title: 143BTK- cell line, rho+, replicate C

description: Gene expression data from 143BTK- cells, undepleted of mitochondrial DNA

source_name: 143BTK- cells, rho+

value: undepleted


title: 143BTK- cell line, rho0, replicate A

status: Public on May 01 2009

type: RNA

city: Kansas City

first: Norman

last: Pavelka

state: MO

address: 1000 E. 50th Street

country: USA

institute: Stowers Institute for Medical Research

description: Gene expression data from 143BTK- cells, depleted of mitochondrial DNA

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip HG-U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station following the EukGE-WS2v4 protocol

scan_protocol: GeneChips were scanned using an Hewlett-Packard GeneArray Scanner

data_processing: 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. Each subset relative to a particular cell line was then independently subjected to a quantile normalization in the R environment for statistical computing. Normalized data were finally rounded to the first decimal digit

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 143BTK- cells, rho0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown for 3-4 weeks in Dulbecco’s modified Eagle medium (DMEM), high glucose (Euroclone), supplemented with 10% Fetal Calf Serum (FCS), 1mM NaPyruvate and 50ug/ml uridine

extract_protocol: Total RNA was isolated from 8 millions cells using the Qiagen RNeasy Mini kit (Qiagen)

treatment_protocol: To generate rho0 cells we added 50 ng/ml ethidium bromide (EthBr) to the growth medium, for a period of 3 weeks. No clone selection was performed but the cells were trypsinised and pooled together. One week after the removal of EthBr, absence of mtDNA was checked in rho0 cell lines by either PCR or by southern-blot

tag: cell line

tag: mitochondria

value: depleted


title: 143BTK- cell line, rho+, replicate A


title: 143BTK- cell line, rho0, replicate B


title: PBMC treated with B. anthracis for 6h set 3

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: Control 12 of 12

hyb_protocol: custom cDNA glass array slide were used for hybridization over night at 55 degree celius

scan_protocol: images were scanned using Genepix 4000B (Axon Instruments)

data_processing: Intensities were extracted using Genepix PRO 6, and Lowess normalization and statistical analysis were performed using GeneSpring GX. Lowess normalization and per gene normalization to specific samples. The later normalization made the values of the control signals 1 or approximately one.

source_name: Human: peripheral blood mononuclear cells

label_protocol: dual channel labling were used: human reference RNA was labled with Cy3 and isolated RNA with Cy5

growth_protocol: Cell lines were cultured in standard media

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

treatment_protocol: peripheral blood mononuclear cells exposed to a 1 MOI (multiplicity of infection pathogenic) of the B. anhracis spores. Cells, incubated in the absence and presence of B. anhracis, were collected by centrifugation. Trizol™ (Invitrogen, Carlsbad, CA,) was added for RNA isolation and inactivation of the pathogen.

tag: cell type

value: peripheral blood mononuclear cells

source_name: universal reference RNA

tag: sample

value: Stratagen universal reference RNA


title: A549 cell line, rho+, replicate B

description: Gene expression data from A549 cells, undepleted of mitochondrial DNA

source_name: A549 cells, rho+


title: PBMC treated with B. anthracis for 6h set 2

description: Biological replica 8 of 10


title: 143BTK- cell line, rho+, replicate B


title: A549 cell line, rho+, replicate A


title: PBMC treated with B. anthracis for 8h set 2

description: Biological replica 9 of 10


title: A549 cell line, rho+, replicate C


title: PBMC treated with B. anthracis for 4h set 2

description: Biological replica 7 of 10


title: PBMC 6h control set 3

description: Control 11 of 12


title: PBMC treated with B. anthracis for 24h set 2

description: Biological replica 10 of 10


title: A549 cell line, rho0, replicate C

description: Gene expression data from A549 cells, depleted of mitochondrial DNA

source_name: A549 cells, rho0


title: PBMC 24h control set 2

description: Control 10 of 12


title: PBMC treated with B. anthracis for 2h set 2

description: Biological replica 6 of 10


title: PBMC 4h control set 2

description: Control 7 of 12


title: PBMC 6h control set 2

description: Control 8 of 12


title: A549 cell line, rho0, replicate B


title: A549 cell line, rho0, replicate A


title: PBMC 8h control set 2

description: Control 9 of 12


title: PBMC 24h control set 1

description: Control 5 of 12


title: PBMC treated with B. anthracis for 24h set 1

description: Biological replica 5 of 14


title: PBMC treated with B. anthracis for 12h set 1

description: Biological replica 4 of 10


title: PBMC 2h control set 1

description: Control 1 of 12


title: PBMC 12h control set 1

description: Control 4 of 12


title: PBMC 4h control set 1

description: Control 2 of 12


title: PBMC treated with B. anthracis for 8h set 1

description: Biological replica 3 of 10


title: PBMC 2h control set 2

description: Control 6 of 12


title: PBMC treated with B. anthracis for 2h set 1

description: Biological replica 1 of 10


title: PBMC 8h control set 1

description: Control 3 of 12


title: wt.coc.1396: Striatum from cocaine treated control animal, biological rep. 3

status: Public on Apr 30 2009

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center

description: Gene expression data from mutant animals treated with cocaine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse 430A 2.0 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Analysis of array data was performed using the R 2.4.1/Bioconductor 1.9 (Gentleman et al. 2004) . Data was normalized and expression values were computed using the gcrma method.

organism: Mus musculus

source_name: The striatum including nucleus accumbens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 10 to 15 week-old littermate female mice were single-caged and handled for 5 days

extract_protocol: Whole brains were removed and placed in RNAlater (Ambion) overnight. Brains were sliced into 150 μm-thick vibratome sections and the striatum including the nucleus accumbens was excised with thin needles. Total RNA was prepared with Rneasy RNA Mini kit (Qiagen) and its quality was assessed on RNA LabChips (Agilent).

treatment_protocol: Intra peritoneal injection of 25 mg/kg cocaine, animals were sacrificed one hour after the injection

tag: Female; C57Bl6 backroung; Srf flox/flox, cocaine treated


title: wt.sal.1377: Striatum from saline treated control animal, biological rep. 3

tag: Female; C57Bl6 backroung; Srf flox/flox, saline treated


title: PBMC treated with B. anthracis for 4h set 1

description: Biological replica 2 of 10


title: wt.coc.1368: Striatum from cocaine treated control animal, biological rep. 2

description: Gene expression data from control animals treated with cocaine


title: wt.sal.1304: Striatum from saline treated control animal, biological rep. 1


title: mut.sal.1331: Striatum from saline treated mutant animal, biological rep. 1

tag: Female; C57Bl6 backroung; D1Cre+, Srf flox/flox, saline treated


title: mut.sal.1366: Striatum from saline treated mutant animal, biological rep. 3


title: mut.coc.1337: Striatum from cocaine treated mutant animal, biological rep. 1

description: Gene expression data from control animals treated with saline

tag: Female; C57Bl6 backroung; D1Cre+, Srf flox/flox, cocaine treated


title: mut.coc.1359: Striatum from cocaine treated mutant animal, biological rep. 2


title: mut.sal.1338: Striatum from saline treated mutant animal, biological rep. 2


title: mut.coc.1370: Striatum from cocaine treated mutant animal, biological rep. 3


title: wt.sal.1376: Striatum from saline treated control animal, biological rep. 2


title: tumor_rep3

status: Public on Apr 21 2009

city: Vienna

first: christian

last: haslinger

state: Vienna

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim Austria

description: Gene expression data of thymus tumor.

hyb_protocol: After fragmentation 15 microgram of cRNA was hybridized for 16hrs at 45C on Affymetrix mous430_2 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Agilent GeneArray Scanner, Scanner Type M10.

data_processing: MAS5 normalized expression, target value 100.

source_name: tumor tissue

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microgram total RNA.

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


title: resistant_tumor_rep3

description: Gene expression data of XIST resistant thymus tumor.

source_name: resistant tumor tissue


title: wt.coc.1364: Striatum from cocaine treated control animal, biological rep. 1


title: Akt_Cre mice treated with tamoxifen for 48h upregulating Akt expression in muscle only

city: Padova

first: Reimar

last: Abraham

address: Via Orus 2

country: Italy

institute: Venetian Institute of Molecular Medicine

description: Transgenic mouse expressing a Akt fusion with estrogen receptor binding domain in skeletal muscle only - addition of tamoxifen stabilizes Akt leading to muscle hypertrophy

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Probe set summary values were obtained using Mas5.0

label: Biotin

source_name: Gastrocnemius muscle treated with tamoxifen for 48h upregulating Akt expression

label_protocol: Standard Affymetrix protocol

extract_protocol:
Trizol followed by Qiagen RNeasy cleanup
Integritiy of RNA was checked by OD260/280 ratio and Agilent

tag: strain

tag: genotype/variation

value: Akt_Cre transgenic

tag: tissue

value: gastrocnemius muscle

tag: agent

value: tamoxifen

tag: time


title: Akt_Cre mice treated with tamoxifen for 24h upregulating Akt expression in muscle only

description: Transgenic mice expressing a fusion of Akt with the estrogen binding domain in muscle only - addition of tamoxifen stabilizes Akt

data_processing: Probe sets were summarized using Mas5.0

source_name: Gastrocnemius muscle treated with tamoxifen for 24h upregulating Akt expression

extract_protocol:
Trizol followed by Qiagen RNeasy clean up
Integritiy of the RNA was checked using Agilent Lab-on-a-chip


title: tumor_rep2

description: Gene expression data of thymus tumor.


title: Akt_Cre mice treated with oil for 24h as a control

source_name: Gastrocnemius muscle treated with oil for 24h

value: oil (control)


title: thymus_normal_rep2

description: Gene expressin data of normal mouse thymus.

source_name: thymus normal tissue


title: thymus_normal_rep1


title: resistant_tumor_rep2


title: Fat D298 ad lib rep6

status: Public on Apr 20 2009

city: Ames

first: Sender

last: Lkhagvadorj

state: IA

address: 2255 Kildee

department: Animal Science

institute: Iowa State University

description: 6 months old Yorkshire gilts from a genetic line with high feed efficiency, obtained by selecting for low residual feed intake were used.

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

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

data_processing: Values are probe level measures that were summarized into probe set level expression measures using the "affy" packagein R according to the MAS 5.0 algorithm

organism: Sus scrofa

source_name: fat, 3-day ad libitum fed, D298

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

growth_protocol: The pigs were fed ad libitum and contained at the Lauren Christian swine facility of Iowa State University. The animal was genotyped for MC4R variant and pigs with specific genotypes were transferred to a clean animal facility for experiment.

extract_protocol: Total RNA was isolated from tissues by using the RNeasy Midi kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) based on the manufacturer's protocol.

treatment_protocol: The animal homozygous for MC4R D298 was fed ad libitum for 3-days.

tag: 10th rib middle layer backfat sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant that were fed ad libitum for 3-days


title: Liver D298 fasted rep6

source_name: liver, 3-day fasted, D298

treatment_protocol: The animal homozygous for MC4R D298 was fasted for 3-days.

tag: Liver sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant were fasted for 3-days


title: Fat N298 ad lib rep6

source_name: fat, 3-day ad libitum fed, N298

treatment_protocol: The animal homozygous for MC4R N298 was fed ad libitum for 3-days.

tag: 10th rib middle layer backfat sample from about six month old Yorkshire gilts homozygous for MC4R N298 variant that were fed ad libitum for 3-days


title: tumor_rep1

description: Gene expression data of thymus tumor.


title: Liver D298 ad lib rep6

source_name: liver, 3-day ad libitum fed, D298

tag: Liver sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant that were fed ad libitum for 3-days


title: Liver N298 fasted rep6

source_name: liver, 3-day fasted, N298

treatment_protocol: The animal homozygous for MC4R N298 was fasted for 3-days.

tag: Liver sample from about six month old Yorkshire gilts homozygous for MC4R N298 variant that were fasted for 3-days


title: resistant_tumor_rep1


title: Fat N298 fasted rep6

source_name: fat, 3-day fasted, N298

tag: 10th rib middle layer backfat sample from about six month old Yorkshire gilts homozygous for MC4R N298 variant that were fasted for 3-days


title: Liver N298 ad lib rep6

source_name: liver, 3-day ad libitum fed, N298

tag: Liver sample from about six month old Yorkshire gilts homozygous for MC4R N298 variant that were fed ad libitum for 3-days


title: Fat D298 fasted rep5

source_name: fat, 3-day fasted, D298

tag: 10th rib middle layer backfat sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant were fasted for 3-days


title: thymus_normal_rep3


title: Fat D298 fasted rep6

tag: 10th rib middle layer backfat sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant were fasted


title: Fat N298 fasted rep5

data_processing: Values are probe level measures that were summarized into probe set level expression measures using the "affy" package in R according to the MAS 5.0 algorithm


title: Fat D298 ad lib rep5


title: Liver N298 fasted rep5


title: Fat N298 ad lib rep5


title: Liver D298 fasted rep5


title: Liver D298 ad lib rep5


title: Fat N298 fasted rep4


title: Fat D298 fasted rep4


title: Fat N298 ad lib rep4


title: Liver N298 ad lib rep4


title: Fat D298 ad lib rep3


title: Fat N298 fasted rep3


title: Liver N298 ad lib rep5


title: Liver D298 fasted rep3


title: Liver N298 ad lib rep3


title: Fat N298 ad lib rep3


title: Fat D298 fasted rep3


title: Liver D298 fasted rep4


title: Liver D298 ad lib rep4


title: Liver N298 fasted rep4


title: Fat D298 ad lib rep4


title: Fat D298 ad lib rep2


title: Liver N298 fasted rep3


title: Fat D298 fasted rep2

treatment_protocol: The animal homozygous for MC4R D298 was fasted for 3-days


title: Fat N298 fasted rep2


title: Liver D298 ad lib rep3


title: Fat N298 ad lib rep2


title: Liver N298 fasted rep2


title: Fat N298 ad lib rep1


title: Liver D298 ad lib rep2


title: Fat N298 fasted rep1


title: Fat D298 fasted rep1


title: Liver D298 fasted rep1

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

tag: Liver sample from about six month old Yorkshire gilts homozygous for MC4R D298 variant that were fasted 3-days


title: Liver N298 ad lib rep2


title: Fat D298 ad lib rep1


title: Liver D298 ad lib rep1


title: Liver D298 fasted rep2


title: Liver N298 fasted rep1


title: c35_TCDD1

status: Public on Apr 17 2009

type: genomic

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons-100 Washtenaw Ave.

institute: University of Michigan

description: Whole genome amplification

hyb_protocol: According to standard Affymetrix protocol

data_processing: The raw data were transferred to tab-delimited text format using Affymetrix Tiling Array Software, then normalized using quantile normalization. The processed data file linked below reports normalized log2 intensities.

molecule: genomic DNA

source_name: hepatoma mutant cells, TCDD 8hr

label_protocol: Immunoprecipitated DNA was subjected to whole genome amplification and labeled according to the standard protocol supplied by Affymetrix (Affymetrix® Chromatin Immunoprecipitation Assay Protocol. Amplified DNA (7.5 µg) was  fragmented and labeled by GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) following the manufacturer’s specifications.  Fragmentation analysis was performed using a RNA 6000 LabChip Kit (Agilent) and an Agilent 2100 bioanalyzer.

extract_protocol: Cells were grown in a-minimal essential medium (a-MEM, Gibco) supplemented with 5% (v/v) fetal bovine serum (Sigma), 26 mM NaHCO3 and 1 % (v/v) antibiotic-antimycotic (Gibco) at 37°C in humidified 5% CO2 atmosphere.  When the cells reached 70-80% confluence they were treated with 5 µM B[a]P, 5 nM TCDD, or 0.1% DMSO vehicle.  Cells were then harvested 1.5 h post-treatment for chromatin immunoprecipitation (ChIP). ChIP was performed with minor modifications of published procedures {Wells et al., 2002} as modified in our laboratory {Schnekenburger et al., 2007}  Immunoprecipitation was performed with ChIP-verified anti-AHR antibody (Biomol) or with control non-immune rabbit IgG (upstate).  An aliquot of immunoprecipitated purified DNA was checked for IP efficiency by real-time PCR using primers specific for the mouse Cyp1a1 promoter domains known to be bound or not by AHR.  A significant enrichment (16- to 32-fold) for the specific AHR target was observed relative to the control antibody.

tag: TREATMENT

value: 5 nanomolar 2,3,7,8-tetrachlorodibenzo-p-dioxin in DMSO 8hr

tag: CELL LINE

value: Hepa-1c1c7 mutant derivative with AHR unable to bind DNA

tag: STRAIN

tag: TISSUE

value: Hepatoma

tag: SEX

value: Male

tag: ANTIBODY

value: anti N-terminus AHR


title: c35_TCDD2

description: Whole genome amplification

scan_protocol: According to standard Affymetrix protocol


title: Liver N298 ad lib rep1


title: c35_DMSO1

description: Whole genome amplification

source_name: hepatoma mutant cells, DMSO 8hr

value: control DMSO vehicle 8hr


title: c35_DMSO2

description: Whole genome amplification


title: c35_Igg2

description: Whole genome amplification

source_name: hepatoma mutant cells, IgG

value: non-specific IgG


title: Ahr_TCDD2

description: Whole genome amplification

source_name: hepatoma cells, TCDD 8hr


title: Ahr_TCDD1

description: Whole genome amplification


title: c35_Igg1

description: Whole genome amplification


title: Ahr_BaP1

description: Whole genome amplification

source_name: hepatoma cells, BaP 8hr

value: 5 micromolar benzo[a]pyrene in DMSO 8hr


title: Ahr_DMSO2

description: Whole genome amplification

source_name: hepatoma cells, DMSO 8hr


title: Ahr_DMSO1

description: Whole genome amplification


title: Igg2

description: Whole genome amplification

source_name: hepatoma cells, IgG


title: Igg1

description: Whole genome amplification


title: Igg3

description: Whole genome amplification


title: Igg4

description: Whole genome amplification


title: Ahr_BaP2

description: Whole genome amplification


title: f1 v f26

city: Atlanta

first: David

middle: John

last: Katz

state: GA

address: Rollins Bldg 1510 Clifton Rd

department: Biology

institute: Emory University

description: Hybridizations were performed pair-wise, along with a dye flip, from N2f1 (wild-type) and spr-5(by101) f1, 13 and f26, for a total of 12 arrays.

hyb_protocol: Successive Hybridization of cDNA and 3DNA to Microarray (2-Step Protocol) 1. Following cDNA sample concentration using the Millipore Microcon. YM-30, add Nuclease Free Water (Vial 10) to the cDNA preparation to achieve a total volume of 10 μl. 2. Following the table below, add the appropriate volumes of reagents: Desired Final Hybridizaton Mix Volume: 50 μl Concentrated cDNA (from step 3a/3b) 10 μl 2X MWG Coverslips Hybridization Buffer 25 μl LNA dT Blocker (Vial 9) 2 ml Nuclease Free Water (Vial 10) 13 μl Recommended Hybridization Mix: Dimensions Required - 22 x 60mm Coverslip Total Volume - 25μl 3. Gently vortex and briefly microfuge the Hybridization Mix after addition of all components. 4. Incubate the Hybridization Mix first at 75-80°C for 10 minutes, and then at 42oC until loading the array. 5. Gently vortex and briefly microfuge the Hybridization Mix (Pre-warming the microarray to the hybridization temperature may reduce background). 6. Carefully pipette 50ul under the coverslip covering the arrayed surface. Ensure that the array is completely covered and incubate overnight in a dark humidified chamber (fill the humidity wells of the chamber with the manufacturers recommended amount of 1X MWG Buffer) at 42oC. 7 Post cDNA Hybridization Wash: After hybridization the slides are washed briefly several times to remove unbound cDNA molecules. Bath #1 (2x SSC, 0.2% SDS) Bath #2 (2x SSC) Bath #3 (0.2x SSC) Place solutions on orbital shaker and rotate during washes. 1. Prewarm the 2X SSC, 0.2% SDS wash buffer to 42oC 2. Remove slides from chambers using forceps and place in slide rack in bath #1. Make sure the coverslip separates from each slide. Be most careful not to let the coverslip scratch the surface of the arrayed area as it comes off. The most effective method to separate the coverslip from the slide is to place the slide in the bath with the array side facing up. Once the slide is submerged, quickly move the slide downward. Occasionally, shaking the slide side to side may be required. Once the coverslip is separated, place the slide in the slide rack. 3. Shake for 12 min. 4. Transfer slides individually to the slide rack in bath #2 and shake for 12 min. 5. Transfer slides individually to the slide rack in bath #3 and shake for 12 min. 6. Wash for 1-2 minutes at room temperature in 95% ethanol to fix the cDNA molecules to the probes. Note: this step can be omitted if 95% Ethanol is not available. 7. After final wash is complete, remove slides, one at a time, from 95% ethanol and spin immediately in microcentrifuge for 30 seconds, or alternatively transfer the array to a dry 50mL centrifuge tube. Do this quickly to avoid streaky background on the slide and orient the slide so that any label is down in the tube. Centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide. Avoid contact with the array surface. 8 3DNA Hybridization: 1. The Anti-Fade Reagent (Vial 8) reduces fading of the fluorescent dyes post hybridization. Prepare a stock solution by adding 1μl of Anti-Fade to 100μl of MWG Hybridization. Store any unused hybridization buffer at –20°C and use within two weeks. 2. Prepare the 3DNA Array 350 Capture Reagent (Vial 1). It is necessary to break up aggregates that may form as a result of the freezing process. a. Thaw the 3DNA Array 350 Capture Reagent (Vial 1) in the dark at room temperature for 20 minutes. b. Vortex at the maximum setting for 3 seconds and microfuge briefly (1 second). c. Incubate at 50-55°C for 10 minutes. d. Vortex at the maximum setting for 3-5 seconds. e. Microfuge the tube briefly to collect the contents at the bottom. f. Be sure to check the sample for aggregates prior to use and repeat vortex mixing if necessary. Aggregates may appear as small air bubbles or flakes at the side of the tube below the surface of the solution. Repeat steps 4a-4f if necessary. 3. Following the table below, add the appropriate volumes of the 3DNA Array 350 kit components to a fresh tube to make the Hybridization Mix based upon the final desired volume: Desired Final Hybridizaton Mix Volume: 50μl 2X MWG Hybridization Buffer 25μ 3DNA Capture Reagent #1 (Vial 1, e.g. Cy3) 2.5μl 3DNA Capture Reagent #2 (Vial 1, e.g. Cy5) 2.5μl Nuclease Free Water (Vial 10) 20μl Note: For single channel expression analysis, use 2.5μl of Nuclease Free Water (Vial 10) in place of the second 3DNA Capture Reagent. Gently vortex and briefly microfuge the Hybridization Mix after addition of all components. 4. Incubate the Hybridization Mix first at 75-80°C for 10 minutes, and then at 50oC until loading the array. 5. Gently vortex and briefly microfuge the Hybridization Mix (Pre-warming the microarray to the hybridization temperature may reduce background). 6. Carefully pipette 50ul under the coverslip covering the arrayed surface. Ensure that the array is completely covered and incubate 2.5-3 hours in a dark humidified chamber (fill the humidity wells of the chamber with the manufacturers recommended amount of 1X MWG Buffer) at 50oC. 9 Post 3DNA Hybridization Wash: After hybridization the slides are washed briefly several times to remove unbound 3DNA molecules. Perform these washes in the dark to avoid photobleaching and fading of the fluorescent dyes. Bath #1 (2x SSC, 0.2% SDS) Bath #2 (2x SSC) Bath #3 (0.2x SSC) Place solutions on orbital shaker and rotate during washes. 1. Prewarm the 2X SSC, 0.2% SDS wash buffer to 50oC 2. Remove slides from chambers using forceps and place in slide rack in bath #1. Make sure the coverslip separates from each slide. Be most careful not to let the coverslip scratch the surface of the arrayed area as it comes off. The most effective method to separate the coverslip from the slide is to place the slide in the bath with the array side facing up. Once the slide is submerged, quickly move the slide downward. Occasionally, shaking the slide side to side may be required. Once the coverslip is separated, place the slide in the slide rack. 3. Shake for 12 min. 4. Transfer slides individually to the slide rack in bath #2 and shake for 12 min. 5. Transfer slides individually to the slide rack in bath #3 and shake for 12 min. 6. After final wash is complete, remove slides, one at a time, and spin immediately in microcentrifuge for 30 seconds, or alternatively transfer the array to a dry 50mL centrifuge tube. Do this quickly to avoid streaky background on the slide and orient the slide so that any label is down in the tube. Centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide. Avoid contact with the array surface. 7. Store the array in the dark until scanned. (scanning should be performed as soon as possible

scan_protocol: High intensity scan using the Scan Array microarray scanner at Washington University Microarray Facility

data_processing: Data was processed at the Washington University Microarray Facility

organism: Caenorhabditis elegans

source_name: spr-5 f1

label_protocol: RNA was labelled with the Genisphere Array350 system

extract_protocol: To generate total RNA 3 10cM plates of worms were flash frozen in 500ul of PBS. Following freezing 1ml of Trizol reagent was added to the pellet and the pellet was thawed, vortexed and re-frozen 4 times. After 4 cycles, the sample was chloroform extracted, precipitated with isopropanol, washed with 75% ethanol and cleaned up with the Qiagen RNeasy kit. For the microarray analysis 8ug of total RNA was hybridized.

tag: spr-5 mutant f1

source_name: spr-5 f26

tag: spr-5 mutant f26


title: N2 (wild-type) v f26

tag: N2 (wild-type)


title: f13 v f1

source_name: spr-5 f13

tag: spr-5 mutant f13


title: N2 (wild-type) v f13


title: Mouse 1, Sample:SZ18, Sex:M, Primary lung cancer, Adenocarcinoma

status: Public on Apr 15 2009

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Mouse1, Sample:SZ18, Sex:M, Primary lung cancer, Adenocarcinoma

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430A GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values

source_name: Primary lung adenocarcinoma from p53R172H∆g/+ K-rasLA1/+ mice

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

growth_protocol: Primary lung adenocarcinomas and metastases from p53R172H∆g/+ K-rasLA1/+ mice or syngeneic tumors were isolated, carefully dissected to remove the adjacent tissue.

extract_protocol: Total RNA was extracted by Trizol (Invitrogen) and purified with an RNeasy kit (Qiagen). RNA quality and quantity were evaluated on an Agilent Bioanalyzer following the manufacture’s recommendations (Agilent Technologies).


title: Mouse 6, Sample:SZ15, Sex:F, Primary lung cancer, Adenocarcinoma

description: Mouse6, Sample:SZ15, Sex:F, Primary lung cancer, Adenocarcinoma


title: Mouse 2, Sample:SZ22, Sex:M, Primary lung cancer, Adenocarcinoma

description: Mouse2, Sample:SZ22, Sex:M, Primary lung cancer, Adenocarcinoma


title: f26 v N2


title: Mouse 7, Sample:SZ17, Sex:M, Primary lung cancer, Adenocarcinoma

description: Mouse7, Sample:SZ17, Sex:M, Primary lung cancer, Adenocarcinoma


title: Mouse 4, Sample:SZ31, Sex:M, Primary lung cancer, Adenocarcinoma

description: Mouse4, Sample:SZ31, Sex:M, Primary lung cancer, Adenocarcinoma


title: N2 (wild-type) v f1


title: f26 v f13


title: Mouse 3, Sample:SZ24, Sex:M, Primary lung cancer, Adenocarcinoma

description: Mouse3, Sample:SZ24, Sex:M, Primary lung cancer, Adenocarcinoma


title: Mouse 5, Sample:SZ14, Sex:M, Primary lung cancer, Adenocarcinoma

description: Mouse5, Sample:SZ14, Sex:M, Primary lung cancer, Adenocarcinoma


title: f26 v f1


title: Mouse 3, Sample:SZ25, Sex:M, Metastasis, heart met

description: Mouse3, Sample:SZ25, Sex:M, Metastasis, heart met

source_name: Metastases from p53R172H∆g/+ K-rasLA1/+ mice


title: f1 v f13

hyb_protocol: Successive Hybridization of cDNA and 3DNA to Microarray (2-Step Protocol) 1. Following cDNA sample concentration using the Millipore Microcon. YM-30, add Nuclease Free Water (Vial 10) to the cDNA preparation to achieve a total volume of 10 μl. 2. Following the table below, add the appropriate volumes of reagents: Desired Final Hybridizaton Mix Volume: 50 μl Concentrated cDNA (from step 3a/3b) 10 μl 2X MWG Coverslips Hybridization Buffer 25 μl LNA dT Blocker (Vial 9) 2 ml Nuclease Free Water (Vial 10) 13 μl Recommended Hybridization Mix: Dimensions Required - 22 x 60mm Coverslip Total Volume - 25μl 3. Gently vortex and briefly microfuge the Hybridization Mix after addition of all components. 4. Incubate the Hybridization Mix first at 75-80°C for 10 minutes, and then at 42oC until loading the array. 5. Gently vortex and briefly microfuge the Hybridization Mix (Pre-warming the microarray to the hybridization temperature may reduce background). 6. Carefully pipette 50ul under the coverslip covering the arrayed surface. Ensure that the array is completely covered and incubate overnight in a dark humidified chamber (fill the humidity wells of the chamber with the manufacturers recommended amount of 1X MWG Buffer) at 42oC. 7 Post cDNA Hybridization Wash: After hybridization the slides are washed briefly several times to remove unbound cDNA molecules. Bath #1 (2x SSC, 0.2% SDS) Bath #2 (2x SSC) Bath #3 (0.2x SSC) Place solutions on orbital shaker and rotate during washes. 1. Prewarm the 2X SSC, 0.2% SDS wash buffer to 42oC 2. Remove slides from chambers using forceps and place in slide rack in bath #1. Make sure the coverslip separates from each slide. Be most careful not to let the coverslip scratch the surface of the arrayed area as it comes off. The most effective method to separate the coverslip from the slide is to place the slide in the bath with the array side facing up. Once the slide is submerged, quickly move the slide downward. Occasionally, shaking the slide side to side may be required. Once the coverslip is separated, place the slide in the slide rack. 3. Shake for 12 min. 4. Transfer slides individually to the slide rack in bath #2 and shake for 12 min. 5. Transfer slides individually to the slide rack in bath #3 and shake for 12 min. 6. Wash for 1-2 minutes at room temperature in 95% ethanol to fix the cDNA molecules to the probes. Note: this step can be omitted if 95% Ethanol is not available. 7. After final wash is complete, remove slides, one at a time, from 95% ethanol and spin immediately in microcentrifuge for 30 seconds, or alternatively transfer the array to a dry 50mL centrifuge tube. Do this quickly to avoid streaky background on the slide and orient the slide so that any label is down in the tube. Centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide. Avoid contact with the array surface. 3DNA Hybridization: 1. The Anti-Fade Reagent (Vial 8) reduces fading of the fluorescent dyes post hybridization. Prepare a stock solution by adding 1μl of Anti-Fade to 100μl of MWG Hybridization. Store any unused hybridization buffer at –20°C and use within two weeks. 2. Prepare the 3DNA Array 350 Capture Reagent (Vial 1). It is necessary to break up aggregates that may form as a result of the freezing process. a. Thaw the 3DNA Array 350 Capture Reagent (Vial 1) in the dark at room temperature for 20 minutes. b. Vortex at the maximum setting for 3 seconds and microfuge briefly (1 second). c. Incubate at 50-55°C for 10 minutes. d. Vortex at the maximum setting for 3-5 seconds. e. Microfuge the tube briefly to collect the contents at the bottom. f. Be sure to check the sample for aggregates prior to use and repeat vortex mixing if necessary. Aggregates may appear as small air bubbles or flakes at the side of the tube below the surface of the solution. Repeat steps 4a-4f if necessary. 3. Following the table below, add the appropriate volumes of the 3DNA Array 350 kit components to a fresh tube to make the Hybridization Mix based upon the final desired volume: Desired Final Hybridizaton Mix Volume: 50μl 2X MWG Hybridization Buffer 25μ 3DNA Capture Reagent #1 (Vial 1, e.g. Cy3) 2.5μl 3DNA Capture Reagent #2 (Vial 1, e.g. Cy5) 2.5μl Nuclease Free Water (Vial 10) 20μl Note: For single channel expression analysis, use 2.5μl of Nuclease Free Water (Vial 10) in place of the second 3DNA Capture Reagent. Gently vortex and briefly microfuge the Hybridization Mix after addition of all components. 4. Incubate the Hybridization Mix first at 75-80°C for 10 minutes, and then at 50oC until loading the array. 5. Gently vortex and briefly microfuge the Hybridization Mix (Pre-warming the microarray to the hybridization temperature may reduce background). 6. Carefully pipette 50ul under the coverslip covering the arrayed surface. Ensure that the array is completely covered and incubate 2.5-3 hours in a dark humidified chamber (fill the humidity wells of the chamber with the manufacturers recommended amount of 1X MWG Buffer) at 50oC. 9 Post 3DNA Hybridization Wash: After hybridization the slides are washed briefly several times to remove unbound 3DNA molecules. Perform these washes in the dark to avoid photobleaching and fading of the fluorescent dyes. Bath #1 (2x SSC, 0.2% SDS) Bath #2 (2x SSC) Bath #3 (0.2x SSC) Place solutions on orbital shaker and rotate during washes. 1. Prewarm the 2X SSC, 0.2% SDS wash buffer to 50oC 2. Remove slides from chambers using forceps and place in slide rack in bath #1. Make sure the coverslip separates from each slide. Be most careful not to let the coverslip scratch the surface of the arrayed area as it comes off. The most effective method to separate the coverslip from the slide is to place the slide in the bath with the array side facing up. Once the slide is submerged, quickly move the slide downward. Occasionally, shaking the slide side to side may be required. Once the coverslip is separated, place the slide in the slide rack. 3. Shake for 12 min. 4. Transfer slides individually to the slide rack in bath #2 and shake for 12 min. 5. Transfer slides individually to the slide rack in bath #3 and shake for 12 min. 6. After final wash is complete, remove slides, one at a time, and spin immediately in microcentrifuge for 30 seconds, or alternatively transfer the array to a dry 50mL centrifuge tube. Do this quickly to avoid streaky background on the slide and orient the slide so that any label is down in the tube. Centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide. Avoid contact with the array surface. 7. Store the array in the dark until scanned. (scanning should be performed as soon as possible


title: f1 v N2 (wild-type)


title: f13 v f26


title: Mouse 1, Sample:SZ19, Sex:M, Metastasis, Liver met

description: Mouse1, Sample:SZ19, Sex:M, Metastasis, Liver met


title: f13 v N2 (wild-type)


title: Mouse 3, Sample:SZ27, Sex:M, Metastasis, s.c. met

description: Mouse3, Sample:SZ27, Sex:M, Metastasis, s.c. met


title: Mouse 1, Sample:SZ21, Sex:M, Metastasis, Inguinal met

description: Mouse1, Sample:SZ21, Sex:M, Metastasis, Inguinal met


title: Mouse 2, Sample:SZ23, Sex:M, Metastasis, Liver met

description: Mouse2, Sample:SZ23, Sex:M, Metastasis, Liver met


title: Mouse 4, Sample:SZ33, Sex:M, Metastasis, Parietal pleural nodule

description: Mouse4, Sample:SZ33, Sex:M, Metastasis, Parietal pleural nodule


title: Mouse 3, Sample:SZ26, Sex:M, Metastasis, Mediastinal LN

description: Mouse3, Sample:SZ26, Sex:M, Metastasis, Mediastinal LN


title: Mouse 1, Sample:SZ20, Sex:M, Metastasis, s.c. met/body wall

description: Mouse1, Sample:SZ20, Sex:M, Metastasis, s.c. met/body wall


title: Control liver_4 pm_rep3

status: Public on Apr 07 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: each sample contains RNA from two lox control animals

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5). The resulting data were imported into Rosetta Resolver (v7.0) and normalized intensities were exported.

source_name: Lox control liver, ad lib, 4:00pm

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

tag: genotype

tag: gender

value: male

tag: age

value: 10 weeks

tag: tissue

value: Liver

tag: diet

value: chow diet


title: Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis, sample1_cy3

status: Public on Apr 10 2009

city: Los Altos

first: Manoj

last: Samanta

state: CA

address: 2240 Homestead Court #309

institute: Systemix Institute

description:
BLOCK    Cy3            Cy5
block 1,"dcl1-7-F#3","hyl1-2-F#2"
block 2,"Ler-0#2","hen1-1W#2"
block 3,"hyl1-2-F#3","dcl1-7-F#5"
block 4,"hen1-1-W#4","Ler-0#3"
block 5,"dcl1-7-F#5","ColF#1"
block 6,"hyl1-2-F#5","Col-F#7"
block 7,"Col-F#3","dcl1-7-F#3"
block 8,"Col-F#1","hyl1-2-F#4"

hyb_protocol: Standard Agilent protocol was used - (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf). Water bath was equilibrated at 60 C. In a 1.5 mL nuclease-free microfuge tube, the following components were added - 300 ng cyanine 3-labelted linearly amplified cRNA, 10X blocking agent, nuclease free water and 25X fragmentation buffer. The mixture was incubated at 60 C for exactly 30 minutes to fragment RNA. 2x GEx Hybridization Buffer HI-RPM was added to 8x15K array formats at the appropriate volume to stop the  fragmentation reaction.  It was spinned for 1 minute at room temperature at 13,000 rpm in a microcentrifuge  to drive the sample off the walls and lid and to aid in bubble reduction. Sample was added on the array.

scan_protocol: After washing, arrays were scanned using a GenePix Autoloader 4200AL with laser excitation at 532 and 635 nm, and saved as 16-bit grayscale TIFF images.

data_processing: Intensity values were extracted using GenePix Pro,  and the data for each sample were normalized using quantile normalization of data from 8 blocks x 2 channels. Data for target of miR859, miR780 and miR856 are not shown, because either the targets of those genes are not validated or the correct target locations were not covered by the array probes.

organism: Arabidopsis thaliana

source_name: seeds of various genotype samples

label_protocol:
Standard Agilent protocol was used - (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf).
1. Add 50 to 5000 ng of total or polyA RNA to a 1.5-mL microcentrifuge tube in  an appropriate volume of 8.3 μL or less. Samples should be diluted such  that at least 2 μL of sample is pipetted into the tube.
2. Prepare tubes for both Spike A Mix/cyanine 3-CTP and Spike B Mix/cyanine  5-CTP dyes.
3. Add 1.2 μL of T7 Promoter Primer (from the Agilent Quick Amp Kit,  Two-Color).
4. Add 2 μL of diluted Spike-Mix (A or B).
5. Use nuclease-free water to bring the total reaction volume to 11.5 μL.
6. Denature the primer and the template by incubating the reaction at 65°C in  a circulating water bath for 10 minutes.
7. Place the reactions on ice and incubate for 5 minutes.
8. Immediately prior to use, gently mix the components listed in Table 3 of Agilent document for the cDNA Master Mix by adding in the order indicated, and put on ice. 9. Prewarm the 5X first strand buffer at 80°C for 3 to 4 minutes to ensure  adequate resuspensions of the buffer components. For optimal  resuspension, briefly mix on a vortex mixer and spin the tube in a  microcentrifuge to drive down the contents from the tube walls. Keep at  room temperature until needed. MMLV-RT and RNaseOUT are enzymes, which need to be kept on ice and  are to be added to the cDNA Master Mix just before starting the reactions. Be sure to use the 10 mM dNTP mix tube from the kit.
10. Briefly spin each sample tube in a microcentrifuge to drive down the  contents from the tube walls and the lid. Return the tubes to ice.
11. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting  up and down.
12. Incubate samples at 40°C in a circulating water bath for 2 hours.
13. Move samples to a 65°C circulating water bath and incubate for 15 minutes.
14. Move samples to ice. Incubate for 5 minutes.
15. Spin samples briefly in a microcentrifuge to drive down tube contents from  the tube walls and lid.
16. Immediately prior to use, gently mix the components listed in Table 4 in the  order indicated for the Transcription Master Mix by pipetting at room  temperature.
17. Prewarm the 50% PEG solution at 40°C for 1 minute. For optimal  resuspension, briefly mix on a vortex mixer and spin the tube in a  microcentrifuge to drive down the contents from the tube walls. Careful  pipetting is required to ensure accurate volume. Keep at room temperature  until needed. RNaseOUT, inorganic pyrophosphatase, and T7 RNA polymerase are  enzymes, which need to be kept on ice and should be added to the  Transcription Master Mix just before starting the reactions.
18. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by  pipetting.
19. Incubate samples in a circulating water bath at 40°C for 2 hours.

growth_protocol: Arabidopsis thaliana seeds were sown to the soil directly, stratified for 72 h at 4 C, and then placed at 21 C under long day condition of 16 h of light.

extract_protocol: RNA was extracted with TriZol reagent (Life Technologies) or using RNAqueous-Micro isolation kit (Ambion), including the DNAse treatment step, from plants harvested 4 weeks after stratification.

value: seeds

value: Col-F


title: SIRT1 LKO liver_4 pm_rep3

description: each sample contains RNA from two SIRT1 LKO animals

source_name: SIRT1 LKO liver, ad lib, 4:00pm


title: SIRT1 LKO liver_4 pm_rep2


title: KO LK GFPhi, biological rep3

status: Public on Apr 03 2009

city: Cambridge

first: Jiangwen

last: Zhang

state: MA

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LK GFPhi(GMP) from KO mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were were normalized by robust multi-chip analysis (RMA) (Bioconductor release 1.9) using PM-only models.

source_name: mouse hematopoietic LK cells with Ikaros-based GFP reporter that allows a clean separation of functionally distinct progenitor subsets

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: The transgenic mice (B-p-GFP-C line, C57BL/6 x C3H)(Kaufmann et al., 2003) and Ikaros null mice (I74 line, C57BL/6 x 129SV) (Wang et al., 1996)  were bred and maintained under specific pathogen free condition in the animal facility.

treatment_protocol: LK GFPhi (GMP) were isolated from KO B-p-GFP-C mice

tag: cell type

value: hematopoietic LK GFPhi(GMP)

value: KO

tag: protocol

value: Ikaros-based GFP reporter with high level expression (GFPhi) of GFP


title: Mouse 4, Sample:SZ32, Sex:M, Metastasis, Mediastinal LN

description: Mouse4, Sample:SZ32, Sex:M, Metastasis, Mediastinal LN


title: KO LK GFPneg, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LK GFPneg(MEP) from KO mouse

treatment_protocol: LK GFPneg (MEP) were isolated from KO B-p-GFP-C mice

value: hematopoietic LK GFPneg(MEP)

value: Ikaros-based GFP reporter with negative level expression (GFPneg) of GFP


title: Control liver_4 pm_rep2


title: Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis, sample2_cy3

description:
BLOCK    Cy3            Cy5
block 1,"rdr6-15-F#5","sgs3-14-F#3"
block 2,"Ler-0#4","hen1-1-W#4"
block 3,"sgs3-14-F#4","rdr6-15-F#6"
block 4,"hen1-1-W#2","Ler-0#3"
block 5,"rdr6-15-F#5","Col-F#1"
block 6,"sgs3-14-F#4","Col-F#7"
block 7,"Col-F#3","rdr6-15-F#1"
block 8,"Col-F#1","sgs3-14-F#5"

data_processing: Intensity values were extracted using GenePix Pro, and the data for each sample were normalized using quantile normalization of data from 8 blocks x 2 channels. Data for target of miR859, miR780 and miR856 are not shown, because either the targets of those genes are not validated or the correct target locations were not covered by the array probes.


title: Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis, sample2_cy5


title: SIRT1 LKO liver_4 pm_rep1


title: Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis, sample1_cy5

value: ColF


title: KO LSK GFPhi, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LSK GFPhi (LMPP) from KO mouse

source_name: mouse hematopoietic progenitors LSK cells with Ikaros-based GFP reporter that allows a clean separation of functionally distinct progenitor subsets

treatment_protocol: LSK GFPhi (LMPP) were isolated from KO B-p-GFP-C mice

value: hematopoietic LSK GFPhi (LMPP)


title: KO LK GFPneg, biological rep2


title: Control liver_4 pm_rep1


title: KO LK GFPhi, biological rep2


title: KO LSK GFPhi, biological rep2


title: KO LSK GFPneg-lo, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LSK GFPneg-lo (HSC) from KO mouse

treatment_protocol: LSK GFPneg-lo (HSC) were isolated from KO B-p-GFP-C mice

value: hematopoietic LSK GFPneg-lo (HSC)

value: Ikaros-based GFP reporter with negative to very low level expression (GFPneg-lo) of GFP


title: KO LK GFPneg, biological rep1


title: KO LSK GFPhi, biological rep1

data_processing: The data were were normalized by robust multi-chip analysis (RMA) (Bioconductor release 2.1) using PM-only models.


title: KO LK GFPhi, biological rep1


title: KO LSK GFPneg-lo, biological rep1


title: KO LSK GFPneg-lo, biological rep2


title: WT ProB, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
proB cells

source_name: proB from bone marrow

growth_protocol: mice were bred and maintained under specific pathogen free condition in the animal facility.

treatment_protocol: For proB cell isolation, wt bone marrow cells were depleted with antibodies against Ter119, Mac-1, Gr-1, IgM, CD3, CD8a, TCRbeta, TCRgamma-delta, DX5 and remaining cells with a c-Kitlo CD19+ phenotype were sorted.

value: proB

value: wt


title: WT ProB, biological rep2


title: WT LK GFPhi, biological rep1

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LK GFPhi(GMP) from wt mouse

treatment_protocol: LK GFPhi (GMP) were isolated from wt B-p-GFP-C mice


title: WT LK GFPhi, biological rep3


title: WT ProB, biological rep1


title: WT LK GFPneg, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LK GFPneg(MEP) from wt mouse

treatment_protocol: LK GFPneg (MEP) were isolated from wt B-p-GFP-C mice


title: WT LSK GFPhi, biological rep2

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LSK GFPhi (LMPP) from wt mouse

treatment_protocol: LSK GFPhi (LMPP) were isolated from wt B-p-GFP-C mice


title: WT LSK GFPhi, biological rep3


title: WT LSK GFPneg-lo, biological rep3

description:
Gene expression data from mouse hematopoietic cells.
mouse hematopoietic LSK GFPneg-lo (HSC) from wt mouse

treatment_protocol: LSK GFPneg-lo (HSC) were isolated from wt B-p-GFP-C mice


title: WT LSK GFPhi, biological rep1


title: WT LSK GFPneg-lo, biological rep1


title: WT LSK GFPneg-lo, biological rep2


title: WT LK GFPneg, biological rep1


title: WT LK GFPhi, biological rep2


title: HepG2_p53_NoDoxy200nMAdriamycin_48h

status: Public on Apr 01 2009

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Microarray analysis has been useful for identifying the targets of many transcription factors. However, gene expression changes in response to transcription factor perturbation reveal both direct transcriptional targets and secondary gene regulation. By integrating RNA interference, gene expression profiling, and chromatin immunoprecipitation technologies, we identified a set of 32 direct transcriptional targets of the tumor suppressor p53. Of these 32 genes, 11 are not currently associated with the core p53 pathway. From among these novel pathway members, we focused on understanding the connection between p53 and SULF2, which encodes an extracellular heparan sulfate 6-O-endosulfatase that modulates the binding of growth factors to their cognate receptors and that has been shown to function as a tumor suppressor. Genetic and pharmacologic perturbation of p53 directly influences SULF2 expression, and similar to silencing of TP53, RNA interference-mediated suppression of SULF2 results in an impaired senescence response of cells to genotoxic stress. Thus, our integrated genomic approach has led to the identification of a novel mediator of p53 network biology.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA. The biotin binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

extract_protocol:
Qiagen RNeasy spin columns with DNAse treatment
Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: conditions

tag: cell line

tag: agent

value: Adriamycin (syn. Doxorubicin)

tag: time


title: HepG2_p53_w/Doxy200nMAdriamycin_48h

value: Doxycycline, Adriamycin (syn. Doxorubicin)


title: HepG2_p53_w/Doxy200nMAdriamycin_72h


title: HepG2_p53_w/Doxy200nMAdriamycin_24h


title: HepG2_p53_NoDoxy200nMAdriamycin_72h


title: WT LK GFPneg, biological rep2


title: HepG2_p53_NoDoxy200nMAdriamycin_24h


title: Susceptible clone 146

city: Seattle

first: Robert

last: Strauss

state: WA

address: 1705 NE Pacific st.

department: Medicine

institute: University of Washington

description: Susceptible culture (experiment/reference)

scan_protocol: Array slides were scanned and data extracted using GenePix Pro 3.0 software at Fred Hutchinson Cancer Research Center microarray facility

data_processing: Microarray data were normalized using the LOWESS algorithm and processed in Bioconductor Limma package.

source_name: ovc316m clonal culture susceptible to adenoviral lysis after 8 days

label_protocol: The aRNA was coupled with Cy5 and Cy3 (dyes were swapped) and hybridized to Human Oligonucleotide 22K microarrays at Fred Hutchinson Cancer Research Center microarray facility.

growth_protocol: Single cell clonal cultures derived from primary ovarian cancer culture ovc316m and SKOV3-ip1 cells (for reference RNA) were maintained in MEGM medium (LONZA) supplemented with 10% FBS and Ciprofloxacin

extract_protocol: Uninfected control wells of cells either resistant or susceptible to oncolytic adenoviruses were lysed in RLT buffer (Qiagen). Total RNA was prepared using RNAeasy columns (Qiagen) its quality assessed by Agilent 2100 bioanalyzer. RNA from SKOV3-1ip cells was used as a reference. mRNA samples were amplified by linear in vitro transcription using Ambion Amino Allyl MessageAmp aRNA kit.

treatment_protocol: Clonal cultures were treated with oncolytic adenoviruses (Ad5/35.IR.E1A/TRAIL, MOI 100) for 8 days and cell survival determined by MTT assay.

tag: cells

value: primary squamous epithelial ovarian cancer stage IV

source_name: ovarian cancer cell line SKOV3-ip1

value: epithelial ovarian cancer cell line


title: Susceptible clone 143

hyb_protocol: Human Oligonucleotide 22K microarrays at Fred Hutchinson Cancer Research Center microarray facility.


title: Susceptible clone 151


title: DLBCL patient 08-290

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: DLBCL patient

hyb_protocol: standard Affymetrix procedures using Fluidics Station

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing: Affymetrix GeneChip GCOS 1.4, GTYPE 4.1. Tables contain CN data as Log2Ratio from mBPCR (Rancoita, BMC Bioinformatics, 2009), and LOH as computed by dCHIP. Female HapMap were used as reference.

source_name: DLBCL patient

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: genomic DNA was extracted using the Qiagen DNA Mini kit (Qiagen, Hilden, Germany)

value: diffuse large B-cell lymphoma clinical sample


title: Susceptible clone 151 dye swap

description: Susceptible culture (reference/experiment)


title: Susceptible clone 146 dye swap


title: Susceptible clone 143 dye swap


title: Susceptible clone 144 dye swap


title: DLBCL patient 08-291

description: DLBCL patient


title: Susceptible clone 155 dye swap


title: Susceptible clone 48 dye swap


title: DLBCL patient 08-292

description: DLBCL patient


title: Susceptible clone 48


title: DLBCL patient 08-294

description: DLBCL patient


title: Susceptible clone 155


title: Susceptible clone 144


title: Susceptible clone 75


title: DLBCL patient 07-212

description: DLBCL patient


title: Susceptible clone 99 dye swap


title: Susceptible clone 99


title: DLBCL patient 08-287

description: DLBCL patient


title: DLBCL patient 07-210

description: DLBCL patient


title: Susceptible clone 137


title: Susceptible clone 139 dye swap


title: Susceptible clone 139


title: DLBCL patient 07-216

description: DLBCL patient


title: Susceptible clone 75 dye swap


title: DLBCL patient 08-289

description: DLBCL patient


title: Susceptible clone 136


title: Susceptible clone 113 dye swap


title: Susceptible clone 127 dye swap


title: Susceptible clone 129 dye swap


title: DLBCL patient 07-215

description: DLBCL patient


title: DLBCL patient 05-292

description: DLBCL patient


title: Susceptible clone 129


title: Susceptible clone 136 dye swap


title: Susceptible clone 113


title: Susceptible clone 137 dye swap


title: Isolated hepatocytes_fresh_Cre(+) rep 3

city: La Jolla

first: Dr. Hyam

middle: L.

last: Leffert

address: 9500 Gilman Drive

department: Pharmacology

institute: UCSD School of Medicine

description: replicate 12

hyb_protocol: ILLUMINA WG-6 V2 mouse bead-chips (#BD 201-0202) were used. Hybridization conditions employed Illumina HYB buffer, 18 hours @ 58○C

scan_protocol: Illumina BeadArray Reader, PMT setting 100%, 532nm for Cy3.

data_processing: Standard Illumina BeadStudio processing of images plus multiple loess normalization of all samples

source_name: Isolated hepatocytes, IkkβDhep mouse

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

growth_protocol: Liver tissues and freshly isolated hepatocytes were obtained as described in KS Koch et al. BBRC 380: 349-354 (2009)(PMID: 19171122).

extract_protocol: RNA was extracted with guanidine thiocyanate reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by standard gel electrophoresis and with Agilent 2100 Bioanalyser.

treatment_protocol: Liver tissues and freshly isolated hepatocytes were subjected directly to extraction of total RNA (for microarray profiling) and DNA (for genotyping and deletion analyses) as described above in KS Koch et al. BBRC 380: 349-354 (2009).

tag: strain

value: Male, adult C57BL6/J

tag: genotype/variation

value: IkkβDhep

value: 4-6 weeks

value: Isolated hepatocytes


title: Resistant clone 69

description: Resistant culture (experiment/reference)

source_name: ovc316m clonal culture resistant to adenoviral lysis after 8 days


title: Resistant clone 49


title: Isolated hepatocytes_fresh_Cre(+) rep 1

description: replicate 10


title: Resistant clone 69 dye swap

description: Resistant culture (reference/experiment)


title: Isolated hepatocytes_fresh_Cre(-) rep 3

description: replicate 9

source_name: Isolated hepatocytes, IkkβF/F mouse

value: IkkβF/F


title: Isolated hepatocytes_fresh_Cre(+) rep 2

description: replicate 11


title: Resistant clone 68 dye swap


title: Resistant clone 49 dye swap


title: Isolated hepatocytes_fresh_Cre(-) rep 2

description: replicate 8


title: Resistant clone 68


title: Isolated hepatocytes_fresh_Cre(-) rep 1

description: replicate 7


title: Resistant clone 65


title: Liver_fresh_Cre(-) rep 3

description: replicate 3

source_name: Liver, IkkβF/F mouse

value: Fresh liver


title: Susceptible clone 127


title: Liver_fresh_Cre(-) rep 2

description: replicate 2


title: Liver_fresh_Cre(+) rep 2

description: replicate 5

source_name: Liver, IkkβDhep mouse


title: DLBCL patient 07-208

description: DLBCL patient


title: Liver_fresh_Cre(+) rep 3

description: replicate 6


title: Liver_fresh_Cre(+) rep 1

description: replicate 4


title: Resistant clone 60 dye swap


title: Resistant clone 60


title: Liver_fresh_Cre(-) rep 1

description: replicate 1


title: Resistant clone 65 dye swap


title: Resistant clone 30 dye swap


title: Resistant clone 76 dye swap


title: Resistant clone 47


title: Resistant clone 47 dye swap


title: Resistant clone 35


title: Resistant clone 30


title: Resistant clone 76


title: Resistant clone 35 dye swap


title: Resistant clone 141


title: Resistant clone 124


title: Resistant clone 124 dye swap


title: Resistant clone 110


title: Resistant clone 50 (dye swap)


title: Resistant clone 141 dye swap


title: Resistant clone 53 (dye swap)


title: Susceptible clone 31 (dye swap)


title: Susceptible clone 52 (dye swap)


title: Resistant clone 56 (dye swap)


title: mf late el12

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. EL1 late

hyb_protocol: Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2min at 99°C then allowed to cool at room temperature for 5 minutes. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B scanner.

data_processing: Spot intensities were extracted, background subtracted, and block-wise lowess normalized using TIGR Spotfinder 2.2.4 (Saeed et al., 2003). Duplicated spots were averaged over the median of intensities. Only genes that were called in 2 out of 3 arrays for every experimental condition were subjected to further analysis.

organism: Orbicella faveolata

source_name: reference

label_protocol: 1 µg of total RNA was amplified using the MessageAmp II aRNA kit (Ambion). For cDNA synthesis, 3 µg of aRNA per sample were primed with 3.5 nmol random pentadecamer for 10min at 70°C. Reverse transcription (RT) lasted for 2 hours at 42°C using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP.  Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 uL 0.5M EDTA and 10 uL 1M NaOH for 15min at 65°C.  After hydrolysis, RT reactions were cleaned using the MinElute Cleanup kit (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark.  Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen).

extract_protocol: Total RNA of coral larvae was isolated using Qiazol (Qiagen) according to manufacturer’s instructions. Larvae were homogenized for 2 minutes using a Mini-Beadbeater (Biospec) with 0.1 mm and 0.55 mm silica beads to disrupt cellular structures. RNA pellets were cleaned further with RNeasy Mini columns (Qiagen).

tag: developmental stage

value: larva

tag: other

value: reference

source_name: mf late el12

value: sample

value: inoculated with Symbiodinium sp. EL1

value: late


title: mf late el13

source_name: mf late el13


title: mf late el11

source_name: mf late el11


title: mf late 1052

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. Mf1.05b late

source_name: mf late 1052


title: mf late 1051

source_name: mf late 1051

value: inoculated with Symbiodinium sp. Mf1.05b


title: Resistant clone 50


title: Susceptible clone 52


title: Susceptible clone 31


title: Resistant clone 56


title: mf late 1053

source_name: mf late 1053


title: mf late con1

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled untreated control larvae late

source_name: mf late con1

value: untreated


title: mf early el12

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. EL1

source_name: mf early el12

value: early


title: mf late con3

source_name: mf late con3


title: mf early el13

source_name: mf early el13


title: Resistant clone 53

source_name: ovarian cancer cell line SKOV3-ip1

value: primary squamous epithelial ovarian cancer stage IV


title: mf early el11

source_name: mf early el11


title: mf early 105b1

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. Mf1.05b

source_name: mf early 105b1


title: Resistant clone 110 dye swap

value: epithelial ovarian cancer cell line

source_name: ovc316m clonal culture resistant to adenoviral lysis after 8 days


title: mf early 105b2

source_name: mf early 105b2


title: mf early 105b3

source_name: mf early 105b3


title: mf early con3

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled untreated control larvae

source_name: reference

source_name: mf early con3


title: mf late con2

source_name: mf late con2


title: apal late el1 1

organism: Acropora palmata

source_name: apal late el1 1


title: apal late el1 2

source_name: apal late el1 2


title: apal late el1 3

source_name: apal late el1 3


title: apal late kb8 3

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. CassKB8 late

source_name: apal late kb8 3


title: mf early con2

source_name: mf early con2


title: apal late kb8 2

source_name: apal late kb8 2

value: inoculated with Symbiodinium sp. CassKB8


title: apal late con 3

source_name: apal late con 3


title: apal late kb8 1

source_name: apal late kb8 1


title: apal late con 1

source_name: apal late con 1


title: apal late con 2

source_name: apal late con 2


title: mf early con1

source_name: mf early con1


title: apal early el1 2

source_name: apal early el1 2


title: apal early el1 1

source_name: apal early el1 1


title: apal early kb8 3

description:
Pooled reference made out of equal amounts of RNA from all samples
Pooled larvae inoculated with Symbiodinium sp. CassKB8

source_name: apal early kb8 3


title: apal early con 2

source_name: reference

source_name: apal early con 2


title: apal early kb8 2

source_name: apal early kb8 2


title: apal early con 1

source_name: apal early con 1


title: apal early con 3

source_name: apal early con 3


title: apal early el1 3

source_name: apal early el1 3


title: apal early kb8 1

source_name: apal early kb8 1


title: Herbert Syndrome Control, expression

city: Southport

first: Michael

middle: Richard

last: Green

state: Queensland

address: 58 Parklands Drive

department: Griffith Insitute for Health & Medical Research

country: Australia

institute: Griffith University

description: Peripheral blood taken from control.

hyb_protocol: According to Affymetrix Protocol for HU133 Plus 2.0 Microarrays

source_name: peripheral blood, control

extract_protocol: PaxGene Kit (PreAnalytix)

tag: disease

value: healthy

value: male


title: A549, untreated mock pool from all timepoints vs. A549, 200nM doxorubicin, 12hr

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: all time points

value: A549, 200nM doxorubicin, 12hr

value: doxorubicin


title: A549, untreated mock pool from all timepoints vs. A549, 200nM doxorubicin, 18hr

value: A549, 200nM doxorubicin, 18hr


title: Herbert Syndrome Case, expression

description: Peripheral blood taken from Herberts Immunodeficiency Syndrome case at trough of G-CSF treatment.

scan_protocol: According to Affymetrix Protocol for HU-133 Plus 2.0 Microarrays

source_name: peripheral blood, Herbert Syndrome case

label_protocol: According to Affymetrix Protocol for HU133 Plus 2.0 Microarrays

value: Herbert Immunodeficiency Syndrome

tag: symptom

value: profound immunodeficiency

tag: genotype

value: chromosomal duplication of 14q11.2


title: Herbert Syndrome Control, SNP Array

description: Peripheral blood taken from control.

hyb_protocol: According to Affymetrix Protocol for 250K Sty SNP Microarray

tag: gender

tag: age


title: Herbert Syndrome Case, SNP Array

description: Peripheral blood taken from Herberts Immunodeficiency Syndrome case.

scan_protocol: According to Affymetrix Protocol for 250K Sty SNP Microarray


title: TOV21G, untreated mock pool from all timepoints vs. TOV21G, 200nM doxorubicin, 24hr

value: TOV21G, 200nM doxorubicin, 24hr


title: TOV21G, untreated mock pool from all timepoints vs. TOV21G, 200nM doxorubicin, 6hr

value: TOV21G, 200nM doxorubicin, 6hr


title: TOV21G, untreated mock pool from all timepoints vs. TOV21G, 200nM doxorubicin, 18hr

value: TOV21G, 200nM doxorubicin, 18hr


title: A549, mock 12hr vs. A549, MDM2 esiRNA 2, 10nM, 12hr

value: A549, mock 12hr

value: mock

value: A549, MDM2 esiRNA 2, 10nM, 12hr

value: MDM2 esiRNA


title: A549, mock 12hr vs. A549, MDM2 esiRNA 1, 10nM, 12hr

value: A549, MDM2 esiRNA 1, 10nM, 12hr


title: A549, mock, 48hr vs. A549, MDM2 esiRNA 1, 10nM, 48hr

value: A549, mock, 48hr

value: A549, MDM2 esiRNA 1, 10nM, 48hr


title: A549, untreated mock pool from all timepoints vs. A549, 200nM doxorubicin, 6hr

value: all time points

value: A549, 200nM doxorubicin, 6hr


title: A549, mock, 24hr vs. A549, MDM2 esiRNA 1, 10nM, 24hr

value: A549, mock, 24hr

value: A549, MDM2 esiRNA 1, 10nM, 24hr


title: TOV21G, mock, 12hr vs. TOV21G, MDM2 esiRNA 2, 10nM, 12hr

value: TOV21G, mock, 12hr

value: TOV21G, MDM2 esiRNA 2, 10nM, 12hr


title: A549, untreated mock pool from all timepoints vs. A549, 200nM doxorubicin, 24hr

value: A549, 200nM doxorubicin, 24hr

value: doxorubicin


title: A549, mock, 48hr vs. A549, MDM2 esiRNA 2, 10nM, 48hr

value: A549, MDM2 esiRNA 2, 10nM, 48hr


title: A549, mock, 24hr vs. A549, MDM2 esiRNA 2, 10nM, 24hr

value: A549, MDM2 esiRNA 2, 10nM, 24hr


title: RAW_2.8mM_HOCl_#3

city: Research Triangle Park

first: Courtney

middle: G

last: Woods

address: PO Box 12137, 6 Davis Drive

department: Computational Biology

institute: The Hamner Institutes

description: no additional information

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Robust Multi-array Average

source_name: RNA from RAW Cells

label_protocol: standard Affymetrix protocol

growth_protocol: RAW 264.7 macrophages (RAW Cells) were cultured in DMEM supplemented with 10% FBS, 10mM HEPES, 100 U penicillin/ml, and 100 ug streptomycin/ml

extract_protocol: Triazol

treatment_protocol:
Treatment: 2.8 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%

tag: Array Type; Affymetrix Mouse 430_2

tag: amount

tag: bioanalyzer results

value: Good


title: RAW_3.5mM_HOCl_#1

description: no additional information

source_name: RNA from RAW 264.7 Cells

treatment_protocol:
Treatment: 3.5 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%
Medium: see growth protocol below

tag: cell type


title: RAW_3.5mM_HOCl_#3

description: no additional information

treatment_protocol:
Treatment: 3.5 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_2.8mM_HOCl_#2

description: no additional information

source_name: RNA from RAW 264.7


title: RAW_3.5mM_HOCl_#2

description: no additional information


title: TOV21G, mock, 12hr vs. TOV21G, MDM2 esiRNA 1, 10nM, 12hr

tag: conditions

tag: cell line

value: TOV21G, MDM2 esiRNA 1, 10nM, 12hr


title: RAW_1.4mM_HOCl_#3

description: no additional information

treatment_protocol:
Treatment: 1.4 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: TOV21G, mock, 24hr vs. TOV21G, MDM2 esiRNA 2, 10nM, 24hr

value: TOV21G, mock, 24hr

tag: time

value: TOV21G, MDM2 esiRNA 2, 10nM, 24hr

tag: agent


title: RAW_2.1mM_HOCl_#2

description: no additional information

treatment_protocol:
Treatment: 2.1 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_1.4mM_HOCl_#2

description: no additional information


title: TOV21G, mock, 24hr vs. TOV21G, MDM2 esiRNA 1, 10nM, 24hr

value: TOV21G, MDM2 esiRNA 1, 10nM, 24hr

value: MDM2 esiRNA


title: TOV21G, mock, 48hr vs. TOV21G, MDM2 esiRNA 2, 10nM, 48hr

value: TOV21G, mock, 48hr

value: TOV21G, MDM2 esiRNA 2, 10nM, 48hr


title: RAW_00.35mM_HOCl_#2

description: no additional information

treatment_protocol:
Treatment: 0.35 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_0.7mM_HOCl#3

description: no additional information

treatment_protocol:
Treatment: 0.70 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_1.4mM_HOCl_#1

description: no additional information


title: RAW_0.35mM_HOCl_#3

description: no additional information

source_name: RNA from RAW 264.7 CellsArray Type; Affymetrix Mouse 430_2,


title: RAW_0.7mM_HOCl_#1

description: no additional information


title: RAW_0.7mM_HOCl_#2

description: no additional information


title: RAW_2.1mM_HOCl_#1

description: no additional information


title: TOV21G, mock, 48hr vs. TOV21G, MDM2 esiRNA 1, 10nM, 48hr

value: TOV21G, MDM2 esiRNA 1, 10nM, 48hr


title: RAW_2.8mM_HOCl_#1

description: no additional information


title: RAW_2.1mM_HOCl_#3

description: no additional information


title: RAW_0.14mM_HOCl_#3

description: no additional information

treatment_protocol:
Treatment: 0.14 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_0.35mM_HOCl_#1

description: no additional information

treatment_protocol:
Treatment: 0.35 mM HOCl in mediu
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%


title: RAW_0mM_HOCl_#3

description: no additional information

treatment_protocol:
Treatment: 0 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%

tag: array type

value: Affymetrix Mouse 430_2,


title: infected 6 weeks

city: Daejeon

first: Suk-Jin

last: Yang

address: 111 Gwahanggno, Yuseong-gu

department: Medical Genomics Research Center

country: South Korea

institute: Korea Research Institute of Bioscience & Biottechnology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio

source_name: mouse liver

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

growth_protocol: The FVB/N male mice were maintained in a temperature-controlled (21 ± 1℃) and humidity-controlled (55 ± 5%) barrier system, with a 12 hr light/dark photocycle.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with BIO-RAD Experion.

treatment_protocol: The mice at 6 weeks of age were infected via oral inoculation with 15 metacercariae of C. sinensis in saline.

tag: tissue

value: liver

value: male

tag: strain

value: FVB/N


title: RAW_0.14mM_HOCl_#1

description: no additional information


title: RAW_0mM_HOCl_#4

description: no additional information


title: uninfected 6 weeks


title: infected 4 weeks


title: uninfected 4 weeks


title: RAW_0.14mM_HOCl_#2

description: no additional information


title: HepG2 H1 term vs. HepG2 shRNA TP53

value: HepG2 H1 term

value: HepG2 shRNA TP53

value: shRNA TP53


title: infected 2 weeks


title: U2OS H1 term vs. U2OS shRNA TP53

value: U2OS H1 term

value: U2OS shRNA TP53


title: OAW42 H1 term vs. OAW42 shRNA TP53

value: OAW42 H1 term

value: OAW42 shRNA TP53


title: RAW_0mM_HOCl_#2

description: no additional information

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

label_protocol: standard affymetrix protocol

growth_protocol: RAW 264.7 macrophages (RAW cells) were cultured in DMEM supplemented with 10% FBS, 10 mM HEPES, 100 U penicillin/ml, and 100 µg streptomycin/ml.

treatment_protocol:
Treatment: 0 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hours
Cell Confluency upon Treatment : ~80-90%

value: Affymetrix Mouse 430_2

value: Good


title: RAW_0mM_HOCl_#1

description: no additional information


title: NCIH460 H1 term vs. NCIH460 shRNA TP53

value: NCIH460 H1 term

value: NCIH460 shRNA TP53


title: uninfected 1 week


title: infected 1 week


title: Standard (no IPC) at post-reperfusion, 5

city: Newark

first: Ali

last: Raza

state: NJ

address: 185 South Orange Ave

department: Surgery

institute: UMDNJ

description: Gene expression data from hepatic allograft WITHOUT ischemic preconditioning at post-reperfusion

hyb_protocol: The biotin labeled cDNA was hybridized to the Human Gene 1.0 ST Array for 16 hours at 45ºC using the GeneChip Hybridization Oven 640 (Affymetrix, Santa Carla, CA, USA, #800138).  Washing and staining with streptavidin-phycoerythrin was performed using the GeneChip Fluidics Station 450 (Affymetrix, Santa Carla, CA, USA, # 00-0079).

scan_protocol: Images were acquired using the Affymetrix Scanner 3000 7G Plus (Affymetrix, Santa Carla, CA, USA, # 00-0210).

data_processing: Fluorescence intensities captured by the Affymetrix Scanner were converted to numerical values using the Affymetrix GeneChip Operating Software version 1.0.  These values were subjected to a log2 transformation and were then standardized using quantile normalization with the Robust Multi-array Analysis (RMA) algorithm.  Gene expression values were median centered and then imported into the Multiple Experiment Viewer (MEV 4.0) software.  Principal Component Analysis was performed to check consistency of the experiments to determine if there were any chip outliers. Significant transcripts were selected using a t-test with p values less than 0.05.

source_name: Donor hepatic allograft WITHOUT ischemic preconditioning at post-reperfusion

label_protocol: cRNA end-labeled with biotin was prepared according to the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual Version 4  from 300 ng total RNA (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

extract_protocol: Total RNA was extracted from hepatic tissue using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA, # 74104) according to the manufacturer’s protocol.

treatment_protocol: Hepatic ischemic preconditioning was administered in the donor and consisted of hilar inflow occlusion for 10 minutes followed by reperfusion until circulatory arrest.  Donor graft biopsies were performed at two time points: one immediately before commencement of implantation in the recipient and another at 90 minutes following reperfusion with portal blood.   The remainder of the liver procurement and transplantation protocols in the donor and recipient were as per standard of practice.

tag: recipient gender

value: Male

tag: recipient age

tag: recipient ethnicity

value: White

value: Liver

tag: protocol

value: without IPC at post-reperfusion


title: Standard (no IPC) at preimplantation, 6

description: Gene expression data from hepatic allograft WITHOUT ischemic preconditioning at pre-implantation time point

source_name: Donor hepatic allograft WITHOUT ischemic preconditioning at pre-implantation time point

value: without IPC at pre-implantation


title: Standard (no IPC) at post-reperfusion, 6


title: Standard (no IPC) at preimplantation, 5


title: Standard (no IPC) at post-reperfusion, 3


title: Standard (no IPC) at post-reperfusion, 4


title: Standard (no IPC) at preimplantation, 3


title: Standard (no IPC) at preimplantation, 4


title: Standard (no IPC) at post-reperfusion, 2


title: Standard (no IPC) at preimplantation, 2


title: Standard (no IPC) at preimplantation, 1


title: Standard (no IPC) at post-reperfusion, 1


title: IPC at preimplantation, 6

description: Gene expression data from hepatic allograft following ischemic preconditioning at pre-implantation time point

source_name: Donor hepatic allograft following ischemic preconditioning at pre-implantation time point

value: Asian

value: IPC at pre-implantation


title: IPC at post-reperfusion, 5

description: Gene expression data from hepatic allograft following ischemic preconditioning at post-reperfusion

source_name: Donor hepatic allograft following ischemic preconditioning at post-reperfusion

value: IPC at post-reperfusion


title: ES cells ctrl (GLUT4) RNAi rep2

first: Matthias

middle: D

last: Kaeser

address: 10010 North Torrey Pines Road

department: RBIO-E

institute: The Salk Institute

description: shRNA targeting GLUT4 (as a control)

hyb_protocol: according to standard Affymetrix protocol

data_processing: GCOS using standard parameters

source_name: Mouse ES treated with lentiviral ctrl (GLUT4) RNAi

label_protocol: 5 micrograms of RNA was RTed using Superscript from Invitrogen and labelled using the RNA transcript labelling kit from Enzo Life Science

growth_protocol: Cells were grown according to ATCC guidelines

extract_protocol: Trizol (Invitrogen) according to manufacturers protocol

treatment_protocol: Cells were harvested 67h after lentiviral infection

tag: Mouse R1 cells


title: IPC at post-reperfusion, 6


title: IPC at post-reperfusion, 4


title: FHV infected S2 cells, biological replicate 3

last: Miller

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

description: Miller S2 FHV infected 3

hyb_protocol: Fragmented cRNAs were hybridized to Affymetrix Drosophila genome array chips for 16 h at 45C, washed, and stained using an Affymetrix microfluids station.

scan_protocol: Chips were scanned with an Affymetrix Scanner 3000.

data_processing: The data were analyzed using the Affymetrix package of Bioconductor - expression values were calculated using a robust multi-array average (RMA).

organism: Drosophila melanogaster

source_name: Drosophila S2 cells, FHV infected for 12 h

label_protocol: Biotinylated cRNAs were prepared from 5-10 ug total RNA using standard Affymetix protocol.

growth_protocol: Cells cultured at 25C in Schneider's Drosophila media supplemented with 10% heat-inactivated fetal bovine serum, 10 U/ml penicillin, and 10 ug/ml streptomycin.

extract_protocol: Trizol extraction of total RNA done per the manufacturer's instruction.  Total RNA digested with RQ1 DNAse and reisolated with RNAsy columns per the manufacturer's instructions.

treatment_protocol: Samples either infected with FHV at an multiplicity of infection (MOI) = 10 or mock infected and cultured for 12 h prior to RNA extraction.

tag: infection

value: FHV infected for 12 h


title: IPC at post-reperfusion, 3


title: ES cells Brg1 RNAi rep 2

description: shRNA targeting Brg1

scan_protocol: according to standard Affymetrix protocol

source_name: Mouse ES treated with lentiviral Brg1 RNAi


title: uninfected 2 weeks

value: liver

tag: gender

value: male

value: FVB/N


title: mock infected S2 cells, biological replicate 3

description: Miller S2 FHV mock 3

source_name: Drosophila S2 cells, mock infected

value: mock infected


title: IPC at preimplantation, 5


title: IPC at preimplantation, 4


title: IPC at preimplantation, 3


title: ES cells ctrl (GLUT4) RNAi rep1

description: shRNA targeting GLUT4 (as a control)


title: IPC at post-reperfusion, 2


title: IPC at preimplantation, 2


title: IPC at post-reperfusion, 1

value: Female


title: ES cells Brg1 RNAi rep 1

description: shRNA targeting Brg1


title: mock infected S2 cells, biological replicate 2

description: Miller S2 FHV mock 2


title: IPC at preimplantation, 1


title: FHV infected S2 cells, biological replicate 2

description: Miller S2 FHV infected 2


title: FHV infected S2 cells, biological replicate 1

description: Miller S2 FHV infected 1


title: mock infected S2 cells, biological replicate 1

description: Miller S2 FHV mock 1


title: Synchronized HCT116_Nocodazole_10h

status: Public on Mar 31 2009

city: Kamakura

first: Hideaki

last: Mizuno

state: Kanagawa

address: 200 Kajiwara

department: Discovery research dept.

country: Japan

institute: Chugai Pharmaceutical Co., Ltd.

hyb_protocol: The cRNA products were fragmented, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was carried out using the GeneChip Scanner and image analysis was performed using GeneChip Operating Software.

data_processing: GCRMA

source_name: Synchronized HCT116, Nocodazole, 10h

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (Affymetrix Expression Analysis Technical Manual, Rev. 4).

growth_protocol: The HCT116 colorectal cancer cell line (ATCC) was grown in McCoy's 5A medium modified (Sigma-Aldrich) with 10% FBS (JBS) and maintained at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated with RNeasy kits (Qiagen) according to the manufacturers' instructions.

treatment_protocol: Synchronous culture was obtained by incubating cells for 19 h in 2 mM of thymidine, followed by a 9-h incubation in normal medium and a second 16-h incubation in thymidine (2 mM). Cells were washed with normal medium followed by treatment with DMSO for 0, 2, 4, 6, 7, 8, 9, and 10 h as a control or 0.1 mg/ml nocodazole (Sigma-Aldrich) for 7, 8, 9, and 10 h.

tag: Cell line

tag: Treatment

value: Nocodazole

tag: Time course


title: Synchronized HCT116_Nocodazole_9h

source_name: Synchronized HCT116, Nocodazole, 9h


title: Synchronized HCT116_DMSO_10h

source_name: Synchronized HCT116, DMSO, 10h

value: DMSO


title: Synchronized HCT116_DMSO_9h

source_name: Synchronized HCT116, DMSO, 9h


title: Synchronized HCT116_DMSO_7h

source_name: Synchronized HCT116, DMSO, 7h


title: Synchronized HCT116_Nocodazole_8h

source_name: Synchronized HCT116, Nocodazole, 8h


title: Synchronized HCT116_Nocodazole_7h

source_name: Synchronized HCT116, Nocodazole, 7h


title: Synchronized HCT116_DMSO_4h

source_name: Synchronized HCT116, DMSO, 4h


title: Synchronized HCT116_DMSO_8h

source_name: Synchronized HCT116, DMSO, 8h


title: Synchronized HCT116_DMSO_2h

source_name: Synchronized HCT116, DMSO, 2h


title: Synchronized HCT116_DMSO_0h

source_name: Synchronized HCT116, DMSO, 0h


title: Synchronized HCT116_DMSO_6h

source_name: Synchronized HCT116, DMSO, 6h


title: Mycobacterium bovis BCG_Peracetic acid_10min_replicate3

city: Fort Meade

first: Chantal

middle: Wheko

last: Nde

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: Peracetic acid treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Operating Software (GCOS) version 1.2

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Mycobacterium bovis BCG_Peracetic acid

label_protocol: Standard Affymetrix procedures. Approximately 10 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated M. bovis cultures at 37°C with shaking at 250 rpm using sterilized Middlebrook 7H9 broth for 5days, (ii) Mycobacteria were harvested, washed and resuspended in sterilized Lurria-Bertani (LB) broth with 0.1% (v/v) Tween 80.  The cultures were incubated for a further 24 hours with shaking at 37°C. To test the efficacy of an antimicrobial against mycobacteria, several concentrations of peracetic acid were added to the cells.

extract_protocol: Total RNA was isolated after 10 and 20 min incubation with and without (control)  peracetic acid using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX)[16]. The mycobacterial cells treated with peracetic acid and untreated cells as controls were harvested and resuspended in PBS buffer.  The mini-bead beater-16 (Bio spec products Inc, Bartlesville, OK) was used to break down the cells for 1 minute (5 times) with intermittent holding on ice for 2 minutes after each beating period.

treatment_protocol: 0.1mM Peracetic acid

value: Pasteur 1173P2 Wild type


title: Mycobacterium bovis BCG_Peracetic acid_20min_replicate1

description: Peracetic acid treatment


title: Mycobacterium bovis BCG_Peracetic acid_20min_replicate2

description: Peracetic acid treatment


title: Mycobacterium bovis BCG_no treatment_0min_replicate1

description: No treatment

source_name: Mycobacterium bovis BCG_no treatment

extract_protocol: Total RNA was isolated after 10 and 20 min incubation with and without (control) peracetic acid using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX)[16]. The mycobacterial cells treated with peracetic acid and untreated cells as controls were harvested and resuspended in PBS buffer.  The mini-bead beater-16 (Bio spec products Inc, Bartlesville, OK) was used to break down the cells for 1 minute (5 times) with intermittent holding on ice for 2 minutes after each beating period.

treatment_protocol: No treatment


title: Mycobacterium bovis BCG_Peracetic acid_20min_replicate3

description: Peracetic acid treatment


title: Mycobacterium bovis BCG_Peracetic acid_10min_replicate1

description: Peracetic acid treatment


title: Mycobacterium bovis BCG_Peracetic acid_10min_replicate2

description: Peracetic acid treatment


title: Mycobacterium bovis BCG_no treatment_0min_replicate2

description: No treatment


title: Mycobacterium bovis BCG_no treatment_0min_replicate3

description: No treatment


title: bERKO PMSG vs. Het PMSG

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.    For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.    Chips were wahed and then scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using the Rosetta Resolver® system (version 7.1) (Rosetta Biosoftware, Kirkland, WA).

source_name: ERb-null granulosa cell, PMSG, 48h

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was extracted using TriZol according to the manufacturer's instructions, then further purified using the QIAGEN (Valencia, CA) RNeasy Mini kit (Cat. No. 74104) clean-up protocol.

tag: Strain

value: C57/Bl6 Esr2-/-, Gender:female, Age:23-25d, Granulosa cells isolated from mice treated with PMSG for 48h

source_name: ERb-het granulosa cell, PMSG, 48h

value: C57/Bl6 Esr2+/-, Gender:female, Age:23-25d, Granulosa cells isolated from mice treated with PMSG for 48h


title: Het PMSG vs. bERKO PMSG

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.