title: GM17773 (550K)

source_name: lymphoblastoid cell line GM17773

tag: ethnic group

tag: cell line (coriell id)


title: GM17771 (550K)

status: Public on Sep 25 2010

type: genomic

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

country: USA

institute: Mayo Clinic

description: Genomic DNA extracted from lymphoblastoid cell line was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: Samples are applied to each BeadChip. The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50mers (covalently linked to one of over 500,000 bead types) during hybridization. One bead type corresponds to each allele per SNP locus.  Unhybridized and non-specifically hybridized DNA is washed away. The chip undergoes staining and extension in capillary flow-through chambers. Singlebase extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates detectable labels on the BeadChip and determines the genotype call for the sample.

scan_protocol: The Illumina BeadArray Reader scans the BeadChip, using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores.

data_processing: Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using HumanHap550 v3.0 Whole-Genome Genotyping Kit (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblastoid cell line GM17771

label_protocol: 750 ng of high quality DNA samples are denatured and neutralized, and then are isothermally amplified in an overnight step.  The amplified product is fragmented by a controlled enzymatic process that does not require gel electrophoresis. The process uses end-point fragmentation to avoid overfragmenting the sample.  After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4ºC, and resuspended in a hybridization buffer.

extract_protocol: Genomic DNA was purchased from the Coriell Cell Repository (Camden, NJ), which was extracted from the cell cultures in the Repositories

value: HCA Han Chinese-American

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17800 (510S)

data_processing: Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using Infinium HumanExon510S-2 DNA Analysis Kit (Illumina).

source_name: lymphoblastoid cell line GM17800


title: GM17774 (550K)

source_name: lymphoblastoid cell line GM17774


title: GM17803 (510S)

source_name: lymphoblastoid cell line GM17803


title: GM17799 (510S)

source_name: lymphoblastoid cell line GM17799


title: GM17798 (510S)

source_name: lymphoblastoid cell line GM17798


title: GM17796 (510S)

source_name: lymphoblastoid cell line GM17796


title: liver; Thioacetamide; 0 mg/kg; 24 hours; 212350856_91802

type: RNA

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description:
Liver toxicants vs. non-toxicants based on overall necrosis score
MAQC_Distribution_Status: MAQC_T -- Training

hyb_protocol: The biotin-labeled cRNA was fragmented and hybridized to the Rat Genome 230 2.0 Array (Affymetrix, Inc.) for 17 hours, prior to washing and scanning.

scan_protocol: Data were extracted from scanned images using the Affymetrix Scanner and GeneChip Operating Software (Affymetrix, Inc.).

data_processing: Affymetrix MAS5

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

label_protocol: 1 μg of total RNA from the left liver lobe of each individual rat was labeled using the GeneChip One-Cycle Target Labeling kit (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocol.

growth_protocol: F344/N male rats grow to 10-12 weeks old before exposed to one of eight hepatotoxicants

extract_protocol: Total RNA was isolated from the flash frozen portion of the left lateral liver lobe using RNeasy Midi columns (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Rats were exposed for 6, 24 or 48 hours to a low, medium or high dose of one of eight hepatotoxicants. All animals were fasted for 12-18 hours prior to exposure.

tag: tissue

value: left lateral liver lobe

tag: strain

tag: gender

value: male

tag: age

value: 10-12 weeks

tag: compound

value: Thioacetamide

tag: hybdate

tag: route

value: Gavage

tag: vehicle

value: Corn Oil

tag: control

value: Y

tag: dose

value: 0 mg/kg

tag: time of exposure

value: 24 hours

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: GM17795 (510S)

source_name: lymphoblastoid cell line GM17795

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17770 (550K)

source_name: lymphoblastoid cell line GM17770


title: GM17769 (550K)

source_name: lymphoblastoid cell line GM17769


title: GM17794 (510S)

source_name: lymphoblastoid cell line GM17794


title: liver; Thioacetamide; 0 mg/kg; 24 hours; 212350854_91741

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17828 (510S)

source_name: lymphoblastoid cell line GM17828


title: liver; Thioacetamide; 0 mg/kg; 6 hours; 212350851_91746

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 6 hours


title: GM17787 (550K)

source_name: lymphoblastoid cell line GM17787


title: GM17802 (510S)

source_name: lymphoblastoid cell line GM17802


title: GM17793 (510S)

source_name: lymphoblastoid cell line GM17793


title: GM17767 (550K)

source_name: lymphoblastoid cell line GM17767


title: GM17792 (510S)

source_name: lymphoblastoid cell line GM17792


title: liver; Thioacetamide; 150 mg/kg; 48 hours; 212350824_90965

tag: control

value: N

tag: dose

value: 150 mg/kg

tag: time of exposure

value: 48 hours

tag: necrosis score


title: liver; Thioacetamide; 0 mg/kg; 24 hours; 212350855_91740

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17789 (510S)

source_name: lymphoblastoid cell line GM17789

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17768 (550K)

source_name: lymphoblastoid cell line GM17768


title: GM17797 (510S)

source_name: lymphoblastoid cell line GM17797


title: GM17791 (510S)

source_name: lymphoblastoid cell line GM17791


title: GM17782 (550K)

source_name: lymphoblastoid cell line GM17782


title: liver; Thioacetamide; 150 mg/kg; 48 hours; 212350821_91101

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17780 (550K)

source_name: lymphoblastoid cell line GM17780


title: liver; Thioacetamide; 150 mg/kg; 48 hours; 212350822_91066

source_name: Liver

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17766 (550K)

source_name: lymphoblastoid cell line GM17766


title: liver; Thioacetamide; 50 mg/kg; 48 hours; 212350820_91056

tag: control

tag: dose

value: 50 mg/kg

tag: time of exposure

tag: necrosis score


title: GM17785 (510S)

source_name: lymphoblastoid cell line GM17785

value: HCA Han Chinese-American


title: GM17790 (510S)

source_name: lymphoblastoid cell line GM17790

value: EBV-transformed lymphoblastoid cells


title: GM17805 (510S)

source_name: lymphoblastoid cell line GM17805


title: GM17765 (550K)

source_name: lymphoblastoid cell line GM17765


title: GM17787 (510S)

source_name: lymphoblastoid cell line GM17787


title: liver; Thioacetamide; 50 mg/kg; 48 hours; 212350818_91001

value: left lateral liver lobe

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17783 (510S)

source_name: lymphoblastoid cell line GM17783

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17776 (510S)

source_name: lymphoblastoid cell line GM17776


title: liver; Thioacetamide; 50 mg/kg; 48 hours; 212350817_91028

tag: tissue

tag: strain

tag: gender

value: male

tag: age


title: GM17764 (550K)

source_name: lymphoblastoid cell line GM17764


title: GM17780 (510S)


title: GM17775 (510S)

source_name: lymphoblastoid cell line GM17775


title: GM17774 (510S)

source_name: lymphoblastoid cell line GM17774


title: GM17782 (510S)


title: liver; Thioacetamide; 15 mg/kg; 48 hours; 212350815_90964

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 15 mg/kg


title: liver; Thioacetamide; 15 mg/kg; 48 hours; 212350816_91002

value: Thioacetamide

value: Gavage

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17762 (550K)

source_name: lymphoblastoid cell line GM17762


title: GM17779 (510S)

source_name: lymphoblastoid cell line GM17779


title: GM17773 (510S)

source_name: lymphoblastoid cell line GM17773


title: GM17761 (550K)

source_name: lymphoblastoid cell line GM17761


title: GM17768 (510S)

source_name: lymphoblastoid cell line GM17768


title: GM17759 (550K)

source_name: lymphoblastoid cell line GM17759


title: GM17771 (510S)

source_name: lymphoblastoid cell line GM17771


title: GM17769 (510S)

source_name: lymphoblastoid cell line GM17769


title: GM17770 (510S)

source_name: lymphoblastoid cell line GM17770


title: liver; Thioacetamide; 15 mg/kg; 48 hours; 212350813_90995

source_name: Liver

value: Corn Oil

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Thioacetamide; 150 mg/kg; 24 hours; 212350620_91016


title: GM17766 (510S)

source_name: lymphoblastoid cell line GM17766

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17757 (550K)

source_name: lymphoblastoid cell line GM17757


title: liver; Thioacetamide; 150 mg/kg; 24 hours; 212350619_90976

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17767 (510S)

source_name: lymphoblastoid cell line GM17767


title: GM17758 (550K)

source_name: lymphoblastoid cell line GM17758


title: liver; Thioacetamide; 150 mg/kg; 24 hours; 212350617_90990

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17764 (510S)

source_name: lymphoblastoid cell line GM17764


title: GM17761 (510S)


title: GM17762 (510S)


title: GM17765 (510S)

source_name: lymphoblastoid cell line GM17765


title: GM17756 (550K)

source_name: lymphoblastoid cell line GM17756


title: GM17754 (550K)

source_name: lymphoblastoid cell line GM17754


title: liver; Thioacetamide; 50 mg/kg; 24 hours; 212350616_90968

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17755 (550K)

source_name: lymphoblastoid cell line GM17755


title: liver; Thioacetamide; 50 mg/kg; 24 hours; 212350614_91014

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17759 (510S)

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17758 (510S)


title: GM17753 (550K)

source_name: lymphoblastoid cell line GM17753


title: GM17756 (510S)


title: GM17757 (510S)


title: liver; Thioacetamide; 15 mg/kg; 24 hours; 212350611_93840

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17752 (550K)

source_name: lymphoblastoid cell line GM17752


title: liver; Thioacetamide; 15 mg/kg; 24 hours; 212350610_93833

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Thioacetamide; 15 mg/kg; 24 hours; 212350609_93850

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17754 (510S)


title: GM17753 (510S)


title: liver; Thioacetamide; 150 mg/kg; 6 hours; 212350566_93871

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17746 (510S)

source_name: lymphoblastoid cell line GM17746

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17752 (510S)


title: GM17745 (550K)

source_name: lymphoblastoid cell line GM17745


title: GM17755 (510S)


title: GM17749 (550K)

source_name: lymphoblastoid cell line GM17749


title: liver; Thioacetamide; 150 mg/kg; 6 hours; 212350564_93855

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17745 (510S)


title: GM17742 (510S)

source_name: lymphoblastoid cell line GM17742


title: GM17744 (550K)

source_name: lymphoblastoid cell line GM17744


title: GM17744 (510S)


title: GM17743 (510S)

source_name: lymphoblastoid cell line GM17743


title: liver; Thioacetamide; 150 mg/kg; 6 hours; 212350563_90861

source_name: Liver

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17747 (510S)

source_name: lymphoblastoid cell line GM17747


title: GM17740 (510S)

source_name: lymphoblastoid cell line GM17740


title: GM17741 (550K)

source_name: lymphoblastoid cell line GM17741


title: GM17749 (510S)


title: GM17743 (550K)


title: liver; Thioacetamide; 50 mg/kg; 6 hours; 212350560_90862

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Thioacetamide; 50 mg/kg; 6 hours; 212350559_90840

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17741 (510S)

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17742 (550K)


title: GM17737 (510S)

source_name: lymphoblastoid cell line GM17737


title: liver; Thioacetamide; 15 mg/kg; 6 hours; 212350558_90866

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17736 (510S)

source_name: lymphoblastoid cell line GM17736


title: GM17740 (550K)


title: GM17738 (510S)

source_name: lymphoblastoid cell line GM17738


title: liver; Thioacetamide; 15 mg/kg; 6 hours; 212350555_90822

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17739 (550K)

source_name: lymphoblastoid cell line GM17739


title: GM17739 (510S)


title: GM17738 (550K)


title: liver; N-Nitrosomorpholine; 300 mg/kg; 48 hours; 212304992_90587

value: N-Nitrosomorpholine

tag: control

tag: dose

value: 300 mg/kg

tag: time of exposure

tag: necrosis score


title: liver; N-Nitrosomorpholine; 300 mg/kg; 48 hours; 212347551_90596

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: GM17734 (510S)

source_name: lymphoblastoid cell line GM17734

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17296 (510S)

source_name: lymphoblastoid cell line GM17296

value: CA Caucasian-American


title: GM17735 (510S)

source_name: lymphoblastoid cell line GM17735


title: GM17736 (550K)


title: GM17737 (550K)


title: GM17733 (510S)

source_name: lymphoblastoid cell line GM17733


title: liver; N-Nitrosomorpholine; 50 mg/kg; 48 hours; 212304987_90601

tag: tissue

tag: strain

tag: gender

tag: age

value: N


title: liver; N-Nitrosomorpholine; 50 mg/kg; 48 hours; 212304986_90632

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17293 (510S)

source_name: lymphoblastoid cell line GM17293


title: GM17295 (510S)

source_name: lymphoblastoid cell line GM17295


title: GM17294 (510S)

source_name: lymphoblastoid cell line GM17294


title: liver; N-Nitrosomorpholine; 50 mg/kg; 48 hours; 212304985_90628

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17733 (550K)


title: GM17292 (510S)

source_name: lymphoblastoid cell line GM17292


title: GM17291 (510S)

source_name: lymphoblastoid cell line GM17291


title: GM17735 (550K)


title: GM17289 (510S)

source_name: lymphoblastoid cell line GM17289


title: GM17288 (510S)

source_name: lymphoblastoid cell line GM17288


title: GM17287 (510S)

source_name: lymphoblastoid cell line GM17287


title: GM17734 (550K)


title: GM17260 (550K)

source_name: lymphoblastoid cell line GM17260


title: GM17290 (510S)

source_name: lymphoblastoid cell line GM17290


title: liver; N-Nitrosomorpholine; 10 mg/kg; 48 hours; 212304984_90589

source_name: Liver

value: 10 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17285 (510S)

source_name: lymphoblastoid cell line GM17285

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17281 (510S)

source_name: lymphoblastoid cell line GM17281


title: liver; N-Nitrosomorpholine; 10 mg/kg; 48 hours; 212304983_90625

tag: tissue

tag: strain

tag: gender

tag: age

value: 48 hours


title: GM17259 (550K)

source_name: lymphoblastoid cell line GM17259


title: liver; N-Nitrosomorpholine; 10 mg/kg; 48 hours; 212304982_90598

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17286 (510S)

source_name: lymphoblastoid cell line GM17286


title: liver; N-Nitrosomorpholine; 10 mg/kg; 48 hours; 212304981_90610

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17278 (510S)

source_name: lymphoblastoid cell line GM17278


title: GM17280 (510S)

source_name: lymphoblastoid cell line GM17280


title: liver; N-Nitrosomorpholine; 0 mg/kg; 48 hours; 212304980_90620

value: Y

value: 0 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17282 (510S)

source_name: lymphoblastoid cell line GM17282

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17258 (550K)

source_name: lymphoblastoid cell line GM17258


title: GM17284 (510S)

source_name: lymphoblastoid cell line GM17284


title: GM17277 (510S)

source_name: lymphoblastoid cell line GM17277


title: liver; N-Nitrosomorpholine; 0 mg/kg; 48 hours; 212304979_90611

tag: tissue

value: left lateral liver lobe

tag: strain

tag: gender

tag: age


title: GM17275 (510S)

source_name: lymphoblastoid cell line GM17275


title: GM17279 (510S)

source_name: lymphoblastoid cell line GM17279


title: GM17256 (550K)

source_name: lymphoblastoid cell line GM17256


title: GM17283 (510S)

source_name: lymphoblastoid cell line GM17283


title: GM17257 (550K)

source_name: lymphoblastoid cell line GM17257


title: liver; N-Nitrosomorpholine; 0 mg/kg; 48 hours; 212304977_90602

value: male

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17276 (510S)

source_name: lymphoblastoid cell line GM17276


title: liver; N-Nitrosomorpholine; 300 mg/kg; 24 hours; 212304976_90627

source_name: Liver

value: 10-12 weeks

tag: control

tag: dose

tag: time of exposure

value: 24 hours

tag: necrosis score


title: GM17255 (550K)

source_name: lymphoblastoid cell line GM17255


title: GM17273 (510S)

source_name: lymphoblastoid cell line GM17273


title: liver; N-Nitrosomorpholine; 300 mg/kg; 24 hours; 212304975_90616

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17274 (510S)

source_name: lymphoblastoid cell line GM17274

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17254 (550K)

source_name: lymphoblastoid cell line GM17254


title: GM17268 (510S)

source_name: lymphoblastoid cell line GM17268


title: liver; N-Nitrosomorpholine; 300 mg/kg; 24 hours; 212304973_90590

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17253 (550K)

source_name: lymphoblastoid cell line GM17253


title: GM17267 (510S)

source_name: lymphoblastoid cell line GM17267


title: GM17250 (550K)

source_name: lymphoblastoid cell line GM17250


title: GM17270 (510S)

source_name: lymphoblastoid cell line GM17270


title: GM17266 (510S)

source_name: lymphoblastoid cell line GM17266


title: liver; N-Nitrosomorpholine; 50 mg/kg; 24 hours; 212304972_90639

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 50 mg/kg


title: GM17251 (550K)

source_name: lymphoblastoid cell line GM17251


title: GM17252 (550K)

source_name: lymphoblastoid cell line GM17252


title: GM17265 (510S)

source_name: lymphoblastoid cell line GM17265


title: liver; N-Nitrosomorpholine; 50 mg/kg; 24 hours; 212304970_90645

value: Gavage

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17271 (510S)

source_name: lymphoblastoid cell line GM17271


title: GM17272 (510S)

source_name: lymphoblastoid cell line GM17272


title: GM17264 (510S)

source_name: lymphoblastoid cell line GM17264


title: GM17269 (510S)

source_name: lymphoblastoid cell line GM17269


title: liver; N-Nitrosomorpholine; 50 mg/kg; 24 hours; 212304969_90607

source_name: Liver

value: Corn Oil

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; N-Nitrosomorpholine; 10 mg/kg; 24 hours; 212304968_90662

value: N-Nitrosomorpholine


title: GM17249 (550K)

source_name: lymphoblastoid cell line GM17249

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17261 (510S)

source_name: lymphoblastoid cell line GM17261


title: GM17263 (510S)

source_name: lymphoblastoid cell line GM17263


title: GM17258 (510S)

source_name: lymphoblastoid cell line GM17258


title: GM17248 (550K)

source_name: lymphoblastoid cell line GM17248


title: GM17260 (510S)

source_name: lymphoblastoid cell line GM17260


title: GM17259 (510S)

source_name: lymphoblastoid cell line GM17259


title: GM17247 (550K)

source_name: lymphoblastoid cell line GM17247


title: liver; N-Nitrosomorpholine; 10 mg/kg; 24 hours; 212304967_90664

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17262 (510S)

source_name: lymphoblastoid cell line GM17262


title: liver; N-Nitrosomorpholine; 0 mg/kg; 24 hours; 212304964_90629

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17246 (550K)

source_name: lymphoblastoid cell line GM17246


title: GM17257 (510S)

source_name: lymphoblastoid cell line GM17257


title: GM17253 (510S)

source_name: lymphoblastoid cell line GM17253


title: GM17252 (510S)

source_name: lymphoblastoid cell line GM17252


title: GM17255 (510S)

source_name: lymphoblastoid cell line GM17255


title: GM17244 (550K)

source_name: lymphoblastoid cell line GM17244


title: liver; N-Nitrosomorpholine; 300 mg/kg; 6 hours; 212304960_90781

tag: control

tag: dose

value: 300 mg/kg

tag: time of exposure

value: 6 hours

tag: necrosis score


title: GM17245 (550K)

source_name: lymphoblastoid cell line GM17245

value: CA Caucasian-American


title: liver; N-Nitrosomorpholine; 0 mg/kg; 24 hours; 212304961_90772

source_name: Liver

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: GM17242 (550K)

source_name: lymphoblastoid cell line GM17242

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17251 (510S)

source_name: lymphoblastoid cell line GM17251


title: GM17243 (550K)

source_name: lymphoblastoid cell line GM17243


title: liver; N-Nitrosomorpholine; 300 mg/kg; 6 hours; 212304959_90774

tag: tissue

tag: strain

tag: gender

tag: age

value: N


title: liver; N-Nitrosomorpholine; 300 mg/kg; 6 hours; 212304958_90786

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17249 (510S)

source_name: lymphoblastoid cell line GM17249


title: GM17254 (510S)

source_name: lymphoblastoid cell line GM17254


title: liver; N-Nitrosomorpholine; 300 mg/kg; 6 hours; 212304957_90780

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17241 (550K)

source_name: lymphoblastoid cell line GM17241


title: GM17256 (510S)

source_name: lymphoblastoid cell line GM17256


title: GM17247 (510S)

source_name: lymphoblastoid cell line GM17247


title: GM17246 (510S)


title: liver; N-Nitrosomorpholine; 50 mg/kg; 6 hours; 212304956_90758

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17243 (510S)

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; N-Nitrosomorpholine; 10 mg/kg; 6 hours; 212304951_90745

tag: tissue

tag: strain

tag: gender

tag: age

value: 10 mg/kg


title: GM17239 (550K)

source_name: lymphoblastoid cell line GM17239


title: GM17238 (550K)

source_name: lymphoblastoid cell line GM17238


title: GM17244 (510S)


title: GM17248 (510S)

source_name: lymphoblastoid cell line GM17248


title: GM17237 (550K)

source_name: lymphoblastoid cell line GM17237


title: GM17239 (510S)


title: GM17250 (510S)

source_name: lymphoblastoid cell line GM17250


title: GM17245 (510S)


title: GM17241 (510S)


title: GM17240 (510S)

source_name: lymphoblastoid cell line GM17240


title: GM17236 (550K)

source_name: lymphoblastoid cell line GM17236


title: liver; N-Nitrosomorpholine; 0 mg/kg; 6 hours; 212304948_90757

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: Y


title: liver; N-Nitrosomorpholine; 0 mg/kg; 6 hours; 212304947_90738

tag: control

tag: dose

value: 0 mg/kg

tag: time of exposure

tag: necrosis score


title: GM17237 (510S)

value: EBV-transformed lymphoblastoid cells


title: GM17234 (550K)

source_name: lymphoblastoid cell line GM17234


title: GM17236 (510S)


title: liver; N-Nitrosomorpholine; 0 mg/kg; 6 hours; 212304946_90777

source_name: Liver

value: left lateral liver lobe

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17235 (510S)

source_name: lymphoblastoid cell line GM17235

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 6 hours; 212276302_90793

tag: tissue

tag: strain

tag: gender

value: male

tag: age

value: 1, 4-Dichlorobenzene

value: 150 mg/kg


title: GM17234 (510S)


title: GM17242 (510S)

source_name: lymphoblastoid cell line GM17242


title: GM17232 (510S)

source_name: lymphoblastoid cell line GM17232


title: GM17233 (550K)

source_name: lymphoblastoid cell line GM17233


title: GM17231 (510S)

source_name: lymphoblastoid cell line GM17231


title: GM17229 (510S)

source_name: lymphoblastoid cell line GM17229


title: GM17238 (510S)


title: GM17231 (550K)


title: GM17230 (510S)

source_name: lymphoblastoid cell line GM17230


title: liver; N-Nitrosomorpholine; 0 mg/kg; 6 hours; 212304945_90776

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 6 hours; 212276300_90747

value: Gavage

tag: control

tag: dose

value: 15 mg/kg

tag: time of exposure

tag: necrosis score


title: GM17227 (510S)

source_name: lymphoblastoid cell line GM17227


title: GM17228 (510S)

source_name: lymphoblastoid cell line GM17228


title: GM17235 (550K)


title: GM17230 (550K)


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 6 hours; 212276298_90763

value: Corn Oil

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17225 (510S)

source_name: lymphoblastoid cell line GM17225

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 6 hours; 212276296_90740

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17222 (510S)

source_name: lymphoblastoid cell line GM17222


title: GM17226 (510S)

source_name: lymphoblastoid cell line GM17226


title: GM17229 (550K)


title: GM17223 (510S)

source_name: lymphoblastoid cell line GM17223


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 6 hours; 212276295_90778

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17232 (550K)


title: GM17220 (510S)

source_name: lymphoblastoid cell line GM17220


title: GM17227 (550K)


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 6 hours; 212276294_90744

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17233 (510S)


title: GM17224 (510S)

source_name: lymphoblastoid cell line GM17224


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 6 hours; 212276297_90736

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17219 (510S)

source_name: lymphoblastoid cell line GM17219

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17218 (510S)

source_name: lymphoblastoid cell line GM17218


title: GM17226 (550K)


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 48 hours; 212276289_90719

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age

value: 48 hours


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 48 hours; 212276293_90790

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17225 (550K)


title: GM17217 (510S)

source_name: lymphoblastoid cell line GM17217


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 48 hours; 212276288_90716

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17223 (550K)


title: GM17216 (510S)

source_name: lymphoblastoid cell line GM17216


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 48 hours; 212276287_90725

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17212 (510S)

source_name: lymphoblastoid cell line GM17212

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17210 (510S)

source_name: lymphoblastoid cell line GM17210


title: GM17222 (550K)


title: GM17213 (510S)

source_name: lymphoblastoid cell line GM17213


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 48 hours; 212276286_90720

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17214 (510S)

source_name: lymphoblastoid cell line GM17214


title: GM17211 (510S)

source_name: lymphoblastoid cell line GM17211


title: GM17224 (550K)


title: GM17209 (510S)

source_name: lymphoblastoid cell line GM17209


title: GM17220 (550K)


title: GM17207 (510S)

source_name: lymphoblastoid cell line GM17207


title: GM17203 (510S)

source_name: lymphoblastoid cell line GM17203


title: GM17215 (510S)

source_name: lymphoblastoid cell line GM17215


title: GM17228 (550K)

source_name: lymphoblastoid cell line GM17228


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 48 hours; 212276283_90705

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17221 (550K)

source_name: lymphoblastoid cell line GM17221


title: GM17208 (510S)

source_name: lymphoblastoid cell line GM17208


title: GM17204 (510S)

source_name: lymphoblastoid cell line GM17204


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 48 hours; 212276285_90676

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17217 (550K)


title: GM17205 (510S)

source_name: lymphoblastoid cell line GM17205


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 48 hours; 212276282_90674

source_name: Liver

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 48 hours; 212276279_90726


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 24 hours; 212276276_90686

value: 24 hours


title: GM17219 (550K)

source_name: lymphoblastoid cell line GM17219

tag: ethnic group

value: CA Caucasian-American

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17218 (550K)

source_name: lymphoblastoid cell line GM17218


title: GM17199 (510S)

source_name: lymphoblastoid cell line GM17199

value: AA African-American


title: GM17201 (510S)

source_name: lymphoblastoid cell line GM17201


title: GM17216 (550K)

source_name: lymphoblastoid cell line GM17216


title: GM17198 (510S)

source_name: lymphoblastoid cell line GM17198


title: GM17202 (510S)

source_name: lymphoblastoid cell line GM17202


title: GM17206 (510S)

source_name: lymphoblastoid cell line GM17206


title: GM17221 (510S)


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 24 hours; 212276275_90724

tag: tissue

tag: strain

tag: gender

tag: age

value: N

value: NIEHS/Cogenics


title: GM17215 (550K)


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 24 hours; 212276273_90661

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 24 hours; 212276274_90666

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17194 (510S)

source_name: lymphoblastoid cell line GM17194


title: GM17193 (510S)

source_name: lymphoblastoid cell line GM17193


title: GM17197 (510S)

source_name: lymphoblastoid cell line GM17197


title: GM17213 (550K)

source_name: lymphoblastoid cell line GM17213


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 24 hours; 212276272_90710

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17196 (510S)

source_name: lymphoblastoid cell line GM17196

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17211 (550K)

source_name: lymphoblastoid cell line GM17211


title: GM17195 (510S)

source_name: lymphoblastoid cell line GM17195


title: GM17192 (510S)

source_name: lymphoblastoid cell line GM17192


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 24 hours; 212276271_90699

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17212 (550K)

source_name: lymphoblastoid cell line GM17212


title: GM17200 (510S)

source_name: lymphoblastoid cell line GM17200


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 24 hours; 212276270_90677

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17190 (510S)

source_name: lymphoblastoid cell line GM17190


title: GM17209 (550K)

source_name: lymphoblastoid cell line GM17209


title: GM17210 (550K)

source_name: lymphoblastoid cell line GM17210


title: GM17187 (510S)

source_name: lymphoblastoid cell line GM17187


title: GM17188 (510S)

source_name: lymphoblastoid cell line GM17188


title: GM17191 (510S)

source_name: lymphoblastoid cell line GM17191


title: GM17186 (510S)

source_name: lymphoblastoid cell line GM17186


title: GM17189 (510S)

source_name: lymphoblastoid cell line GM17189


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 24 hours; 212276267_90698

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: wild-type roots - Fe, biological rep3

city: Saarbrücken

first: Mara

last: Schuler

address: Campus SB, Geb.A2 4

country: Germany

institute: Saarland University

description: Roots of wild-type, ecotype Columbia, grown under Fe deficiency

hyb_protocol: (see label protocol)

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Data were processed by Affymetrix GeneChip Operating software (GCOS) and quantile normalized using R.

organism: Arabidopsis thaliana

source_name: wild-type, Roots grown under - Fe, ecotype Columbia

label_protocol: 5 µg RNA of each sample were processed into biotin-labeled cRNA and hybridized to Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays (Affymetrix, High Wycombe, U.K.), using the Affymetrix One-Cycle Labeling and Control (Target) kit

growth_protocol: Wild-type and nas4x-1 plants were grown in hydroponic solution containing a quarter strength of Hoagland salts supplied with 10µM FeNa-EDTA. The medium was exchanged weekly. Four weeks after germination, plants were divided into two groups, one of them was kept in the same conditions as mentioned above (10µM FeNa-EDTA, + Fe) while the other group was transferred to Hoagland solution without Fe (0 µM FeNa-EDTA, - Fe). Cultivation took place at 21°C/19°C and 16-h-light, 8-h-dark cycles and a light intensity of 150 µmol x m-2 x s-1.

extract_protocol: Total RNA was extracted from 100 mg of root and leaf material with the Quiagen RNeasy Plant Mini Prep Kit.

treatment_protocol: No special treatment has been applied

value: Roots


title: GM17185 (510S)

source_name: lymphoblastoid cell line GM17185


title: GM17208 (550K)

source_name: lymphoblastoid cell line GM17208


title: GM17181 (510S)

source_name: lymphoblastoid cell line GM17181


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 24 hours; 212276269_90708

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17182 (510S)

source_name: lymphoblastoid cell line GM17182

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17207 (550K)

source_name: lymphoblastoid cell line GM17207


title: GM17183 (510S)

source_name: lymphoblastoid cell line GM17183


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 24 hours; 212276262_33311

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age

value: Y

value: 0 mg/kg


title: GM17180 (510S)

source_name: lymphoblastoid cell line GM17180

value: EBV-transformed lymphoblastoid cells


title: GM17203 (550K)

source_name: lymphoblastoid cell line GM17203


title: GM17205 (550K)

source_name: lymphoblastoid cell line GM17205


title: GM17179 (510S)

source_name: lymphoblastoid cell line GM17179


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 6 hours; 212276260_33357

value: left lateral liver lobe

value: male

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 6 hours


title: GM17184 (510S)

source_name: lymphoblastoid cell line GM17184


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 24 hours; 212276266_90706

value: 10-12 weeks

value: 1, 4-Dichlorobenzene

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 24 hours; 212276263_33338

value: Gavage

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: wild-type roots + Fe, biological rep1

description: Roots of wild-type, ecotype Columbia, grown under Fe supply

source_name: wild-type, Roots grown under + Fe, ecotype Columbia


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 6 hours; 212276257_33344

value: Corn Oil

value: 150 mg/kg


title: GM17178 (510S)

source_name: lymphoblastoid cell line GM17178

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17174 (510S)

source_name: lymphoblastoid cell line GM17174


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 6 hours; 212276259_33336

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17204 (550K)

source_name: lymphoblastoid cell line GM17204


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 48 hours; 210759919_33290

tag: compound

value: 1, 2-Dichlorobenzene

tag: hybdate

tag: route

tag: vehicle

value: 48 hours


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 48 hours; 210759918_55249

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17172 (510S)

source_name: lymphoblastoid cell line GM17172

value: AA African-American


title: GM17176 (510S)

source_name: lymphoblastoid cell line GM17176


title: GM17173 (510S)

source_name: lymphoblastoid cell line GM17173


title: GM17202 (550K)

source_name: lymphoblastoid cell line GM17202

value: CA Caucasian-American


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 48 hours; 210759916_55261

value: N

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 48 hours; 210759915_55281


title: GM17167 (510S)

source_name: lymphoblastoid cell line GM17167

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17175 (510S)

source_name: lymphoblastoid cell line GM17175


title: GM17177 (510S)

source_name: lymphoblastoid cell line GM17177


title: GM17201 (550K)

source_name: lymphoblastoid cell line GM17201


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 48 hours; 210759914_55279

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17166 (510S)

source_name: lymphoblastoid cell line GM17166


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 48 hours; 210759913_55242

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 15 mg/kg


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 48 hours; 210759911_55264

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 48 hours; 210759910_55265

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17165 (510S)

source_name: lymphoblastoid cell line GM17165

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17158 (510S)

source_name: lymphoblastoid cell line GM17158


title: GM17160 (510S)

source_name: lymphoblastoid cell line GM17160


title: GM17159 (510S)

source_name: lymphoblastoid cell line GM17159


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 48 hours; 210759907_55283

tag: tissue

tag: strain

tag: gender

tag: age

value: Y

value: 0 mg/kg


title: GM17162 (510S)

source_name: lymphoblastoid cell line GM17162

value: EBV-transformed lymphoblastoid cells


title: GM17170 (510S)

source_name: lymphoblastoid cell line GM17170


title: GM17171 (510S)

source_name: lymphoblastoid cell line GM17171


title: GM17157 (510S)

source_name: lymphoblastoid cell line GM17157


title: GM17161 (510S)

source_name: lymphoblastoid cell line GM17161


title: GM17148 (510S)

source_name: lymphoblastoid cell line GM17148


title: GM17149 (510S)

source_name: lymphoblastoid cell line GM17149


title: GM17145 (510S)

source_name: lymphoblastoid cell line GM17145


title: GM17146 (510S)

source_name: lymphoblastoid cell line GM17146


title: GM17155 (510S)

source_name: lymphoblastoid cell line GM17155


title: GM17156 (510S)

source_name: lymphoblastoid cell line GM17156


title: GM17150 (510S)

source_name: lymphoblastoid cell line GM17150


title: GM17143 (510S)

source_name: lymphoblastoid cell line GM17143


title: GM17168 (510S)

source_name: lymphoblastoid cell line GM17168


title: GM17147 (510S)

source_name: lymphoblastoid cell line GM17147


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 48 hours; 210759906_55271

source_name: Liver

value: left lateral liver lobe

value: male

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 24 hours; 210759904_72004

value: 10-12 weeks

tag: control

tag: dose

tag: time of exposure

value: 24 hours

tag: necrosis score


title: GM17154 (510S)

source_name: lymphoblastoid cell line GM17154


title: GM17144 (510S)

source_name: lymphoblastoid cell line GM17144


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 24 hours; 210759900_72024

value: Gavage

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17142 (510S)

source_name: lymphoblastoid cell line GM17142

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 24 hours; 210759902_72026

tag: tissue

tag: strain

tag: gender

tag: age

value: Corn Oil


title: GM17139 (510S)

source_name: lymphoblastoid cell line GM17139


title: GM17163 (510S)

source_name: lymphoblastoid cell line GM17163


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 24 hours; 210759899_72183

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 150 mg/kg


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 24 hours; 210759896_72155

value: 1, 2-Dichlorobenzene

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 24 hours; 210759897_72198

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17138 (510S)

source_name: lymphoblastoid cell line GM17138

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17140 (510S)

source_name: lymphoblastoid cell line GM17140


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 24 hours; 210759893_55254

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17137 (510S)

source_name: lymphoblastoid cell line GM17137


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 24 hours; 210759892_55263

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 6 hours; 210759886_33308

tag: control

tag: dose

tag: time of exposure

value: 6 hours

tag: necrosis score


title: GM17164 (510S)

source_name: lymphoblastoid cell line GM17164

value: AA African-American


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 6 hours; 210759885_33312

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 6 hours; 210759882_33288


title: GM17136 (510S)

source_name: lymphoblastoid cell line GM17136

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17141 (510S)

source_name: lymphoblastoid cell line GM17141


title: GM17135 (510S)

source_name: lymphoblastoid cell line GM17135


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 6 hours; 210759888_33298

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17132 (510S)

source_name: lymphoblastoid cell line GM17132


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 6 hours; 210759881_33282

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17129 (510S)

source_name: lymphoblastoid cell line GM17129


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 6 hours; 210759880_33346

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17133 (510S)

source_name: lymphoblastoid cell line GM17133


title: GM17125 (510S)

source_name: lymphoblastoid cell line GM17125


title: GM17124 (510S)

source_name: lymphoblastoid cell line GM17124


title: GM17126 (510S)

source_name: lymphoblastoid cell line GM17126


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 6 hours; 210759879_33341

source_name: Liver

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17134 (510S)

source_name: lymphoblastoid cell line GM17134

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17131 (510S)

source_name: lymphoblastoid cell line GM17131


title: GM17121 (510S)

source_name: lymphoblastoid cell line GM17121


title: GM17117 (510S)

source_name: lymphoblastoid cell line GM17117


title: GM17120 (510S)

source_name: lymphoblastoid cell line GM17120


title: GM17122 (510S)

source_name: lymphoblastoid cell line GM17122


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 6 hours; 210759877_33317

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17123 (510S)

source_name: lymphoblastoid cell line GM17123


title: GM17119 (510S)

source_name: lymphoblastoid cell line GM17119


title: Induced G1E-ER-GATA-1_LMO2 knockdown_Rep2

city: Sendai

first: Tohru

last: Fujiwara

address: 2-1 Seiryo-cho, Aoba-ku

department: Hematology and Rheumatology

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Cy5- and Cy3-labeled cRNAs were combined with blocking agent and fragmentation buffer and incubated 60℃ 30 min to fragment RNA, and GEx Hybridization buffer was added to stop the reaction. The mixture was hybridized to the Agilent 4 x 44K whole mouse genome microarray (G4122F) at 65℃ 17h.

scan_protocol: After washing with GE wash buffer data were collected using Agilent microarray scanner. The settings were as follows: Dye channel: Red & Green, Scan resolution: 5um, Scanning Mode: single pass

data_processing: VALUE was determined as log10 ratio of normalized Cy5 (red) signal to normalized Cy3 (green) signal. Normalization was based on EDGE3 software Liner&LOWNESS (Locally Weighted Liner Regression).

organism: Mus musculus

source_name: Control siRNA-treated G1E-ER-GATA-1_Cy5

label_protocol: 1.2 ug of total RNA in a total volume of 8.3 uL was incubated with T7 promoter primer and Cy3-CTP. After denaturation at 65℃, MMLV-RT, dNTP, RNaseOUT, DTT and 5x buffer were added and incubated at 40℃ for 2h. Transcription master mix, containing 4x buffer, DTT, NTPmix, PEG, RNaseOUT, pyrophosphatase, T7 RNA polymerase and Cy5-CTP, were added and incubated 40℃ for 2h.

extract_protocol:
Total RNA was extracted using TRIZOL (Invitrogen).
RNA quality was checked by Nanodrop: A260/280>1.7 and 260/230>1.6

tag: cell line

value: Control siRNA-treated/b-estradiol-treated murine ES cells

value: erythroid

source_name: LMO2 siRNA-treated G1E-ER-GATA-1_Cy3

value: LMO2 siRNA-treated/b-estradiol-treated murine ES cells


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 6 hours; 210759876_33331

tag: compound

tag: hybdate

tag: route

tag: vehicle

tag: control

value: NIEHS/Cogenics


title: Induced G1E-ER-GATA-1_LMO2 knockdown_Rep1


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 6 hours; 210759878_33323

value: N

tag: dose

value: 15 mg/kg

tag: time of exposure

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: GM17115 (510S)

source_name: lymphoblastoid cell line GM17115

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

value: EBV-transformed lymphoblastoid cells


title: GM17113 (510S)

source_name: lymphoblastoid cell line GM17113

tag: cell type


title: GM17128 (510S)

source_name: lymphoblastoid cell line GM17128


title: GM17116 (510S)

source_name: lymphoblastoid cell line GM17116


title: GM17114 (510S)

source_name: lymphoblastoid cell line GM17114


title: GM17110 (510S)

source_name: lymphoblastoid cell line GM17110


title: GM17130 (510S)

source_name: lymphoblastoid cell line GM17130


title: GM17127 (510S)

source_name: lymphoblastoid cell line GM17127


title: GM17112 (510S)

source_name: lymphoblastoid cell line GM17112


title: non-progressive sural nerve, patient 8

status: Public on Sep 24 2010

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute.  The samples were Robust Multi-array Average (RMA) normalized using the BrainArray Custom CDF HGU133Plus2_Hs_ENTREZG version 12. Cyber-T and ChipInspector (Genomatix, Germany) were used to analyze the expression data.

label: biotin

source_name: non-progressive DN sural nerve 52 weeks

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit protocol from 75 ng total RNA (Ovation RNA Amplification System V2 Manual, 2007, NuGEN).

extract_protocol: Total RNA was isolated from a 1 cm segment of each sural nerve biopsy using a commercially available kit (RNeasy Mini Kit; QIAGEN, Inc., Valencia, CA), including an on-column deoxyribonuclease digestion and following the manufacturer’s protocol. RNA quality and quantity were assessed by microfluid electrophoresis using an RNA 6000 Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: tissue

value: sural nerve


title: non-progressive sural nerve, patient 10


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 6 hours; 210759875_33326

source_name: Liver

value: left lateral liver lobe

tag: strain

tag: gender

value: male

tag: age

value: Y

value: 0 mg/kg

tag: necrosis level (ekl)

tag: institution


title: non-progressive sural nerve, patient 9


title: non-progressive sural nerve, patient 17


title: non-progressive sural nerve, patient 16


title: non-progressive sural nerve, patient 7


title: non-progressive sural nerve, patient 11


title: non-progressive sural nerve, patient 6


title: non-progressive sural nerve, patient 14


title: GM17118 (510S)

source_name: lymphoblastoid cell line GM17118


title: non-progressive sural nerve, patient 12


title: non-progressive sural nerve, patient 13


title: non-progressive sural nerve, patient 4


title: GM17111 (510S)

source_name: lymphoblastoid cell line GM17111


title: Induced G1E-ER-GATA-1_ETO2 knockdown_Rep2

label_protocol: 1.2 ug of total RNA in a total volume of 8.3 uL was incubated with T7 promoter primer and Cy5-CTP. After denaturation at 65℃, MMLV-RT, dNTP, RNaseOUT, DTT and 5x buffer were added and incubated at 40℃ for 2h. Transcription master mix, containing 4x buffer, DTT, NTPmix, PEG, RNaseOUT, pyrophosphatase, T7 RNA polymerase and Cy5-CTP, were added and incubated 40℃ for 2h.

tag: cell line

source_name: ETO2 siRNA-treated G1E-ER-GATA-1_Cy3

label_protocol: 1.2 ug of total RNA in a total volume of 8.3 uL was incubated with T7 promoter primer and Cy3-CTP. After denaturation at 65℃, MMLV-RT, dNTP, RNaseOUT, DTT and 5x buffer were added and incubated at 40℃ for 2h. Transcription master mix, containing 4x buffer, DTT, NTPmix, PEG, RNaseOUT, pyrophosphatase, T7 RNA polymerase and Cy3-CTP, were added and incubated 40℃ for 2h.

value: ETO2 siRNA-treated/b-estradiol-treated murine ES cells


title: non-progressive sural nerve, patient 15


title: Gene expression profiling in 3A6 MSCs

city: Taipei

first: Chih

middle: Chien

last: Tsai

address: No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan

country: Taiwan

institute: Taipei Vaterans General Hospital

description: HPV E6/E7/hTERT transfected Mesenchymal stem cells

hyb_protocol: standard Affymetrix procedures

scan_protocol: Scanned on Affymatrix GeneArray® scanner and images was analyzed by GeneChip Operating Software (Affymatrix, USA)

data_processing: GeneChip Operating Software (Affymatrix, USA) was used for background subtraction and MAS5 normalization.

label_protocol: standard Affymetrix procedures

growth_protocol: 3A6 MSCs was kept in DMEM-LG medium with 10% FBS

extract_protocol: Total RNA was extracted from samples using QIAGEN RNeasy Mini Kit

treatment_protocol: No treatment

value: Bone marrow


title: Induced G1E-ER-GATA-1_ETO2 knockdown_Rep1


title: progressive sural nerve, patient 18

source_name: progressive DN sural nerve 52 weeks


title: progressive sural nerve, patient 17


title: non-progressive sural nerve, patient 3


title: non-progressive sural nerve, patient 1


title: GM17107 (510S)

source_name: lymphoblastoid cell line GM17107


title: progressive sural nerve, patient 13


title: progressive sural nerve, patient 12


title: non-progressive sural nerve, patient 2


title: GM17106 (510S)

source_name: lymphoblastoid cell line GM17106


title: progressive sural nerve, patient 14


title: progressive sural nerve, patient 15


title: GM17105 (510S)

source_name: lymphoblastoid cell line GM17105


title: progressive sural nerve, patient 8


title: progressive sural nerve, patient 9


title: GM17109 (510S)

source_name: lymphoblastoid cell line GM17109


title: progressive sural nerve, patient 10


title: progressive sural nerve, patient 7


title: progressive sural nerve, patient 6


title: progressive sural nerve, patient 5


title: Withering II WII_3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20)

scan_protocol: Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were scale-normalized

label: Alexa Fluor 647

organism: Vitis vinifera

source_name: Corvina berry, withering II

label_protocol: Total RNA (1 ug) was amplified by using the SuperScript Indirect RNA Amplification System (Invitrogen), to incorporate amino-allyl UTP molecules (aRNA) and fluorescently labelled by using the Alexa Fluor 647 reactive Dye

growth_protocol: Vitis vinifera cv Corvina (clone 48) were grown in a vineyard of Pasqua Vini e Cantine (Verona, Italy)

extract_protocol: Total RNA was extracted according to Rezaian and Krake (doi:10.1016/S0166-0934(00)00211-1

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 112 days after fruit set and stored in the for 56 days in special room (fruttaio) normally used for this process, at room temperature and a relative humidity not exceeding 65%.

value: berry

tag: time point

value: withering II

tag: cultivar

value: Corvina


title: progressive sural nerve, patient 4


title: progressive sural nerve, patient 11


title: Withering III WIII_3

source_name: Corvina berry, withering III

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 112 days after fruit set and stored in the for 91 days in special room (fruttaio) normally used for this process, at room temperature and a relative humidity not exceeding 65%.

value: withering III


title: non-progressive sural nerve, patient 5


title: Withering III WIII_1


title: Withering III WIII_2


title: GM17104 (510S)

source_name: lymphoblastoid cell line GM17104

value: AA African-American


title: progressive sural nerve, patient 3


title: Withering II WII_1

value: whitering II


title: Withering II WII_2


title: GM17101 (510S)

source_name: lymphoblastoid cell line GM17101


title: Withering I WI_3

source_name: Corvina berry, withering I

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 112 days after fruit set and stored in the for 35 days in special room (fruttaio) normally used for this process, at room temperature and a relative humidity not exceeding 65%.

value: whitering I


title: GM17102 (510S)

source_name: lymphoblastoid cell line GM17102


title: GM17103 (510S)

source_name: lymphoblastoid cell line GM17103


title: progressive sural nerve, patient 2


title: Withering I WI_2

value: withering I


title: progressive sural nerve, patient 1


title: Withering I WI_1


title: 24 hours post mating - female brain - replicate 4

city: Los Angeles

first: Justin

last: Dalton

state: CA

address: 1050 Child's Way, RRI

department: Biological Sciences

institute: University of Southern California

description: Biological replicate 4 of 4: 24 hours post-mating female brains to age matched virgin female brains

hyb_protocol: cDNA or cRNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO). Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA). Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

scan_protocol: All arrays were scanned using the GenePix 4100A scanner and GenePix Pro 5.0 software from Axon Instruments (Molecular Diagnostics, Sunnyvale, CA).

data_processing: Visual inspection of the microarray images filtered out florescence most likely not due to labeled cDNA binding; the data from these array elements was discarded. Array elements were only considered for further analysis if at least one channel (Cy3 or Cy5) had greater than 75% of the pixels with intensity values one standard deviation above background levels. All microarray normalization and statistical analyses were performed using the limma package of BioConductor in the program R.

organism: Drosophila melanogaster

source_name: Adult Virgin Female

label_protocol: For head isolated RNA, cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 20 µg of total RNA was used as a starting template. The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL). The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM). After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA). For brain isolated RNA, cRNA probes were made and Cy-labeled from RNA derived from CNS tissue using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion). The cRNA samples were then purified (Gel-Purification Kit, Qiagen, Valencia, CA).

growth_protocol: Flies were raised at 25°C under a 12-hour light and 12-hour dark cycle, on standard cornmeal food media.

extract_protocol: Adult heads were snapped-off from the body by shaking the frozen flies in the cryovial. The frozen heads were sorted from the bodies on plastic cooled on dry ice. Total RNA was extracted from ~100 heads per sample, or 20 brains,  by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA).

treatment_protocol: Virgin Canton S females and w; P[UAS-dj-GFP] males were collected within 5-8 hours of eclosion and aged for 5 days. On the fifth day, females and males were combined at a ratio of 10 females: 20 males for two hours between the time period of 6-8 hours after the lights on. Females were then sorted under CO2 anesthesia using a fluorescence microscope. Only females that showed strong GFP expression in the lower abdomen were collected and aged on food. The mated females were then collected 24, 48 or 72 hours post-mating by tapping them without anesthesia into a cryovial, and immediately snap frozen in liquid nitrogen.  Age matched virgin females were collected in a similar manner. For the 0-2 hour time point, animals were anaesthetized after the 2 hour mating period, identified as mated females and were immediately snap frozen in liquid nitrogen. The virgin females collected for the 0-2 hour time point were not exposed to males, but were anaesthetized to control for gene expression differences due to CO2 exposure, and snap frozen. For experiments analyzing gene expression in dissected brain tissues, flies were mated as above and 24 hours after mating were lightly anaesthetized individually on ice. Brain tissue was dissected in ice-cold RNase-free 1X phosphate buffered saline (PBS). The brain tissue was rinsed in 1X PBS to remove non-brain tissue and immediately placed in ice-cold Trizol (Invitrogen) until RNA extraction.

value: Canton S

value: Female

tag: stage

value: Adult

value: Brain

tag: hours post-mating

value: 24 hours

tag: treatment

value: Virgin

source_name: Adult Mated Female

value: Mated


title: Ripening R_2

source_name: Corvina berry, ripening

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 112 days after fruit set

value: ripening


title: 24 hours post mating - female brain - replicate 3

description: Biological replicate 3 of 4: 24 hours post-mating female brains to age matched virgin female brains


title: 24 hours post mating - female brain - replicate 2

description: Biological replicate 2 of 4: 24 hours post-mating female brains to age matched virgin female brains


title: Ripening R_1


title: 72 hours post mating - female head - replicate 4

description: Biological replicate 4 of 4: 72 hours post-mating female heads to age matched virgin female heads

value: Head

value: 72 hours


title: 24 hours post mating - female brain - replicate 1

description: Biological replicate 1 of 4: 24 hours post-mating female brains to age matched virgin female brains


title: Pre-ripening PR_3

source_name: Corvina berry, pre-ripening

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 98 days after fruit set

value: berry

value: pre-ripening


title: Veraison V_3

source_name: Corvina berry, veraison

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 71 days after fruit set

value: veraison

value: Corvina


title: Veraison V_1


title: 72 hours post mating - female head - replicate 3

description: Biological replicate 3 of 4: 72 hours post-mating female heads to age matched virgin female heads


title: Pre-ripening PR_2


title: 72 hours post mating - female head - replicate 2

description: Biological replicate 2 of 4: 72 hours post-mating female heads to age matched virgin female heads


title: Pre-ripening PR_1


title: progressive sural nerve, patient 16

source_name: progressive DN sural nerve 52 weeks

value: sural nerve


title: Veraison V_2


title: Ripening R_3


title: 48 hours post mating - female head - replicate 4

description: Biological replicate 4 of 4: 48 hours post-mating female heads to age matched virgin female heads

value: 48 hours


title: 72 hours post mating - female head - replicate 1

description: Biological replicate 1 of 4: 72 hours post-mating female heads to age matched virgin female heads


title: Pre-veraison PV_2

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were scale-normalized.

source_name: Corvina berry, pre-veraison

extract_protocol: Total RNA was extracted according to Rezaian and Krake (doi:10.1016/S0166-0934(00)00211-1)

treatment_protocol: A pool of deseeded berries was obtained from grapevine clusters harvested at 59 days after fruit set

value: pre-veraison


title: Pre-veraison PV_3


title: 48 hours post mating - female head - replicate 2

description: Biological replicate 2 of 4: 48 hours post-mating female heads to age matched virgin female heads

value: Canton S


title: Muscle_TotalRNA_CN2535

city: Liege

first: Florian

last: Caiment

address: 1 avenue de l'hopital

department: GIGA

country: Belgium

institute: University of Liege

description: Labelling, hybridization, washing, scanning and normalisation were performed by Exiqon (Denmark).

hyb_protocol: Using Tecan hybridization stations, the hybridization and washing steps are fully automated. The arrays were incubated at 56°C for 16 h.

scan_protocol: Arrays were scanned using an Agilent G2505B Microarray Scanner System. The scanning is normally performed with 10 ìm. The sensitivity should be adjusted to 100% PMT. To avoid ozone bleaching, we scanned the microarrays in an ozone-free environment (less than 2 ppb ozone).

data_processing: Starting from raw data, the normalisation was made by background subtraction and normalisation with a global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm (using ImaGene). This within-slide normalisation was performed to minimize differences between the colors in an intensity-dependent manner.

organism: Ovis aries

source_name: Longissimus dorsi, CN

label_protocol: miRCURY™ LNA Array Power labeling kit.

growth_protocol: Frozen tissue in liquid nitrogen.

extract_protocol: Trizol (Invitrogen) standard extraction protocol.

value: 8 weeks

tag: genotype

value: maternal heterozygous callipyge (Cmat/+pat)

value: Longissimus dorsi muscle

tag: identfier

source_name: Longissimus dorsi, reference

value: NN, CN, NC, CC

tag: sample type

value: pool of the 8 samples used in this microarray experiment


title: Pre-veraison PV_1


title: Muscle_TotalRNA_NC2538

source_name: Longissimus dorsi, NC

value: paternal heterozygous callipyge (+mat/Cpat)


title: 48 hours post mating - female head - replicate 3

description: Biological replicate 3 of 4: 48 hours post-mating female heads to age matched virgin female heads

value: Female

value: Adult

value: Virgin

value: Mated


title: Muscle_TotalRNA_CC2523

source_name: Longissimus dorsi, CC

value: homozygous callipyge (Cmat/Cpat)


title: Muscle_TotalRNA_CC2521


title: 48 hours post mating - female head - replicate 1

description: Biological replicate 1 of 4: 48 hours post-mating female heads to age matched virgin female heads

value: Head


title: 24 hours post mating - female head - replicate 2

description: Biological replicate 2 of 4: 24 hours post-mating female heads to age matched virgin female heads

value: 24 hours


title: 24 hours post mating - female head - replicate 4

description: Biological replicate 4 of 4: 24 hours post-mating female heads to age matched virgin female heads


title: Muscle_TotalRNA_CN2566


title: Muscle_TotalRNA_NC2519


title: 24 hours post mating - female head - replicate 3

description: Biological replicate 3 of 4: 24 hours post-mating female heads to age matched virgin female heads


title: 24 hours post mating - female head - replicate 1

description: Biological replicate 1 of 4: 24 hours post-mating female heads to age matched virgin female heads


title: 0-2 hours post mating - female head - replicate 4

description: Biological replicate 4 of 4: 0-2 hours post-mating female heads to age matched virgin female heads

value: 0-2 hours


title: 0-2 hours post mating - female head - replicate 3

description: Biological replicate 3 of 4: 0-2 hours post-mating female heads to age matched virgin female heads


title: 0-2 hours post mating - female head - replicate 2

description: Biological replicate 2 of 4: 0-2 hours post-mating female heads to age matched virgin female heads


title: Muscle_TotalRNA_NN2530

source_name: Longissimus dorsi, NN

value: wild type (+mat/+pat)


title: GM17108 (510S)

description: Genomic DNA extracted from lymphoblastoid cell line was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

source_name: lymphoblastoid cell line GM17108

tag: ethnic group

value: AA African-American

tag: cell line (coriell id)

tag: wei id

value: EBV-transformed lymphoblastoid cells


title: Sample 31 contralateral white matter

city: Barcelona

first: Sophie

last: Domingues

address: Pg Vall d’Hebron 119-129

department: Department of Neurology

country: Spain

institute: Institut de Recerca Hospital Vall d’Hebron

description: Gene expression data from human brain samples 5h after intracerebral hemorrhage.

hyb_protocol: cRNA was hybridizated in Human Genome U133 Plus 2.0 Affymetrix microarrays.

scan_protocol: Microarrays were scanned in Affymetrix Genechip Scanner 3000 7G.

data_processing: Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized. Log2 RMA signal estimates were obtained using R-2.8 and Bioconductor 2.3 Packages.

source_name: Human brain sample of intracerebral hemorrhage contralateral white matter

label_protocol:
Samples were amplified using Two Cycle cDNA Synthesis Affymetrix kit.
Samples were chemically fragmented and biotinylated using the IVT Labelling Kit (Affymetrix)

growth_protocol: Samples from perihematomal areas (PH), contralateral grey matter (CG) and contralateral white matter (CW) were obtained within the first 5 h after death of human individuals.

extract_protocol: Total RNA was extracted from fresh peripheral blood mononuclear cells using an RNeasy kit (Quiagen, Santa Clarita, USA)

treatment_protocol: Samples were snap frozen in liquid nitrogen and stored at -80ºC until RNA isolation.

tag: tissue

value: brain

value: male


title: Sample 31 perihematomal area

source_name: Human brain sample of intracerebral hemorrhage perihematomal area

tag: gender


title: Sample 28 contralateral grey matter

source_name: Human brain sample of intracerebral hemorrhage contralateral grey matter

tag: age

value: female


title: Muscle_TotalRNA_NN2565

value: 8 weeks

value: Longissimus dorsi muscle

value: NN, CN, NC, CC


title: Sample 27 contralateral white matter


title: Sample 30 perihematomal area


title: PPARg KO macrophages rep 1

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix (Santa Clara, CA) arrays according to the manufacturer’s instructions.

scan_protocol: Standard protocol from Affymetrix

data_processing: Data were analyzed with the MICROARRAY suite (Affymetrix), GENESPRING (Silicon Genetics), and in-house software developed by Sasik et al. 2002 (Bioinformatics).

source_name: Thioglycollate-elicited PPARg KO macrophages

label_protocol: cRNA was generated from 10 ug of total RNAby using the SuperScript kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

growth_protocol: Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3 days after peritoneal injection of 2.5 ml of 3% thioglycollate (Difco). Cells were plated in RPMI and 10% FBS and washed after 5 h, the medium was removed, and cells were fed with fresh medium containing 0.5% FBS.

extract_protocol: Cells were lysed with TRIzol (Invitrogen),and total RNA was purified by using RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: After plating, PPAR WT and PPAR KO macrophages were incubated for 24hrs in RPMI medium supplemented with 0,5% FBS and antibiotics

tag: strain

value: mixed background of 129/SV and C57BL/6

tag: cell type

value: macrophage

tag: genotype/variation

value: PPARg KO


title: PPARg KO macrophages rep 2


title: Sample 31 contralateral grey matter


title: Sample 28 perihematomal area


title: PPARg WT macrophages rep 2

source_name: Thioglycollate-elicited PPARg WT macrophages

value: PPARg WT


title: PPARg WT macrophages rep 1


title: Sample 30 contralateral grey matter


title: Sample 28 contralateral white matter


title: Sample 27 perihematomal area


title: Sample 27 contralateral grey matter


title: Rice primordia Replicate 1 (Fixed)

status: Public on Sep 23 2010

city: New Haven

first: Timothy

last: Nelson

state: CT

department: MCDB

institute: Yale University

description: Biological replicate 1 of 4.

hyb_protocol: Hybridization were carried out using a modified protocol as described previously (Jiao et al., Plant Cell 17:3239).

scan_protocol: Scanned on a GenePix 4200A Images were quantified using GenePix 5.0

data_processing: GenePix 5.0 version of the software was used for data analysis. LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal. The ratio of test/reference is provided in the data table below. Details are available in (Jiao et al., Nature Genetics 41:258-263).

organism: Oryza sativa

source_name: Amplified RNA from rice suspension cultured cells (red).

label_protocol: A two-round T7 polymerase-based linear amplification systems, RiboAmp (Arcturus Engineering), was used according to the manufacturer to amplify and label RNA. For details, see http://bioinformatics.med.yale.edu/riceatlas/protocols.jspx. These samples were processed a bit differently in that after amplification of the RNA, the RNA was labelled using a TUrbo labelling kit from Arcturus(KIT0609 and kit0610).

extract_protocol: Arcturus Picopure RNA isolation Kit

value: Nipponbare

value: Undifferentiated rice suspension cultured cells

source_name: Amplified RNA from rice Embryo - Coleoptile - Dry Seed (green)

value: Rice primordia

value: embryo Coleoptile from dry seeds


title: Spikelet primordia Replicate 2 (Fixed)

description: Biological replicate 1 of 4.

value: Spikelet primordia


title: NA12155_vs_NA19240_rep1

city: Cambridge

first: Peter

last: Sudmant

state: MA

address: 77 Massachusetts Ave

institute: MIT

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

source_name: DNA from Coriell NA12155

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers (for test and control samples, respectively) per Nimblegen protocol (http://www.nimblegen.com/products/lit/lit.html) but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: DNA was extracted from lymphoblastoid cell lines by Coriell cell repositories.

tag: cell line

value: lymphoblastoid cells

source_name: DNA from Coriell NA19240

value: reference


title: Anther Replicate 4 (Fixed)

description: Biological replicate 1 of 4.

tag: cultivar

value: Anther


title: Spikelet primordia Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Carpel Replicate 2 (Fixed)

description: Biological replicate 1 of 4.

value: Carpel


title: Carpel Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Carpel Replicate 3 (Fixed)

description: Biological replicate 1 of 4.


title: 0-2 hours post mating - female head - replicate 1

description: Biological replicate 1 of 4: 0-2 hours post-mating female heads to age matched virgin female heads

source_name: Adult Virgin Female

value: Canton S

value: Female

tag: stage

value: Adult

value: Head

value: 0-2 hours

value: Virgin

source_name: Adult Mated Female

value: Mated


title: Anthers from open flowers, pollen filled Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Spikelet primordia Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: Rice primordia Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: Rice primordia Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: NA10847_vs_NA19240_rep1

source_name: DNA from Coriell NA10847

value: female


title: Carpel Replicate 4 (Fixed)

description: Biological replicate 1 of 4.

value: Nipponbare


title: Anthers from open flowers, pollen filled Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Undifferentiated rice suspension cultured cells


title: Rice primordia Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Rice primordia


title: Anthers from open flowers, pollen filled Replicate 4 (Fixed)

description: Biological replicate 1 of 4.

value: embryo Coleoptile from dry seeds


title: Spikelet primordia Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Spikelet primordia


title: Anther Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Anther Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: NA18956_vs_NA19240_rep1

source_name: DNA from Coriell NA18956

value: lymphoblastoid cells


title: NA18516_vs_NA19240_rep1

source_name: DNA from Coriell NA18516

value: male

value: reference


title: NA12892_vs_NA19240_rep1

source_name: DNA from Coriell NA12892


title: Anthers from open flowers, empty anthers Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from open flowers, empty anthers Replicate 3 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from closed flowers, after fertilization Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from closed flowers, after fertilization Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Anther Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Anther


title: Anthers from open flowers, empty anthers Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from open flowers, pollen filled Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from open flowers, empty anthers Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Anthers from closed flowers, after fertilization Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Palea vascular bundle Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Palea vascular bundle


title: Palea vascular bundle Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: PL-5_3

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA was computed in R/Bioconductor (http://www.R-project.org)

source_name: SGHPL-5 cell line

label_protocol: Affymetrix

growth_protocol: Total RNAs of three consecutive cell passages of each trophoblast cell line were isolated and 5µg of total RNA were then used for preparation of cRNA, hybridization to human U133A GeneChips (Affymetrix).

extract_protocol: Trizol followed by RNeasy Mini kit (Qiagen)

treatment_protocol: no treatment

value: SGHPL-5 cell line


title: Anthers from closed flowers, after fertilization Replicate 3 (Fixed)

description: Biological replicate 1 of 4.


title: Palea vascular bundle Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Palea vascular bundle Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma vascular bundle Replicate 2 (Fixed)

description: Biological replicate 1 of 4.

value: Lemma vascular bundle


title: PL-5_2


title: Palea epidermis Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Palea epidermis


title: Palea epidermis Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: Palea epidermis Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma epidermis Replicate 4 (Fixed)

description: Biological replicate 1 of 4.

value: Lemma epidermis


title: Lemma epidermis Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma vascular bundle Replicate 3 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma epidermis Replicate 3 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma vascular bundle Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: PL-5_1


title: Lemma epidermis Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Palea epidermis Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: Lemma vascular bundle Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: JEG-3_4

source_name: JEG3 choriocarcinoma cell line

value: JEG3 choriocarcinoma cell line


title: HTR-8_2

source_name: HTR-8/SVneo cell line

value: HTR-8/SVneo cell line


title: HTR-8_3


title: Silica cells from Flag leaf tip Replicate 4 (Fixed)

description: Biological replicate 1 of 4.

value: Silica cells from Flag leaf tip


title: HTR-8_1


title: JEG-3_2


title: JEG-3_1


title: JEG-3_3


title: Silica cells from Flag leaf tip Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Nipponbare


title: IRAK2 deficient macrophages, R848 2h

city: Cleveland

first: Youzhong

last: Wan

state: OH

address: 9500 Euclid Avenue, NE20

department: Immunology

institute: Cleveland Clinic Foundation

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Expression data normalization and differential expression analysis was handled through the Illumina BeadStudio Gene Expresson module V3.2.  The data were first normalized by using the quantile normalization algorithm provided by Illumina Beadstudio and then the differential expression analyses were performed by using Illumina’s custom model.

source_name: bone marrow derived macrophages

label_protocol: A single-round of in vitro transcription (IVT) amplification was carried out using the Illumina RNA Amplification Kit, manufactured by Ambion, Inc., to amplify mRNA and thus to obtain ample amounts of biotinylated cRNA to perform the whole human genome gene expression assay using the mouseRef-8 v2 expression beadchips micro-array (Illumina, San Diego, CA).

growth_protocol: Bone marrow cells were obtained from tibias and femurs by flushing with DMEM, and cultured in L929 cells-conditioned medium for 5 days for differentiation.

extract_protocol: total RNA was isolated from the treated or untreated bone marrow derived macrophages with TRIZOL following the protocol from manufacturer

treatment_protocol: Bone marrow dericed macrophages were treated with CpG B (1ug/ml) or R848 (1ug/ml) for 2 hours

value: female

value: IRAK2 knockout

tag: agent


title: Silica cells from Flag leaf base Replicate 3 (Fixed)

description: Biological replicate 1 of 4.

value: Undifferentiated rice suspension cultured cells

value: Silica cells from Flag leaf base

value: embryo Coleoptile from dry seeds


title: ACH-3P_1

source_name: ACH3P cell line

value: ACH3P cell line


title: IRAK2 deficient macrophages, CpG B 2h

value: CpG B


title: ACH-3P_3


title: wild type macrophages, R848 2h

value: wild type


title: ACH-3P_2


title: Silica cells from Flag leaf tip Replicate 1 (Fixed)

description: Biological replicate 1 of 4.


title: ach4_rco1_2

city: Kansas City

first: Samantha

middle: Gail

last: Pattenden

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: Biological repeat 2 of 3, anti-acetylated histone H4 antibody (Upstate #06-866)

hyb_protocol: Input was labeled with Cy3 dye, while immunoprecipitated samples were labeled with Cy5 dye.  Samples were combined 1:1 based on quantity (ng).  Before hybridization, labeled aRNA samples were fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.  The hybridization mixture was set up for the Agilent yeast 4x44K platform (Agilent Technologies) according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo.

scan_protocol: Scanning was performed on the Agilent DNA Microarray Scanner (Agilent Technologies, Model#G2505B)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used to quantify images. Data was read into R and normalized within arrays using median normalization and between arrays using Aquantile normalization from the limma package (Smyth, 2005)

organism: Saccharomyces cerevisiae

source_name: AcH4 ChIP DNA, rco1 deletion cells

label_protocol: For the labeling reactions, 4-6 ug amino allyl-incorporated aRNA in a 5 uL volume of 0.1M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) monofunctional NHS-ester Cy3 or Cy5 dye in DMSO (Sigma) and incubated at 22°C for 2 hours.  Reactions were quenched with 5 uL 4M hydroxylamine at 22°C for 15 minutes, cleaned with an RNeasy MinElute Cleanup Kit (Qiagen), and the efficiency of dye incorporation measured using the Nanodrop 2000 spectrophotometer (Thermo Scientific).  Samples with a label incorporation efficiency of 2-4% were used for micorarray hybridization.

growth_protocol: All yeast strains were grown in 200 mL YPD cultures to OD600=1.0-1.2

extract_protocol: ChIP and input samples were amplified using double T7 Linear Amplification

treatment_protocol: Chromatin immunoprecipitation (ChIP) assays were performed as previously described (Li et al., 2007 Genes & development 21, 1422-1430), except 50 uL of protein G Dynabeads (Invitrogen) was used for the immunoprecipitation.

tag: yeast strain

tag: growth media

value: YPD

tag: antibody

value: anti-acetylated histone H4 antibody

tag: type

value: ChIP

value: input


title: IRAK2 deficient macrophages, untreated

value: untreated


title: Silica cells from Flag leaf base Replicate 2 (Fixed)

description: Biological replicate 1 of 4.


title: wild type macrophages, CpG B 2h


title: Silica cells from Flag leaf base Replicate 4 (Fixed)

description: Biological replicate 1 of 4.


title: ach4_rsc2_2

source_name: AcH4 ChIP DNA, rsc2 deletion cells


title: ach4_rco1_1

description: Biological repeat 1 of 3, anti-acetylated histone H4 antibody (Upstate #06-866)


title: Silica cells from Flag leaf tip Replicate 2 (Fixed)

description: Biological replicate 1 of 4.

source_name: Amplified RNA from rice suspension cultured cells (red).


title: ach4_rsc2_1


title: ach4_rco1_3

description: Biological repeat 3 of 3, anti-acetylated histone H4 antibody (Upstate #06-866)


title: ach4_rsc2_3


city: Berlin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

institute: Max-Delbrueck Center for Molecular Medicine

description: Gene expression data from a freshly isolated subclone of the mouse inner medullary collecting duct cell line (mIMCD-3)

hyb_protocol: Fifteen micrograms of fragmented target cRNA per chip was used in duplicate hybridizations according to standard Affymetrix protocols (Affymetrix Genechip Fluidics Workstation).

scan_protocol: Hybridized chips were read on an Affymetrix Scanner Type M10.

data_processing: Robust multichip analysis (RMA) was carried out using the Affymetrix microarray *.cel files. The RMA data were generated using RMA Express.

source_name: mIMCD-3 cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: A subclone of mIMCD-3 cells was grown to confluency in Dulbecco's Modified Eagle Medium (DMEM). The detailed protocol for microdissection of E12.5 embryonic kidneys was described previously (Schmidt-Ott, K. M., Yang, J., Chen, X., Wang, H., Paragas, N., Mori, K., Li, J. Y., Lu, B., Costantini, F., Schiffer, M. et al. (2005). Novel regulators of kidney development from the tips of the ureteric bud. J Am Soc Nephrol 16, 1993-2002)

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, Valencia, CA) with on-column DNase digestion according to the manufacturer’s instructions.

tag: developmental stage


title: mouse E12.5 ureteric bud tip_biological replicate 1

description: Gene expression data from mouse E12.5 microdissected ureteric bud tip

source_name: microdissected ureteric bud tips

value: microdissected ureteric bud tips


title: wild type macrophages, untreated


title: ach4_rsc1_3

source_name: AcH4 ChIP DNA, rsc1 deletion cells


title: mouse E12.5 ureteric bud tip_biological replicate 2


title: mouse E12.5 ureteric bud stalk_biological replicate 2

description: Gene expression data from mouse E12.5 microdissected ureteric bud stalk

source_name: microdissected ureteric bud stalks

value: microdissected ureteric bud stalks


title: mouse E12.5 ureteric bud stalk_biological replicate 1


title: ach4_rsc1_2


title: ach4_rsc1_1


title: ach4_wt_3

source_name: AcH4 ChIP DNA, wild type cells


title: ach4_wt_2


title: CovR_Red_K6

status: Public on Sep 22 2010

city: Cincinnati

first: Rita

middle: G

last: Kansal

address: 3235 Eden Avenue

institute: University Of Cincinnati

description: RNA from bacteria grown in vitro to early-stationary phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

hyb_protocol: Dendrimer-labeled cDNA samples from different pairs of isolates were combined and hybridised to the microarray slide for 16 h. Slides were washed to remove unbound cDNA and labeled with dendrimer-targeted Alexa Fluor 546 and Alexa Fluor 647 dyes (Genisphere) for 5 h. Following a final wash to remove excess fluorescent dye, slides were coated in DyeSaver2 (Genisphere) to preserve the fluorescent signal, and subsequently polished with toluene/acetone (3:1) to minimize background fluorescence immediately prior to scanning .

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner (Axon Instruments, Inc.)

data_processing: All transcriptional and statistical analyses were undertaken in silico using GeneSpring GX 10 (Agilent Technologies). Background-subtracted data were filtered and raw fluoresecene values below 50 were discareded as fold-changes at this level may lead to misinterpretation. Data were normalized to the median and presented in log scale for analysis based on fold-change.

organism: Streptococcus pyogenes

source_name: CovR deleted 5448

label_protocol: Purified RNA was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit according to the manufaturer.

growth_protocol: Overnight  cultures were sub-inoculated 1:10 into fresh pre-warmed Todd-Hewitt broth supplemented with yeast extract and grown to early-stationary phase

extract_protocol: early-stationary phase in vitro-grown bacteria were harvested by centrifugation and lysed by mechanical disruption. Bacterial RNA for microarray was extracted using the RNeasy Mini Kit (Qiagen) and treated with TURBO DNA-free DNase (Ambion) to remove contaminating DNA.

tag: growth phase and conditions

value: Early-Stationary phase in vitro


title: WT_Green_K3

label: Alexa Fluor 546


title: CovR_Green_K4


title: AP_Green_K5

source_name: Animal Passaged strain of WT 5448


title: CovS_Red_K5

source_name: CovS deleted 5448


title: AP_Green_K6


title: CovS_Red_K4


title: CovS_Red_K26


title: mouse E12.5 metanephric mesenchyme_biological replicate 1

description: Gene expression data from mouse E12.5 microdissected metanephric mesenchyme

source_name: microdissected metanephric mesenchyme

value: microdissected metanephric mesenchyme


title: CovR_Green_K26


title: mouse E12.5 metanephric mesenchyme_biological replicate 2


title: Silica cells from Flag leaf base Replicate 1 (Fixed)

description: Biological replicate 1 of 4.

value: Nipponbare

source_name: Amplified RNA from rice Embryo - Coleoptile - Dry Seed (green)


title: SRC111976 - CGH

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

description: Normal sample 1

hyb_protocol: Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol

scan_protocol: Agilent's user manual (Agilent scanner)

data_processing: Tumor samples were assayed on Agilent Human Genome CGH 244A Microarrays. Human male genomic DNA (Promega P/N G1471) was used as reference.  Individual log2 ratios of background-subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5.

source_name: Normal prostate

label_protocol: Agilent's Genomic DNA Labeling Kit Plus

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

tag: sampleID

tag: organ

value: Prostate

tag: subtype

value: Adjacent normal prostate

source_name: Diploid reference

tag: reference

value: Male genomic DNA (Promega P/N G1471)


title: SRC113063 - CGH

description: Normal sample 3


title: ach4_wt_1


title: Purified naïve CD8+ alpha/beta T cells

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol with an Affymetrix 7G/4C scanner

data_processing: .cel files were analyzed using Affymetrix Expression Console 1.0 using default settings for MAS5.0 signal extraction

source_name: Lymph nodes of C57BL/6 mice

label_protocol: Standard One-Cycle Affymetrix labeling

extract_protocol: Qiagen RNeasy

value: alpha/beta T cells purified by negative selection

tag: tissue

value: lymph nodes

tag: strain


title: WT_Green_K25


title: CovR_Red_K24


title: AP_Red_K25


title: Purified naïve CD44- gamma/delta T cells

tag: cell type

value: gamma/delta T cells purified by negative selection


title: CovR_Red_K3


title: SRC113061 - CGH

description: Tumor sample 3

source_name: Prostate adenocarcinoma

value: Prostate adenocarcinoma


title: AP_Green_K24


title: CovS_Red_K23


title: AP_Green_K23


title: WT_Green_K21


title: CovR_red_K21


title: CovS_Green_K2


title: WT_Red_K2


title: CovS_Green_K20


title: SRC112038 - CGH

description: Tumor sample 2


title: SRC111995 - CGH

description: Tumor sample 1


title: WT_Green_K19


title: CovR_Green_K16


title: CovR_Green_K22


title: CovR_Red_K18


title: AP_Red_K19


title: CovS_Red_K16


title: AP_Green_K18


title: AP_Green_K17


title: CovS_Red_K17


title: WT_Red_K20


title: WT_Green_K15


title: CovR_red_K15


title: WT_Red_K14


title: Chimp 1618 - HEV infection SAR55 - week 8 - mAdbID:109729

city: Bethesda

first: Claro

last: Yu

email: clyu@niaid.nih.gov, boond@mail.nih.gov

state: MD

address: 50 South Drive

department: Hepatitis Viruses Section

institute: NIAID

description: mAdb experiment ID: :109729

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 15 micrograms of cRNA was hybridized for 16 hours at 45C on arrays from Affymetrix. Arrays were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner with a 7G upgrade.

data_processing:
Calculation Method: The Genomatix ChipInspector software, which uses CEL files as input, was used to map probes to transcripts in the human (version 37) and chimpanzee (version 2) genome sequences in ElDorado (Genomatix proprietary genome annotation database), in order to remove probes without 100 % sequence identity, to perform a linear total intensity normalization of probes of each chip (.cel file).

Normalized probe set level data points not available from the Genomatix software.
Processed data files that are available, as listed in Description field, are linked as supplementary files on Series GSE22160 record.

organism: Pan troglodytes

source_name: HEV-infection with SAR55 - week 8

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from mRNA.

extract_protocol:
Trizol Extraction
Other: Frozen liver needle biopsies embedded in OCT were homogenized with a PRO 200 Homogenizer with Multi-Gen 7mm 316 Stainless Generators (Pro Scientific, Oxford, CT). Total RNA was isolated with TRIZOL Reagent (Invitrogen, Carlsbad, CA) and purified with an RNEasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol:
Treatment time: week 8 post-inoculation
In-vivo treatment: A chimpanzee was inoculated intravenously with the hepatitis E virus: 0.5 ml of the HEV SAR55 strain (genotype 1) at approximately 10^6 ID.

tag: chimp

tag: infection

value: HEV

tag: time

value: week 8

tag: madbid

value: liver

tag: disease state

value: Hepatitis E


title: CovS_Red_K22


title: WT_Green_K1


title: AP_Red_K13


title: CovS_Green_K14


title: AP_Red_K1


title: WT_Green_K13


title: SRC112036 - CGH

description: Normal sample 2