam


title: Piriform Cortex_animal N76_0.2 mL saline_no seize_drugs_24hr

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

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: genomic DNA from colon cancer tissue_CRC2025T

description: tumor colon sample

tag: gender

value: Male

tag: tissue

value: Colon cancer tissue

tag: disease state

value: tumor


title: B[a]P_Test Centre3_BioRep2_TechRepA

tag: cell line

tag: test centre

tag: treatment

tag: biological replicate

tag: technical replicate

value: A


title: genomic DNA from colon cancer tissue_CRC2027T

description: tumor colon sample

value: Female


title: DMSO_Test Centre3_BioRep1_TechRepNA

value: DMSO


title: genomic DNA from colon cancer adjacent normal tissue_CRC2028N

description: normal colon sample

value: normal


title: DMSO_Test Centre3_BioRep2_TechRepNA


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

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

tag: animal number

value: Piriform Cortex

tag: agent

tag: amount administered

value: Sprague-Dawley

value: Y

tag: presence of seizure

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: DMSO_Test Centre3_BioRep3_TechRepNA


title: DMH_Rep2

description: Gene expression in mice of DMH group

source_name: Normal colonic mucosa,DMH group ,replicate 2

tag: strain

tag: tumor status


title: genomic DNA from colon cancer adjacent normal tissue_CRC2027N

description: normal colon sample

tag: gender


title: genomic DNA from colon cancer tissue_CRC2026T

description: tumor colon sample

tag: tissue


title: Butyrate-DMH-Tumor_Rep3

description: Gene expression in mice of Butyrate group with tumors

source_name: Normal colonic mucosa,Butyrate group with tumors,replicate 3

value: without tumors

value: Butyrate-DMH


title: genomic DNA from colon cancer adjacent normal tissue_CRC2025N

description: normal colon sample

tag: disease state


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

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

value: Sarin

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: genomic DNA from colon cancer adjacent normal tissue_CRC2026N

description: normal colon sample


title: Piriform Cortex_animal N75_0.2 mL sarin_no seize_no drugs_3hr

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

tag: animal number

tag: agent

tag: amount administered

value: N


title: Piriform Cortex_animal N73_0.2 mL sarin_no seize_no drugs_1hr

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

tag: presence of seizure


title: Butyrate-DMH-Tumor_Rep2

source_name: Normal colonic mucosa,Butyrate group with tumors,replicate 2

value: ICR

value: normal colonic mucosa


title: B[a]P_Test Centre2_BioRep2_TechRepNA

tag: cell line

tag: test centre

tag: treatment

value: B[a]P

tag: biological replicate

tag: technical replicate


title: DMSO_Test Centre2_BioRep2_TechRepNA


title: Piriform Cortex_animal N71_0.2 mL sarin_no seize_no drugs_6hr

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

tag: tissue

tag: strain

tag: animal weight (g)


title: DMH_Rep1

description: Gene expression in mice of DMH group

source_name: Normal colonic mucosa,DMH group ,replicate 1

tag: tumor status

value: control

value: DMH


title: genomic DNA from colon cancer tissue_CRC2023T

description: tumor colon sample

tag: gender

value: Colon cancer tissue

tag: disease state

value: tumor


title: DMSO_Test Centre2_BioRep1_TechRepNA


title: B[a]P_Test Centre2_BioRep1_TechRepNA


title: Piriform Cortex_animal N69_0.23 mL sarin_no seize_no drugs_24hr

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

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed


title: genomic DNA from colon cancer tissue_CRC2024T

description: tumor colon sample

value: Male


title: genomic DNA from colon cancer adjacent normal tissue_CRC2024N

description: normal colon sample


title: DMSO_Test Centre2_BioRep3_TechRepB

tag: cell line

value: DMSO

value: B


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

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

tag: animal number

value: Piriform Cortex

tag: agent

tag: amount administered

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency


title: B[a]P_Test Centre2_BioRep3_TechRepB

tag: test centre

tag: treatment

tag: biological replicate

tag: technical replicate


title: Piriform Cortex_animal N68_0.22 mL saline_no seize_drugs_24hr

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

tag: tissue

value: Saline

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

tag: animal weight (g)


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

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

value: Y

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed


title: Butyrate-DMH-Notumor_Rep2

description: Gene expression in mice of Butyrate group without tumors

source_name: Normal colonic mucosa,Butyrate group without tumors,replicate 2

tag: tumor status

value: with tumors

tag: agent

value: Butyrate-DMH


title: genomic DNA from colon cancer adjacent normal tissue_CRC2023N

description: normal colon sample

tag: gender

value: Female

tag: disease state

value: normal


title: Butyrate-DMH-Notumor_Rep1

source_name: Normal colonic mucosa,Butyrate group without tumors,replicate 1

value: ICR

value: normal colonic mucosa


title: DMSO_Test Centre2_BioRep3_TechRepA

tag: cell line

tag: test centre

value: A


title: genomic DNA from colon cancer tissue_CRC2021T

description: tumor colon sample


title: Butyrate-DMH-Tumor_Rep1

source_name: Normal colonic mucosa,Butyrate group with tumors,replicate 1

value: without tumors


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

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

tag: animal number

value: Sarin

tag: amount administered

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency


title: Butyrate-DMH-Notumor_Rep3

source_name: Normal colonic mucosa,Butyrate group without tumors,replicate 3

tag: strain

tag: tissue


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

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

tag: agent dose

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: animal weight (g)


title: genomic DNA from colon cancer tissue_CRC2020T

description: tumor colon sample

source_name: Colon

tag: gender

value: Colon cancer tissue

value: tumor


title: B[a]P_Test Centre2_BioRep3_TechRepA

tag: treatment

value: B[a]P

tag: biological replicate

tag: technical replicate


title: B[a]P_Test Centre1_BioRep1_TechRepC

tag: cell line

tag: test centre

value: C


title: genomic DNA from colon cancer adjacent normal tissue_CRC2020N

description: normal colon sample

value: Male

tag: disease state


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

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

tag: animal number

value: Piriform Cortex

tag: agent

tag: amount administered

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: B[a]P_Test Centre1_BioRep1_TechRepA


title: Piriform Cortex_animal N59_0.2 mL sarin_no seize_no drugs_6hr

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

tag: tissue

tag: agent dose

tag: strain

value: Sprague-Dawley

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)


title: Piriform Cortex_animal N63_0.2 mL sarin_no seize_no drugs_24hr

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

tag: date injected

tag: animal weight (g)


title: Piriform Cortex_animal N60_0.2 mL sarin_no seize_no drugs_3hr

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


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

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

value: Y

tag: seizure time

tag: seizure latency


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

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


title: DMSO_Test Centre1_BioRep2_TechRepNA

tag: cell line

tag: test centre

tag: treatment

value: DMSO

tag: biological replicate

tag: technical replicate


title: genomic DNA from colon cancer adjacent normal tissue_CRC2017N

description: normal colon sample

tag: gender

value: Female

tag: disease state


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

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

tag: animal number

tag: agent

tag: amount administered

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer tissue_CRC2017T

description: tumor colon sample

tag: tissue


title: B[a]P_Test Centre1_BioRep3_TechRepNA


title: genomic DNA from colon cancer adjacent normal tissue_CRC2021N

description: normal colon sample

value: normal


title: DMSO_Test Centre1_BioRep1_TechRepNA


title: genomic DNA from colon cancer tissue_CRC2018T

description: tumor colon sample


title: DMSO_Test Centre1_BioRep3_TechRepNA


title: Piriform Cortex_animal N61_0.21 mL sarin_no seize_no drugs_1hr

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

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2018N

description: normal colon sample


title: B[a]P_Test Centre1_BioRep1_TechRepB

tag: cell line

tag: test centre

tag: treatment

tag: biological replicate

tag: technical replicate

value: B


title: Piriform Cortex_animal N58_0.21 mL sarin_no seize_no drugs_0.25hr

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

tag: animal number

tag: agent

tag: amount administered


title: genomic DNA from colon cancer tissue_CRC2016T

description: tumor colon sample

tag: gender

tag: disease state


title: B[a]P_Test Centre1_BioRep2_TechRepNA


title: genomic DNA from colon cancer adjacent normal tissue_CRC2016N

description: normal colon sample

tag: tissue


title: Piriform Cortex_animal N54_0.2 mL saline_no seize_drugs_6hr

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

value: Saline

tag: agent dose

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2015N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2015T

description: tumor colon sample


title: genomic DNA from colon cancer tissue_CRC2014T

description: tumor colon sample


title: 16425-16429-Cy3

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

description: log2 ratio Cy3/Cy5

hyb_protocol: Hybridization was performed using the gene expression hybridization kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions. Each sample was hybridized against the same reference (human adult whole brain RNA pool from 5 donors). Washing was performed using the gene expression wash buffer kit (Agilent).

scan_protocol: Hybridized microarray slides were washed according to the manufacturer's instructions, and were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution. The scanned images were analyzed numerically using the Agilent Feature Extraction Software.

data_processing: Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).

label_protocol: Amplification and labeling with Cy3 (sample) or Cy5 (reference) were done using the low RNA input linear amplification kit plus (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was purified using the Qiagen miRNeasy Mini Kit. RNA was examined for integrity and purity using an Agilent RNA 6000 Series II Nano kit on a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

tag: sample type

value: sample

tag: diagnosis

value: Glioma

tag: inducing agent

value: poly (I:C)

value: control

value: normal brain


title: 16296-16297-Cy3

description: log2 ratio Cy3/Cy5


title: Pituitary Bmal1-/- mice 6

city: MARSEILLE Cedex 15

first: Anne-Marie

last: Francois-Bellan

address: Bd Pierre DRAMARD

country: France

institute: CNRS

description:
Gene expression data from  Bmal1-/- pituitary
D70330_VPA011_6KO_3mcgM430A_2

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

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

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

source_name: Pituitary Bmal1-/- mice 6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from1 ug total RNA.

growth_protocol: All animals were housed in a 12-h light/12-h dark cycle (light/dark, 12:12) with lights on at 7 A.M., in a temperature- and humidity-controlled environment and fed ad libitum

extract_protocol: total RNA was isolated with a nucleospin RNA II kit (Macherey-Nagel)

treatment_protocol: Mice were sacrificed by decapitation at ZT12 (light off)

tag: strain

value: male

value: pituitary

tag: genotype/variation


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

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

value: Sarin

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: 16424-16431-Cy3

description: log2 ratio Cy3/Cy5


title: Piriform Cortex_animal N47_0.2 mL saline_no seize_drugs_1hr

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

tag: animal number

tag: tissue

value: Piriform Cortex

tag: agent

tag: amount administered


title: genomic DNA from colon cancer adjacent normal tissue_CRC2014N

description: normal colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: Pituitary Wild type 3

description:
Gene expression data from wild type pituitary.
D70330_VPA011_3WT_3mcgM430A_2

source_name: Pituitary Wild type 3

value: wild type


title: Piriform Cortex_animal N51_0.22 mL sarin_no seize_no drugs_0.25hr

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

tag: agent dose

value: Sprague-Dawley

value: N

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: Piriform Cortex_animal N46_0.2 mL sarin_no seize_no drugs_3hr

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

tag: strain

tag: atropine, 2-pam, diazepam


title: genomic DNA from colon cancer tissue_CRC2012T

description: tumor colon sample

value: Male

value: tumor


title: 16425-16430-Cy3

description: log2 ratio Cy3/Cy5

tag: sample type

tag: diagnosis

tag: inducing agent


title: Pituitary Wild type 2

description:
Gene expression data from wild type pituitary.
D70330_VPA011_2WT_3mcgM430A_2

source_name: Pituitary Wild type 2

tag: genotype/variation


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

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

tag: animal number

value: Y

tag: time point (hr)

tag: date injected

tag: seizure time

tag: seizure latency

tag: animal weight (g)


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

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

tag: tissue

tag: agent

tag: amount administered

tag: agent dose


title: genomic DNA from colon cancer tissue_CRC2013T

description: tumor colon sample

tag: gender

value: Female

tag: disease state


title: Pituitary Bmal1-/- mice 5

description:
Gene expression data from  Bmal1-/- pituitary
D70330_VPA011_5KO_3mcgM430A_2

source_name: Pituitary Bmal1-/- mice 5

tag: strain


title: Piriform Cortex_animal N44_0.21 mL sarin_no seize_no drugs_6hr

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

tag: atropine, 2-pam, diazepam

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2012N

description: normal colon sample

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2013N

description: normal colon sample


title: Pituitary Bmal1-/- mice 4

description:
Gene expression data from  Bmal1-/- pituitary
D70330_VPA011_4KO_3mcgM430A_2

source_name: Pituitary Bmal1-/- mice 4

tag: genotype/variation


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

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

tag: animal number

tag: time point (hr)

tag: date injected


title: 16423-16433-Cy3

description: log2 ratio Cy3/Cy5

tag: sample type

value: sample

tag: diagnosis

value: Glioma

tag: inducing agent


title: genomic DNA from colon cancer adjacent normal tissue_CRC2011N

description: normal colon sample

tag: tissue


title: Pituitary Wild type 1

description:
Gene expression data from wild type pituitary.
D70330_VPA011_1WT_3mcgM430A_2

source_name: Pituitary Wild type 1


title: 16426-16427-Cy3

description: log2 ratio Cy3/Cy5

value: control


title: 16424-16432-Cy3

description: log2 ratio Cy3/Cy5

value: normal brain


title: 16426-16428-Cy3

description: log2 ratio Cy3/Cy5

value: poly (I:C)


title: genomic DNA from colon cancer tissue_CRC2011T

description: tumor colon sample


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

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

tag: agent

tag: amount administered

tag: agent dose

tag: seizure time

tag: seizure latency

tag: animal weight (g)


title: 16296-16298-Cy3

description: log2 ratio Cy3/Cy5


title: 16423-16434-Cy3

description: log2 ratio Cy3/Cy5


title: Piriform Cortex_animal N41_0.2 mL saline_no seize_drugs_24hr

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

value: Saline

tag: strain

tag: atropine, 2-pam, diazepam

tag: time injected

tag: date sacrificed


title: Piriform Cortex_animal N40_0.21 mL saline_no seize_drugs_3hr

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

tag: animal number

tag: time sacrificed

tag: presence of seizure


title: L591 vs KMH2 rep1

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Cells  untreated, harvested after several passages.

hyb_protocol: Oligoarray, 850 ng of each cy3 and cy5 labeled cRNA were fragmented at 60°C for 10 min, then equal volume of Agilent Hybridization buffer (50 ul) was added and hybridized using Agilent hybridization chambers at 65°C for 17 hours in an rotatory oven.  After hybridization, slides were washed sequentially using 50 ml Falcon tubes; Agilent buffer1 for 1 minute; Agilent buffer 2 at 37°C for 1 min; Acetoniltrile for 10 seconds; Agilent stabilization and drying solution for 30 seconds.

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Cell line KMH2 - Not EBV infected

label_protocol: cRNA was labeled usind Quick-Amp labeling kit (Agilent, USA, cat # 5190-0424). Briefly 250 ng of total RNA plus RNAs spikes (Spike A-cy3 or Spike B-cy5) and were primed with T7 DNA primer at 70°C for 10 min, then the first and second cDNA molecules were synthesized at 42°C for 2 h in the presence of RTase. The cRNA were made  by T7 RNA polymerase plus rNTPs mixture and UTP labeled CY3 or Cy5.

growth_protocol: Cells were grown in RPMI medium supplemented with 10% Fetal Bovine Serum.

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

treatment_protocol: Not treated cells

tag: cell line

tag: infection

value: Not EBV infected

source_name: Cell line L591- EBV infected

value: EBV infected


title: genomic DNA from colon cancer adjacent normal tissue_CRC2010N

description: normal colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2010T

description: tumor colon sample

tag: tissue


title: genomic DNA from colon cancer tissue_CRC2009T

description: tumor colon sample


title: L591 vs KMH2 rep2


title: Piriform Cortex_animal N38_0.2 mL sarin_no seize_no drugs_24hr

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

value: Piriform Cortex

tag: agent

value: Sarin

tag: amount administered

tag: time point (hr)

tag: date injected


title: genomic DNA from colon cancer tissue_CRC2008T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2009N

description: normal colon sample


title: L591 vs L1236 rep1

source_name: Cell line L1236 - Not EBV infected


title: L591 vs L1236 rep2


title: Piriform Cortex_animal N37_0.19 mL saline_no seize_drugs_3hr

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

tag: agent dose

value: Sprague-Dawley

value: N

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2008N

description: normal colon sample

value: Male


title: L591 vs L428 rep2

source_name: Cell line L428- Not EBV infected


title: Piriform Cortex_animal N36_0.2 mL saline_no seize_drugs_0.25hr

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

tag: strain

tag: atropine, 2-pam, diazepam

value: Y


title: genomic DNA from colon cancer adjacent normal tissue_CRC2006N

description: normal colon sample


title: Piriform Cortex_animal N35_0.2 mL saline_no seize_drugs_6hr

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

tag: time injected

tag: date sacrificed


title: L591 vs L428 rep1


title: Piriform Cortex_animal N34_0.22 mL saline_no seize_drugs_3hr

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

tag: animal number

tag: time sacrificed


title: L591 vs L591 rep1

description: Hybridization control untreated, harvested after several passages.

tag: cell line


title: genomic DNA from colon cancer tissue_CRC2006T

description: tumor colon sample

value: tumor


title: genomic DNA from colon cancer adjacent normal tissue_CRC2007N

description: normal colon sample

value: Female

value: normal


title: Piriform Cortex_animal N33_0.2 mL saline_no seize_drugs_1hr

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

tag: presence of seizure


title: WT2(Cy3) vs. WT_Blap 2 (Cy5)

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

description: no further description

hyb_protocol: Slides were hybridised using manual chambers according to manufacturer. Briefly, slides were prehybridized in 5 x SSC,0.1% SDS, and 0.1 mg/mL BSA for 45m, and rinse in 0.1 x SSC two times before drying. Both samples were resuspended in 50% formamide, 5 x SSC, 0.1% SDS, and 0.1 mg/mL of  sonicated salmon sperm DNA, denatured for 5 m and injected between slide and coverslip (Lifterslips). Hyb was performed overnight at 42ºC. Washes a) Arrays were inmersed in 2 x SSC, 0.1% SDS at 42°C until the coverslip moves freely away from the slide. b) Transferred to 2 x SSC, 0.1% SDS at 42°C for 5 minutes. c) Transferred  to 0.1 x SSC, 0.1% SDS at room temperature for 5 minutes. Repeat step d) Transferred  to 0.1 x SSC at room temperature for 1 minute. Repeated 4 times e) Rinsed  in 0.01 x SSC for 10 seconds. 9. Dried by centrifugation at 1,600 x g for 2 minutes.

scan_protocol: Slides were scanning at 10um resolution using a 4200B Molecular Devices scanner, adjusting PMT values so that ratio Cy5/Cy3 total intensity is close to 1. Image analysis was performed using GenePix 6.0 software.

data_processing: ocal background was used for background sustraction. Background-substrated signals were used for ratio calculations. Data were normalized by global-median and print-tip loess. Features whose background-substrated intensity do not reach two times background intensity were flagged as bad and rejected for further analysis (Value=null). Equal for features affected by hyb and washing artefacts, if any. Original value data are log ratios of lowess-normalized Cy5/Cy3 signals.

organism: Saccharomyces cerevisiae

source_name: Wt BY4741 strain in log phase culture

label_protocol: Indirect labelling

extract_protocol: standard protocol (acid-phenol extraction).

treatment_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6. 50 ml of yeast culture was treated with  vehicle (1% DMSO)  for 1 hour. Cells were then harvested by centrifugation and washed with cold water. Dried cell pellet was kept at-80 until RNA purification

tag: genotype

value: :MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ0

source_name: Wt BY4741 strain in log phase culture treated with b-lapachone

treatment_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6. 50 ml of yeast culture was treated with 10 ug/ml b-lapachone in DMSO for 1 hour. Cells were then harvested by centrifugation and washed with cold water. Dried cell pellet was kept at-80 until RNA purification


title: genomic DNA from colon cancer tissue_CRC2007T

description: tumor colon sample

tag: gender

tag: disease state


title: WT4(Cy3) vs. WT_Blap 4 (Cy5)

description: no further description


title: liver_highfat_rep3

city: Hohhot

first: Heping

last: Zhang

address: No.306 Zhaowuda road

institute: Inner Mongolia Agricultural University

description: Gene expression data of liver of hypercholesterolemic rat

hyb_protocol: Purified cRNA was broken down to 35 to 200 base fragments and incubated at 94℃ for 35 min. The fragmented and labelled cRNA was applied to the Rat Genome 230 2.0 Array. Hybridization was carried out in a mixture containing probe array controls, BSA (Invitrogen, Carlsbad, CA, USA) and herring sperm DNA (Promega, Madison, WI, USA) for 16 h at 45℃.

scan_protocol: GeneChips were scanned using GeneArrayTM scanner 3000

data_processing: Gene expression values were calculated from the fluorescence signal by Affymetrix GeneChip Operating Software, as described by Affymetrix GeneChip standard procedures.

source_name: Hypercholesterolemic rat as control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rats in high fat and probiotic treated group were fed with fat-rich diet to form hypercholesterol models in the first 30 d. In the next 30 d, in addition to fat-rich diet, rats in high fat group were daily supplied with 1 ml of normal saline and rats in probiotic treated group were daily supplied with L. casei Zhang (2 × 108cfu) dissolved in 1 ml of normal saline by intragastric administration.

tag: tissue

value: liver

tag: treatment

value: high fat control


title: L591 vs L591 rep2

tag: infection


title: genomic DNA from colon cancer adjacent normal tissue_CRC2005N

description: normal colon sample


title: WT3(Cy5) vs. WT_Blap 3 (Cy3)

description: no further description


title: liver_highfat_rep2