title: GD 14, Replicate 1

status: Public on Dec 01 2010

type: mixed

city: louisville

first: Guy

last: Brock

state: KY

address: 485 E. Gray St

department: Bioinformatics and Biostatistics

country: USA

institute: University of Louisville

description:
Biological replicate 1 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 14.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt

hyb_protocol: Samples were hybridized to miRXplore™ Microarrays (Miltenyi Biotec GmbH) using the a-Hyb™ Hybridization Station (Miltenyi Biotec GmbH).

scan_protocol: Fluorescence signals of the hybridized miRXplore™ Microarrays were detected using a laser scanner from Agilent Technologies.

data_processing: Mean and median signal and local background intensities for the Hy3 and Hy5 channels were obtained for each spot on each of the nine microarray images using the ImaGene software (BioDiscovery, Inc., El Segundo, CA).  Low quality spots were identified and given relative weights which were subsequently used in data analysis and modeling of miRNA expression values.  A total of 5,404 spots remained after discarding empty spots, dummy spots, extreme outliers, and those with missing background intensities. The pre-processing procedure consisted of three steps. First, all spots for which the mean foreground intensity was smaller than 1.1 times the mean background intensity in three or more arrays were discarded, unless all three samples came from the same day.  Several within-array normalization procedures on the remaining 864 spots were evaluated. Based on visual inspection of the mean log2 expression values versus the log2 expression ratio for each spot (“MA” plots), it was decided that “no within-array” normalization gave the best results and the 72 control spots were subsequently removed. In the second step, a simple background correction was performed by subtracting background from the foreground intensities.  Log2 ratios of Hy5 (red, experimental) versus Hy3 (green, control) expression were calculated for each spot. Seven spots (in all nine arrays) exhibited negative intensities after the background procedure. These were treated as missing and then imputed using the K-nearest neighbor imputation scheme.  Lastly, the between-array normalization using the quantile method was performed to align the distributions of the log-ratios on each chip.  After all preprocessing steps, the total number of miRNA left was 198.

molecule: total RNA

organism: Mus musculus

source_name: First branchial arch–derived tissue (including primary and secondary palatal tissue)

label_protocol: RNA samples (1 µg) isolated from mouse embryonic orofacial tissues (GD-12 – GD-14) as well as the miRXplore Universal Reference (control) were fluorescently labeled with Hy5 (red) or Hy3 (green), respectively.

growth_protocol: Mature male and female ICR mice (Harlan, Indianapolis, IN), maintained in an American Association for Accreditation of Laboratory Animal Care (AAALAC) approved facility, on a 12-hour light/dark cycle and provided ad libitum food and water, were mated overnight.

extract_protocol: Total RNA (including miRNAs) was isolated using the miRVANA Kit from Ambion following manufacturer's instructions

treatment_protocol: The presence of a vaginal plug the following morning was considered as evidence of mating, and the time designated as gestational day 0 (GD 0). On GD-12, GD-13, and GD-14, which represent the critical period of palate development in the mouse, female mice were euthanized by asphyxiation and embryos were dissected from uteri in sterile calcium/magnesium-free PBS.  Extraembryonic membranes were removed from the embryos, and first branchial arch–derived tissue, including primary and secondary palatal tissue, was excised.  Excised tissue was minced and stored at minus 80°C in PrepProtect™ Stabilization Buffer (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) for subsequent shipment to Miltenyi Biotec for miRNA expression analysis. For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH).

tag: developmental stage

value: Embryo

tag: strain

value: ICR

tag: tissue

value: first branchial arch–derived tissue (including palate)

tag: age

value: GD 14

molecule: other

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

source_name: miRXplore Universal Reference

extract_protocol: miRXplore Universal Reference purchased from Miltenyi Biotec GmbH. The reference comprises all human, mouse, rat, and virus microRNAs according to the miRBase Sequence Database version 9.2 released by the Sanger Institute.

tag: control

value: defined pool of synthetic microRNAs


title: GD 12, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 12.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt

value: GD 12


title: GD 12, Replicate 1

description:
Biological replicate 1 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 12.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 12, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 12.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 14, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 14.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 13, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 13.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt

value: GD 13


title: GD 9.5, Replicate 1

description:
Biological replicate 1 of 3.  Mouse embryonic developing neural tubes, GD 9.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt

data_processing: Mean and median signal and local background intensities for the Hy3 and Hy5 channels were obtained for each spot on each of the nine microarray images using the ImaGene software (BioDiscovery, Inc., El Segundo, CA).  Low quality spots were identified and given relative weights which were subsequently used in data analysis and modeling of miRNA expression values.  A total of 5,620 spots remained after discarding empty spots, dummy spots, extreme outliers, and those with missing background intensities. The pre-processing procedure consisted of three steps. First, all spots for which the mean foreground intensity was smaller than 1.1 times the mean background intensity in three or more arrays were discarded, unless all three samples came from the same day. Several within-array normalization procedures on the remaining 360 spots were evaluated. Based on visual inspection of the mean log2 expression values versus the log2 expression ratio for each spot (“MA” plots), it was decided that “no within-array” normalization gave the best results and the 72 control spots were subsequently removed. In the second step, a simple background correction was performed by subtracting background from the foreground intensities.  Log2 ratios of Hy5 (red, experimental) versus Hy3 (green, control) expression were calculated for each spot. None of the spots (in all nine arrays) exhibited negative intensities after the background procedure. Lastly, the between-array normalization using the quantile method was performed to align the distributions of the log-ratios on each chip.  After all preprocessing steps, the total number of miRNA left was 72.

label_protocol: RNA samples (1 µg) isolated from mouse embryonic orofacial tissues (GD-8.5 – GD-9.5) as well as the miRXplore Universal Reference (control) were fluorescently labeled with Hy5 (red) or Hy3 (green), respectively.

treatment_protocol: The presence of a vaginal plug the following morning was considered as evidence of mating, and the time designated as gestational day 0 (GD 0). On GD-8.5, GD-9.0, and GD-9.5, which represent the critical period of neural tube  development in the mouse, female mice were euthanized by asphyxiation and embryos were dissected from uteri in sterile calcium/magnesium-free PBS.  Developing neural tubes from the most rostral aspect of the forebrain to the caudal aspect of the hindbrain (above the otic vesicle) were excised.  Excised tissue was minced and stored at minus 80°C in PrepProtect™ Stabilization Buffer (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) for subsequent shipment to Miltenyi Biotec for miRNA expression analysis. For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH).

value: neural tube


title: GD 13, Replicate 1

description:
Biological replicate 1 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 13.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 14, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 14.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 13, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic First branchial arch–derived tissue, GD 13.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 9.0, Replicate 1

description:
Biological replicate 1 of 3.  Mouse embryonic developing neural tubes, GD 9.0.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt

source_name: Developing neural tubes from the most rostral aspect of the forebrain to the caudal aspect of the hindbrain


title: GD 9.5, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic developing neural tubes, GD 9.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 9.5, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic developing neural tubes, GD 9.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 9.0, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic developing neural tubes, GD 9.0.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 9.0, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic developing neural tubes, GD 9.0.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 8.5, Replicate 3

description:
Biological replicate 3 of 3.  Mouse embryonic developing neural tubes, GD 8.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: GD 8.5, Replicate 1

description:
Biological replicate 1 of 3.  Mouse embryonic developing neural tubes, GD 8.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: self-to-self experiment

type: RNA

city: Nanjing

first: miao

last: weiguo

address: Weigang

country: China

institute: Nanjing Agricultural Uiversity

description: self-to-self experiment

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

organism: Gossypium hirsutum

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP,ambion) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction.  We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: All plants were cultured in a sterile incubator at 28˚C

extract_protocol: Total RNA samples were extracted from 1 g of cotton true leaves and roots from Z35 and T-34 using the Plant Total RNA Extract Kit (Autolab Biotech, Beijing, China) according to the manufacturer’s instructions.

treatment_protocol: Before microarray analysis of transgenic T-34, homozygous plants were further confirmed by kanamycin-resistance screening, PCR analysis, and Southern and western blot analyses.

tag: gentype/variation

tag: tissue type

value: leaf

tag: genotype/variation


title: GD 8.5, Replicate 2

description:
Biological replicate 2 of 3.  Mouse embryonic developing neural tubes, GD 8.5.
ch1 raw data file: *_1b.txt
ch2 raw data file: *_2b.txt


title: 4 week skeletal muscle, untreated, biological replicate 2

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

description: Gene expression data from 4 week old mice muscle, control.

hyb_protocol: Hybridization was done according to the manufacturer's (Affymetrix Inc., Santa Clara, CA, USA) instructions

scan_protocol: Scanning was done according to the manufacturer's (Affymetrix Inc., Santa Clara, CA, USA) instructions

data_processing: The data were analyzed using R and Bioconductor using justRMA with default settings

label: biotin

source_name: 4 week old C57BL/6 mice, control

label_protocol: RNA labelling was done according to the manufacturer's (Affymetrix Inc., Santa Clara, CA, USA) instructions

extract_protocol: RNA was extracted from muscle and liver tissue using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer

treatment_protocol: Pregnant dams recieved either water or 1% taurine in water from day 1 of pregnancy. Offspring was killed and tissue taken out at 4 weeks.

value: quadriceps muscle

tag: genotype


title: 4 week skeletal muscle, in utero taurine supplementation, biological replicate 3

description: Gene expression data from 4 week old mice muscle, gestational taurine supplementation

source_name: 4 week old C57BL/6 mice, in utero taurine supplemented


title: 4 week liver, in utero taurine supplementation, biological replicate 3

description: Gene expression data from 4 week old mice liver, gestational taurine supplementation

value: liver


title: 4 week skeletal muscle, untreated, biological replicate 3


title: 4 week liver, untreated, biological replicate 3

description: Gene expression data from 4 week old mice liver, control.


title: 4 week skeletal muscle, in utero taurine supplementation, biological replicate 1


title: 4 week skeletal muscle, untreated, biological replicate 1


title: 4 week skeletal muscle, in utero taurine supplementation, biological replicate 2


title: 4 week liver, untreated, biological replicate 1


title: 4 week liver, in utero taurine supplementation, biological replicate 1


title: 4 week liver, in utero taurine supplementation, biological replicate 2


title: ECRS_WT

city: wuhan

first: heng

last: wang

address: jiefang avenue 1095#

institute: tongji hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using cubic spline normalisation with Illumina BeadStudio Application.

source_name: sinonasal mucosa from wild type mice with allergic eosinophilic chronic rhinosinusitis

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: Total RNA was extracted by using an RNeasy kit (Qiagen, Valencia, Calif) following manufacturer's instructions. Equal quantities of total RNA from 5 mice in the same study group were pooled together.

value: wild type

value: 6-8 weeks old

value: sinonasal mucosa

tag: disease


title: Liver_LEP_ICVN_1008

status: Public on Nov 10 2010

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

hyb_protocol: Approximately 750ng of labeled cRNA was hybridized to the MouseRef-8 v2.0 Expression BeadChips as per manufacturer’s instructions.

scan_protocol: After hybridization, arrays were washed, stained with Cy3-conjugated streptavidin, and scanned.

data_processing: Image data were analyzed with BeadStudio V2.0. Raw intensity data from BeadStudio were exported for further statistical analyses. Microarray data were normalized using the lumi package in R, using the variance stabilizing transformation (VST) of the package and robust spline normalization (RSN).

source_name: Liver

label_protocol: Purified RNA (200 ng) was further used for cRNA amplification and labeling with biotin using Target Amp cDNA synthesis kit (Epicenter catalog no. TAB1R6924).

extract_protocol: Total RNA was isolated using TRI REAGENT (Sigma), according to the manufacturer’s protocol.

value: ob/ob

tag: treatment

value: Leptin

tag: route

value: ICVN


title: d1 (Gα) mutant vs. wild type

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

hyb_protocol: Agilent’s In situ Hybridzation kit 5184-3568 was used for hybridization as per the directions of the manufacturer

scan_protocol: Scanning was performed with AGILENT DNA Microarray scanner SureScan High-Resolution Technology with GeneSpring software and image analyses were performed using the same.

data_processing: The normalization was done using GeneSpring GX as per the recommended Per Spot and Per Chip protocol. Ratio of intensities values above 1.5 were considered significant for upregulated genes while ratio less than 0.66 was considered for down regulated genes.

organism: Oryza sativa

source_name: Oryza sativa japonica d1 (Gα) mutant

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA using Agilent's Low input RNA linear amplification Kit Cat # 5184-3523. Protocol was followed as per manufacturers directions.cRNA was purified using Qiagen’s RNeasy minikit Cat#74104

growth_protocol: Seeds of the rice d1 (Gα) mutant (O. sativa japonica Nipponbare) were obtained from the Faculty of Agriculture, Kyushu University, Japan. They were surface-sterilized with 70 % ethanol and 0.01 % Triton-X 100 and grown on B-5 agar media at 25 °C with a light intensity of 1 kilo lux. Photoperiod of 12 hr light and 12 hr dark were maintained throughout the growth. The seedlings were grown for 25 days till the emergence of the tertiary leaves and were excised and used for microarray analysis.

extract_protocol: Hot-Phenol method for total RNA isolation was used for the current experiment.

value: d1 (Gα) mutant

source_name: Oryza sativa japonica wild type

growth_protocol: Seeds of the rice wild type (O. sativa japonica Nipponbare) were obtained from the Faculty of Agriculture, Kyushu University, Japan. The were surface-sterilized with 70 % ethanol and 0.01 % Triton-X 100 and grown on B-5 agar media at 25 °C with a light intensity of 1 kilo lux. Photoperiod of 12 hr light and 12 hr dark were maintained throughout the growth. The seedlings were grown for 25 days till the emergence of the tertiary leaves and were excised and used for microarray analysis.


title: Liver_LEP_ICV_1003

value: ICV


title: d1 (Gα) mutant vs. wild type (Flip dye)

description: The normalization was done using GeneSpring GX as per the recommended Per Spot and Per Chip protocol.

growth_protocol: Seeds of the rice (O. sativa japonica Nipponbare) were obtained from the Faculty of Agriculture, Kyushu University, Japan. They were surface-sterilized with 70 % ethanol and 0.01 % Triton-X 100 and grown on B-5 agar media at 25 °C with a light intensity of 1 kilo lux. Photoperiod of 12 hr light and 12 hr dark were maintained throughout the growth. The seedlings were grown for 25 days till the emergence of the tertiary leaves and were excised and used for microarray analysis.


title: Liver_VEH_ICV_1011

value: Vehicle


title: Liver_LEP_ICV_1019


title: Liver_VEH_ICV_1012


title: Cholera toxin and nitrate treatment vs. nitrate treatment in etiolated rice plants

source_name: Oryza sativa indica treated with cholera toxin and nitrate

growth_protocol: Rice seedlings were germinated on cotton in plastic trays and grown for 8-10 days in the absence of light and nutrients on distilled water prior to treatment.

treatment_protocol: 8-10 day old etiolated rice plantlets were treated with 25 µg/ml cholera toxin (CTX) and 120mM nitrate for 2 hours in total darkness. Total RNA was isolated from the tissue and used for labeling.

tag: cultivar

value: oryza sativa indica var. panvel

value: 8-10 days

tag: growth conditions

value: 25 °C with 80-90% humidity

source_name: Oryza sativa indica treated with nitrate

treatment_protocol: Total RNA was isolated from 8-10 day old etiolated rice plantlets floated in 120 mM nitrate in total darkness for two hours.


title: 4 week liver, untreated, biological replicate 2


title: Control_WT

source_name: sinonasal mucosa from normal wild type mice

value: control


title: Liver_LEP_ICVN_1016


title: Liver_LEP_ICVN_1001


title: Liver_LEP_ICVN_1004


title: Cholera toxin and nitrate treatment vs. nitrate treatment in etiolated rice plants (Flip-dye)

treatment_protocol: 8-10 day old etiolated rice plantlets were treated with 120mM nitrate for 2 hours in total darkness. Total RNA was isolated from the tissue and used for labeling.

source_name: Oryza sativa treated with cholera toxin and nitrate


title: ECRS_KO

source_name: sinonasal mucosa from CC10-knockout mice with allergic eosinophilic chronic rhinosinusitis

value: CC10 knockout


title: Liver_LEP_ICV_1017


title: Liver_LEP_ICV_1014


title: Liver_LEP_SQ_1041

value: SQ


title: Liver_VEH_SQ_1040


title: Liver_VEH_ICV_1002


title: Liver_B6_2035

value: Baseline


title: Liver_LEP_SQ_1039


title: Liver_VEH_SQ_1035


title: Liver_B6_5542


title: Liver_VEH_SQ_1007


title: Liver_VEH_ICV_1010


title: Liver_B6_5543


title: EpiSCs, biological replicate 2

status: Public on Oct 30 2010

city: La Jolla

first: Hongyan

last: Zhou

state: CA

address: 10550 North Torrey Pines Road

institute: the scripps research institute

description: Gene expression data from mouse epiblast stem cells

hyb_protocol: The hybridization mix containing 750 ng of labeled amplified cRNA was prepared according to the Illumina BeadStation 500X System Manual (Illumina, San Diego, CA, USA) using the supplied reagents and GE Healthcare Streptavidin-Cy3 staining solution. Hybridization to the Illumina Array MouseRef-8 v2 was for 18 h at 55 °C on a BeadChip Hyb Wheel.

scan_protocol: The array was scanned using the Illumina BeadArray Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

label: Biotin

source_name: EpiSCs

label_protocol: Biotin-16-UTP-labeled cRNA was synthesized from 500 ng total RNA with the  Illumina TotalPrep RNA amplification kit (Ambion AMIL1791, Foster City, CA, USA).

growth_protocol: EpiSCs were cultured at 37°C with 5% CO2. EpiSCs were maintained on irradiated MEF feeders in DF12 (GIBCO), supplemented with 20% KSR (GIBCO), 0.1 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, and 10 ng/ml of bFGF (Chemicon).

extract_protocol: Total RNA was extracted and purified with RNeasy Plus minikit (Qiagen).

tag: cell type

value: pluripotent epiblast stem cells


title: parnate/mAMFGi, biological replicate 2

description: Gene expression data from converted cells

source_name: parnate/mAMFGi

growth_protocol: ES cells were cultured at 37°C with 5% CO2. mES cells were maintained on irradiated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 10% fetal bovine serum (FBS; GIBCO), 0.1 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, and 1,000 units/ml of LIF (Chemicon).

value: converted mouse ESCs


title: Liver_B6_2029


title: Liver_LEP_SQ_1029


title: Liver_B6_2021


title: parnate/mAMFGi, biological replicate 1


title: Liver_VEH_SQ_1034


title: Liver_B6_5541


title: Maize-sh1_endosperm at 15DAP, biological rep2

status: Public on Oct 01 2010

city: Taian

first: xiang

last: li

address: No. 61 Daizong street

department: College of life science

institute: Shandong Agricultural University

description: Gene expression data from endosperm of sh1 inbred at 15 DAP.

hyb_protocol: Hybridization was performed on GeneChip maize Genome Array by using Affymetrix® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software Version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and dChip as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Zea mays

source_name: endosperm at 15 DAP

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

growth_protocol: The maize inbred lines B73, ae wx and sh1 were planted in the field of the north campus of Shandong Agricultural University during August 2007.

extract_protocol:
Nine endosperm tissues were collected and frozen in liquid nitrogen and stored subsequently at -70℃.
Total RNA was isolated by using the RNA Extraction Kit purchased from Beijing Autolab Biotechnology Co., Ltd, and was cleaned up by using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s instructions.

value: endosperm

value: sh1 inbred line

value: 15DAP (days after pollination)


title: Maize-sh1_endosperm at 15DAP, biological rep1


title: Liver_LEP_SQ_1032

value: ob/ob

value: Leptin


title: Maize-sh1_endosperm at 15DAP, biological rep3


title: Maize-ae wx_endosperm at 15DAP, biological rep3

description: Gene expression data from endosperm of ae wx inbred at 15 DAP.

value: ae wx inbred line


title: Maize-ae wx_endosperm at 15DAP, biological rep2


title: Maize-B73_endosperm at 15DAP, biological rep3

description: Gene expression data from endosperm of B73 inbred at 15 DAP.

value: B73 inbred line


title: Maize-ae wx_endosperm at 15DAP, biological rep1


title: EpiSCs, biological replicate 1


title: Maize-B73_endosperm at 15DAP, biological rep2


title: Maize-B73_endosperm at 15DAP, biological rep1


title: endometrium_progesterone+estrogen-treated_rep3

status: Public on Sep 30 2010

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

description: endometrial tissue; ovariectomized cow

hyb_protocol: fragmented cRNA was hybridized to Affymetrix GeneChip Bovine Genome Arrays and washed and stained with Affymetrix Wash&Stain Kit on an Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: RMA Normalization

organism: Bos taurus

source_name: endometrial tissue, treated with progesterone+estrogen

label_protocol: total RNA was transcribed and labeled with Ambion Kit MessageAmp II Biotin Enhanced according to the manufacturers protocol

growth_protocol: The cows (n=12) were ovariectomized, maintained in a free-stall barn throughout the experimental period, and had free access to food and water.

extract_protocol: deep frozen tissue was transferred to 5 ml RNAlater-ICE (Ambion, Austin, TX, USA) and allowed to impregnate at -20°C during two days for optimal RNA protection. Total RNA was extracted from bovine mammary gland tissue with the Trizol method according to the manufacturers protocol

treatment_protocol: Ovariectomized cows (n=12) were randomly divided into four groups; the control group (n=3) received saline treatment at Day 0 (beginning of the experiment), E2 groups (n=3) received saline and 1 mg estradiol benzoate (EB) at Day 0 and Day 5, respectively, two CIDR were inserted to the uterus of animals of the P4 group (n=3) from Day 0 to Day 6, and the E2+P4 group (n=3) received two CIDR at Day 0 and injection of 1 mg EB immediately after removal of the CIDR at Day 6. Blood samples (5 ml) in control and P4 groups were collected at Day 5 after saline or CIDR treatment, and in E2 and E2+P4 groups blood samples were collected after EB treatment. All animals were slaughtered 2 days after blood sampling, and endometrium samples were collected as described in Bauersachs et al J Mol Endocrinol 2005). The tissue samples were snap-frozen and stored at -80°C until analysis.

value: endometrium

tag: agent

value: progesterone+estrogen


title: endometrium_progesterone-treated_rep3

description: endometrial tissue; ovariectomized cow

source_name: endometrial tissue, treated with progesterone

value: progesterone


title: endometrium_progesterone-treated_rep1

description: endometrial tissue; ovariectomized cow


title: endometrium_progesterone+estrogen-treated_rep2

description: endometrial tissue; ovariectomized cow


title: endometrium_progesterone+estrogen-treated_rep1

description: endometrial tissue; ovariectomized cow


title: endometrium_progesterone-treated_rep2

description: endometrial tissue; ovariectomized cow


title: endometrium_estrogen-treated_rep2

description: endometrial tissue; ovariectomized cow

source_name: endometrial tissue, treated with estrogen

value: estrogen


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M6_R1_B

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

description: This experiment was performed with two independent biological replicates (R1 and R2). The whole genome microarray consisting of a total of ~45,000 oligonucleotides was printed on two separate slides (Slides A and B).

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 5X SSC, 0.1% SDS, 0.2 mg/ml of yeast tRNA, 0.2 mg/ml of polyadenylic acid and 25% super-pure formamide. Hybridization was performed by applying the labeled mixture of control and transgenic rice samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified hybridization chamber (Genomictree). The chamber was submerged into 42C water from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

scan_protocol: Microarrays were scanned at 635nm and 532nm using the Axon GenePix 4000B scanner (Molecular Devices). Scan image was acquired and processed by the GenePix Pro 5.1.

data_processing: Quality flagging was performed on the microarray scans using GenePix Pro 5.1. A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatics analysis of the gene expression data. Gene expression data in each image was normalized globally prior to high level analysis. VALUES represent the log2 of the ratio between the background subtracted intensity values at Cy5 (635 nm) and Cy3 (532 nm) (635/532). Data sorting was performed by MS Access. All high level (T-tests and hierarchical clustering) analyses were performed with the MeV Bioinformatics tools (TIGR).

organism: Oryza sativa Japonica Group

source_name: WT rice seedlings at ambient temperature (29C)

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP. The resulting aRNA molecules were chemically labeled with Cy3 fluorescent dye.

growth_protocol: Seedlings were germinated in ample water and allowed in soil to develop to V3-stage at ambient temperature (29C) in a growth room.

extract_protocol: Total RNA was isolated from control seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Control samples (seedlings at V3 stage) were at ambient temperature (29C)

tag: subspecies

value: japonica

value: Nipponbare

value: seedlings

value: WT

source_name: Transgenic Rice (line_M6) seedlings at ambient temperature (29C)

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP. The resulting aRNA molecules were chemically labeled with Cy5 fluorescent dye.

extract_protocol: Total RNA was isolated from transgenic rice (line_M6) seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Transgenic rice (line_M6 seedlings at V3 stage) were at ambient temperature (29C)

value: OsMYB4 transgenic

tag: transgenic line

tag: replicate


title: endometrium_estrogen-treated_rep3

description: endometrial tissue; ovariectomized cow

tag: tissue


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M6_R2_B

tag: developmental stage


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M2_R1_B

source_name: Transgenic Rice (line_M2) seedlings at ambient temperature (29C)

extract_protocol: Total RNA was isolated from transgenic rice (line_M2) seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Transgenic rice (line_M2 seedlings at V3 stage) were at ambient temperature (29C)


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M2_R2_B


title: endometrium_estrogen-treated_rep1

description: endometrial tissue; ovariectomized cow


title: endometrium_mock-treated_rep1

description: endometrial tissue; ovariectomized cow

source_name: endometrial tissue, mock-treated

value: control


title: endometrium_mock-treated_rep3

description: endometrial tissue; ovariectomized cow


title: Ko 2

city: Farmington

first: Anupinder

last: Kaur

state: CT

address: 400 Farmington Avenue

department: Genetics and Developmental Biology

institute: UCHC

description: Replicate Ko

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization using GenomeStudio.

source_name: Peritoneal macrophages

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: peritoneal macrophages

tag: genome/variation

value: CD13 knock out


title: WT 2

description: Replicate WT

value: wild type


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M2_R1_A


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M6_R1_A


title: WT 1

description: Sample WT


title: Ko 1

description: Sample Ko


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M6_R2_A


title: Nipponbare_WT_vs_Nipponbare_OsMYB4_OX_M2_R2_A


title: DR-HFS_vs_DR-LFS1

status: Public on Sep 25 2010

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

hyb_protocol: The hybridizations were performed using the MAUI hybridization system at 48oC (BioMicro Systems, Inc, Salt Lake City, UT).

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.

data_processing: The data generated by GenePix® Pro version 5.0 software was analyzed to identify differentially expressed genes. Data normalization was performed in two steps for each microarray separately (21). First, background adjusted intensities were log-transformed and the differences (M) and averages (A) of log-transformed values were calculated as M = log2(X1) - log2(X2) and A = [log2(X1) + log2(X2)]/2, where X1 and X2 denote the Cy5 and Cy3 intensities, respectively.  Second, normalization was performed by fitting the array-specific local regression model of M as a function of A.

organism: Rattus norvegicus

source_name: LCM captured rat MECs

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.

growth_protocol: Virgin female obesity-prone (OP) (Crl:OP(CD) and obesity-resistant (OR) (Crl:OR(CD) rats (Charles River Labs, Kingston NY) were purchased at weaning (PND 23 days). These rats were originally developed by Dr. Barry Levin  (42; 54) and have been maintained at Charles River since 2001. Upon arrival, rats were placed on either a low fat n-6 PUFA diet (10% fat by kcal; primarily from safflower oil) or a high fat n-6 PUFA diet (39% fat by kcal; primarily from safflower oil) (Research Diets, Inc. New Brunswick, NJ) (see Table 1), both diets were devoid of phytoestrogens). Importantly, these diets differed only in their fat level, carbohydrate level and caloric density; all other nutrients such as protein and micro- and macro-nutrients were matched between the diets. All rats were ad libitum fed, were individually housed on phytoestrogen-free hardwood Sani-chip bedding (P.J. Murphy Forest Products Corp., Montville, NJ), and maintained in temperature- and humidity-controlled rooms in the AALAC approved University of Cincinnati facility under a 12h light-dark cycle. All animal procedures were approved by the University of Cincinnati Institutional Animal Care and Use Committee and experiments were performed following the guidelines of the National Institutes of Health for the proper and humane use of animals in biomedical research

extract_protocol: A cohort of female rats (strains OR and OP as described above) were sacrificed at PND50 and mammary tissue removed and frozen (-80oC) in Optimal Cutting Temperature (OCT) Compound (Sakura, Baltimore, MD). The frozen mammary tissue was sectioned to 10 µm thickness using a cryostat (Leica Bannockburn, IL), stained with hematoxylin and eosin, followed immediately by laser capture micro-dissection (LCM) using the PixCell II Arcturus LCM System (Arcturus, Sunnydale, CA). Mammary ductal epithelial cells were captured at a total rate of 10-12,000 hits per sample. Total RNA was isolated using Tri Reagent according to manufacturer’s protocol TRI118 (Molecular Research Center, Inc., Cincinnati, OH).

value: OR

tag: diet

value: High fat

tag: gender

value: female

value: Low fat


title: Breast Vasculature Tumor P

status: Public on Sep 19 2010

city: Montreal

first: Francois

last: Pepin

state: Quebec

address: 1160 Pine Av W

country: Canada

institute: McGill University

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (500 ng) were subjected to fragmentation followed by 18 h hybridization, washing, and scanning (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90030). Samples were hybridized against Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA). Duplicate hybridizations were performed for all samples using reverse-dye labeling.

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 7.5.1) from Agilent with the default parameters.

data_processing: Outlier features on arrays were flagged by the software. Arrays were required to have an average raw signal intensity of 800 in each channel, and a signal to noise ratio above 16 per channel. MvA plots were examined for signs of hybridization or labeling problems. Data preprocessing and normalization were automated using the BIAS system. Raw feature intensities were background corrected using the RMA background correction algorithm. Resulting expression estimates were converted to log2-ratios. Within array normalization was performed using spatial and intensity-dependent loess. Median absolute deviation scale normalization was used to normalize between arrays.

organism: Homo sapiens

source_name: Breast tumor-associated vasculature (laser capture microdissected)

label_protocol: 2 to 4 ng of total RNA was subjected to two rounds of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and labeled with Cy3 and Cy5 dyes according to the manufacturer’s procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours following tissue staining. Total RNA was extracted from each population of microdissected cells using a GITC (guanidinium isothiocyanate) extraction protocol. Briefly, LCM caps were incubated for 5 minutes (room temperature) in 200 μl GITC extraction buffer supplemented with 1.6 μl β-mercaptoethanol (4 M GITC, 25 mM sodium citrate pH 7.0, 0.1 M β-mercaptoethanol, 0.5% N-lauroylsarcosine). Subsequently, 20 μl of 2 M NaOAc, pH 4.0, 220 μl of water-saturated phenol and 60 μl of chloroform-isoamyl alcohol (23:1) were added to the extraction buffer. Following 15 minutes incubation on ice and centrifugation (12,000 rpm, 15 minutes) the aqueous phase was removed and RNA was precipitated with 2 μl glycogen (GenHunter, Nashville, Tennessee, USA) and 200 μl isopropanol. Samples were placed at -80°C for 30 minutes and centrifuged at 4°C (12,000 rpm) for 30 minutes to pellet RNA. Pellets were washed with 70% ethanol, air dried and subjected to DNAseI treatment (Roche, Basel, Switzerland). DNAseI treatment was performed in the presence of an RNase inhibitor (Invitrogen, Carlsbad, California, USA). Subsequently, samples were re-extracted as described above and re-suspended in 10 μl of diethylpyrocarbonate-treated water. RNA was quantified using a RiboGreen assay (Molecular Probes, Carlsbad, California, USA).

value: Breast Vasculature Tumor

tag: patient

value: P

tag: age

tag: tumor size (mm)

tag: tumor pecam1 staining

value: high

tag: er status

value: Positive

tag: pr status

value: Negative

tag: her2 status

tag: grade

value: III

tag: ln status

tag: recurrence

value: No

tag: follow up (years)

source_name: Universal Reference

tag: sample

value: Universal Reference


title: Breast Vasculature Tumor O

tag: tissue

value: O


title: DIO-LFS_vs_DIO-HFS2

treatment_protocol: Upon arrival, rats were placed on either a low fat n-6 PUFA diet (10% fat by kcal; primarily from safflower oil) or a high fat n-6 PUFA diet (39% fat by kcal; primarily from safflower oil) (Research Diets, Inc. New Brunswick, NJ) (see Table 1), both diets were devoid of phytoestrogens). Importantly, these diets differed only in their fat level, carbohydrate level and caloric density; all other nutrients such as protein and micro- and macro-nutrients were matched between the diets.

tag: strain

value: OP


title: DIO-LFS_vs_DIO-HFS1


title: DIO-HFS_vs_DIO-LFS3


title: DR-LFS_vs_DR-HFS2


title: Breast Vasculature Tumor N

value: N

value: low

value: II


title: DR-HFS_vs_DR-LFS3

value: OR


title: Breast Vasculature Tumor J

value: J


title: DR-HFS_vs_DR-LFS2

value: High fat

value: female


title: Breast Vasculature Tumor K

value: Breast Vasculature Tumor

value: K

value: Yes


title: Breast Vasculature Tumor M

value: M

value: Positive


title: Breast Vasculature Tumor Q

value: Q

value: high

value: Negative

value: III


title: Breast Vasculature Tumor G

value: G

value: Universal Reference


title: Breast Vasculature Tumor F

value: F

value: low

value: I

value: No


title: Breast Vasculature Tumor I

value: II


title: DIO-HFS_vs_DIO-LFS1

value: OP

value: High fat

value: female

value: Low fat


title: DIO-HFS_vs_DIO-LFS2


title: Breast Vasculature Tumor H

value: Breast Vasculature Tumor

value: H

value: Yes


title: DR-LFS_vs_DR-HFS1

value: OR


title: Breast Vasculature Tumor L

value: L

value: Positive

value: Negative


title: Breast Vasculature Tumor E

value: E

value: III

value: Universal Reference


title: Breast Vasculature Tumor C

value: C

value: low


title: Breast Vasculature Tumor D

value: D

value: II

value: No


title: Breast Vasculature Tumor B

value: B


title: Breast Vasculature Tumor A

value: A

value: high


title: Breast Vasculature Reduction  V

source_name: Normal vasculature derived from breast reduction patient (laser capture microdissected)

value: Breast Vasculature Reduction

value: V


title: Breast Vasculature Normal Q

source_name: Morphologically normal vasculature derived from breast cancer patient (laser capture microdissected)

value: Breast Vasculature Normal

value: Q

value: Yes


title: Breast Vasculature Normal G

value: G

value: Positive

value: Negative


title: Breast Vasculature Normal E

value: E

value: III

value: Universal Reference


title: endometrium_mock-treated_rep2

description: endometrial tissue; ovariectomized cow

value: endometrium

tag: agent

value: control


title: Breast Vasculature Normal F

value: F

value: low

value: I

value: No


title: Breast Vasculature Normal I

value: high

value: II


title: Breast Vasculature Normal D

value: Breast Vasculature Normal

value: D


title: Breast Vasculature Normal N

value: N


title: Breast Vasculature Normal O

value: O


title: Breast Vasculature Normal T

value: T


title: Breast Vasculature Normal B

value: B

value: Positive

value: Negative


title: Breast Vasculature Normal A

value: A

value: III

value: Yes

value: Universal Reference


title: Breast Vasculature Normal R

value: R


title: HBx-16 months (non-tumor)

status: Public on Sep 16 2010

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: No. 35 Keyan Road

department: Division of Molecular and Genomic medicine

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: HBx-16 months ( non-tumor )

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Follow NimbleGen’s ds cDNA synthesis protocol. This protocol uses Invitrogen’s SuperScriptII double stranded cDNA synthesis kit, followed by RNase treatment.

tag: disease stage

value: non-tumor

tag: age (months)

tag: genetic background

value: HBx transgenic


title: HBx-12 months (non-tumor)

source_name: HBx-12 months ( non-tumor )


title: HBx-6 weeks

source_name: HBx-6 weeks


title: WT-8 months

source_name: WT-8 months

value: Wild Type


title: WT-16 months

source_name: WT-16 months


title: WT-14 months

source_name: WT-14 months


title: HBx-14 months (non-tumor)

source_name: HBx-14 months ( non-tumor )


title: Breast Vasculature Normal S

tag: patient

value: S

tag: age

value: II

value: No


title: WT-12 months

source_name: WT-12 months


title: HBx-16 months (tumor)

source_name: HBx-16 months ( tumor )

value: tumor


title: HBx-14 months (tumor)

source_name: HBx-14 months ( tumor )


title: Liver  (SAMPLE 95)

status: Public on Sep 15 2010

city: Madrid

first: Gloria

last: Muñoz

address: Crta. Coruña km 7

department: Mejora Genetica Animal

country: Spain

institute: INIA

data_processing: The data were normalized using the Loess followed by the Robust Spline Normalization (RSN) methods with the Lumi package in R.

source_name: Mouse liver

label_protocol: Biotinilated cRNA syntheses were generated using the Ambion Total Prep RNA Amplification Kit for Illumina arrays following the manufacturer´s instructions.

extract_protocol: Total RNA was extracted with Trizol reagent, following manufacturer´s protocol. Quality control was performed with Agilent 2100 Bioanalyser.

tag: gender

value: male

value: M16i x MB2 F2 intercross

value: Liver

tag: haplotype class

tag: scanning day

tag: scanning position

value: 15 weeks


title: Liver  (SAMPLE 90)

value: female


title: Liver  (SAMPLE 96)


title: HBx-8 months (non-tumor)

source_name: HBx-8 months ( non-tumor )


title: Liver  (SAMPLE 87)


title: WT-6 weeks

source_name: WT-6 weeks


title: Breast Vasculature Normal U

value: Breast Vasculature Normal

value: U

tag: tumor size (mm)

tag: tumor pecam1 staining

tag: er status

value: Negative

tag: pr status

tag: her2 status

tag: grade

value: Positive


title: Liver  (SAMPLE 84)

tag: strain

tag: tissue


title: Liver  (SAMPLE 85)


title: Liver  (SAMPLE 91)


title: Liver  (SAMPLE 92)


title: Liver  (SAMPLE 86)


title: Liver  (SAMPLE 83)


title: Liver  (SAMPLE 89)


title: Liver  (SAMPLE 82)


title: Liver  (SAMPLE 94)


title: Liver  (SAMPLE 78)


title: Liver  (SAMPLE 93)


title: Liver  (SAMPLE 88)


title: Liver  (SAMPLE 81)


title: Liver  (SAMPLE 80)


title: Liver  (SAMPLE 76)


title: Liver  (SAMPLE 74)


title: Liver  (SAMPLE 77)


title: Liver  (SAMPLE 75)


title: Liver  (SAMPLE 73)


title: Liver  (SAMPLE 79)


title: Liver  (SAMPLE 70)


title: Liver  (SAMPLE 72)


title: Liver  (SAMPLE 68)


title: Liver  (SAMPLE 65)


title: Liver  (SAMPLE 67)


title: Liver  (SAMPLE 62)


title: Liver  (SAMPLE 66)


title: Liver  (SAMPLE 64)


title: Liver  (SAMPLE 61)


title: Liver  (SAMPLE 71)


title: Liver  (SAMPLE 58)


title: Liver  (SAMPLE 57)


title: Liver  (SAMPLE 55)


title: Liver  (SAMPLE 69)


title: Liver  (SAMPLE 60)


title: Liver  (SAMPLE 52)


title: Liver  (SAMPLE 59)


title: Liver  (SAMPLE 56)


title: Gonadal fat (SAMPLE 47)

source_name: Mouse gonadal fat

value: Gonadal fat


title: Liver  (SAMPLE 53)


title: Gonadal fat (SAMPLE 44)


title: Liver  (SAMPLE 54)


title: Liver  (SAMPLE 49)


title: Gonadal fat (SAMPLE 46)


title: Liver  (SAMPLE 51)


title: Liver  (SAMPLE 50)


title: Liver  (SAMPLE 63)


title: Gonadal fat (SAMPLE 48)


title: Gonadal fat (SAMPLE 43)


title: Gonadal fat (SAMPLE 40)


title: Gonadal fat (SAMPLE 37)


title: Gonadal fat (SAMPLE 45)


title: Gonadal fat (SAMPLE 38)


title: Gonadal fat (SAMPLE 36)


title: Gonadal fat (SAMPLE 42)


title: Gonadal fat (SAMPLE 33)


title: Gonadal fat (SAMPLE 35)


title: Gonadal fat (SAMPLE 29)


title: Gonadal fat (SAMPLE 27)


title: Gonadal fat (SAMPLE 31)


title: Gonadal fat (SAMPLE 28)


title: Gonadal fat (SAMPLE 39)


title: Gonadal fat (SAMPLE 32)


title: Gonadal fat (SAMPLE 25)


title: Gonadal fat (SAMPLE 34)


title: Gonadal fat (SAMPLE 23)


title: Gonadal fat (SAMPLE 26)


title: Gonadal fat (SAMPLE 22)


title: Gonadal fat (SAMPLE 24)


title: Gonadal fat (SAMPLE 15)


title: Gonadal fat (SAMPLE 13)


title: Gonadal fat (SAMPLE 17)


title: Gonadal fat (SAMPLE 41)


title: Gonadal fat (SAMPLE 16)


title: Gonadal fat (SAMPLE 14)


title: Gonadal fat (SAMPLE 30)


title: Gonadal fat (SAMPLE 18)


title: Gonadal fat (SAMPLE 12)


title: Gonadal fat (SAMPLE 19)


title: Gonadal fat (SAMPLE 21)


title: Gonadal fat (SAMPLE 8)


title: Gonadal fat (SAMPLE 9)


title: Gonadal fat (SAMPLE 5)


title: Gonadal fat (SAMPLE 6)


title: Gonadal fat (SAMPLE 20)


title: Gonadal fat (SAMPLE 7)


title: Gonadal fat (SAMPLE 10)


title: Testis, Cmpd8, biological rep4

status: Public on Sep 01 2010

city: Amsterdam

first: Xiaolian

last: Yuan

state: North Holland

address: Science Park 904

department: Microarray department

country: Netherlands

institute: Amsterdam University

description: Gene expression data from testes isolated at 24 h after DOP treatment of rat.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).

source_name: Rat testes, DOP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.

extract_protocol: Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).

treatment_protocol: After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.

value: testes

value: 10 weeks old

tag: compound

value: DOP

tag: harmfulness

value: Non-reprotoxic Phthalate

tag: labelblock

value: Label  block 2

tag: hybblock

value: Hybridization block 4


title: Testis, Cmpd10, biological rep5

description: Gene expression data from testes isolated at 24 h after DMP treatment of rat.

source_name: Rat testes, DMP

tag: age

value: DMP

value: Label  block 3

value: Hybridization block 5


title: Gonadal fat (SAMPLE 2)

tag: gender

value: male

value: M16i x MB2 F2 intercross


title: Testis, Cmpd8, biological rep5


title: Testis, Cmpd9, biological rep4

description: Gene expression data from testes isolated at 24 h after DEP treatment of rat.

source_name: Rat testes, DEP

value: DEP


title: Testis, Cmpd10, biological rep4


title: Testis, Cmpd9, biological rep1

value: Label  block 1

value: Hybridization block 1


title: Testis, Cmpd9, biological rep3

value: Hybridization block 3


title: Gonadal fat (SAMPLE 11)

value: female

tag: haplotype class

value: 15 weeks


title: Gonadal fat (SAMPLE 4)

value: Gonadal fat

tag: scanning day


title: Testis, Cmpd10, biological rep3

value: testes

value: 10 weeks old


title: Testis, Cmpd11, biological rep3

description: Gene expression data from testes isolated at 24 h after MEHP treatment of rat.

source_name: Rat testes, MEHP

value: MEHP

value: Reprotoxic Phthalate


title: Gonadal fat (SAMPLE 1)

tag: scanning position


title: Testis, Cmpd9, biological rep5

value: Non-reprotoxic Phthalate


title: Testis, Cmpd11, biological rep1

value: Hybridization block 2


title: Testis, Cmpd11, biological rep2

value: Label  block 2


title: Testis, Cmpd9, biological rep2


title: Gonadal fat (SAMPLE 3)


title: Testis, Cmpd10, biological rep2

value: DMP


title: Testis, Cmpd8, biological rep1

value: male

value: DOP


title: Testis, Cmpd7, biological rep4

description: Gene expression data from testes isolated at 24 h after DPrP treatment of rat.

source_name: Rat testes, DPrP

value: DPrP

value: Hybridization block 4


title: Testis, Cmpd10, biological rep1

value: Label  block 1

value: Hybridization block 1


title: Testis, Cmpd6, biological rep5

description: Gene expression data from testes isolated at 24 h after DBP treatment of rat.

source_name: Rat testes, DBP

value: DBP

value: Label  block 3

value: Hybridization block 5


title: Testis, Cmpd7, biological rep3

value: testes

value: Hybridization block 3


title: Testis, Cmpd7, biological rep2

value: 10 weeks old


title: Testis, Cmpd7, biological rep1


title: Testis, Cmpd8, biological rep2


title: Testis, Cmpd6, biological rep4

value: Reprotoxic Phthalate


title: Testis, Cmpd4, biological rep1

description: Gene expression data from testes isolated at 24 h after DHP treatment of rat.

source_name: Rat testes, DHP

value: DHP


title: Testis, Cmpd5, biological rep4

description: Gene expression data from testes isolated at 24 h after DPeP treatment of rat.

source_name: Rat testes, DPeP

value: DPeP


title: Testis, Cmpd6, biological rep1


title: Testis, Cmpd5, biological rep1


title: Testis, Cmpd11, biological rep4

value: MEHP


title: Testis, Cmpd8, biological rep3

value: Non-reprotoxic Phthalate

value: Label  block 2


title: Testis, Cmpd4, biological rep4

value: male


title: Testis, Cmpd4, biological rep2

value: Hybridization block 2


title: Testis, Cmpd5, biological rep2


title: Testis, Cmpd6, biological rep3


title: Testis, Cmpd6, biological rep2


title: Testis, Cmpd2, biological rep4

description: Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.

source_name: Rat testes, 2-ME

value: Positive control

value: Hybridization block 4


title: Testis, Cmpd2, biological rep5


title: Testis, Cmpd3, biological rep2

description: Gene expression data from testes isolated at 24 h after DEHP treatment of rat.

source_name: Rat testes, DEHP

value: DEHP

value: Label  block 1


title: Testis, Cmpd4, biological rep5

value: Label  block 3


title: Testis, Cmpd3, biological rep5

value: Hybridization block 5


title: Testis, Cmpd4, biological rep3

value: testes


title: Testis, Cmpd2, biological rep2


title: Testis, Cmpd3, biological rep4


title: Testis, Cmpd2, biological rep1

value: Hybridization block 1


title: Testis, Cmpd2, biological rep3

value: 10 weeks old

value: Hybridization block 3


title: Testis, Cmpd1, biological rep3

description: Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.

source_name: Rat testes, mock

value: mock

value: Negative control


title: Testis, Cmpd1, biological rep4


title: Testis, Cmpd3, biological rep3

value: Reprotoxic Phthalate


title: Testis, Cmpd1, biological rep5


title: Testis, Cmpd5, biological rep3

value: DPeP


title: Testis, Cmpd1, biological rep1


title: Animal 25

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

department: Genetics

institute: Univ of Alabama at Birmingham

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF25_HF_SAT

hyb_protocol: A total of 0.75 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with streptavidin-Cy3 prior to visualization.

scan_protocol: BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value).  Both non-normalized and normalized (quantile) data were generated for each sample.

source_name: Left ventricle, heart failure surgery, saturated fat diet

label_protocol: Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.

growth_protocol: Tissue from a separate set of animals (n=6/group) was quick frozen in liquid nitrogen for microarray analysis.

extract_protocol: RNA was extracted from all tissues using a standard protocol and Tri-reagent.

treatment_protocol: Rats were randomly assigned to receive either a sham-operation (SH) or coronary ligation to induce cardiac dysfunction (HF). Following surgery, rats were immediately fed either a normal rodent chow (NC) or a high saturated fat chow (SAT) with 60% caloric content derived from fat (25% palmitic, 33% stearic, 33% oleic acid, Research Diets).

value: Wistar

value: left ventricle

tag: surgery

value: coronary ligation

tag: coronary status

value: heart failure

tag: diet

value: high saturated fat


title: Testis, Cmpd1, biological rep2

value: male

value: Hybridization block 2


title: Testis, Cmpd3, biological rep1

value: DEHP

value: Label  block 1


title: Animal 35

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF35_SHAM_SAT

source_name: Left ventricle, sham surgery, saturated fat diet

value: sham

value: normal


title: Animal 18

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF18_HF_SAT


title: Animal 37

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF37_HF_SAT


title: Animal 28

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF28_HF_SAT


title: Animal 34

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF34_SHAM_SAT


title: Animal 40

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF40_SHAM_NORM

source_name: Left ventricle, sham surgery, normal diet


title: Animal 12

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF12_SHAM_SAT


title: Animal 4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF4_HF_NORM

source_name: Left ventricle, heart failure surgery, normal diet


title: Animal 17

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF17_SHAM_SAT


title: Animal 21

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF 21_HF_NORM


title: Animal 20

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF20_SHAM_SAT


title: Animal 5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF5_HF_SAT


title: Animal 39

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF39_HF_SAT


title: Animal 16

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF16_HF_NORM


title: Animal 38

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF38_HF_NORM


title: Animal 22

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF22_SHAM_NORM


title: Animal 13

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF13_SHAM_NORM


title: Animal 9

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF9_SHAM_NORM


title: Animal 23

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF23_HF_NORM


title: Animal 11

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF11_SHAM_SAT


title: Animal 15

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF15_SHAM_NORM


title: Pellicle formation/MR-1, 3

city: Norman

first: Yili

last: Liang

state: OK

address: 101 David L. Boren Blvd,

department: Botany and Microbiology

institute: Insitute Institute for Environmental Genomics, University of Oklahoma

description: Global Transcriptome Analysis of pellicle formation of Shewanella oneidensis MR-1 and mutational analysis of its iron transport proteins.

hyb_protocol: The two labeled cDNA pools (pellicle cells and planktonic cells) to be compared were mixed and hybridized simultaneously to the array on UltraGAPS slides (Corning) in a solution containing 5x SSC, 0.1% SDS, and 0.1 mg/mL of herring sperm DNA (Gibco BRL). The entire process of hybridization, including prehybridization, hybridization, and post-hybridization wash, was performed according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned using the confocal laser microscope of the ScanArray Gx Microarray Analysis System (PerkinElmer) at a resolution of 5 µm per pixel. Scanning parameters (laser power and photomultiplier tube or PMT gain) were adjusted, so that overall intensities in both fluorescence channels were relatively equal and few spots were saturated.

data_processing: To determine fluorescence intensity (pixel density) and background intensity, 16-bit TIFF scanned images were analyzed using the software ImaGene version 7.0 (Biodiscovery). The text files from ImaGene were then analyzed with the software GeneSpring GX (Agilent).

organism: Shewanella oneidensis MR-1

source_name: Pellicle cells

label_protocol: Fluorescently labeled cDNA copies of total cellular RNA extracted from pellicle cells and planktonic cells were prepared by incorporation of fluorescein-labeled nucleotide analogs during a first-strand reverse transcription reaction according to the manufacturer's instructions (Invitrogen). RNA from the pellicle cells was fluorescently labeled with Cy3, and that from the planktonic was labeled with Cy5.

growth_protocol: MR-1 was grown still in LB medium for pellicle formation at the room temperature. Pellicle cells were collected.

extract_protocol: Total cellular RNAs from pellicle cells and planktonic cells of S. oneidensis were isolated using the TRIzol Reagent (Gibco BRL) according to the manufacturer's instructions. After precipitation, RNA samples were purified with the Qiagen RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MR-1 was grown still in 50-ml Pyrex beakers and allowed to develop a complete but thin layer of pellicles at the room temperature. To separate cells in pellicle and underneath, cultures were withdrawn through the stop-cock even for collecting planktonic cells and cells from the pellicle were gathered.

source_name: Planktonic cells

growth_protocol: MR-1 was grown still in LB medium for pellicle formation at the room temperature. Planktonic cells were collected.


title: Spleen_CON.Null.NoLPS_ABAIMMUN06_Rep.2

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

hyb_protocol: The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

scan_protocol: The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were normalized using GC-RMA algorithm in R statistical environment. Linear modeling was performed using the bioconductor package 'limma'.

source_name: Spleen; Control; PPARg null; No LPS

label_protocol: RNA was processed and labeled according to the standard target labeling protocols.

growth_protocol: Splenocytes were obtained from wild-type and spleen-specific PPARγ -null mice fed on a control or ABA-enriched diet without or with LPS challenge.

extract_protocol: After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

treatment_protocol: PPAR g flfl; MMTV-Cre+ (n=40) and control PPAR g flfl; MMTV-Cre- (n=40) mice fed control or ABA-supplemented diets were used for these experiments. These mice express a transgenic recombinase under the control of the MMTV-Cre promoter .  The mice were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 750 F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.

value: Control diet

tag: genotype

value: Conditional PPAR g-null

value: PPAR g flfl; MMTV-Cre+

tag: stimulus

value: No LPS


title: Spleen_CON.Null.LPS_ABAIMMUN06_Rep.1

source_name: Spleen; Control; PPARg null; LPS

value: LPS


title: Pellicle formation/MR-1, 2

tag: MR-1 was grown still in LB medium for pellicle formation at the room temperature. Pellicle cells were collected.

tag: MR-1 was grown still in LB medium for pellicle formation at the room temperature. Planktonic cells were collected.


title: Animal 7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF7_SHAM_NORM

tag: strain

tag: tissue


title: Pellicle formation/MR-1, 1


title: Spleen_CON.WT.LPS_ABAIMMUN06_Rep.1

source_name: Spleen; Control; wild-type; LPS

value: Wild-type

value: PPAR g flfl; MMTV-Cre-


title: Spleen_CON.Null.LPS_ABAIMMUN06_Rep.2


title: Spleen_ABA.WT.NoLPS_ABAIMMUN06_Rep.1

source_name: Spleen; ABA; wild-type; No LPS

value: Abscisic acid (ABA) supplementation


title: Spleen_CON.WT.NoLPS_ABAIMMUN06_Rep.2

source_name: Spleen; Control; wild-type; No LPS


title: Spleen_ABA.WT.LPS_ABAIMMUN06_Rep.1

source_name: Spleen; ABA; wild-type; LPS


title: Spleen_CON.WT.NoLPS_ABAIMMUN06_Rep.1


title: Spleen_CON.WT.LPS_ABAIMMUN06_Rep.2


title: Spleen_NoLPS.ABA_ABAIMMUN05_Rep.2


title: Spleen_ABA.WT.LPS_ABAIMMUN06_Rep.2


title: Spleen_ABA.Null.NoLPS_ABAIMMUN06_Rep.2

source_name: Spleen; ABA; PPARg null; No LPS


title: Spleen_NoLPS.CON_ABAIMMUN05_Rep.1


title: Spleen_ABA.Null.LPS_ABAIMMUN06_Rep.1

source_name: Spleen; ABA; PPARg null; LPS


title: Spleen_CON.Null.NoLPS_ABAIMMUN06_Rep.1


title: Spleen_ABA.WT.NoLPS_ABAIMMUN06_Rep.2


title: Spleen_LPS.CON_ABAIMMUN05_Rep.3


title: Spleen_ABA.Null.NoLPS_ABAIMMUN06_Rep.1


title: Spleen_NoLPS.CON_ABAIMMUN05_Rep.2


title: Spleen_LPS.CON_ABAIMMUN05_Rep.4


title: Spleen_NoLPS.ABA_ABAIMMUN05_Rep.1


title: Spleen_ABA.Null.LPS_ABAIMMUN06_Rep.2


title: Animal 24

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
INF24_HF_NORM

value: Wistar

value: left ventricle

value: coronary ligation


title: Spleen_LPS.CON_ABAIMMUN05_Rep.2


title: Spleen_LPS.ABA_ABAIMMUN05_Rep.4


title: Spleen_LPS.ABA_ABAIMMUN05_Rep.1


title: Spleen_LPS.ABA_ABAIMMUN05_Rep.3


title: Spleen_LPS.ABA_ABAIMMUN05_Rep.2


title: Spleen_LPS.CON_ABAIMMUN05_Rep.1


title: E.coli_salt_3

status: Public on Aug 20 2010

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

hyb_protocol: Nimblegen Hybridization System

scan_protocol: Surescan high-resolution DNA microarry scanner

data_processing: Data was normalized using the Standard Normalization routine included with JMP Genomics 4.1. This routine mean centers the data around 0 and divides by the standard deviation.

organism: Escherichia coli

source_name: salt

label_protocol: Standard Nimblegen protocol.

growth_protocol: incubated at 37 C under shaking conditions at 250 rpm until mid-log phase

extract_protocol: Total cellular RNA extracted after resuspension in TE buffer and incubated with 1 mg/ml lysozyme

treatment_protocol: cerium chloride 50 mg/L

tag: treatment

value: cerium chloride salt


title: E.coli_salt_4


title: E.coli_Nano_4

source_name: Nano

treatment_protocol: prewarmed cerium oxide nanoparticles

value: cerium oxide nanoparticles


title: 3T3-L1 adipocyte tissue culture, phenformin, biological rep3

status: Public on Aug 10 2010

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm.

data_processing:
The data was analysed using R  2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

The limma data are linked to the Series GSE17404 record as supplementary files 'GSE17404_limma_CLAvsLA.txt', 'GSE17404_limma_PFMvsLA.txt', and 'GSE17404_limma_PFMvsCLA.txt'.

source_name: 3T3-L1 adipocyte tissue culture, phenformin fed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell line

tag: cell type

value: adipocyte

value: phenformin


title: E.coli_salt_1


title: E.coli_Nano_2


title: E.coli_Nano_3


title: 3T3-L1 adipocyte tissue culture, LA, biological rep3

source_name: 3T3-L1 adipocyte tissue culture, LA fed

value: linoleic acid


title: T6PNE cells, E47 induced (1273001003_G)

status: Public on Aug 07 2010

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: no additional information

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing:
Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine
VALUE = Quantile-normalized signal

label: streptavidin Cy3

source_name: T6PNE cells were isolated from human fetal islets; E47 was induced by tamoxifen treatment

label_protocol: As suggested by illumina

growth_protocol: TRM 6  cells were derived from human fetal islets. They were engineered to express PDX-1, NeuroD1  and inducible E45. Both islets and T6PNE RPMI media with 5.5mM glucose 10% FBS and 1% pen/strep.

extract_protocol: Cells were harvested with RLT buffer and βME. RNA was extracted with  DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: E47 was induced in T6PNE with Tamoxifen (0.5-4µM). Islets were untreated.

value: pancreas islets

value: fetal islet cell line T6PNE

tag: protocol

value: E47 induction


title: 3T3-L1 adipocyte tissue culture, CLA, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, CLA fed

value: conjugated linoleic acid


title: E.coli_control_3

source_name: control

treatment_protocol: control

value: untreated


title: E.coli_control_4


title: 3T3-L1 adipocyte tissue culture, CLA, biological rep2


title: T6PNE cells, E47 induced (1273001003_C)

description: no additional information


title: 3T3-L1 adipocyte tissue culture, CLA, biological rep3


title: islets (1273001001_B)

description: no additional information

source_name: Human islets; untreated


title: T6PNE cells (1273001002_A)

description: no additional information

source_name: T6PNE cells were isolated from human fetal islets

value: uninduced


title: E.coli_control_1


title: E.coli_salt_2


title: E.coli_Nano_1


title: 3T3-L1 adipocyte tissue culture, LA, biological rep1


title: 3T3-L1 adipocyte tissue culture, phenformin, biological rep1


title: islets (1273001005_F)

description: no additional information


title: 3T3-L1 adipocyte tissue culture, LA, biological rep2


title: E.coli_control_2


title: 3T3-L1 adipocyte tissue culture, phenformin, biological rep2


title: T6PNE cells, E47 induced (1273001006_B)

description: no additional information


title: T6PNE cells (1354661001_E)

description: no additional information


title: islets (1273001005_B)

description: no additional information


title: T6PNE cells, E47 induced (1354661001_F)

description: no additional information


title: T6PNE cells, E47 induced (1354661001_A)

description: no additional information


title: T6PNE cells, E47 induced (1354661002_B)

description: no additional information


title: T6PNE cells (1354661002_C)

description: no additional information


title: T6PNE cells, E47 induced (1354661002_D)

description: no additional information


title: T6PNE cells (1354661001_G)

description: no additional information


title: RDX/0/B

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: RDX(rear)/CONTROLchallenge/Rep(B)

hyb_protocol: 1 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 021219_G2_D_F_20080811.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by 75th percentile shift and conduct baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.  The resulting gene list was utilized to conduct pair-wise comparisons to determine statistically significant differences in gene expression between control and RDX-exposed fish within each time point via unpaired t-test and 2-fold cutoff.

organism: Pimephales promelas

source_name: RDX(rear)/CONTROLchallenge

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The P. promelas sub-adults were exposed individually in a 1L glass beaker (n=6) for a period of 96-h with no renewal of the exposure water.  Temperature and photoperiod were kept the same as the chronic, year-long study.  Each beaker was aerated by trickle flow aeration using a glass pipette.

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The P. promelas were exposed individually in a 1L glass beaker (n=6) for a period of 96-h with no renewal of the exposure water.  Temperature and photoperiod were kept the same as the year-long, chronic study.  Each beaker was aerated by trickle flow aeration using a glass pipette.  The fish were not fed for the duration of this study.     Sub-adult fish were cut in half longitudinally with one half being immediately transferred to RNA Later (Ambion, Austin TX) and RNA fixed following manufacturer's recommendations for genomic analysis while the other half was flash frozen in liquid nitrogen and transferred to -70°C for later analytical chemistry analysis.

value: liver


title: Cont/0/E

description: CONTROL(rear)/CONTROLchallenge/Rep(B)

source_name: CONTROL(rear)/CONTROLchallenge


title: Cont/0/A

description: CONTROL(rear)/CONTROLchallenge/Rep(A)


title: Cont/5/E


title: RDX/5/B


title: RDX/0/C

description: RDX(rear)/CONTROLchallenge/Rep(C)


title: Cont/0/D

description: CONTROL(rear)/CONTROLchallenge/Rep(D)


title: Cont/5/F


title: RDX/0/A

description: RDX(rear)/CONTROLchallenge/Rep(A)


title: Cont/0/B

description: CONTROL(rear)/CONTROLchallenge/Rep(B)


title: Cont/0/F

description: CONTROL(rear)/CONTROLchallenge/Rep(F)


title: RDX/0/D

description: RDX(rear)/CONTROLchallenge/Rep(D)


title: Cont/0/C

description: CONTROL(rear)/CONTROLchallenge/RepC


title: RDX/5/D


title: RDX/0/E

description: RDX(rear)/CONTROLchallenge/Rep(E)


title: RDX/5/F


title: Cont/5/A


title: RDX/0/F

description: RDX(rear)/CONTROLchallenge/Rep(F)


title: RDX/5/A


title: Cont/5/D


title: RDX/5/C


title: Cont/5/B


title: T6PNE cells (1354661002_A)

description: no additional information


title: RDX, 9 month: 251959710083_GE1-v5_95_Feb07_1_4

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

source_name: RDX, 9 month

growth_protocol: Fathead minnow were maintained in 10 gallon aquaria including glass wool filtration systems, air stones, breeding substrates (3 PVC pipe cut in longitudinal section) where water changes were conducted every 28d.  Fish were fed frozen brine shrimp daily.

treatment_protocol: 2 male and 4 female adult fish were allocated to each experimental unit (10 gallon aquarium).  Eight experimental units were maintained as controls and another 8 were dosed with RDX that averaged 0.83mg/L over the course of the year long Assay.  5 male fish were collected from each the control and RDX-exposure condition at 1d, 1mo, 3mo, 6mo, 9mo, and 12 mo time periods.  Both liver and brain tissues were collected and immediately transferred to RNA Later (Ambion, Austin TX) and RNA fixed following manufacturer's recommendations.


title: RDX, 9 month: 251959710088_GE1-v5_95_Feb07_2_1


title: RDX/5/E


title: RDX, 6 month: 251959710088_GE1-v5_95_Feb07_2_4

source_name: RDX, 6 month


title: RDX, 6 month: 251959710089_GE1-v5_95_Feb07_1_4


title: RDX, 9 month: 251959710087_GE1-v5_95_Feb07_1_3


title: RDX, 9 month: 251959710085_GE1-v5_95_Feb07_1_2


title: RDX, 6 month: 251959710084_GE1-v5_95_Feb07_2_1


title: RDX, 12 month: 251959710088_GE1-v5_95_Feb07_1_3

source_name: RDX, 12 month


title: RDX, 3 month: 251959710084_GE1-v5_95_Feb07_1_4

source_name: RDX, 3 month


title: RDX, 9 month: 251959710086_GE1-v5_95_Feb07_1_3


title: RDX, 3 month: 251959710090_GE1-v5_95_Feb07_1_3


title: RDX, 1 day: 251959710090_GE1-v5_95_Feb07_1_1

source_name: RDX, 1 day


title: RDX, 12 month: 251959710086_GE1-v5_95_Feb07_2_1


title: RDX, 6 month: 251959710087_GE1-v5_95_Feb07_2_2


title: RDX, 3 month: 251959710089_GE1-v5_95_Feb07_2_2


title: RDX, 3 month: 251959710085_GE1-v5_95_Feb07_1_3


title: RDX, 3 month: 251959710088_GE1-v5_95_Feb07_1_1


title: RDX, 6 month: 251959710083_GE1-v5_95_Feb07_1_1


title: RDX, 12 month: 251959710087_GE1-v5_95_Feb07_1_1


title: RDX, 1 day: 251959710084_GE1-v5_95_Feb07_1_3


title: RDX, 1 day: 251959710084_GE1-v5_95_Feb07_2_3


title: RDX, 12 month: 251959710083_GE1-v5_95_Feb07_2_2


title: RDX, 1 day: 251959710088_GE1-v5_95_Feb07_2_2


title: RDX, 1 day: 251959710087_GE1-v5_95_Feb07_2_4


title: RDX, 1 month: 251959710086_GE1-v5_95_Feb07_2_3

source_name: RDX, 1 month


title: RDX, 1 month: 251959710089_GE1-v5_95_Feb07_1_1


title: RDX, 1 month: 251959710089_GE1-v5_95_Feb07_2_3


title: RDX, 1 month: 251959710085_GE1-v5_95_Feb07_2_1


title: RDX, 1 month: 251959710083_GE1-v5_95_Feb07_1_2


title: Control, 9 month: 251959710085_GE1-v5_95_Feb07_2_4

source_name: Control, 9 month


title: Control, 9 month: 251959710083_GE1-v5_95_Feb07_2_4


title: Control, 9 month: 251959710087_GE1-v5_95_Feb07_1_2


title: Control, 6 month: 251959710084_GE1-v5_95_Feb07_1_2

source_name: Control, 6 month


title: Control, 1 day: 251959710088_GE1-v5_95_Feb07_1_4

source_name: Control, 1 day


title: Control, 1 day: 251959710090_GE1-v5_95_Feb07_1_2


title: Control, 6 month: 251959710089_GE1-v5_95_Feb07_2_4


title: Control, 12 month: 251959710085_GE1-v5_95_Feb07_1_1

source_name: Control, 12 month


title: Control, 6 month: 251959710084_GE1-v5_95_Feb07_1_1


title: Control, 9 month: 251959710086_GE1-v5_95_Feb07_1_1


title: Control, 12 month: 251959710088_GE1-v5_95_Feb07_2_3


title: Control, 6 month: 251959710089_GE1-v5_95_Feb07_1_2


title: Control, 1 day: 251959710089_GE1-v5_95_Feb07_1_3


title: Control, 9 month: 251959710089_GE1-v5_95_Feb07_2_1


title: Control, 1 day: 251959710084_GE1-v5_95_Feb07_2_4


title: Control, 6 month: 251959710086_GE1-v5_95_Feb07_1_4


title: Control, 1 day: 251959710085_GE1-v5_95_Feb07_2_2


title: Control, 12 month: 251959710087_GE1-v5_95_Feb07_2_3


title: Control, 12 month: 251959710087_GE1-v5_95_Feb07_2_1


title: Control, 12 month: 251959710085_GE1-v5_95_Feb07_2_3


title: Control, 1 month: 251959710086_GE1-v5_95_Feb07_2_4

source_name: Control, 1 month


title: Control, 1 month: 251959710090_GE1-v5_95_Feb07_1_4


title: Cont/5/C


title: 13747864_R9B_1

description: RDX, 9 month vs Reference

hyb_protocol: Products of the cDNA synthesis reactions were hybridized onto microarrays.  Two µL of blocking agent, locked nucleic acid (LNA) dT Blocker (Genisphere) was included in each hybridization.  RNA sample probes were hybridized at 55 ºC overnight (~16h) then washed for 20 min in 60 ºC 2x standard saline citrate (SSC) including 0.2% sodium dodecyl sulfate (SDS), 20 min in 2x SSC at room temperature, and 20 min in 0.2x SSC also at room temperature.  Slides were then spin dried for 2 min at 800 rcf.  Slides were subsequently hybridized to A647 and Cy3 labeled secondary hybridization probes in 100 µL hybridization buffer with 1 µL of Anti-Fade Reagent for 4h at 60ºC.  reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.  Grids were manually fit to microarray spots using GenePix Software (Molecular Devices).  Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from analysis.

data_processing: Data were LOWESS-normalized using Acuity Software (Molecular Devices) providing Cy3:A647 ratio values calculated using background-normalized median-signal intensities.  Statistical analyses were conducted using Bayesian Analysis of Gene Expression Levels (BAGEL) software version 3.62 (Townsend and Hartl, 2002).  Non-overlapping 97.5% confidence intervals (C.I.) among treatments were established a priori as statistically significant differences in expression.

label_protocol: Experimental samples were labeled with Cyanine-3 (Cy3) and the Reference fathead minnow brain samples were labeled with A647 dye.  Probes for microarray hybridizations were prepared from 500 ng total RNA / sample following the Genisphere®, Array 900™ Alexa Fluor 647 and Cy3 secondary hybridization labeling protocol (Genisphere, Hatfield, PA) according to the manufacturer’s instructions.

value: brain

source_name: Reference Sample

value: Pooled brain tissue reference used for main experiment


title: 13747860_R9B_3

description: RDX, 9 month vs Reference


title: 13747861_R9B_4

description: RDX, 9 month vs Reference


title: 13722795_r6b2

description: RDX, 6 month vs Reference


title: 13759400_r3b3

description: RDX, 3 month vs Reference


title: Control, 1 month: 251959710085_GE1-v5_95_Feb07_1_4


title: 13722591_r3b4

description: RDX, 3 month vs Reference


title: 13722786_r3b1

description: RDX, 3 month vs Reference


title: Control, 1 month: 251959710086_GE1-v5_95_Feb07_1_2


title: 13747862_R9B_5

description: RDX, 9 month vs Reference


title: Control, 1 month: 251959710084_GE1-v5_95_Feb07_2_2


title: 13748243_r1db5

description: RDX, 1 day vs Reference


title: 13748236_r6b1

description: RDX, 6 month vs Reference


title: 13722781_r6b5

description: RDX, 6 month vs Reference


title: 13759715_r1db2

description: RDX, 1 day vs Reference


title: 13748242_r1db4

description: RDX, 1 day vs Reference


title: 13748245_r1db3

description: RDX, 1 day vs Reference


title: 13759370_r1db1

description: RDX, 1 day vs Reference


title: 13747879_R12B_1

description: RDX, 12 month vs Reference


title: 13748234_r6b3

description: RDX, 6 month vs Reference


title: 13747873_R12B_4

description: RDX, 12 month vs Reference


title: 13747878_R12B_5

description: RDX, 12 month vs Reference


title: 13748249_r6b4

description: RDX, 6 month vs Reference


title: 13747859_R9B_2

description: RDX, 9 month vs Reference


title: 13747868_R12B_2

description: RDX, 12 month vs Reference


title: 13722779_r1b2

description: RDX, 1 month vs Reference


title: 13748258_r1b4

description: RDX, 1 month vs Reference


title: 13722576_r1b1

description: RDX, 1 month vs Reference


title: 13747869_R12B_3

description: RDX, 12 month vs Reference


title: 13747863_C9B_1

description: Control, 9 month vs Reference


title: 13748254_c6b2

description: Control, 6 month vs Reference


title: 13759397_r1b5

description: RDX, 1 month vs Reference


title: RDX, 12 month: 251959710083_GE1-v5_95_Feb07_2_3


title: 13747854_C9B_4

description: Control, 9 month vs Reference


title: 13759369_c6b3

description: Control, 6 month vs Reference


title: 13747857_C9B_3

description: Control, 9 month vs Reference


title: 13759366_c3b5

description: Control, 3 month vs Reference

source_name: Control, 3 month


title: 13760153a_c3b3_2ndscan

description: Control, 3 month vs Reference


title: 13719431_c3b4

description: Control, 3 month vs Reference


title: 13747883_C9B_2

description: Control, 9 month vs Reference


title: 13760154_r1b3

description: RDX, 1 month vs Reference


title: 13748238_c6b1

description: Control, 6 month vs Reference


title: 13722785_c1db5

description: Control, 1 day vs Reference


title: 13748235_c1db2

description: Control, 1 day vs Reference


title: 13747856_C9B_5

description: Control, 9 month vs Reference


title: 13722575_c6b5

description: Control, 6 month vs Reference


title: 13722796_c1db3

description: Control, 1 day vs Reference


title: 13759399_c1db1

description: Control, 1 day vs Reference


title: 13722783_c3b2

description: Control, 3 month vs Reference


title: 13747876_C12B_4

description: Control, 12 month vs Reference


title: 13747877_C12B_3

description: Control, 12 month vs Reference


title: 13748260_c3b1

description: Control, 3 month vs Reference


title: 13747875_C12B_5

description: Control, 12 month vs Reference


title: 13748256_c1b4

description: Control, 1 month vs Reference


title: 13719428_c1b2

description: Control, 1 month vs Reference


title: 13747874_C12B_1

description: Control, 12 month vs Reference


title: 13759368_c3b2

description: Control, 3 month vs Reference


title: 13760087_c1b3

description: Control, 1 month vs Reference


title: 13748252_c1db4

description: Control, 1 day vs Reference


title: 13722784_c1b5

description: Control, 1 month vs Reference


title: 13564930_refvsref

description: Reference vs Reference


title: 13564929_refvsref

description: Reference vs Reference


title: 13564924_refvsref

description: Reference vs Reference


title: 13747872_C12B_2

description: Control, 12 month vs Reference


title: 13564908_refvsref

description: Reference vs Reference


title: 13564927_refvsref

description: Reference vs Reference


title: 13759398_c1b1

description: Control, 1 month vs Reference


title: 13722791_r3b5

description: RDX, 3 month vs Reference


title: Gill_19C_steadyacclim_rep6

status: Public on Jul 15 2010

city: Pacific Grove

first: Cheryl

last: Logan

address: 120 Ocean View Blvd

institute: Stanford University

hyb_protocol: Hybridizations were conducted overnight at 65°C in Genetix (Boston, MA, USA) humid hybridization chambers. After hybridization, slides were washed by repeated vigorous immersion in 0.5x SSC and 0.01% SDS for 2 min to remove unbound dye. Slides were then washed in 0.6x SSC on a shaker for 15 min and dried by centrifugation.

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner in GenePix 4.0 (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing: Raw data for each gene (median pixel intensity of each spot with background correction) were imported from GenePix 4.0 into GeneSpring version 7.3 (Silicon Genetics, Redwood, CA, USA) for subsequent analysis. We normalized the data using intensity-dependent locally weighted linear regression (lowess) transformation to correct for spatial variation in the array due to inconsistencies in printing pins, slide surface variability, and differences in local hybridization conditions across a slide. We normalized and filtered our data in Genespring 7.3. To obtain a set of reliable genes from the normalized data, we discarded all probes that were flagged as irregular by Genepix 4.0 software or by hand (irregularities are generally due to specks of dust or scratches on slides) and genes that showed standard deviations of >1.4. All subsequent analyses were performed on this filtered list comprising 7,488 probes.

organism: Gillichthys mirabilis

source_name: Gillichthys mirabilis, gill tissues, 19C acclim,1 month

label_protocol: Single stranded cDNA was labeled with either Cy3 (reference samples) or Cy5 (acclimation samples) cyanine monoreactive dye (Amersham, Piscataway, NJ, USA), prepared in 80 µl of dimethylsulfoxide.

extract_protocol: Total RNA was extracted from gill tissue using the Qiagen Tissuelyser for homogenization and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).  Total RNA was determined by A260 absorbance using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA).  Samples were run on 1% agarose gels to confirm RNA integrity. 15 µg of total RNA from each sample were reverse transcribed with 3 µl of AffinityScript enzyme (Agilent Technologies, Santa Clara, CA, USA), 0.75 µl oligo(dT15) and 0.75 µl pdN9 random hexamer primers, and amino-allyl modified dNTPs. RNA templates were removed from the RT reactions by incubation at 65°C for 30 min in 0.2 mol l-1 NaOH and 0.1 mol l-1 EDTA. cDNA was precipitated at -80°C for 20 min in 4.5 µl 3M sodium acetate and 2.5 volumes on 100% ethanol. Samples were centrifuged at 10,000 rpm for 20 min at 4°C and resuspended in 8 µl of nuclease free water and 2 µl of fresh 0.5 M sodium bicarbonate.

tag: temperature

tag: tissue type

value: Gill tissue

source_name: Gillichthys mirabilis, gill tissue, flow-through seawater tank (~13C), pooled total RNA for reference

tag: reference


title: Gill_28C_steadyacclim_rep3

source_name: Gillichthys mirabilis, gill tissues, 28C acclim,1 month

value: flow-through seawater tank (~13C), pooled total RNA


title: Gill_19C_steadyacclim_rep3


title: Gill_28C_steadyacclim_rep5


title: Gill_28C_steadyacclim_rep7


title: Gill_9C_steadyacclim_rep9

source_name: Gillichthys mirabilis, gill tissues, 9C acclim,1 month


title: Gill_28C_steadyacclim_rep4


title: Gill_9C_steadyacclim_rep5


title: Gill_19C_steadyacclim_rep5