title: shallow_yorkshire_20_wk_s58

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #58. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time

value: 20 wk

tag: breed

value: yorkshire

tag: depth

value: shallow


title: shallow_yorkshire_12_wk_s53

status: Public on Dec 31 2011

type: RNA

city: Ames

first: Oliver

last: Couture

state: IA

address: 2255 Kildee

country: USA

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

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: shallow, yorkshire, 12 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 #54. 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: 12 wk


title: young adult_24hr BTF mix exposure_rep1

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

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

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

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

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

organism: Danio rerio

source_name: mRNA isolated from wildtype young adult, BTF mix

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

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

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

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

tag: line

value: AB

tag: genotype

value: wildtype

tag: gender

value: hemaphrodite

tag: developmental stage

value: young adult

tag: treatment

value: benzene, toluene, formaldehyde

tag: treatment time

value: 24 hours


title: deep_yorkshire_12_wk_s52

source_name: deep, yorkshire, 12 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #51. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: deep


title: genomic DNA from colon cancer tissue_CRC2087T

type: genomic

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

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

value: Male

tag: tissue

value: Colon cancer tissue

tag: disease state

value: tumor


title: Slide#17_12980428

city: Beaumont

first: Jeff

last: Wilkinson

state: tx

address: 635 Parson

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

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

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

organism: Aspergillus parasiticus

source_name: 5-AC 16hr rep5

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

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

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

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

value: mycelia

source_name: SerTrans 16hr rep5


title: Slide#16_12980475

source_name: 5-AC 24hr rep3

source_name: SerTrans 24hr rep6


title: Slide#14_12980478

source_name: SerTrans 24hr rep4

source_name: WT 24hr rep4


title: Slide#13_12980479

source_name: SerTrans 16hr rep4

source_name: SerTrans 24hr rep3


title: Slide#11_12980419

source_name: SerTrans 16hr rep2

source_name: WT 16hr rep5


title: Slide#12_12980420

source_name: WT 16hr rep6

source_name: SerTrans 16hr rep3


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

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

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

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

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)

organism: Rattus norvegicus

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

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

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

tag: animal number

value: Hippocampus

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: genomic DNA from colon cancer adjacent normal tissue_CRC2086N

description: normal colon sample

tag: gender

value: Female

value: normal


title: genomic DNA from colon cancer tissue_CRC2085T

description: tumor colon sample


title: deep_yorkshire_12_wk_s50

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #49. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: breed

value: yorkshire

tag: time

value: 12 wk

tag: depth


title: Slide#10_12980480

source_name: SerTrans 24hr rep2

tag: tissue

source_name: SerTrans 16hr rep1


title: shallow_yorkshire_12_wk_s51

source_name: shallow, yorkshire, 12 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #52. 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: shallow


title: Slide#15_12980476

source_name: SerTrans 24hr rep5

source_name: 5-AC 24hr rep1


title: Hippocampus_animal N259_naive_no agent_0hr

description: Gene expression data from Hippocampus of animal N259_naive_no agent_0hr

tag: animal number

tag: agent

value: Naive


title: genomic DNA from colon cancer tissue_CRC2086T

description: tumor colon sample

source_name: Colon

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2084T

description: tumor colon sample


title: Slide#9_12980418

source_name: WT 24hr rep6

source_name: SerTrans 24hr rep1


title: Hippocampus_animal N257_naive_no agent_0hr

description: Gene expression data from Hippocampus of animal N257_naive_no agent_0hr


title: Hippocampus_animal N258_naive_no agent_0hr

description: Gene expression data from Hippocampus of animal N258_naive_no agent_0hr


title: shallow_yorkshire_3_wk_s47

source_name: shallow, yorkshire, 3 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #48. 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: 3 wk


title: Slide#8_12980482

source_name: WT 24hr rep5

source_name: 5-AC 24hr rep6


title: deep_yorkshire_3_wk_s46

source_name: deep, yorkshire, 3 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #45. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: genomic DNA from colon cancer tissue_CRC2083T

description: tumor colon sample


title: shallow_yorkshire_3_wk_s45

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #46. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: shallow_yorkshire_12_wk_s49

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #50. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Hippocampus_animal N251_0.21 mL saline_no seize_no drugs_1hr

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

tag: amount administered

tag: agent dose

tag: strain


title: deep_yorkshire_3_wk_s48

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #47. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: genomic DNA from colon cancer adjacent normal tissue_CRC2084N

description: normal colon sample


title: deep_yorkshire_3_wk_s44

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #43. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Hippocampus_animal N256_0.2 mL saline_no seize_no drugs_24hr

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

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected


title: Hippocampus_animal N254_0.2 mL saline_no seize_no drugs_24hr

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

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: genomic DNA from colon cancer adjacent normal tissue_CRC2085N

description: normal colon sample

tag: gender


title: Hippocampus_animal N252_0.2 mL saline_no seize_no drugs_24hr

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

tag: presence of seizure

tag: animal weight (g)


title: Slide#6_12980415

source_name: 5-AC 16hr rep4

source_name: WT 16hr rep3


title: genomic DNA from colon cancer adjacent normal tissue_CRC2082N

description: normal colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2083N

description: normal colon sample


title: Slide#5_12918591

source_name: 5-AC 24hr rep5

source_name: 5-AC 16hr rep3


title: Slide#7_12980413

source_name: WT 16hr rep4

source_name: WT 24hr rep3


title: genomic DNA from colon cancer adjacent normal tissue_CRC2081N

description: normal colon sample


title: Slide#4_12918594

source_name: WT 16hr rep2

source_name: 5-AC 16hr rep2


title: shallow_yorkshire_3_wk_s43

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #44. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time

tag: breed

tag: depth


title: Slide#3_12918593

source_name: WT 24hr rep2

tag: tissue

source_name: WT 16hr rep1


title: Slide#2_12980481

source_name: 5-AC 24hr rep4

source_name: WT 24hr rep1


title: genomic DNA from colon cancer tissue_CRC2081T

description: tumor colon sample

source_name: Colon

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2082T

description: tumor colon sample


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

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

tag: animal number

tag: agent

tag: amount administered


title: shallow_yorkshire_2_wk_s41

source_name: shallow, yorkshire, 2 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #42. 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: 2 wk


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

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

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam


title: genomic DNA from colon cancer adjacent normal tissue_CRC2080N

description: normal colon sample


title: Slide#1_12980417

source_name: 5-AC 16hr rep1

source_name: 5-AC 24hr rep2


title: Hippocampus_animal N248_0.2 mL saline_no seize_no drugs_1hr

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

tag: time point (hr)

tag: date injected

tag: time injected


title: Hippocampus_animal N246_0.18 mL saline_no seize_no drugs_6hr

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

tag: date sacrificed

tag: time sacrificed


title: Hippocampus_animal N245_0.2 mL saline_no seize_no drugs_3hr

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

tag: presence of seizure

tag: animal weight (g)


title: deep_yorkshire_2_wk_s42

source_name: deep, yorkshire, 2 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #41. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: breed

tag: time

value: deep


title: Hippocampus_animal N250_0.21 mL saline_no seize_no drugs_3hr

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

tag: tissue


title: deep_yorkshire_2_wk_s38

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #37. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: depth


title: genomic DNA from colon cancer tissue_CRC2080T

description: tumor colon sample

tag: gender

value: Male

tag: disease state


title: genomic DNA from colon cancer adjacent normal tissue_CRC2079N

description: normal colon sample

value: Colon cancer tissue


title: genomic DNA from colon cancer tissue_CRC2079T

description: tumor colon sample

value: tumor


title: shallow_yorkshire_2_wk_s39

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #40. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Exposed to 70% RH for 36hr , biological rep3

city: Irvine

first: Mei-Hui

last: Wang

state: CA

address: 3501B Hewitt Hall UCI

institute: UC irvine

description: Exposed to 70% RH for 36hr

hyb_protocol: 2.2 μg of the resulting fragmented, biotin-tagged cDNA  was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix array (GeneChip® Plasmodium/Anopheles Genome Array). The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol

scan_protocol: Scanning on an Affymetrix GeneChip 3000 Scanner 7G

data_processing: Results were quantified and analyzed using Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values (Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

label: Biotin

organism: Anopheles gambiae

source_name: Female adult, exposed to 70% RH for 36hr

label_protocol: 3.75 μg of the resulting amplified cDNA material for each sample was first fragmented and subsequently end-labeled using the NuGEN FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos CA)

growth_protocol: There were 250 adult (male:female=1:1) for each cage. Adults had access to raisins and cotton balls saturated with dd-water. Mosquito colonies were maintained by blood feeding on anesthetized rabbits very five days.

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

treatment_protocol: Mosquitoes were exposed to 70% (standard) or 30% (desiccated) RH without any access to sugar and water. A total of 4 cages of mosquitoes were set up simultaneously. For each humidity condition, twelve surviving mosquitoes were collected and at 0 hr (right before the desiccation experiment was initiated), 18 and 36 hr post exposure except in 30% RH treatment 36 hr post exposure did not yield any surviving mosquitoes (9 mosquitoes collected only). All samples were preserved in RNAlater® (Ambion Inc.) and in -80 oC freezer until RNA extraction.

value: whole body

tag: genotype

tag: desiccation

value: Exposed to 70% RH for 36hr


title: deep_yorkshire_2_wk_s40

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #39. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: shallow_yorkshire_2_wk_s37

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #38. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Exposed to 70% RH for 36hr , biological rep4

description: Exposed to 70% RH for 36hr


title: deep_yorkshire_1_wk_s36

source_name: deep, yorkshire, 1 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #35. 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: 1 wk


title: genomic DNA from colon cancer tissue_CRC2078T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2078N

description: normal colon sample


title: Exposed to 70% RH for 36hr , biological rep2

description: Exposed to 70% RH for 36hr


title: shallow_yorkshire_1_wk_s35

source_name: shallow, yorkshire, 1 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #36. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Exposed to 70% RH for 36hr , biological rep1

description: Exposed to 70% RH for 36hr


title: deep_yorkshire_1_wk_s34

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #33. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: genomic DNA from colon cancer tissue_CRC2077T

description: tumor colon sample


title: total mRNAs in LNCaP cells treated with DHT at 48h

city: Shanghai

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: Life School

country: China

institute: Fudan University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LNCaP cell line

growth_protocol: The androgen-sensitive human prostate cancer cell line LNCaP was obtained from ATCC and maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin (100 units/ml)-streptomycin (100g/ml) at 37 ℃ in a humidified 5% CO2 cell incubator.

extract_protocol: For cell samples at each time point, the total RNA was extracted and purified using the RNeasy Mini kit following the manufacturer’s instructions. The isolated RNA was stored at -70℃ for the Illumina microarrays.

treatment_protocol: Before androgen treatment, the LNCaP cells were cultivated with Phenol Red -free RPMI 1640 (GIBCO/ BRL) supplemented with 10% charcoal-dextran-stripped FBS for 5 days. Then the cells were induced with androgen dihydrotestosterone (DHT), at ultimate concentration 10 nM, which has been proven by pre-experiment to be optimum for LNCaP cell growth (data not shown). The cell response to androgen treatment was analyzed at ten time points — 0h, 20min, 40min, 1h, 2 h, 4 h, 8 h, 16h, 24 h and 48 h, where ‘0h’ refers to cell status before androgen action.

tag: treatment group

value: dihydrotestosterone (DHT) at 48h

tag: hormone status

value: androgen-sensitive

value: prostate cancer

tag: cell line

value: LNCaP


title: total mRNAs in LNCaP cells treated with DHT at 24h

description: replicate 1

label_protocol: The isolated RNA was stored at -70℃ for the Illumina microarrays.

value: dihydrotestosterone (DHT) at 24h


title: total mRNAs in LNCaP cells treated with DHT at 16h

description: replicate 1

value: dihydrotestosterone (DHT) at 16h


title: shallow_yorkshire_1_wk_s31

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #32. 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: yorkshire

value: shallow


title: Exposed to 70% RH for 18hr , biological rep3

description: Exposed to 70% RH for 18hr

source_name: Female adult, exposed to 70% RH for 18hr

value: Exposed to 70% RH for 18hr


title: genomic DNA from colon cancer adjacent normal tissue_CRC2076N

description: normal colon sample

value: normal


title: Exposed to 70% RH for 18hr , biological rep4

description: Exposed to 70% RH for 18hr


title: total mRNAs in LNCaP cells treated with DHT at 8h

description: replicate 1

value: dihydrotestosterone (DHT) at 8h


title: Exposed to 30% RH for 36hr , biological rep2

description: Exposed to 30% RH for 36hr

source_name: Female adult, exposed to 30% RH for 36hr

value: Exposed to 30% RH for 36hr


title: deep_yorkshire_1_wk_s32

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #31. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: deep


title: genomic DNA from colon cancer tissue_CRC2076T

description: tumor colon sample

value: Male

value: Colon cancer tissue

value: tumor


title: shallow_yorkshire_1_wk_s33

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #34. 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: 1 wk


title: genomic DNA from colon cancer adjacent normal tissue_CRC2077N

description: normal colon sample


title: Exposed to 30% RH for 36hr , biological rep3

description: Exposed to 30% RH for 36hr

value: whole body


title: total mRNAs in LNCaP cells treated with DHT at 4h

description: replicate 1

value: dihydrotestosterone (DHT) at 4h

value: androgen-sensitive


title: Exposed to 30% RH for 36hr , biological rep1

description: Exposed to 30% RH for 36hr


title: genomic DNA from colon cancer tissue_CRC2075T

description: tumor colon sample


title: genomic DNA from colon cancer adjacent normal tissue_CRC2075N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2074T

description: tumor colon sample

value: Female


title: deep_duroc_20_wk_s28

source_name: deep, duroc, 20 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #27. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: 20 wk

value: duroc


title: total mRNAs in LNCaP cells treated with DHT at 40min

description: replicate 1

value: dihydrotestosterone (DHT) at 40min

value: prostate cancer

value: LNCaP


title: deep_duroc_20_wk_s30

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #29. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Exposed to 70% RH for 18hr , biological rep2

description: Exposed to 70% RH for 18hr

value: Exposed to 70% RH for 18hr


title: total mRNAs in LNCaP cells treated with DHT at 2h

description: replicate 1

value: dihydrotestosterone (DHT) at 2h


title: Exposed to 70% RH for 18hr , biological rep1

description: Exposed to 70% RH for 18hr


title: genomic DNA from colon cancer tissue_CRC2072T

description: tumor colon sample


title: shallow_duroc_20_wk_s29

source_name: shallow, duroc, 20 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #30. 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: shallow


title: total mRNAs in LNCaP cells treated with DHT at 1h

description: replicate 1

value: dihydrotestosterone (DHT) at 1h


title: genomic DNA from colon cancer adjacent normal tissue_CRC2072N

description: normal colon sample

value: Male

value: normal


title: total mRNAs in LNCaP cells treated with DHT at 20min

description: replicate 1

value: dihydrotestosterone (DHT) at 20min


title: shallow_duroc_20_wk_s25

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #26. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: genomic DNA from colon cancer adjacent normal tissue_CRC2074N

description: normal colon sample

value: Colon cancer tissue


title: LM6567_DscrABC_biological rep 1

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

department: Microbiology

institute: University of Iowa

hyb_protocol: Samples  were hybridized to the chips at the University of Washington Center for Expression Arrays.

scan_protocol: Analysis was done Affymetrix Microarray Suite v. 5.

data_processing: Data processing was done using Affymetrix Microarray Suite v. 5 and Cyber-T.

organism: Vibrio parahaemolyticus

source_name: DscrABC translucent strain grown on plate

label_protocol: cDNA was synthesized according to the Affymetrix Prokaryotic Target Preparation Protocol using the Superscript II Reverse Transcriptase kit (Invitrogen) and pD(N)6 random hexamers (GE Healthcare). Approximately 36 g of RNA was converted to ~7 g cDNA, which was purified with the MinElute PCR purification kit (Qiagen) and fragmented with RQ1 DNase to yield fragments between 50 and 200 bp. cDNA was labeled with Biotin-ddUTP using the BioArray Terminal Labeling Kit (Enzo).

growth_protocol: Strains were pre-grown on plates, suspended to an OD600nm of 0.05, and 100 l were spread onto multiple fresh Heart Infusion swarm plates. Plates were incubated at 30oC and after 8 h of incubation RNA was collected.

extract_protocol: cells were suspended in 5 ml of a solution containing 2 parts of RNA protect agent (QIAGEN, Germantown, MD) and 1 part of PBS buffer (Dulbecco’s phosphate buffered saline 10x, Sigma, St Louis, MO). The RNA was processed using the RNeasy Mini Kit (QIAGEN). The RNA integrity was checked by electrophoresis on agarose gels. There was no detectable DNA contamination as assessed by PCR using primers to amplify the protein translation elongation factor Tu gene (RVF105355f and RVF104794r)

treatment_protocol: harvested cells were used for RNA isolation

tag: colony morphology

value: crinkly


title: LM6567_DscrABC_biological rep 2


title: Exposed to 30% RH for 18hr , biological rep3

description: Exposed to 30% RH for 18hr

source_name: Female adult, exposed to 30% RH for 18hr

value: whole body

value: Exposed to 30% RH for 18hr


title: Exposed to 30% RH for 18hr , biological rep4

description: Exposed to 30% RH for 18hr


title: genomic DNA from colon cancer tissue_CRC2071T

description: tumor colon sample

value: Female

value: tumor


title: Exposed to 30% RH for 18hr , biological rep1

description: Exposed to 30% RH for 18hr


title: deep_duroc_12_wk_s24

source_name: deep, duroc, 12 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #23. 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

value: 12 wk

value: deep


title: deep_duroc_20_wk_s26

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

value: 20 wk


title: shallow_duroc_12_wk_s23

source_name: 12 wk, duroc, shallow

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #24. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: LM5674_DopaR_biological rep 2

source_name: wt translucent strain grown on plate

value: translucent


title: genomic DNA from colon cancer adjacent normal tissue_CRC2071N

description: normal colon sample

source_name: Colon


title: shallow_duroc_20_wk_s27

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #28. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: total mRNAs in LNCaP cells treated with DHT at the beginning

description: replicate 1

value: dihydrotestosterone (DHT) at the beginning

value: androgen-sensitive

value: prostate cancer

value: LNCaP


title: deep_duroc_12_wk_s22

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #21. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: shallow_duroc_12_wk_s11

source_name: shallow, duroc, 12 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #22. 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: shallow


title: Exposed to 30% RH for 18hr , biological rep2

description: Exposed to 30% RH for 18hr

treatment_protocol: Mosquitoes were exposed to 70% (standard) or 30% (desiccated) RH without any access to sugar and water. A total of 4 cages of mosquitoes were set up simultaneously. For each humidity condition, twelve surviving mosquitoes were collected and at 0 hr (right before the desiccation experiment was initiated), 18 and 36 hr post exposure except in 30% RH treatment 36 hr post exposure did not yield any surviving mosquitoes (9 mosquitoes collected only). All samples were preserved in RNAlater® (Ambion Inc.) and in -80 oC freezer until RNA extraction.


title: No desiccation stress exposure, biological rep4

description: No desiccation stress exposure

source_name: Female adult, no desiccation exposed

value: No desiccation stress exposure


title: genomic DNA from colon cancer adjacent normal tissue_CRC2070N

description: normal colon sample

value: Male

value: Colon cancer tissue

value: normal


title: LM5674_DopaR_biological rep 1


title: infected with LUMANdp retrovirus for 18h

city: Nijmegen

first: Anna

last: Sanecka

address: Geert Grooteplein 26/28

department: Tumor Immunology Lab

country: Netherlands

institute: UMC St Radboud Nijmegen, NCMLS

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction by Partek software

organism: Mus musculus

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: D2SC/1 cells were cultured in IMDM supplemented with 5% heat-inactivated FCS and 0.5% antibiotic-antimycotic.

extract_protocol: Rneasy column purification

treatment_protocol: For transduction,D2SC/1 cells were cultured on retronectin-coated 35 mm Petri dishes together with 2 ml of thawed virus containing supernatant for indicated time and then washed with PBS

tag: treatment

value: infected with LUMANdp retrovirus


title: No desiccation stress exposure, biological rep2

description: No desiccation stress exposure

value: whole body


title: infected with GFP retrovirus for 18h

source_name: infected with GFP retrovirus for 18h

value: infected with GFP retrovirus


title: deep_duroc_12_wk_s20

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #19. 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


title: No desiccation stress exposure, biological rep1

description: No desiccation stress exposure


title: genomic DNA from colon cancer tissue_CRC2068T

description: tumor colon sample

value: Female

value: tumor


title: genomic DNA from colon cancer tissue_CRC2070T

description: tumor colon sample


title: shallow_duroc_12_wk_s19

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #20. 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: 12 wk


title: Hepa1c1c7_DMSO_24h_3

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.

source_name: murine hepatoma cells treated for 24h with Vehicle

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.

value: Hepa 1c1c7

tag: cell type

value: hepatoma

tag: concentration of chemical

value: Vehicle

tag: time of exposure


title: No desiccation stress exposure, biological rep3

description: No desiccation stress exposure


title: Hippocampus_animal N244_0.18 mL saline_no seize_no drugs_1hr

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

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

tag: animal number

value: Hippocampus

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: infected with LUMANdp retrovirus for 6h

source_name: infected with LUMANdp retrovirus for 6h

tag: treatment

tag: time

tag: cell line


title: genomic DNA from colon cancer tissue_CRC2069T

description: tumor colon sample

tag: gender

value: Male

tag: tissue

tag: disease state


title: Hippocampus_animal N243_0.21 mL saline_no seize_no drugs_3hr

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

tag: animal number

tag: agent

tag: amount administered


title: shallow_duroc_3_wk_s17

source_name: shallow, duroc, 3 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #18. 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: 3 wk

tag: breed

tag: depth

value: shallow


title: genomic DNA from colon cancer adjacent normal tissue_CRC2069N

description: normal colon sample

value: Colon cancer tissue

value: normal


title: genomic DNA from colon cancer adjacent normal tissue_CRC2068N

description: normal colon sample


title: deep_duroc_3_wk_s18

source_name: deep, duroc, 3 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #17. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: deep


title: Hepa1c1c7_50nMBaP_24h_3

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

tag: cell type

tag: concentration of chemical

tag: time of exposure


title: infected with GFP retrovirus for 6h

source_name: infected with GFP retrovirus for 6h

value: infected with GFP retrovirus


title: Hepa1c1c7_5uMBaP_24h_3

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

value: 5 µM


title: deep_duroc_3_wk_s16

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #15. 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


title: Hippocampus_animal N242_0.2 mL saline_no seize_no drugs_6hr

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

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed


title: Hepa1c1c7_DMSO_12h_3

source_name: murine hepatoma cells treated for 12h with Vehicle

tag: cell line


title: untreated

source_name: untreated

treatment_protocol: For transduction, D2SC/1 cells were cultured on retronectin-coated 35 mm Petri dishes together with 2 ml of thawed virus containing supernatant for indicated time and then washed with PBS

tag: treatment

value: untreated

tag: time


title: deep_duroc_3_wk_s14

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #13. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Hippocampus_animal N241_0.2 mL saline_no seize_no drugs_6hr

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

tag: animal number

tag: tissue

tag: agent

tag: amount administered

tag: presence of seizure

tag: animal weight (g)


title: genomic DNA from colon cancer adjacent normal tissue_CRC2066N

description: normal colon sample

tag: gender

tag: disease state


title: genomic DNA from colon cancer tissue_CRC2067T

description: tumor colon sample

value: Female

value: tumor


title: Hepa1c1c7_5uMBaP_12h_3

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

value: Hepa 1c1c7

tag: cell type

value: hepatoma

tag: concentration of chemical

tag: time of exposure


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

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

value: Hippocampus

value: Saline

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: date injected

tag: time injected


title: shallow_duroc_3_wk_s15

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #16. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time

tag: breed

tag: depth


title: genomic DNA from colon cancer adjacent normal tissue_CRC2067N

description: normal colon sample

tag: tissue


title: genomic DNA from colon cancer tissue_CRC2066T

description: tumor colon sample

value: Male


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

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

tag: animal number

tag: agent

value: Sarin

tag: amount administered

value: Sprague-Dawley

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: seizure time

tag: seizure latency


title: shallow_duroc_3_wk_s13

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #14. 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: 3 wk

value: shallow


title: Hepa1c1c7_DMSO_4h_3

source_name: murine hepatoma cells treated for 4h with Vehicle

tag: cell line

tag: cell type

tag: concentration of chemical

value: Vehicle

tag: time of exposure


title: Hepa1c1c7_50nMBaP_4h_3

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


title: Hepa1c1c7_50nMBaP_12h_3

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


title: genomic DNA from colon cancer tissue_CRC2065T

description: tumor colon sample

source_name: Colon

tag: gender

value: Colon cancer tissue

tag: disease state


title: Hepa1c1c7_5uMBaP_4h_3

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

value: 5 µM


title: shallow_duroc_2_wk_s9

source_name: shallow, duroc, 2 wk

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

tag: breed

value: duroc

tag: time

value: 2 wk


title: genomic DNA from colon cancer adjacent normal tissue_CRC2064N

description: normal colon sample

value: Female

tag: tissue

value: normal


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

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

tag: animal number

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

value: N

tag: time point (hr)

tag: date injected

tag: time injected

tag: animal weight (g)


title: Hippocampus_animal N172_0.21 mL sarin_no seize_no drugs_24hr

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

tag: agent

tag: amount administered

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: deep_duroc_2_wk_s12

source_name: deep, duroc, 2 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #11. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: depth

value: deep


title: shallow_duroc_2_wk_s11

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #12. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: breed


title: genomic DNA from colon cancer adjacent normal tissue_CRC2065N

description: normal colon sample

tag: gender

tag: disease state


title: Hippocampus_animal N81_0.24 mL saline_no seize_drugs_1hr

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

tag: animal number

tag: tissue

value: Hippocampus


title: Hippocampus_animal N82_0.2 mL saline_no seize_drugs_1hr

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

value: Saline

tag: agent dose

tag: strain


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

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

tag: atropine, 2-pam, diazepam

value: Y

tag: time point (hr)

tag: seizure time

tag: seizure latency


title: deep_duroc_2_wk_s10

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #9. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: time


title: deep_duroc_2_wk_s8

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


title: genomic DNA from colon cancer tissue_CRC2064T

description: tumor colon sample

value: tumor


title: genomic DNA from colon cancer tissue_CRC2063T

description: tumor colon sample

value: Male


title: Hepa1c1c7_50nMBaP_2h_3

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

tag: cell line

value: Hepa 1c1c7

tag: cell type

value: hepatoma

tag: concentration of chemical

tag: time of exposure


title: Hepa1c1c7_5uMBaP_2h_3

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


title: Hippocampus_animal N79_0.22 mL sarin_no seize_no drugs_1hr

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

tag: agent

value: Sarin

tag: amount administered

value: Sprague-Dawley

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure

tag: animal weight (g)


title: Hepa1c1c7_DMSO_2h_3

source_name: murine hepatoma cells treated for 2h with Vehicle

value: Vehicle


title: Hepa1c1c7_DMSO_24h_2

source_name: murine hepatoma cells treated for 24h with Vehicle


title: Hepa1c1c7_50nMBaP_24h_2

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


title: Hippocampus_animal N78_0.23 mL saline_no seize_drugs_6hr

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

tag: animal number

tag: tissue

tag: agent dose

tag: strain

tag: atropine, 2-pam, diazepam


title: Hepa1c1c7_5uMBaP_24h_2

tag: cell line

value: 5 µM


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

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

tag: time point (hr)


title: Hippocampus_animal N76_0.2 mL saline_no seize_drugs_24hr

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


title: genomic DNA from colon cancer adjacent normal tissue_CRC2063N

description: normal colon sample

tag: gender

value: Colon cancer tissue

tag: disease state


title: shallow_duroc_2_wk_s7

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

tag: breed

value: duroc

tag: time

value: 2 wk

tag: depth

value: shallow


title: deep_duroc_1_wk_s4

source_name: deep, duroc, 1 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #3. 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: 1 wk


title: genomic DNA from colon cancer adjacent normal tissue_CRC2062N

description: normal colon sample

value: Female

value: normal


title: Hepa1c1c7_50nMBaP_12h_2

tag: cell type

tag: concentration of chemical

tag: time of exposure


title: shallow_duroc_1_wk_s5

source_name: shallow, duroc, 1 wk

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #6. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: genomic DNA from colon cancer tissue_CRC2062T

description: tumor colon sample


title: Hippocampus_animal N75_0.2 mL sarin_no seize_no drugs_3hr

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

value: Hippocampus

tag: agent

tag: amount administered

value: N

tag: date injected

tag: time injected

tag: date sacrificed

tag: time sacrificed

tag: presence of seizure


title: genomic DNA from colon cancer tissue_CRC2061T

description: tumor colon sample

tag: tissue

value: tumor


title: deep_duroc_1_wk_s2

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #1. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

value: deep


title: deep_duroc_1_wk_s6

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #5. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.


title: Hippocampus_animal N73_0.2 mL sarin_no seize_no drugs_1hr

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

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: agent dose

tag: strain

tag: atropine, 2-pam, diazepam

tag: time point (hr)

tag: animal weight (g)


title: shallow_duroc_1_wk_s3

treatment_protocol: THIS SAMPLE IS TO BE PAIRED WITH SAMPLE #4. After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: breed

tag: depth

tag: time


title: genomic DNA from colon cancer tissue_CRC2060T

description: tumor colon sample

tag: gender

tag: disease state


title: genomic DNA from colon cancer adjacent normal tissue_CRC2061N

description: normal colon sample

value: Male


title: Hepa1c1c7_5uMBaP_12h_2

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: genomic DNA from colon cancer adjacent normal tissue_CRC2060N

description: normal colon sample