title: 9_182; Sample ID: M9_M182

status: Public on Apr 18 2007

city: Delhi

first: Anu

last: Sharma

email: anukaush@gmail.com, ramuigib@gmail.com

state: Delhi

address: Mall Road, Near Jubilee Hall

department: Functional Genomics Unit,

country: India

institute: Institute of Genomics and Integrative Biology

description: Normalized and background corrected intensities were used for comparison studies. A brightness (intensity) threshold of 1000 units was used to filter very low intensity spots. The hybridization to spots was screened on the basis of reproducibility in duplicates. Spots that had less than 50% variation in intensity among duplicates were taken for further analysis. Average Cy5/Cy3 ratio was calculated for each spot and the observations for all the experiments of were collated in a single MS-Excel file. The genes were further classified on the basis of fold change variation they showed. The genes varying between 0.5-2 fold were considered as equally expressed. Genes that differed at >2 fold or at <0.5 fold were classified as increase in expression or decrease in expression with respect to a given sample respectively . The genes were also classified into 6 different functional classes namely, ‘Information’, ‘Cell cycle’, ‘Metabolism’, ‘Signalling and communication’, ‘Immune and related functions’ and ‘Structure and motility’

hyb_protocol: Equal amounts of labelled targets (7 ul each) were mixed along with 20 ug human cot-1 DNA and were denatured in boiling water bath for about 2 minutes. Equal volume of hybridization buffer (50% formamide, 10X SSC and 0.2 % SDS) was added to the denatured labelled targets. The labelled cDNA targets were pipetted onto the microarray, covered by a coverslip and kept in Corning’s hybridization chamber in a water bath maintained at 42 oC for 16-18 hours for hybridization. The stringency washes were performed at room temperature and according to manufacturer’s protocol. Microarray slide was first immersed in 0.5X SSC, 0.01% SDS wash solution to remove the coverslip from the array and then transferred to another conical 50 ml tube containing the 30 ml of the same wash solution. It was washed with gentle shaking for 5 minutes and subsequently transferred to other tube containing 30 ml of 0.06X SSC, 0.01% SDS and again washed with gentle shaking for 5 minutes. Lastly the microarray slide was transferred to tube containing 30 ml of 0.06X SSC and washed with gentle shaking for 2 minutes. After the stringency washes the detection of microarray spots is carried out using TSA. The details of the reagents used for TSA detection are listed in Appendix I. The procedure for TSA detection is as under •	Blocking: Slide was blocked by overlaying with 600ul of TNB buffer (0.1 M Tris-HCl, pH 7.5, 0.15 M NaCl, 0.5% blocking reagent) and incubating for 10 minutes. The slide was then washed with 30 ml of TNT buffer (0.1 M Tris-HCl, pH 7.5, 0.15 M NaCl, 0.05% Tween-20) for 1 minute with gentle shaking. •	Introduction of HRP: Slide was incubated with 300 ul of Anti-FL-HRP conjugate solution for 10 minutes, followed by washing 3 times with 30 ml of TNT buffer for 1 minute each. This antibody-HRP conjugate binds specifically to the hybridized fluorescein labelled cDNA. •	Introduction of Cyanine 3 Tyramide: Microarray slide was incubated with 300 ul of cyanine-3-tyramide solution for 10 minutes and the slide rinsed 3 times with 30 ml of TNT buffer for 5 minutes each. HRP catalyses the local deposition of cyanine 3 labelled tyramide. This being an enzymatic process, the amount of tyramide relative to fluorescein labelled cDNA is greatly amplified. •	HRP Inactivation: Slide was incubated with 300 ul of HRP Inactivation solution for 10 minutes and subsequently washed 3 times with 30 ml of TNT buffer for 1 minute. This is done to inactivate the residual HRP. •	Introduction of HRP: Slide was incubated with 300 ul of Streptavidin-HRP conjugate solution for 10 minutes, followed by washing 3 times with 30 ml of TNT buffer for 1 minute each. This antibody-HRP conjugate binds specifically to the hybridized biotin labelled cDNA. •	Introduction of Cyanine 5 Tyramide: Microarray slide was incubated with 300 ul of cyanine-5-tyramide solution for 10 minutes and the slide is rinsed 3 times with 30 ml of TNT buffer for 5 minutes each. In this case also, the amount of tyramide relative to biotin labelled cDNA is greatly amplified. Another wash with 30ml of 0.06X SSC is given for 1 minute. •	Dry Slide: The slide was spin dried at a low centrifuge speed at room temperature in a 50 ml conical tube.

scan_protocol: All the hybridized cDNA microarray slides were scanned with ScanArray Lite microarray scanner (Packard BioSciences) at a resolution of 10 microns. The scanner has in-built two lasers of wavelengths of 543nm and 633nm corresponding to excitation wavelengths of Cyanine 3 and Cyanine 5 dyes respectively. The laser power and PMT gain of the scanner was decided by doing a ‘line scan’ on selected spots as suggested by the manufacturer. These spots were generally positive control genes, housekeeping genes like beta-actin that had been printed on the microarray along with other gene probes. In the line scan, intensity for the selected spots was compared for both Cy3 and Cy5 channels, and the power and PMT gain was adjusted to make the intensity values approximately same. The default values for power and PMT gain was set at 80%. For most of the microarray slides, power setting of 60% and PMT gain settings of 75% worked successfully. The images were acquired for both Cy3 and Cy5 channels by ScanArray software (Packard BioSciences, USA). Quantification of the images was carried out by QuantArray software (Packard BioSciences, USA). Grid patterns of the different microarrays used in the study,  Hu2304, Hu800  were fed to QuantArray to generate a composite image for relative comparisons of gene expression between the two samples. The spots were sometimes adjusted manually in the grid; very low-intensity spots, bad spots or smudged spots were flagged not to be included in Quantitation of the image. Adaptive circle segmentation method was used for Quantitation . Spot intensity was calculated by subtracting background signal from the foreground signal. The raw comparison data obtained was stored as a tab delimited ‘text’ file and used for subsequent analysis.

data_processing: Raw data was normalized against whole slide intensity in all the cases. This normalization was done by an in-built tool in QuantArray software using background subtracted intensity values for each spot. A normalization factor was calculated taking Cy3 values as baseline and Cy5 values were re-scaled according the calculated normalization factor. The fold change was calculated based on the background corrected and normalized intensity values in the ratio of Cy5/Cy3.

source_name: M9 blood leukocytes

label_protocol: An indirect labeling procedure described in Tyramide signal amplification kit (PE Lifesciences) was used to label targets during first strand synthesis. About 5ug total RNA sample was used per reaction and labelled with Biotin or Fluorescein dCTP during first strand synthesis using the reaction mix concentrate and labelled nucleotide provided in the kit. A small modification in the protocol was done by increasing the amount of reaction mix and biotin/fluorescein nucleotide to 2 ul instead of 1 ul. This was done to compensate for a still high amount of RNA used by us compared to amount suggested by the manufacturer (5 ug vs. 2 ug). Both the biotin and fluorescein labelled first strand cDNAs were separately purified by precipitation by adding 0.8 volumes of isopropanol, in the presence of 0.3M Ammonium acetate and 5 ug glycogen. Mix was vortexed and incubated at 4 oC for 30 minutes and centrifuged at 12,000 g for 15 minutes to collect the pellet. The pellet was subsequently washed twice with 100 ul of cold 70% ethanol. Washed pellet was air-dried and resuspended in 8 ul sterile water. 1ul of the labelled cDNA was analysed for incorporation of label by comparing with pre-labelled controls provided by manufacturer and the rest of the cDNA is stored at –20 oC till further use. Equal amounts of labelled targets (7 ul each) were mixed along with 20 ug human cot-1 DNA and were denatured in boiling water bath for about 2 minutes. Equal volume of hybridization buffer (50% formamide, 10X SSC and 0.2 % SDS) was added to the denatured labelled targets. The labelled cDNA targets were pipetted onto the microarray, covered by a coverslip and kept in Corning’s hybridization chamber in a water bath maintained at 42 oC for 16-18 hours for hybridization. The stringency washes were performed at room temperature and according to manufacturer’s protocol. Microarray slide was first immersed in 0.5X SSC, 0.01% SDS wash solution to remove the coverslip from the array and then transferred to another conical 50 ml tube containing the 30 ml of the same wash solution. It was washed with gentle shaking for 5 minutes and subsequently transferred to other tube containing 30 ml of 0.06X SSC, 0.01% SDS and again washed with gentle shaking for 5 minutes. Lastly the microarray slide was transferred to tube containing 30 ml of 0.06X SSC and washed with gentle shaking for 2 minutes.

extract_protocol:
15ml of the total 20ml collected blood was used to isolate total RNA from white blood cells (WBCs) to carry out microarray experiments. Since RNA is very sensitive to degradation all precautions like use of fresh sterile gloves was used to prevent degradation of total RNA during the isolation procedure. All the reagents used for RNA isolation were prepared in diethylpyrocarbonate (DEPC) treated water and RNase, DNase  free plasticware was used.

Blood was transferred to Nuclease free 50ml conical centrifuge tubes and RBCs were lysed by adding 45ml of ice-cold 1X RBC lysis buffer (150mM NH4Cl, 10mM NaHCO3, 1mM EDTA, pH 8.0) per 5ml of whole blood. WBC pellet was collected by centrifuging at 250g for 10 min at 40oC and removing the supernatant. EZ-RNA isolation kit from Biological Industries, Israel, was used to isolate RNA from the WBC pellet. The kit is based on the protocol described by Chomczynski and Sacchi (1987). 500ul of solution A (containing guanidine thiocynate) of the kit was added to the cell pellet obtained from 5 ml of blood. The pellet was suspended in solution A and transferred to a 1.5 ml nuclease free microfuge tube and the mix kept at room temperature for 5 minutes. 500ul of solution B (acidic Phenol and chloroform mixture) was added after incubation and mixed thoroughly and further incubated at room temperature for 10 minutes. The mixture was centrifuged at 12,000 g for 15 minutes at 40oC to separate the aqueous layer containing total RNA from the organic layer. The aqueous layer was transferred to a fresh 1.5 ml tube and equal volume of isopropanol was added to precipitate the RNA. The contents of the tube were mixed by vortexing and kept at –200oC overnight for efficient precipitation of total RNA. The RNA pellet was collected by centrifuging the contents at 12,000 g for 15 minutes and washed twice by 70% ice-cold ethanol. The pellet was dried and dissolved in 20ul DEPC treated water and kept at 650oC dry bath for not more than 2 hours for dissolving the pellet.

The quality of RNA was checked for its integrity and any contamination of genomic DNA by quick electrophoresis run on 1% agarose TAE gel. 2ul of the isolated total RNA was loaded on 1% agarose gel prepared in DEPC treated 1X TAE buffer and electrophoresced at 100V for not more than 10 minutes. RNA was kept at –700oC until further use.

tag: 37 yr old normal male

source_name: M182 blood leukocytes

tag: 58 yr old normal male


title: JIR1212 gdn44

status: Public on May 01 2007

type: genomic

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

description: Random primers were annealed to 2ug of restriction-digested genomic DNA and labelled and unlabelled nucleotide were added using Klenow polyermase.

data_processing: Expression and p-values are attached to series file

molecule: genomic DNA

organism: Dichelobacter nodosus

tag: D. nodosus strain JIR1212

source_name: JIR3356 wild-type

tag: D. nodosus wild-type strain JIR3356


title: JIR1201 gdn38

tag: D. nodosus strain JIR1201

tag: Wild-type strain


title: JIR1212 gdn40

tag: D. nodosus wild-type JIR3356


title: olfactory epithelium with out OMP-GFP expressing OSNs

status: Public on Apr 30 2007

type: RNA

city: Lexington

first: Neeraja

last: Sammeta

state: KY

address: 800 Rose Street,

department: Physiology

country: USA

institute: University of Kentucky

description: RNA isolated from approximately 2,500,000 cells cells

hyb_protocol: According to the instructions provided  in Affymetrix Genechip expression analysis technical manual.

data_processing: Using MAS5.0, scaled to 500

label: Biotin-Strptavidin-Phycoerythrin

molecule: total RNA

organism: Mus musculus

source_name: olfactory epithelium without mature OSNs from OMP-GFP mice

label_protocol: According to the instructions provided for eukaryotic one cycle target labeling in Affymetrix Genechip expression analysis technical manual.

growth_protocol: Normal laboratory animal rearing conditions

extract_protocol: RNA extraction using TRI reagent from Molecular Research Center Inc

tag: Strain- Mixed 129XC57Bl6

tag: Gender -Both male and female

tag: Age - P10

tag: Tissue- OE with out mature OSNs


title: cueO 2500V

status: Public on Apr 28 2007

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Triplicate cultures of E. coli MG1655 and the isogenic cueO mutant were grown to mid-exponential phase (OD600 0.8) in M9C supplemented with 2M FeSO4. RNA was extracted using Qiagen RNAprotect and RNeasy Mini Kit. Reference RNA was similarly purified from triplicate cultures of E. coli MG1655 grown on M9C supplemented with 2M FeCl3. RNA concentration and quality was assessed using an Aligent Bioanalyser 2100 NanoLabchip.

data_processing: Raw data, prior to normalisation

organism: Escherichia coli

source_name: cueO mutant + Fe(II)

tag: Strain

value: MG1655 cueO mutant

tag: OD

tag: Media

value: Minimal - M9C

source_name: wt + Fe(II)

value: MG1655 wild type


title: olfactory epithelium with out OMP-GFP expressing OSNs on Chip B

description: RNA isolated from approximately 2,500,000 cells

hyb_protocol: According to the instructions provided in Affymetrix Genechip expression analysis technical manual

data_processing: Using MAS 5.0, scaled to 500

label: Biotin-Streptavidin-Phycoerythrin

source_name: Olfactory epithelium without mature OSNs from OMP-GFP mice

label_protocol: According to the instructions provided for eukaryotic one cycle target labeling in Affymetrix Genechip expression analysis technical manual

tag: Strain - Mixed 129XC57Bl6

tag: Gender- Both Male and Female

tag: Age -P10


title: 18_19; Sample ID: F18_F19

organism: Homo sapiens

source_name: F18 blood leukocytes

tag: 41 yr old normal female

source_name: F19 blood leukocytes


title: cueO 1500V

description: Triplicate cultures of E. coli MG1655 and the isogenic cueO mutant were grown to mid-exponential phase (OD600 0.8) in M9C supplemented with 2M FeSO4. RNA was extracted using Qiagen RNAprotect and RNeasy Mini Kit. Reference RNA was similarly purified from triplicate cultures of E. coli MG1655 grown on M9C supplemented with 2M FeCl3. RNA concentration and quality was assessed using an Aligent Bioanalyser 2100 NanoLabchip. Microarrays,

value: minimal - M9C

value: Mininal - M9C


title: 15_185; Sample ID: F15_M185

source_name: F15 blood leukocytes

tag: 26 yr old normal female

source_name: F185 blood leukocytes

tag: 23 yr old normal male


title: OMP-GFP homozygous 1

description: OE from mice homozygous for OMP-GFP

hyb_protocol: According to the instructions provided in the Affymetrix Gene Chip expression analysis technical manual

source_name: olfactory epithelium

label_protocol: According to the instructions for eukaryotic one cycle target labeling provided in the Affymetrix Gene Chip expression analysis technical manual

extract_protocol: Using TRI reagent from Molecular Research Center Inc

tag: strain- Mixed 129XC57bl6

tag: Gender- Both male and female

tag: Age -P11

tag: Tissue - olfactory epithelium


title: OMP-GFP positive Olfactory sensory neurons on B chip

description: RNA isolated from approximately 500,000 cells

scan_protocol: According to the instructions provided in Affymetrix Genechip expression analysis technical manual

source_name: FACS sorted OSNs from OMP-GFP mice

tag: strain - Mixed 129X C57Bl6

tag: Gender- both male and female

tag: Age- P10

tag: Tissue- FACS sorted mature OSNs


title: JIR1201 gdn42

tag: D. nodosus strain JIR1201

tag: Wild-type D. nodosus JIR3356


title: OMP-GFP heterozygous 3

description: OE from mice heterozygous for OMP-GFP

scan_protocol: According to the instructions provided in the Affymetrix Gene Chip expression analysis technical manual

source_name: Olfactory epithelium

tag: strain - mixed 129XC57Bl6

tag: Age- P11

tag: Tissue- Olfactory epithelium


title: 15_184; sample ID: F15_F184

source_name: F184 blood leukocytes

tag: 23 yr old normal female


title: 19_24; Sample ID: F19_F24

tag: 41 yr old normal female

source_name: F24 blood leukocytes

tag: 33 yr old normal female


title: OMP-GFP homozygous 3

description: OE from mice homozygous for OMP-GFP

tag: Strain- Mixed 129XC57Bl6

tag: Tissue- olfactory epithelium


title: 18_23; Sample ID: F18_M23

source_name: M23 blood leukocytes

tag: 39 yr old normal male


title: 18_22; Sample ID: F18_M22

source_name: M22 blood leukocytes

tag: 10 yr old normal male child


title: OMP-GFP homozygous 2

description: OE from mice homozygous for OMP-GFP

tag: Gender- Both male and female

tag: Tissue - olfactory epithelium


title: 15_183; sample ID: F15_F183

tag: 26 yr old normal female

source_name: F183 blood leukocytes

tag: 51 yr old normal female


title: cueO 3500V

tag: Strain

tag: OD

tag: Media


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger67

status: Public on Jun 01 2007

type: mixed

city: Stanford

first: Susan

middle: Nelle

last: Thayer

state: CA

address: 260 Panama St.

department: Plant Biology

institute: Carnegie Institution of Washington

hyb_protocol: The combined labeled G. dissectum cDNA samples and Arabidopsis genomic DNA were hybridized to the microarrays in a hybridization buffer containing 0.16 µg yeast tRNA, 0.47 µg PolyA, 0.02 µg PolyT in 5X SSC, 25% formamide and 0.3% SDS in a total of 42.47 uL in a 42°C water bath for 16 h using ArrayIt Hybridization Cassettes. After hybridization, slides were washed sequentially with 2X SSC/0.03% SDS, followed by 1X SSC then 0.05X SSC (2 minutes each) and spun dry before scanning.

scan_protocol: Used a Genepix (Axon) 4000B scanner (Molecular Devices, Sunnyvale, CA). Images were quantified using SpotReader Software (Niles Scientific, Portola Valley, CA)

data_processing: Only features having >90% of Ch1 pixels above background were included. Flagged (saturated, low signal or bad) features were omitted, arrays were print tip normalized in Genespring v7.2 (Agilent Technologies), quantile normalized using Microsoft Excel, features with normalized Ch2/Ch1 ratio <0.65 omitted.

organism: Arabidopsis thaliana

source_name: Columbia strain

label_protocol: We labeled 2 ug of the Arabidopsis genomic DNA using random primers, the Klenow enzyme (Amersham) and Cy5 dUTP (Amersham). The reaction products were purified using QiaQuick columns (Qiagen)and concentrated in a speed vac.

growth_protocol: sterilized seeds grown axenically on agar

extract_protocol: Tissue was ground in liquid nitrogen and extracted using an equal volume of buffer containing 100 mM Tris pH 8.0, 50 mM EDTA, 750 mM NaCl and 10 mM ?-mercaptoethoanol. Per 15 mL extraction buffer, 1 mL 20% SDS and 50 uL 20 mg/mL Proteinase K were added and incubated at 65 ºC for 20-30 min. with gentle mixing 2-3 times during incubation. To this 1/7 volume 5 M NaCl was added and mixed gently. Then 0.1 volume 10% hexadecyltrimethylammonium bromide (CTAB), 0.7 M NaCl was added, mixed gently, incubated at 37 ºC for 15-30 min., and then extracted with chloroform/isoamyl alcohol (24:1, vol:vol). To the aqueous phase, 0.1 volume 10% CTAB, 0.7M NaCl was added; mixed gently and re-extracted with chloroform:isoamyl alcohol. To the aqueous phase, 2 volumes of 1% CTAB, 100 mM Tris pH 8.0, 50 mM EDTA was added to precipitate the DNA. After overnight incubation at 37 ºC, the precipitate was suspended in 10 mM Tris pH 8.0, 10 mM EDTA containing 1 M NaCl, warming to 65 ºC as needed. The DNA was precipitated in isopropanol, dried and treated with RNaseA. The DNA was precipitated and washed with 70% ethanol.

tag: genomic DNA sheared to 1000 bp

organism: Geranium dissectum

source_name: Total RNA from multiple individuals in experimental field plot.

label_protocol: cDNA was made from 18.6 to 50 µg of total RNA using Invitrogen Superscript II. Any remaining RNA was then degraded with RNase A and H. cDNAs were purified using Microcon YM-30 columns (Millipore). We labeled the second strand using random primers, the Klenow enzyme (Amersham) and Cy5 dUTP (Amersham). The reaction products were purified using QiaQuick columns (Qiagen)and concentrated using a speed vac.

growth_protocol: natural grassland plants grown in 2001-2002 growing season subjected to 4 global change factors each at 2 levels: ambient or elevated CO2, ambient temperature or ambient + 1 degree C warming, natural rainfall (601.2 mm/yr) or natural rainfall supplemented with 50% of every storm added immediately following each storm with a 3 week season extension, ambient growth nitrogen or ambient supplemented with 7 g N m-2 y-1, supplied as Ca(NO3)2. There were 16 treatments applied in a nested design.

extract_protocol: Tissue ground in liquid nitrogen and then homogenized and extracted using a CTAB-based extraction buffer (Pine Tree Method, Chang and Puryear, 1993). Following two chloroform:isoamyl alcohol extractions, the RNA was precipitated overnight at 4°C, after adding isopropanol and 0.8M sodium citrate/1.2M sodium chloride using half the volume of the aqueous phase each. The precipitate was washed with cold 75% ethanol and resuspended in nuclease-free water. Genomic DNA and a contaminant that was labeled by Cy dyes were removed by precipitation with 2M LiCl for 1 h at -20°C.

tag: naturally growing in Jasper Ridge Global Change experiment, Stanford, CA

tag: leaf tissue

tag: harvested between 10 AM and 2 PM

tag: plants were vegetative at time of harvest


title: OMP-GFP heterozygous 1

description: OE from mice heterozygous for OMP-GFP

tag: Strain - Mixed 129/C57Bl6

tag: Gender - Both male and female

tag: Age -P11


title: Brain tissue without olfactory bulb

description: Olfactory bulbs are excluded from brain tissue

hyb_protocol: According to the instructions provided  in affymetrix Genechip expression analysis technical manual

data_processing: Using MAs 5.0, scaled to 500

source_name: Brain with out olfactory bulb from OMP-GFP mice

label_protocol: According to the instructions provided for eukaryotic one cycle target labeling in affymetrix Genechip expression analysis technical manual

growth_protocol: Normal laboratory animal rearing condition

tag: Strain- Mixed 129XC57Bl6 mice

tag: Gender - Both male and Female

tag: Age- P10

tag: Tissue-Brain with out Olfactory bulb


title: OMP-GFP heterozygous 2

description: OE from mice heterozygous for OMP-GFP

tag: Strain -Mixed 129XC57Bl6

tag: Gender- both male and female

tag: Tissue - olfactory epithelium


title: Brain tissue without olfactory bulb on Chip B

description: RNA isolated from brain with out olfactory bulb

tag: Strain - 129xC57Bl6 mice

tag: Gender- Both Male and Female

tag: Tissue- Brain with out olfactory bulbs


title: MicroRNA Gene Expression in Human Uterine Leiomyomata41

status: Public on Apr 15 2007

city: Newark

first: Tongsheng

last: Wang

state: NJ

address: 225 Warren Street

department: Center For Applied Genomics

institute: Public Health Research Institute

description: Human Uterine Leiomyomata tissue sample 41

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: The raw data were normalized following the guidelines in Ambion mirVanaTM instruction manual (version 0508). A global normalization factor was calculated after applying the following filters to the data: 1) the ratio of means should be in the range 0.2-5.0 to exclude extreme outliers; 2) the sum of median intensities should be greater than 500 to exclude low intensities spots; 3) fewer than 10% of the pixels in a probe spots are saturated. A scaling factor was calculated so that the mean of the ratio of medians (635/532) of the selected miRNAs was equal to one. This scaling factor was then applied to the whole dataset.

source_name: Human matched myometrium tissue

label_protocol: Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail to the 3’ end of each miRNA sample. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy3 dyes (Amersham Bioscience, Piscataway, NJ). Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure

growth_protocol: matched myometrium tissue as control from patients with clinic infomation in age, tumor size, ethnicity, etc.

extract_protocol: Total RNA isolation and small RNA enrichment procedure were performed with the mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX.) according to the manufacturer’s instructions. To isolate miRNA enriched RNA fractions, total RNA samples were fractionated and cleaned up with filter cartridge spin column and different ethanol concentrations per the manufacturer’s recommendation. From 20 to 50 ug of total RNA about 3-8 ug small RNA enriched RNA was recovered. RNA less than 200 nt were quantitatively examined on 20% urea denaturing acrylamide gel.

tag: Human uterine leiomyomata tissue from patients with clinic infomation in age, tumor size, ethnicity, etc.


title: MicroRNA Gene Expression in Human Uterine Leiomyomata51

description: Human Uterine Leiomyomata tissue sample 51


title: MicroRNA Gene Expression in Human Uterine Leiomyomata38

description: Human Uterine Leiomyomata tissue sample 38


title: MicroRNA Gene Expression in Human Uterine Leiomyomata40

description: Human Uterine Leiomyomata tissue sample 40


title: MicroRNA Gene Expression in Human Uterine Leiomyomata50

description: Human Uterine Leiomyomata tissue sample 50


title: MicroRNA Gene Expression in Human Uterine Leiomyomata49

description: Human Uterine Leiomyomata tissue sample 49


title: MicroRNA Gene Expression in Human Uterine Leiomyomata43

description: Human Uterine Leiomyomata tissue sample 43


title: MicroRNA Gene Expression in Human Uterine Leiomyomata45

description: Human Uterine Leiomyomata tissue sample 45


title: MicroRNA Gene Expression in Human Uterine Leiomyomata46

description: Human Uterine Leiomyomata tissue sample 46


title: MicroRNA Gene Expression in Human Uterine Leiomyomata44

description: Human Uterine Leiomyomata tissue sample 44


title: MicroRNA Gene Expression in Human Uterine Leiomyomata47

description: Human Uterine Leiomyomata tissue sample 47


title: MicroRNA Gene Expression in Human Uterine Leiomyomata48

description: Human Uterine Leiomyomata tissue sample 48


title: MicroRNA Gene Expression in Human Uterine Leiomyomata42

description: Human Uterine Leiomyomata tissue sample 42


title: MicroRNA Gene Expression in Human Uterine Leiomyomata36

description: Human Uterine Leiomyomata tissue sample 36


title: MicroRNA Gene Expression in Human Uterine Leiomyomata35

description: Human Uterine Leiomyomata tissue sample 35


title: MicroRNA Gene Expression in Human Uterine Leiomyomata33

description: Human Uterine Leiomyomata tissue sample 33


title: MicroRNA Gene Expression in Human Uterine Leiomyomata34

description: Human Uterine Leiomyomata tissue sample 34


title: MicroRNA Gene Expression in Human Uterine Leiomyomata39

description: Human Uterine Leiomyomata tissue sample 39


title: MicroRNA Gene Expression in Human Uterine Leiomyomata37

description: Human Uterine Leiomyomata tissue sample 37


title: MicroRNA Gene Expression in Human Uterine Leiomyomata32

description: Human Uterine Leiomyomata tissue sample 32


title: MicroRNA Gene Expression in Human Uterine Leiomyomata27

description: Human Uterine Leiomyomata tissue sample 27


title: MicroRNA Gene Expression in Human Uterine Leiomyomata30

description: Human Uterine Leiomyomata tissue sample 30


title: MicroRNA Gene Expression in Human Uterine Leiomyomata31

description: Human Uterine Leiomyomata tissue sample 31


title: OMP-GFP positive olfactory neurons

description: RNA isolated from approximately 500,000 cells cells

scan_protocol: According to the instructions provided  in Affymetrix Genechip expression analysis technical manual.

tag: Strain- Mixed 129XC57Bl6

tag: Gender - Male and female

tag: Age - P10

tag: Tissue- FACS sorted mature OSNs


title: MicroRNA Gene Expression in Human Uterine Leiomyomata22

description: Human Uterine Leiomyomata tissue sample 22


title: MicroRNA Gene Expression in Human Uterine Leiomyomata24

description: Human Uterine Leiomyomata tissue sample 24


title: MicroRNA Gene Expression in Human Uterine Leiomyomata26

description: Human Uterine Leiomyomata tissue sample 26


title: MicroRNA Gene Expression in Human Uterine Leiomyomata25

description: Human Uterine Leiomyomata tissue sample 25


title: MicroRNA Gene Expression in Human Uterine Leiomyomata28

description: Human Uterine Leiomyomata tissue sample 28


title: MicroRNA Gene Expression in Human Uterine Leiomyomata16

description: Human Uterine Leiomyomata tissue sample 16


title: MicroRNA Gene Expression in Human Uterine Leiomyomata17

description: Human Uterine Leiomyomata tissue sample 17


title: MicroRNA Gene Expression in Human Uterine Leiomyomata20

description: Human Uterine Leiomyomata tissue sample 20


title: MicroRNA Gene Expression in Human Uterine Leiomyomata14

description: Human Uterine Leiomyomata tissue sample 14


title: MicroRNA Gene Expression in Human Uterine Leiomyomata15

description: Human Uterine Leiomyomata tissue sample 15


title: MicroRNA Gene Expression in Human Uterine Leiomyomata13

description: Human Uterine Leiomyomata tissue sample 13


title: MicroRNA Gene Expression in Human Uterine Leiomyomata23

description: Human Uterine Leiomyomata tissue sample 23


title: MicroRNA Gene Expression in Human Uterine Leiomyomata29

description: Human Uterine Leiomyomata tissue sample 29


title: MicroRNA Gene Expression in Human Uterine Leiomyomata12

description: Human Uterine Leiomyomata tissue sample 12


title: MicroRNA Gene Expression in Human Uterine Leiomyomata19

description: Human Uterine Leiomyomata tissue sample 19


title: MicroRNA Gene Expression in Human Uterine Leiomyomata18

description: Human Uterine Leiomyomata tissue sample 18


title: MicroRNA Gene Expression in Human Uterine Leiomyomata21

description: Human Uterine Leiomyomata tissue sample 21


title: MicroRNA Gene Expression in Human Uterine Leiomyomata11

description: Human Uterine Leiomyomata tissue sample 11


title: MicroRNA Gene Expression in Human Uterine Leiomyomata9

description: Human Uterine Leiomyomata tissue sample 9


title: MicroRNA Gene Expression in Human Uterine Leiomyomata8

description: Human Uterine Leiomyomata tissue sample 8


title: MicroRNA Gene Expression in Human Uterine Leiomyomata6

description: Human Uterine Leiomyomata tissue sample 6


title: MicroRNA Gene Expression in Human Uterine Leiomyomata3

description: Human Uterine Leiomyomata tissue sample 3

label_protocol: Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail to the 3? end of each miRNA sample. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy3 dyes (Amersham Bioscience, Piscataway, NJ). Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure

extract_protocol: Total RNA isolation and small RNA enrichment procedure were performed with the mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX.) according to the manufacturer?s instructions. To isolate miRNA enriched RNA fractions, total RNA samples were fractionated and cleaned up with filter cartridge spin column and different ethanol concentrations per the manufacturer?s recommendation. From 20 to 50 ug of total RNA about 3-8 ug small RNA enriched RNA was recovered. RNA less than 200 nt were quantitatively examined on 20% urea denaturing acrylamide gel.


title: MicroRNA Gene Expression in Human Uterine Leiomyomata5

description: Human Uterine Leiomyomata tissue sample 5


title: MicroRNA Gene Expression in Human Uterine Leiomyomata10

description: Human Uterine Leiomyomata tissue sample 10


title: MicroRNA Gene Expression in Human Uterine Leiomyomata1

description: Human Uterine Leiomyomata tissue sample 1


title: MicroRNA Gene Expression in Human Uterine Leiomyomata2

description: Human Uterine Leiomyomata tissue sample 2


title: MicroRNA Gene Expression in Human Uterine Leiomyomata4

description: Human Uterine Leiomyomata tissue sample 4


title: LBN_Ctr-2

status: Public on Apr 01 2007

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

description: Gene expression data from native kidneys from Lewis Brown Norway rats

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GMS 418 Array Scanner

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

label: biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: extraction of total RNA was performed using Qiagen Rneasy kit according to the manufacturer's instructions.

tag: Age

value: 10-12 weeks


title: LBN_Ctr-3


title: LBN_sTX-4

description: Gene expression data from syngeneic transplanted kidney from a Lewis rat into a Lewis rat

treatment_protocol: allogeneic transplanted kidney


title: LBN_aTX-3

description: Gene expression data from allogeneic transplanted kidney from a Lewis rat into a Lewis_Brown_Norway_Rat


title: LBN_sTX-3

source_name: syngeneic transplanted kidney from a Lewis rat into a Lewis rat

treatment_protocol: syngeneic transplanted kidney


title: Expression in rad50delta strain at meiosis 0 hr

status: Public on Apr 10 2007

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

country: Japan

institute: Kazusa DNA Research Institute

description: Gene expression data from diploid cells in premeiosis.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip YG-S98. GeneChips were washed and stained using EukGE-WS1 ver3 protocol in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: 0 hr after transfer into sporulation medium

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

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown to a density of 4.0x10^7 cells/ml at 30C in SPS presporulation medium (0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base w/o amino acid and ammonium sulfate, 1% potassium acetate, 0.5% ammonium sulfate, usual level fo amino acids, 50 mM potassium phthalate buffer pH 5.0, and antifoam).

extract_protocol: Total RNA was prepared using glass beads and RNeasy Maxi Kit (QIAGEN). mRNA was isolated the total RNA using Oligotex-dT30 (TaKaRa). These processes were performed according to the manufacturer's instructions.

treatment_protocol: Cells were washed twice with water, frozen in liquid nitrogen, and stored at -80C.

tag: strain

tag: background

tag: genotype


title: Expression in wild type strain at meiosis 0 hr

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen). mRNA was isolated the total RNA using Oligotex-dT30 (TaKaRa). These processes were performed according to the manufacturer's instructions.

value: wt


title: LBN_Ctr-4


title: Wobbler_testis_5997_rep1

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: testis wr/wr 5997

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Strain

value: wr/wr

tag: Mouse ID

source_name: Testis wt pool


title: LBN_aTX-2

source_name: allogeneic transplanted kidney from a Lewis rat into a Lewis_Brown_Norway_Rat


title: Wobbler_testis_5905_rep4

source_name: testis wr/wr 5905


title: Expression in mre11delta strain at meiosis 0 hr


title: LBN_Ctr-1


title: Wobbler_testis_5997_rep2


title: LBN_aTX-1


title: Expression in spo11Y135F strain at meiosis 0 hr


title: LBN_sTX-5


title: LBN_aTX-4


title: LBN_Ctr-5


title: Wobbler_testis_6065_rep3

source_name: testis wr/wr 6065


title: Wobbler_testis_6065_rep2


title: Wobbler_testis_5997_rep3


title: Wobbler_testis_5997_rep4


title: Wobbler_testis_6065_rep4


title: LBN_sTX-1


title: LBN_sTX-2


title: LBN_aTX-5


title: MicroRNA Gene Expression in Human Uterine Leiomyomata7

description: Human Uterine Leiomyomata tissue sample 7


title: Wobbler_testis_6163_rep1

source_name: testis wr/wr 6163


title: Wobbler_testis_6493_rep1

source_name: testis wr/wr 6493


title: Wobbler_testis_6493_rep4


title: Wobbler_testis_6163_rep4


title: Wobbler_testis_5905_rep3


title: Wobbler_testis_5905_rep2


title: Wobbler_testis_6493_rep2


title: Wobbler_testis_6065_rep1


title: Wobbler_testis_6163_rep3


title: Wobbler_testis_5995_rep4

source_name: testis wr/wr 5995


title: Wobbler_testis_5995_rep3


title: Wobbler_testis_5905_rep1


title: gDNA_EColi_S13

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Comparison of gDNA K12/S13

hyb_protocol: Agilent standard protocol 17H at 60 degrees C; Agilent proprietary Buffers

scan_protocol: Images were quantified using Agilent Feature Extraction Software.

data_processing: Local Background Substracted Signal Corrected for unequal Dye incorporation or unequal load of labelled product

label: cyanine 3

organism: Escherichia coli K-12

source_name: gDNA from E.coli K12 cyanine 3

label_protocol: Klenow and random primers

extract_protocol: DNeasy (Qiagen)

tag: gDNA K12

label: Cyanine 5

source_name: strain S13

tag: gDNA S13


title: gDNA_EColi_S05

description: Comparison of gDNA K12/S05

source_name: strain S05

tag: gDNA S05


title: Wobbler_testis_6335_rep2

source_name: testis wr/wr 6335


title: Wobbler_testis_5995_rep1


title: gDNA_EColi_H27

description: Comparison of gDNA K12/H27

source_name: strain H27

tag: gDNA H27


title: Wobbler_testis_6069_rep3

source_name: testis wr/wr 6069


title: Wobbler_testis_6335_rep4


title: gDNA_EColi_H23

description: Comparison of gDNA K12/H23

source_name: strain H23

tag: gDNA H23


title: Wobbler_testis_6493_rep3


title: Wobbler_testis_6335_rep1


title: Wobbler_testis_6335_rep3


title: gDNA_EColi_S04

description: Comparison of gDNA K12/S04

source_name: strain S04

tag: gDNA S04


title: Wobbler_testis_6069_rep4


title: Wobbler_testis_5995_rep2


title: gDNA_EColi_H12

description: Comparison of gDNA K12/H12

source_name: strain H12

tag: gDNA H12


title: gDNA_EColi_H01

description: Comparison of gDNA K12/H01

source_name: strain H01

tag: gDNA H01


title: gDNA_EColi_F02

description: Comparison of gDNA K12/F02

source_name: strain F02

tag: gDNA F02


title: Wobbler_testis_6069_rep2

source_name: Testis wt pool


title: Wobbler_testis_6069_rep1


title: gDNA_EColi_H04

description: Comparison of gDNA K12/H04

source_name: strain H04

tag: gDNA H04


title: Wobbler_testis_5907_rep4

source_name: testis wr/wr 5907


title: Wobbler_testis_5907_rep3


title: gDNA_EColi_H03

description: Comparison of gDNA K12/H03

source_name: strain H03

tag: gDNA H03


title: Wobbler_testis_5907_rep2


title: gDNA_EColi_F01

description: Comparison of gDNA K12/F01

source_name: strain F01

tag: gDNA F01


title: gDNA_EColi_C01

description: Comparison of gDNA K12/C01

source_name: strain C01

tag: gDNA C01


title: gDNA_EColi_H05

description: Comparison of gDNA K12/H05

source_name: gDNA from E.coli K12 cyanine 3

source_name: strain H05

tag: gDNA H05


title: gDNA_EColi_B02

description: Comparison of gDNA K12/B02

source_name: strain B02

tag: gDNA B02


title: gDNA_EColi_C02

description: Comparison of gDNA K12/C02

source_name: strain C02

tag: gDNA C02


title: gDNA_EColi_B05

description: Comparison of gDNA K12/B05

source_name: strain B05

tag: gDNA B05


title: gDNA_EColi_520

description: Comparison of gDNA K12/520

tag: gDNA K12

source_name: strain 520

tag: gDNA 520


title: gDNA_EColi_521

description: Comparison of gDNA K12/521

source_name: strain 521

tag: gDNA 521


title: gDNA_EColi_H02

description: Comparison of gDNA K12/H02

source_name: strain H02

tag: gDNA H02


title: Wobbler_testis_5906_rep2

source_name: testis wr/wr 5906

tag: Strain

tag: Mouse ID


title: Wobbler_testis_5906_rep3


title: Wobbler_spinal cord_5995_rep1

source_name: Wobbler Spinal Cord wr/wr 5995

source_name: Spinal cord Wt pool


title: Wobbler_spinal cord_5995_rep2

source_name: Spinal Cord wr/wr 5995


title: Wobbler_testis_5907_rep1

source_name: Testis wt pool


title: Wobbler_testis_5906_rep4


title: Wobbler_spinal cord_pool2_rep3

source_name: Spinal Cord wr/wr Pool2

tag: Pool1; Mouse ID


title: Wobbler_spinal cord_pool2_rep2


title: Wobbler_spinal cord_pool1_rep1

source_name: Spinal Cord wr/wr Pool1


title: Wobbler_testis_5906_rep1


title: SLIDE 12: wild type vs PerR mutant

city: St. Louis

first: Michael

middle: G

last: Caparon

state: MO

address: 660 S. Euclid Ave.

department: Dept. of Molecular Microbiology

institute: Washington University School of Medicine

description: Wild type strain versus PerR mutant strain in mid-logarithmic phase of growth

hyb_protocol: The tagged cDNAs from the appropriate samples were mixed and then allowed to hybridize with the array using a commercial buffer (MWG) at 42°C overnight. Following washing using 2× SSC, 0.2% SDS, at 65°C to remove unhybridized cDNAs, the detection reagents (Cyanine 3 and Cyanine 5 3DNA dendrimers, Genisphere) were added with incubation at 65°C for 3 h. Unbound detection reagents were removed by washing.

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence.

data_processing: What is submitted is the raw output of Scanarray. VALUE = log2 (test/ref)

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes, PerR mutant, mid-logarithmic phase of growth

label_protocol: Synthesis and labelling of cDNA used a commercial kit (3DNA Array 900, Genisphere).

growth_protocol: Overnight growth in THY medium was diluted 1:100 in fresh THY medium followed by incubation at 37°C to the mid-logarithmic phase (OD600=0.300) of growth

extract_protocol: Total RNA was isolated using glass beads (Lysing Matrix A, Q/BioGene) and a high-speed reciprocating shaking device (FP-120, Savant Instruments). RNA was further purified (RNeasy Mini Kit for RNA clean up, Qiagen) and contaminating DNA was removed by DNase. Total RNA concentration was calculated using absorbance at 260 nm.RNA was further analyzed by a fluorescent assay involving electrophoretic separation of RNA (Agilent 2100 Bioanalyzer), and rejected if the electropherogram (a diagram of fluorescence over time) showed degradation of RNA

tag: Streptoccocus pyogenes strain HdeltaPerR (PerR mutant derived form the wild type strain HSC5) grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY medium) to mid-logarithmic phase of growth

source_name: Streptocococcus pyogenes, wild type strain, mid-logarithmic phase of growth

tag: Streptoccocus pyogenes strain HSC5 (Wild type) grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY medium) to mid-logarithmic phase of growth


title: Wobbler_spinal cord_pool1_rep3


title: HSC ltbp1-/- vs wt 90

status: Public on Mar 31 2007

city: Cologne

first: Sebastian

last: Knoebel

address: Nattermannallee 1

institute: MiltenyiBiotec GmbH

description: 1 µg of linear amplified RNA from wt and ltbp1-/- in vitro activated HSC (6d culture on plastic) were labelled by reverse transcription with Cy3 and Cy5 fluorescence, respectively. Cy3 and Cy5 labeled cDNA were combined and subdivided into two parts to perform co-hybridizations with the PIQOR Immunology Microarray, mouse

scan_protocol: Image capture and signal quantification were done with the Microarray Scanner G2505B (Agilent Technologies) and ImaGene software version 5.0 (BioDiscovery, Los Angeles, MA)

data_processing: PubmedID

source_name: Hepatic stellate cells (HSC)_wt_activated_2

tag: HSC, wt, activated (by in vitro culture on plastic for 6 days), pooled cells of 5 animals

source_name: Hepatic stellate cells (HSC)_ltbp1-/-_activated_2

tag: HSC, ltbp1-/-, activated (by in vitro culture on plastic for 6 days), pooled cells of 5 animals


title: Wobbler_spinal cord_pool2_rep4


title: HSC activated vs quiescent 42

description: 1 µg of linear amplified RNA from quiescent and in vitro activated wt HSC (6d culture on plastic) were labelled by reverse transcription with Cy3 and Cy5 fluorescence, respectively. Cy3 and Cy5 labeled cDNA were combined and subdivided into two parts to perform co-hybridizations with the PIQOR Immunology Microarray, mouse

source_name: Hepatic stellate cells (HSC)_wt_quiescent_2

tag: HSC, wt, quiescent (cultured in vitro on plastic for 1 day), pooled cells of 5 animals

source_name: Hepatic stellate cells (HSC)_wt_quiescent_4


title: HSC activated vs quiescent 40

source_name: Hepatic stellate cells (HSC)_wt_quiescent_1

source_name: Hepatic stellate cells (HSC)_wt_quiescent_3


title: SLIDE 4: wild type vs PerR mutant


title: HSC ltbp1-/- vs wt 33

source_name: Hepatic stellate cells (HSC)_wt_activated_1

source_name: Hepatic stellate cells (HSC)_ltbp1-/-_activated_1


title: SLIDE 11: wild type vs PerR mutant


title: SLIDE 2: wild type vs PerR mutant


title: Wobbler_spinal cord_pool1_rep2


title: expanded cultures_depolarized_rep4

status: Public on Mar 19 2007

city: Naples

first: Umberto

last: di Porzio

address: Via Pietro Castellino 111

department: neurobiology laboratory

country: Italy

institute: Istitute of genetics and biophysics

description: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates in presence of basic fibroblast growth factor (bFGF, 20ng/ml) and Sonic hedgehog (SHH) for 6 days in vitro. For other additional three days in vitro both factors were withdrawn. After 9 days in vitro the cultures were treated for 2h with high KCl and collected 30 min or 2 h after the end of depolarization (2h + 30 min or 2h + 2h). The RNA from the culture duplicates were pooled. RNA obtained from control and depolarized cultures from three independent groups was hybridized on triplicate microarrays.

data_processing: RMA

label: Biotin

source_name: expanded cultures from ventral midbrain, depolarized (2h + 2h)

label_protocol: BioArray High Yiled RNA transcript labeling kit (ENZO Diagnostics, Farmingdale, NY).

growth_protocol: Cells dissected from ventral midbrain of E12 embryos were dissociated using mechanical trituration with a fire polished Pasteur pipette in culture medium and 0.01% pancreatic deoxyribonuclease (Sigma, Milan, Italy); cells were centrifuged 10 min at 800 rpm, suspended in plating medium, counted and plated at a density of 18.000/cm2 in dishes coated with 15ug/ml of poly-D-Lysine (Sigma). Serum was absent from the culture medium, which was complemented with B27 supplement (Invitrogen), basic fibroblast growth factor (bFGF, 20 ng/ml, Sigma), the N-terminal fragment of the Sonic hedgehog (SHH) protein (50ng/ml). Half of the medium was changed every three days. After six days the medium supplements were withdrawn, with the exception of B27 and the cultures were carried for additional three days. After 9 days in vitro the cultures were used for the experiment.

extract_protocol: RNA was extracted from single cultures, using the Tri-Reagent isolation system (Sigma) and following the manufacturer’s instructions. Total RNA was treated with DNA free kit (Ambion Inc., Milan, Italy) to eliminate possible DNA contaminations. After RNA extraction and Dnase treatment an additional clean-up of total RNA was performed using the RNeasy kit (Qiagen, Milan, Italy). Using the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized from total RNA. and was used to obtain

treatment_protocol: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates. After 9 days in vitro the cultures were depolarized with KCl (56mM) for 2 h and then the depolarizing medium was changed and the samples were collected 2 h after the end of depolarization.

value: CD1 rat

tag: Age

value: E12 embryos

tag: Tissue

value: ventral midbrain


title: SLIDE 3: wild type vs PerR mutant


title: Wobbler_spinal cord_pool2_rep1


title: SLIDE 10: wild type vs PerR mutant


title: Wobbler_spinal cord_pool1_rep4


title: SLIDE 5: wild type vs PerR mutant


title: expanded cultures_depolarized_rep3

source_name: expanded cultures from ventral midbrain, depolarized for 2h + 30 min

treatment_protocol: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates. After 9 days in vitro the cultures were depolarized with KCl (56mM) for 2 h and then the depolarizing medium was changed and the samples were collected 30 min after the end of depolarization.


title: expanded cultures_depolarized_rep1

source_name: expanded cultures from ventral midbrain, depolarized (2h + 30 min)


title: expanded cultures_control_rep5

source_name: expanded cultures from ventral midbrain control (2h +2h)

treatment_protocol: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates. After 9 days in vitro the cultures were grown for 2 h + 2 h in a control medium.


title: expanded cultures_depolarized_rep5

source_name: expanded cultures from ventral midbrain, depolarized (2h +2h)


title: expanded cultures_depolarized_rep2


title: HSC ltbp1-/- vs wt 85


title: expanded cultures_control_rep3

source_name: expanded cultures from ventral midbrain, control (2h + 30 min)

treatment_protocol: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates. After 9 days in vitro the cultures were grown for 2 h + 30 min in a control medium.


title: expanded cultures_control_rep4

source_name: expanded cultures from ventral midbrain, control (2h +2h)


title: 1010f; Sample ID: M55_M58

status: Public on Mar 18 2007

description: Normalized and background corrected intensities were used for comparison studies. A brightness (intensity) threshold of 1000 units was used to filter very low intensity spots. The hybridization to spots was screened on the basis of reproducibility in duplicates. Spots that had less than 50% variation in intensity among duplicates were taken for further analysis. Average Cy5/Cy3 ratio was calculated for each spot and the observations for all the experiments of were collated in a single MS-Excel file. The genes were further classified on the basis of fold change variation they showed. The genes varying between 0.5-2 fold were considered as equally expressed. Genes that differed at >2 fold or at <0.5 fold were classified as increase in expression or decrease in expression with respect to a given sample respectively. The genes were also classified into 6 different functional classes namely, ‘Information’, ‘Cell cycle’, ‘Metabolism’, ‘Signalling and communication’, ‘Immune and related functions’ and ‘Structure and motility’

hyb_protocol: Equal amounts of labelled targets (7 ul each) were mixed along with 20 ug human cot-1 DNA and were denatured in boiling water bath for about 2 minutes. Equal volume of hybridization buffer (50% formamide, 10X SSC and 0.2 % SDS) was added to the denatured labelled targets. The labelled cDNA targets were pipetted onto the microarray, covered by a coverslip and kept in Corning’s hybridization chamber in a water bath maintained at 42 oC for 16-18 hours for hybridization. The stringency washes were performed at room temperature and according to manufacturer’s protocol. Microarray slide was first immersed in 0.5X SSC, 0.01% SDS wash solution to remove the coverslip from the array and then transferred to another conical 50 ml tube containing the 30 ml of the same wash solution. It was washed with gentle shaking for 5 minutes and subsequently transferred to other tube containing 30 ml of 0.06X SSC, 0.01% SDS and again washed with gentle shaking for 5 minutes. Lastly the microarray slide was transferred to tube containing 30 ml of 0.06X SSC and washed with gentle shaking for 2 minutes. •	Introduction of HRP: Slide was incubated with 300 ul of Anti-FL-HRP conjugate solution for 10 minutes, followed by washing 3 times with 30 ml of TNT buffer for 1 minute each. This antibody-HRP conjugate binds specifically to the hybridized fluorescein labelled cDNA. •	Introduction of Cyanine 3 Tyramide: Microarray slide was incubated with 300 ul of cyanine-3-tyramide solution for 10 minutes and the slide rinsed 3 times with 30 ml of TNT buffer for 5 minutes each. HRP catalyses the local deposition of cyanine 3 labelled tyramide. This being an enzymatic process, the amount of tyramide relative to fluorescein labelled cDNA is greatly amplified. •	Introduction of HRP: Slide was incubated with 300 ul of Streptavidin-HRP conjugate solution for 10 minutes, followed by washing 3 times with 30 ml of TNT buffer for 1 minute each. This antibody-HRP conjugate binds specifically to the hybridized biotin labelled cDNA. •	Introduction of Cyanine 5 Tyramide: Microarray slide was incubated with 300 ul of cyanine-5-tyramide solution for 10 minutes and the slide is rinsed 3 times with 30 ml of TNT buffer for 5 minutes each. In this case also, the amount of tyramide relative to biotin labelled cDNA is greatly amplified. Another wash with 30ml of 0.06X SSC is given for 1 minute.

scan_protocol: The images were acquired for both Cy3 and Cy5 channels by ScanArray software (Packard BioSciences, USA). Quantification of the images was carried out by QuantArray software (Packard BioSciences, USA). Grid patterns of the different microarrays used in the study, Hu1536, Hu2304, Hu800  were fed to QuantArray to generate a composite image for relative comparisons of gene expression between the two samples. The spots were sometimes adjusted manually in the grid; very low-intensity spots, bad spots or smudged spots were flagged not to be included in Quantitation of the image. Adaptive circle segmentation method was used for Quantitation. Spot intensity was calculated by subtracting background signal from the foreground signal. The raw comparison data obtained was stored as a tab delimited ‘text’ file and used for subsequent analysis.

source_name: M55 blood leukocytes

label_protocol:
An indirect labeling procedure described in Tyramide signal amplification kit (PE Lifesciences) was used to label targets during first strand synthesis. About 5ug total RNA sample was used per reaction and labelled with Biotin or Fluorescein dCTP during first strand synthesis using the reaction mix concentrate and labelled nucleotide provided in the kit. A small modification in the protocol was done by increasing the amount of reaction mix and biotin/fluorescein nucleotide to 2 ul instead of 1 ul. This was done to compensate for a still high amount of RNA used by us compared to amount suggested by the manufacturer (5 ug vs. 2 ug). Both the biotin and fluorescein labelled first strand cDNAs were separately purified by precipitation by adding 0.8 volumes of isopropanol, in the presence of 0.3M Ammonium acetate and 5 ug glycogen. Mix was vortexed and incubated at 4 oC for 30 minutes and centrifuged at 12,000 g for 15 minutes to collect the pellet. The pellet was subsequently washed twice with 100 ul of cold 70% ethanol. Washed pellet was air-dried and resuspended in 8 ul sterile water. 1ul of the labelled cDNA was analysed for incorporation of label by comparing with pre-labelled controls provided by manufacturer and the rest of the cDNA is stored at –20 oC till further use. Equal amounts of labelled targets (7 ul each) were mixed along with 20 ug human cot-1 DNA and were denatured in boiling water bath for about 2 minutes. Equal volume of hybridization buffer (50% formamide, 10X SSC and 0.2 % SDS) was added to the denatured labelled targets. The labelled cDNA targets were pipetted onto the microarray, covered by a coverslip and kept in Corning’s hybridization chamber in a water bath maintained at 42 oC for 16-18 hours for hybridization. The stringency washes were performed at room temperature and according to manufacturer’s protocol. Microarray slide was first immersed in 0.5X SSC, 0.01% SDS wash solution to remove the coverslip from the array and then transferred to another conical 50 ml tube containing the 30 ml of the same wash solution. It was washed with gentle shaking for 5 minutes and subsequently transferred to other tube containing 30 ml of 0.06X SSC, 0.01% SDS and again washed with gentle shaking for 5 minutes. Lastly the microarray slide was transferred to tube containing 30 ml of 0.06X SSC and washed with gentle shaking for 2 minutes.
After the stringency washes the detection of microarray spots is carried out using TSA.

extract_protocol:
15ml of the total 20ml collected blood was used to isolate total RNA from white blood cells (WBCs) to carry out microarray experiments. Since RNA is very sensitive to degradation all precautions like use of fresh sterile gloves was used to prevent degradation of total RNA during the isolation procedure. All the reagents used for RNA isolation were prepared in diethylpyrocarbonate (DEPC) treated water and RNase, DNase  free plasticware was used.

Blood was transferred to Nuclease free 50ml conical centrifuge tubes and RBCs were lysed by adding 45ml of ice-cold 1X RBC lysis buffer (150mM NH4Cl, 10mM NaHCO3, 1mM EDTA, pH 8.0) per 5ml of whole blood. WBC pellet was collected by centrifuging at 250g for 10 min at 40C and removing the supernatant. EZ-RNA isolation kit from Biological Industries, Israel, was used to isolate RNA from the WBC pellet. The kit is based on the protocol described by Chomczynski and Sacchi (1987). 500ul of solution A (containing guanidine thiocynate) of the kit was added to the cell pellet obtained from 5 ml of blood. The pellet was suspended in solution A and transferred to a 1.5 ml nuclease free microfuge tube and the mix kept at room temperature for 5 minutes. 500ul of solution B (acidic Phenol and chloroform mixture) was added after incubation and mixed thoroughly and further incubated at room temperature for 10 minutes. The mixture was centrifuged at 12,000 g for 15 minutes at 40C to separate the aqueous layer containing total RNA from the organic layer. The aqueous layer was transferred to a fresh 1.5 ml tube and equal volume of isopropanol was added to precipitate the RNA. The contents of the tube were mixed by vortexing and kept at –200C overnight for efficient precipitation of total RNA. The RNA pellet was collected by centrifuging the contents at 12,000 g for 15 minutes and washed twice by 70% ice-cold ethanol. The pellet was dried and dissolved in 20ul DEPC treated water and kept at 650C dry bath for not more than 2 hours for dissolving the pellet.

The quality of RNA was checked for its integrity and any contamination of genomic DNA by quick electrophoresis run on 1% agarose TAE gel. 2ul of the isolated total RNA was loaded on 1% agarose gel prepared in DEPC treated 1X TAE buffer and electrophoresced at 100V for not more than 10 minutes. RNA was kept at –700oC until further use.

tag: 34 yrs normal male

source_name: M58 blood leukocytes

tag: 33 yrs normal male


title: 6b6f; Sample ID: F53_F52

source_name: F53 blood leukocytes

tag: 22 yrs normal female

source_name: F52 blood leukocytes

tag: 25 yrs normal female


title: expanded cultures_control_rep2

source_name: expanded cultures from ventral midbrain control (2 h + 30 min)


title: 8b8f; Sample ID: F53_F51

source_name: F51 blood leukocytes

tag: 28 yrs normal female


title: 2b2f; sample ID M58_M57

tag: 27 years male (normal)

source_name: M57 blood leukocytes

tag: 33 years male (normal)


title: 9b9f; Sample ID: F52_M57

tag: 27 yrs normal male


title: 4b4f; Sample ID: M56_M55

source_name: M56 blood leukocytes

tag: 25 yrs normal male


title: 3b3f; Sample ID M57_M56


title: 5b5f; Sample ID: M55_F53


title: 7b7f: Sample ID F52_F51


title: 1b1f; Sample ID F51_M58

source_name: Blood leukocytes

tag: Female 28 years (normal individual)

tag: Male 33 years, normal individual


title: expanded cultures_control_rep6

tag: Strain


title: Dendritic cell tumour IDC7

status: Public on Mar 15 2007

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: see Ullmann et al (submitted)

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website

scan_protocol: Slides were scanned using an Axon 4000B scanner (Axon Instruments, Union City, CA)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen et al., 2005). Background intensities were not subtracted. Signal intensities were normalized by subgrid LOWESS and chromosomal regions sharing the same DNA copy number were segmented by circular binary segmentation. Segments exceeding a log2 ratio of +/- 0.2 were considered as an aberration.

source_name: DNA isolated from frozen tissue

label_protocol: DNA was  labelled by random priming. Detailed protocols are available at our website

extract_protocol: standard proteinase K digestion and phenol-chloroform isoamylalcohol

tag: Gender

value: female

value: dendritic cell tumor

tag: Localization

value: right upper lobe of the lung

source_name: female reference

extract_protocol: cell lysis and salting out

tag: DNA isolated from a lymphoblastoid cell line derived from a healthy female proband


title: expanded cultures_control_rep1

description: To minimize biological variability four pregnant rats were sacrificed and the E12 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled, dissociated and the cells were cultured in duplicates in presence of basic fibroblast growth factor (bFGF, 20ng/ml) and Sonic hedgedog (SHH) for 6 days in vitro. For other additional three days in vitro both factors were withdrawn. After 9 days in vitro the cultures were treated for 2h with high KCl and collected 30 min or 2 h after the end of depolarization (2h + 30 min or 2h + 2h). The RNA from the culture duplicates were pooled. RNA obtained from control and depolarized cultures from three independent groups was hybridized on triplicate microarrays.

tag: Age


title: Dendritic cell tumor FDC1

description: see Ullmann et al (submitted)

source_name: tumour DNA isolated from frozen tissue

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website

tag: Tissue

value: parapharyngeal

source_name: female reference DNA


title: Dendritic cell tumour IDC4

description: see Ullmann et al (submitted)

source_name: DNA isolated from formalin-fixed, paraffin embedded tumor tissue

value: male

value: dendritic cell tumour

value: lymph-node neck

source_name: male reference pool

tag: DNA isolated from formalin-fixed, paraffin embedded non-tumour tissue of 5 males


title: Dendritic cell tumour IDC5

description: see Ullmann et al (submitted)

value: right axillary mass

label_protocol: DNA was labelled by random priming. Detailed protocols are available at our website


title: Dendritic cell tumour IDC8

description: see Ullmann et al (submitted)

value: muscular wall of urinary bladder


title: expanded cultures_depolarized_rep6

source_name: expanded cultures from ventral midbrain, depolarized (2h +2h)


title: Dendritic cell tumour IDC6

description: see Ullmann et al (submitted)

value: right lower eye-lid


title: Dendritic cell tumour FDC1 recurrence

description: see Ullmann et al (submitted)

source_name: formalin-fixed, paraffin embedded tumor tissue

label_protocol: DNA was amplified by means of a commercial kit (GenomePlex, Rubicon) and labelled by random priming. Detailed protocols are available at our website


title: MP G7 control 7 days vs. MP G8 low 7 days (ExpID 1993)

status: Public on Mar 01 2007

city: Chapel Hill

first: James

middle: Todd

last: Auman

state: NC

address: 3304 Kerr Hall, Campus Box 7360

department: Institute for Pharmacogenomics and Individualized Therapy

institute: University of North Carolina at Chapel Hill

description: Male Sprague-Dawley rats were treated with 7 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

data_processing: Five hundred nanograms (500 ng) of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer’s protocol.  For each two color comparison, 750 ng each of Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v. 7.1) using defaults for all parameters.

source_name: MP G7 control 7 days (Cy3)

tag: MP G7 control 7 days

source_name: MP G8 low 7 days (Cy5)

tag: MP G8 low 7 days


title: MP G1 control 1 day vs. MP G2 low 1 day (ExpID 1991B)

description: Male Sprague-Dawley rats were treated with a single dose of 10 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G1 control 1 day (Cy3)

tag: MP G1 control 1 day

source_name: MP G2 low 1 day (Cy5)

tag: MP G2 low 1 day


title: MP G8 high 7 days vs. MP G7 control 7 days (ExpID 1996B)

description: Male Sprague-Dawley rats were treated with 7 daily doses of 100 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G8 high 7 days (Cy3)

tag: MP G8 high 7 days

source_name: MP G7 control 7 days (Cy5)


title: MP G8 low 7 days vs. MP G7 control 7 days (ExpID 1993B)

source_name: MP G8 low 7 days (Cy3)


title: MP G7 control 7 days vs. MP G8 high 7 days (ExpID 1996B)

source_name: MP G8 high 7 days (Cy5)


title: MP G4 control 3 days vs. MP G5 low 3 days (ExpID 1992)

description: Male Sprague-Dawley rats were treated with 3 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G4 control 3 days (Cy3)

tag: MP G4 control 3 days

source_name: MP G5 low 3 days (Cy5)

tag: MP G5 low 3 days


title: Methapyrilene, Control 7 day vs. Methapyrilene, High 7 day (ExpID 1471B)

description: Male Sprague-Dawley rats were treated with 7 daily doses of 100 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Control 7 day (Cy3)

tag: Methapyrilene, Control 7 day

source_name: Methapyrilene, High 7 day (Cy5)

tag: Methapyrilene, High 7 day


title: MP G4 control 3 days vs. MP G6 high 3 days (ExpID 1995)

description: Male Sprague-Dawley rats were treated with 3 daily doses of 100 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G6 high 3 days (Cy5)

tag: MP G6 high 3 days


title: Methapyrilene, High 7 day vs. Methapyrilene, Control 7 day (ExpID 1471B)

source_name: Methapyrilene, High 7 day (Cy3)

source_name: Methapyrilene, Control 7 day (Cy5)


title: Methapyrilene, Control 7 day vs. Methapyrilene, Low 7 day (ExpID 1470B)

description: Male Sprague-Dawley rats were treated with 7 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Low 7 day (Cy5)

tag: Methapyrilene, Low 7 day


title: MP G7 control 7 days vs. MP G8 low 7 days (ExpID 1993B)


title: MP G2 low 1 day vs. MP G1 control 1 day (ExpID 1991B)

source_name: MP G2 low 1 day (Cy3)

source_name: MP G1 control 1 day (Cy5)


title: MP G4 control 3 days vs. MP G5 low 3 days (ExpID 1992B)


title: MP G1 control 1 day vs. MP G3 high 1 day (ExpID 1994B)

description: Male Sprague-Dawley rats were treated with a single dose of 100 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G3 high 1 day (Cy5)

tag: MP G3 high 1 day


title: Methapyrilene, Control 3 day vs. Methapyrilene, High 3 day (ExpID 1469B)

description: Male Sprague-Dawley rats were treated with 3 daily doses of 100 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Control 3 day (Cy3)

tag: Methapyrilene, Control 3 day

source_name: Methapyrilene, High 3 day (Cy5)

tag: Methapyrilene, High 3 day


title: Methapyrilene, Control 1day vs. Methapyrilene, Low 1 day (ExpID 1466B)

description: Male Sprague-Dawley rats were treated with a single dose of 10 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Control 1day (Cy3)

tag: Methapyrilene, Control 1day

source_name: Methapyrilene, Low 1 day (Cy5)

tag: Methapyrilene, Low 1 day


title: Methapyrilene, Control 1day vs. Methapyrilene, High 1 day (ExpID 1467B)

description: Male Sprague-Dawley rats were treated with a single dose of 100 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, High 1 day (Cy5)

tag: Methapyrilene, High 1 day


title: Methapyrilene, Control 3 day vs. Methapyrilene, Low 3 day (ExpID 1468B)

description: Male Sprague-Dawley rats were treated with 3 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Low 3 day (Cy5)

tag: Methapyrilene, Low 3 day


title: HY5 ChIP-chip Rep4

city: New Haven

first: Kun

last: He

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

description: Analysis of transcription factor HY5 genomic binding sites

hyb_protocol: Microarray chips were prehybridized with prehybridization buffer (33.3 mM MES, 0.33 M [Na+], 6.6 mM EDTA, 0.03% Tween 20, 0.03 mg/ml salmon sperm DNA, 0.17 mg/ml BSA) for 15 minutes at 45°C. Arrays were washed with water twice and hybridized with labeled DNA in hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20, 0.1 mg/ml salmon sperm DNA, 0.5 mg/ml BSA) for 14-16 hrs at 57°C. After hybridization, the arrays were washed in non-stringent buffer (6X SSPE, 0.01% [v/v] Tween-20) for 3 min at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 20 min at 45°C. Arrays were rinsed 3 times with non-stringent buffer at room temperature and once with ice-chilled stringent buffer, then were dried with centrifugation (1000 rpm, 5 min). Microarrays were scanned with a GenePix 4000B scanner (Axon, Foster City, CA), and independent TIFF images for both Cy-3 and Cy-5 channels were acquired at 5 µm resolution.

scan_protocol: The microarrays were scanned with GENEPIX Pro 3.0 software, and intensity data were extracted with NimbleScan software (NimbleGen Systems)

data_processing: The signal intensities were normalized by loess normalization method (Yang et al., 2002). A linear model was employed to identify the oligos that were enriched in the ChIP (Cy5) sample channel. The model is given by yijkl=μ+Ai+Dj+Si+VSkl+ADij+DSjl+ASil+εijkl, where yijkl denotes the log-transformed signal for oligo l on slide i labeled with dye j on sample k. μrepresents the overall average signal, and Ai, Dj and Si represent the effect from array, dye and oligos respectively. The interaction terms AD, VS, DS, and AS represent array by dye, sample by oligo, dye by oligo, and array by oligo, respectively. εijkl represents the random error effect. The sample variety term VS is the parameter we want to infer. The linear model described above was performed on each oligo using limma package for R with moderated t-statistics computed to assess the significance of variance (Smyth et al., 2005). The false-discovery rate controlling method (Benjamini and Hochberg, 1995) was used to control for multiple testing errors through an function implemented in limma package.

source_name: HY5 ChIP sample

label_protocol: The DNA product obtained by ChIP was amplified and labeled as previously described with minor modifications (Iyer et al., 2001). In brief, 7 l ChIPed DNA were mixed with 2 l 5X Sequenase buffer and 1 l 50 M primer 1 (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3') and incubated at 94ºC, 2 min, followed by cooling to 8ºC, then 5 l of reaction mixture (1X Sequenase buffer, 0.15 mM dNTP, 0.015 M DTT, 0.75 g BSA, 0.3 l Sequenase (US Biochemical, USA)) was added. The temperature of the mixture was increased to 37ºC over 8 min, then kept at 37ºC for 8 min for polymerization. The DNA in the mixture was denatured at 94ºC for 2 min, cooled down to 8ºC, then 0.24 l of Sequenase was added. The temperature was increased to 37ºC over 8 min, and kept at 37ºC for 8 min for polymerization again. The DNA was diluted to 50 l with 1X TE buffer. From the diluted DNA, 15 l was used for the first PCR reaction, mixed with 10 l 10X PCR buffer, 2.5 l 10 mM dNTP, 2 l 25 mM MgCl2, 2.5 lμM primer 2 (5'-GTTTCCCAGTCACGATC-3'), 1 l Taq polymerase (Qiagen, USA) and water to make 100 l total solution. The first PCR was performed with following conditions: 18-20 cycles of 92°C (30 sec)-40°C (30 sec)-50°C (30 sec)-72°C (2 min). The second PCR reaction for incorporating aminoallyl-dUTP was performed using 15 l of the first PCR product, mixed with 5 l 10X PCR buffer, 0.5 l 50X dNTP mixture (10 l each of 100 mM dA, dC, dG and 2 l of 100 mM dTTP, 8 l 100 mM aminoallyl-dUTP), 1 l 25 mM MgCl2, 1 lM primer 2, 0.5 l Taq polymerase and water to make 50 l total solution with the same PCR condition as above. After purifying the PCR product using microcon-30 filters, 7 l (1-2 g) of purified DNA were mixed with 0.7 l of 1 M sodium bicarbonate (pH 9.0) and 1 l dye of Cy5 or Cy3 (Amersham, dissolved in DMSO), and incubated 90 min at room temperature in the dark, then quenched with 1 l of 2M ethanolamine (Sigma) by incubation for 15 min. The labeled products were purified with QiaQuick PCR purification column (Qiagen).

growth_protocol: 4-day-old seedlings grown under continuous white light

extract_protocol: Seedling tissues 1.5 g were crosslinked with 50 ml of 1% formaldehyde in a vacuum for 15 minutes. 2.5 ml of 2 M glycine was added to stop the crosslinking. After rinsing seedlings with water, tissues were ground with liquid nitrogen and resuspended with 25 ml of Extraction Buffer I (0.4 M sucrose, 10 mM Tris-HCl pH 8, 10 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor, Roche), then filtered through miracloth (Calbiochem). The filtrate was centrifuged at 4000 rpm at 4˚C for 20 mins. The pellet was resuspended in 1 ml of Extraction Buffer II (0.25 M sucrose, 10 mM Tris-HCl pH 8, 10mM MgCl2, 1% Triton X-100, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor) and centrifuged at 14000 rpm, 4˚C for 10 mins. The pellet was resuspended in 300 l of Extraction Buffer III (1.7 M sucrose, 10 mM Tris-HCl pH 8, 0.15% Triton X-100, 2 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor) and loaded on top of the equal amount of clean Extraction Buffer III, then centrifuged at 14000 rpm for 1 hr. The crude nuclear pellet was resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1X complete protease inhibitor, Roche) and sonicated with Branson Sonifier, VWR to achieve an average fragment size of approximately 0.3 to 1.0 kb. The sonicated chromatin was centrifuged and the insoluble pellet was discarded. The soluble chromatin solution was diluted 10 fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl), then after preclearing with protein A-sepharose beads (Sigma), 5 l of HY5 or HA tag specific monoclonal antibody (Santa Cruz Biotech, USA) were added to a 1 ml chromatin solution and incubated overnight at 4ºC. The immunocomplexes were extracted by incubating with 100 l of 50% protein A-sepharose beads for 1 hr at 4ºC. After several washes, immunocomplex was eluted from the beads with 250 l of elution buffer (1% SDS, 0.1 M NaHCO3) twice, then reverse crosslinked with final concentration of 200 mM NaCl at 65ºC for 6-8 hrs. After removing all proteins by treating with proteinase K, DNA was purified by phenol-chloroform extraction and followed by ethanol precipitation. The pellet was resuspended with 50 l of 0.1X TE with RNase A (0.1 mg/ml) and used for probe synthesis or PCR analysis.

tag: 35S HA:HY5 transgenic line

source_name: genomic DNA input

label_protocol: Same with Channel 1

extract_protocol: A small aliquot of untreated sonicated chromatin was reverse-crosslinked and used as the total input DNA control.

tag: Col Wildtype


title: MP G3 high 1 day vs. MP G1 control 1 day (ExpID 1994B)

source_name: MP G3 high 1 day (Cy3)

tag: MP G1 control 1 day


title: MP G7 control 7 days vs. MP G8 high 7 days (ExpID 1996)

source_name: MP G7 control 7 days (Cy3)

tag: MP G7 control 7 days

source_name: MP G8 high 7 days (Cy5)

tag: MP G8 high 7 days


title: Wobbler_testis_6163_rep2

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

source_name: testis wr/wr 6163

tag: Strain

tag: Mouse ID

source_name: Testis wt pool


title: HY5 ChIP-chip Rep3


title: MP G4 control 3 days vs. MP G6 high 3 days (ExpID 1995B)

source_name: MP G4 control 3 days (Cy3)

tag: MP G4 control 3 days

source_name: MP G6 high 3 days (Cy5)


title: Methapyrilene, Control 3 day vs. Methapyrilene, High 3 day (ExpID 1469)


title: Methapyrilene, Low 1 day vs. Methapyrilene, Control 1day (ExpID 1466B)

source_name: Methapyrilene, Low 1 day (Cy3)

source_name: Methapyrilene, Control 1day (Cy5)


title: MP G5 low 3 days vs. MP G4 control 3 days (ExpID 1992B)

source_name: MP G5 low 3 days (Cy3)

tag: MP G5 low 3 days

source_name: MP G4 control 3 days (Cy5)


title: Methapyrilene, Control 3 day vs. Methapyrilene, Low 3 day (ExpID 1468)

description: Male Sprague-Dawley rats were treated with 3 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols

source_name: Methapyrilene, Control 3 day (Cy3)


title: Methapyrilene, High 1 day vs. Methapyrilene, Control 1day (ExpID 1467B)

source_name: Methapyrilene, High 1 day (Cy3)


title: Methapyrilene, Control 7 day vs. Methapyrilene, Low 7 day (ExpID 1470)

source_name: Methapyrilene, Control 7 day (Cy3)

tag: Methapyrilene, Control 7 day

source_name: Methapyrilene, Low 7 day (Cy5)

tag: Methapyrilene, Low 7 day


title: MP G2 low 1 day vs. MP G1 control 1 day (ExpID 1991)

source_name: MP G2 low 1 day (Cy3)

tag: MP G2 low 1 day

source_name: MP G1 control 1 day (Cy5)


title: Methapyrilene, High 7 day vs. Methapyrilene, Control 7 day (ExpID 1471)

source_name: Methapyrilene, High 7 day (Cy3)

tag: Methapyrilene, High 7 day

source_name: Methapyrilene, Control 7 day (Cy5)


title: HY5 ChIP-chip Rep1

source_name: HY5 ChIP sample

extract_protocol: Seedling tissues 1.5 g were crosslinked with 50 ml of 1% formaldehyde in a vacuum for 15 minutes. 2.5 ml of 2 M glycine was added to stop the crosslinking. After rinsing seedlings with water, tissues were ground with liquid nitrogen and resuspended with 25 ml of Extraction Buffer I (0.4 M sucrose, 10 mM Tris-HCl pH 8, 10 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor, Roche), then filtered through miracloth (Calbiochem). The filtrate was centrifuged at 4000 rpm at 4˚C for 20 mins. The pellet was resuspended in 1 ml of Extraction Buffer II (0.25 M sucrose, 10 mM Tris-HCl pH 8, 10mM MgCl2, 1% Triton X-100, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor) and centrifuged at 14000 rpm, 4˚C for 10 mins. The pellet was resuspended in 300 l of Extraction Buffer III (1.7 M sucrose, 10 mM Tris-HCl pH 8, 0.15% Triton X-100, 2 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF, 1X protease inhibitor) and loaded on top of the equal amount of clean Extraction Buffer III, then centrifuged at 14000 rpm for 1 hr. The crude nuclear pellet was resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1X complete protease inhibitor, Roche) and sonicated with Branson Sonifier, VWR to achieve an average fragment size of approximately 0.3 to 1.0 kb. The sonicated chromatin was centrifuged and the insoluble pellet was discarded. The soluble chromatin solution was diluted 10 fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl), then after preclearing with protein A-sepharose beads (Sigma), 5 l of HY5 or HA tag specific monoclonal antibody (Santa Cruz Biotech, USA) were added to a 1 ml chromatin solution and incubated overnight at 4ºC. The immunocomplexes were extracted by incubating with 100 l of 50% protein A-sepharose beads for 1 hr at 4ºC. After several washes, immunocomplex was eluted from the beads with 250 l of elution buffer (1% SDS, 0.1 M NaHCO3) twice, then reverse crosslinked with final concentration of 200 mM NaCl at 65ºC for 6-8 hrs. After removing all proteins by treating with proteinase K, DNA was purified by phenol-chloroform extraction and followed by ethanol precipitation. The pellet was resuspended with 50 l of 0.1X TE with RNase A (0.1 mg/ml) and used for probe synthesis or PCR analysis.

source_name: genomic DNA input


title: 143b doxorubicin treated expt4

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

institute: Cancer Institute (WIA)

description: The scanned images were imported into TIGR'S Spotfinder software. The gridding was done followed by QC setting and checking for quality of spots called. The MEV file output was then loaded into the TIGR'S MIDAS software. The  "One bad channel tolerance policy" was set to Generous. Channel A and B flags were used. Lowess Normalisation was done using Global mode. The MIDAS output files were analysed in TMEV software for data mining.

hyb_protocol: Pre-hybridisation using 5x SSC, 0.1% SDS and 1% BSA for one hour. Slides dried and then placed in Amersham's Lucidea Hybridisation chamber and hybridised with 200ul of the hyb-mixture for 16 hours at 42°C. Wash 1:  1X SSC, 0.2% SDS; 32°C; Wash 2:  0.1X SSC, 0.2% SDS; 20°C; Wash 3:  0.1X SSC; 20°C; The slides were dried before scanning.

scan_protocol: Perkin Elmer's Proscan array was used for scanning the slides. The Image files generated were stored as TIFF images

data_processing: TIGR'S suite of softwares Spotfinder, MIDAS and MEV were used for data processing.

source_name: 143b parental cell line

label_protocol: Amersham Biosciences Cyscribe Post labeling kit and protocol

growth_protocol: Cells grown in DMEM - 10% Fetal calf serum, in 10% carbon dioxide chamber.

extract_protocol: Qiagen's RNeasy kit and protocol

treatment_protocol: no treatment

tag: 143b cell line

tag: human osteosarcoma cell line

source_name: 143b doxorubicin resistant cell line

label_protocol: Amersham Biosciences Cyscribe post labeling kit and protocol

growth_protocol: Cells grown in DMEM - 10% Fetal calf serum, in 10% carbon dioxide chamber in the presence of 75uM Doxorubicin.

treatment_protocol: 143b cells grown in the presence of intermittent exposure to doxorubicin (3 hours at a concentration) and allowing cells to recover before moving to the next higher dose. the 143b doxorubicin drug resistant cell line used for the experiment was grown in the presence of 75um doxorubicin and showed stable resistance to the drug.

tag: 143b doxorubicin drug resistant cell line;

tag: human osteosarcoma cell line selected for doxorubicin resistance by growing the cells in progressively increasing concentration of the drug.


title: Methapyrilene, Control 1day vs. Methapyrilene, Low 1 day (ExpID 1466)

source_name: Methapyrilene, Control 1day (Cy3)

tag: Methapyrilene, Control 1day

source_name: Methapyrilene, Low 1 day (Cy5)

tag: Methapyrilene, Low 1 day


title: 143b doxorubicin treated expt3

description: The scanned images were imported into TIGR'S Spotfinder software. The gridding was done followed by QC setting and checking for quality of spots called. The MEV file output was then loaded into the TIGR'S MIDAS software. The "One bad channel tolerance policy" was set to Generous. Channel A and B flags were used. Lowess Normalisation was done using Global mode. The MIDAS output files were analysed in TMEV software for data mining.


title: 143b doxorubicin treated expt2


title: Methapyrilene, Low 7 day vs. Methapyrilene, Control 7 day (ExpID 1470B)

source_name: Methapyrilene, Low 7 day (Cy3)


title: HY5 ChIP-chip Rep2

tag: 35S HA:HY5 transgenic line

tag: Col Wildtype


title: Methapyrilene, Low 3 day vs. Methapyrilene, Control 3 day (ExpID 1468B)

source_name: Methapyrilene, Low 3 day (Cy3)

tag: Methapyrilene, Low 3 day

source_name: Methapyrilene, Control 3 day (Cy5)

tag: Methapyrilene, Control 3 day


title: Methapyrilene, High 3 day vs. Methapyrilene, Control 3 day (ExpID 1469B)

source_name: Methapyrilene, High 3 day (Cy3)

tag: Methapyrilene, High 3 day


title: Methapyrilene, Low 3 day vs. Methapyrilene, Control 3 day (ExpID 1468)


title: Methapyrilene, High 3 day vs. Methapyrilene, Control 3 day (ExpID 1469)


title: Methapyrilene, Control 7 day vs. Methapyrilene, High 7 day (ExpID 1471)

source_name: Methapyrilene, High 7 day (Cy5)


title: Methapyrilene, Low 1 day vs. Methapyrilene, Control 1day (ExpID 1466)

source_name: Methapyrilene, Low 1 day (Cy3)

source_name: Methapyrilene, Control 1day (Cy5)


title: Methapyrilene, High 1 day vs. Methapyrilene, Control 1day (ExpID 1467)

source_name: Methapyrilene, High 1 day (Cy3)

tag: Methapyrilene, High 1 day


title: MP G8 high 7 days vs. MP G7 control 7 days (ExpID 1996)

source_name: MP G8 high 7 days (Cy3)

tag: MP G8 high 7 days

source_name: MP G7 control 7 days (Cy5)

tag: MP G7 control 7 days


title: 143b doxorubicin treated expt1


title: Methapyrilene, Low 7 day vs. Methapyrilene, Control 7 day (ExpID 1470)

tag: Methapyrilene, Low 7 day

source_name: Methapyrilene, Control 7 day (Cy5)

tag: Methapyrilene, Control 7 day


title: MP G8 low 7 days vs. MP G7 control 7 days (ExpID 1993)

description: Male Sprague-Dawley rats were treated with 7 daily doses of 10 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G8 low 7 days (Cy3)

tag: MP G8 low 7 days


title: MP G6 high 3 days vs. MP G4 control 3 days (ExpID 1995B)

source_name: MP G6 high 3 days (Cy3)

tag: MP G6 high 3 days

source_name: MP G4 control 3 days (Cy5)

tag: MP G4 control 3 days


title: MP G5 low 3 days vs. MP G4 control 3 days (ExpID 1992)

source_name: MP G5 low 3 days (Cy3)

tag: MP G5 low 3 days


title: MP G1 control 1 day vs. MP G2 low 1 day (ExpID 1991)

description: Male Sprague-Dawley rats were treated with a single dose of 10 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G1 control 1 day (Cy3)

tag: MP G1 control 1 day

source_name: MP G2 low 1 day (Cy5)

tag: MP G2 low 1 day


title: MP G1 control 1 day vs. MP G3 high 1 day (ExpID 1994)

source_name: MP G3 high 1 day (Cy5)

tag: MP G3 high 1 day