title: Quercetin-3-glucoside vs vehicle on SAMF H14k part1 replicate 1

hyb_protocol: The labeled cDNA samples were hybridized to the SAMF Human 14K microarray slides (GEO Accession numbers GPL3963 and GPL3964), printed at the University of Calgary. These arrays contain 13,972 70-mer oligos designed against the UniGene database (Operon V1.0) spotted in duplicate.  For more information on the microarray chips used in these experiments, please see the SAMF website (www.microarrays.ucalgary.ca).  The hybridization was carried out at 37°C for 18 hrs in a Boekel InSlide OutTM hybridization oven. The post-hybridization washes were performed as follows: 2 x SSC, 0.2% SDS for 3-4 min, 0.2 x SSC for 1 min followed by 0.1 x SSC for 1 min. The slides were scanned using ScanArray500 at of 550 nm and 649 nm for Cy3 and Cy5, respectively.

data_processing: The quantification and image files were then loaded into Gene Traffic DuoTM (Iobion) for microarray data management and analysis.  The data were filtered to flag spots with intensities less than 100 units, or less than twice the average background.  The data were normalized according to the Lowess method (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15) resident in the Gene Traffic software.

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006). The procedure involved three main steps. The first involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark. In a separate experiment, a reciprocal labeling reaction was carried by incorporating Cy5 into the Q3G treated sample and Cy3 into vehicle treated sample. As a result, two separate reactions were completed per sample. Following several washes, dye coupled cDNA purification was performed using microspin cup and cDNA was eluted from the column.  Following dye incorporation, cDNAs from the control and Q3G samples were combined. These reciprocal labeling reactions were performed twice on two independent experimental samples to yield four replicates. These dye-switching experiments were performed in order to minimize any bias associated with cDNA synthesis.

extract_protocol: Total RNA was extracted using the RNeasy mini column (Qiagen).  The integrity of total RNA was confirmed by gel electrophoresis (1% formaldehyde agarose). Absorbance of RNA was measured at 260/280 nm using a spectrophotometer and RNA samples having a 260/280 ratio > than 1.9 were subsequently used for microarray analysis.

treatment_protocol: The cells were treated with Q3G (10 μM)  for 6h


title: T93-614 DNA 2ug red Vs nDNA 2ug green 150302

status: Public on Oct 31 2006

type: genomic

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: Slides were hybridised at 65C for 1 hour then 47C for 3 nights.

hyb_protocol: slides were rinsed in 4 x SSPE and 10mM EDTA, transferred to a fresh wash solution (4 x SSPE, 10mM EDTA) and gently agitated until the cover slip detached, and then in a third wash solution (4 x SSPE, 10mM EDTA) for 1 minute, all solution were pre warmed to 42ºC. Slides were then transferred a 42ºC wash containing 6 x SSPE and 50% formamide for 5 – 15 seconds, and finally washed for 30 seconds each in 2 x SSPE and 10mM EDTA, and 0.1 x SSPE. Finally slides were rinsed in HPLC grade water and excess solution removed with canned air.

scan_protocol: Hybridised microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments), and images visualised by GenePix software (version 3). Slides were scanned with laser power levels at 100% PMT (Photomultiplyer Tube) voltage levels were altered in order to provide an average Cy5:Cy3 hybridisation ratio across the slide of 1:1.  Individual fluoresce intensities rations (Cy5:Cy3) for each cDNA were determined by the software, with the hybridisation signal for each clone being calculated as the median fluorescence of pixels within a defined area of array spot.  Spots from cDNA clones representing mitochondrial sequences and spots, which didn’t respond, were removed at this point of data analysis.  Data was normalised using Lowess Normalisation.

data_processing: Data were filtered for quality by automated spot flagging and manual inspection in GenePix software and the normalised using a lowess algorithm. Each clone was normalized according to its position on the array to adjust for regional variations in relative signal intensity on the slides. The data set was renormalized to a Log2 ratio of 0.

molecule: genomic DNA

organism: Homo sapiens

source_name: T93-614(Primary Seminoma Testicular Germ Cell Tumour Sample)

label_protocol: DNA was Labelled using a Bioprime labelling kit (Invitrogen) according to the manufacturer’s instructions, except that 2 µg of DNA was labelled in a 40 µl reaction with 75 µM Cy5-dCTP (or Cy3-dCTP) [NEN, Boston, MA], plus 60 µM dCTP, and 120 µM dGTP, dATP, dTTP and 40units of Klenow large fragment DNA polymerase. Samples were then incubated over night at 37ºC. The labelling reaction was terminated by the addition of 90mM EDTA, unincorporated nucleotides were removed by the addition of 32µg of COT-1 DNA and 80mM NaOH and heated to 70ºC for 10 minutes. Samples were clean up and volume reduced by first adding 0.5 x SSPE (5mM Phosphate, pH 7.4, 0.5mM EDTA) to a total volume of 500µl, this was then filtered through a 0.1µm Ultrafree-MC filter column (Millipore) and centrifuged 6500rpm. The volume was then reduced to 3µl/2µg of labelled sample by filtering through a Microcon YM-30 filtration unit (Millipore) at 13K rpm.

extract_protocol: Tumour samples were ground in a pestle and mortar.  DNA was extracted using standard methods ie. cell lysis, proteinase K digestion, phenol extraction followed by precipitation (Sambrook and Russell,2001).

tag: gender

value: male

tag: age

tag: tissue type

value: tumor

source_name: Genomic Male DNA(Genomic Male blood DNA)

value: normal


title: 44_Carcinoma_BAC_par

status: Public on Nov 01 2006

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Copy number analysis of colorectal tumors

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

scan_protocol: Scanned with a GenePix 4100A scanner (Axon Instruments, Westburg BV, Leusden, The Netherlands)

data_processing: limma

source_name: Tumor DNA from patient 44 on BAC platform

label_protocol: overnight random prime labelling reaction (BioPrime Random Prime labelling Kit, Invitrogen, Breda, The Netherlands).

extract_protocol: DNA was extracted with the Chelex extraction method. Briefly, three tissue punches (diameter 0.6 mm) were obtained by a tissue microarrayer (Beecher Instruments, Sun Prairie, WI). DNA was isolated with Chelex and proteinase K. FFPE DNA was subsequently cleaned up using the Genomic Wizard kit (Promega).

tag: Tumor DNA of male patient with colorectal carcinoma

source_name: female reference DNA

extract_protocol: Commercially available pooled DNA (Promega)

tag: Gender mismatched pooled reference DNA


title: 106_Carcinoma_BAC_par

source_name: Tumor DNA from patient 106 on BAC platform

tag: Tumor DNA of female patient with colorectal carcinoma

source_name: male reference DNA


title: RH30 DNA 2ug red Vs Normal DNA 2ug green 120302

source_name: RH30(Primary Nonseminoma Testicular Germ Cell Tumour Sample)


title: L99-82 DNA 2ug red Vs Normal DNA 2ug green 150302

source_name: L99-82(Primary Seminoma Testicular Germ Cell Tumour Sample)


title: T92-5276 DNA 2ug red Vs Normal DNA 2ug green 150302

source_name: T92-5762(Primary Nonseminoma Testicular Germ Cell Tumour Sample)


title: RH38 2ug red Vs Normal DNA 2ug green 060202

description: 65C for 1 hour, 47C 3 nights

source_name: RH38(Primary Seminoma Testicular Germ Cell Tumour Sample)


title: L00-90 DNA 2ug red Vs nDNA 2ug green 150302

source_name: LOO-90(Primary Seminoma Testicular Germ Cell Tumour Sample)


title: LOO-59 DNA 2ug red Vs Normal DNA 2ug green 150302

source_name: LOO-59(Primary Seminoma Testicular Germ Cell Tumour Sample)


title: L99-20 DNA 2ug red Vs Normal DNA 2ug green 150302

source_name: T99-20(Primary Nonseminoma Testicular Germ Cell Tumour Sample)


title: RH24 DNA 2ug red Vs Normal DNA 2ug green 120302

source_name: RH24(Primary Seminoma Testicular Germ Cell Tumour)


title: L00-89 DNA 2ug red Vs nDNA 2ug green 150302

source_name: LOO-89(Primary Seminoma Testicular Germ Cell Tumour Sample)


title: EGDe vs ∆688 BHI RT scan 2 (11_22_05)

type: RNA

city: Boston

first: Aimee

last: Shen

state: MA

address: Armenise Building, rm 313, 200 Longwood Avenue

department: Microbiology and Molecular Genetics

country: USA

institute: Harvard University

description: RNA was harvested from cultures of EGDe and ∆688 grown at RT standing in BHI and competitively hybridized to TIGR microarrays.

hyb_protocol: The differentially labeled samples were then mixed together and competitively hybridized to L. monocytogenes microarrays (TIGR, Rockville, Maryland, United States) that had been UV cross-linked and pre-hybridized at 42˚C in 5X SSC/0.1% SDS/10 mg/mL BSA for a minimum of 1 hr, washed 3 times in dH2O, then immersed in 95% EtOH, and dried by centrifugation. Hybridization was carried out under Lifterslips (Erie Scientific, Portsmouth, New Hampshire, United States) in a sealed wet box at 42°C for 14-16 hr.

scan_protocol: Microarray slides were scanned by using a ScanArray 5000 apparatus (GSI Lumonics, Billerica, Massachusetts, United States) and analyzed with GenePix PRO 3.0 software (Axon Instruments, Molecular Devices, Sunnyvale, California, United States).

data_processing: gene Pix Pro 3.0 software

molecule: total RNA

organism: Listeria monocytogenes

source_name: EGDe wild-type

label_protocol: 10 μg of total RNA was mixed with 2 μg random hexamer DNA (Invitrogen, Carlsbad, California, United States) in a total volume of 9.5 μL. Fluorescently labeled cDNA was prepared by direct incorporation of fluorescent nucleotide analogues (Cy3-dCTP and Cy5-dCTP) during a first-strand, randomly primed reverse transcription reaction using Superscript III reverse transcriptase according to the manufacturer’s instructions (Invitrogen, Carlsbad, California, United States). A modified mix of dNTPs was used (0. 2 mM dG/T/ATP, 0.1 mM dCTP) with 1 μL of Cy3-dCTP or Cy5-dCTP (GE Biosciences, Piscataway, New Jersey, United States). Following reverse transcription, the RNA was degraded by heating samples at 95˚C for 3 min, adding 1 μL of 2 N NaOH, and incubating samples at 37˚C for 10 min. Samples were neutralized by adding 1 μL of 2 N HCl, 5 μL 1 M Tris HCl pH 7.5, and 23 μL of distilled water. Extension products were purified using the QIAquick PCR purification kit (Qiagen, Valencia, California, United States) according to the manufacturer’s instructions, except that samples were eluted in 2 x 100 μL elution buffer. DNA was precipitated by adding 2.5 μL of 1 mg/mL salmon sperm DNA, 40 μL 3 M sodium acetate, and 720 μL of 100% ethanol. Labeled DNA was recovered by centrifugation, washed once in 70% ethanol, air-dried for 3 min at RT, then resuspended in 30 μL hybridization buffer (25% formamide/5X SSC/1% SDS) by gentle vortexing, followed by heating at 95˚C for 5 min, then pipeting to re-suspend, followed by heating at 95 ˚C for a second time.

extract_protocol: RNA was harvested from 8 mL standing culture using the FastRNA Pro Blue kit (Qbiogene, Carlsbad, CA)

tag: wild-type EGDe grown standing for 18 hr at RT in BHI broth

tag: ∆lmo0688 grown standing for 18 hr at RT in BHI broth


title: EGde vs ∆688 BHI RT scan 2 (11_24_05)

tag: EGDe was grown standing for 18 hr at RT in BHI broth

tag: ∆688 was grown standing for 18 hr at RT in BHI broth


title: EGDe vs ∆688 BHI RT

tag: ∆688 was grown for 18 hr at RT standing in BHI broth

tag: EGDe was grown for 18 hr at RT standing in BHI broth


title: EGDe vs ∆688 BHI RT scan 1

tag: ∆lmo0688 strain grown standing overnight in BHI broth at RT for 18 hr

tag: wild-type grown for 18 hr at RT standing in BHI broth


title: LVHeart_Diabetic648_16wks, biological rep4

city: Auckland

first: Sarah

last: Glyn-Jones

address: 3A Symonds St

department: School of Biological Sciences

country: New Zealand

institute: University of Auckland

description: Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: This data was 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. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method  was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).

label: biotin

organism: Rattus norvegicus

source_name: Diabetic, left ventricle (LV) heart tissue, 16wks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)

extract_protocol: RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol

treatment_protocol: Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C

tag: Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study


title: LVHeart_Diabetic465_16wks, biological rep7


title: LVHeart_Diabetic968_16wks, biological rep5


title: LVHeart_Diabetic370_16wks, biological rep2


title: LVHeart_Diabetic481_16wks, biological rep3


title: LVHeart_Diabetic035_16wks, biological rep1


title: LVHeart_Normal796_16wks, biological rep7

description: Gene expression data from LV heart tissue of normal animal 16wks after saline injection

source_name: control (no diabetes), left ventricle (LV) heart tissue, 16wks

growth_protocol: Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)

tag: Wistar, control animal, saline injection, left ventricle heart tissue


title: LVHeart_Diabetic226_16wks, biological rep6


title: LVHeart_Normal260_16wks, biological rep5


title: LVHeart_Normal791_16wks, biological rep6


title: GATA6 (-/-) -RA vs +RA

city: Philadelphia

first: Xiangxi

last: Xu

state: PA

address: 333 Cottman Ave

department: Ovarian Cancer and Tumor Cell Biology

institute: Fox Chase Cancer Center

description: PMT was set at 30 for Cy5, and 35 for Cy3.

hyb_protocol: Hybridization to microarrays was performed overnight at 42°C in hybridization buffer (25% formamide, 5 x SSC, 0.1% SDS, and 100 ug/ml sonicated salmon sperm DNA). After hybridization, the arrays were washed two times in washing buffer A (2 x SSC, 0.1% SDS) at 42°C for 5 min and then three times in washing buffer B (0.1 x SSC, 0.1% SDS) at room temperature for 10 min. The slides were brieﬂy dipped into distilled water and dried in a stream of nitrogen before scanning.

scan_protocol: Images were obtained by scanning of the arrays in an Affymetrix 428 scanner.

data_processing: Signal intensities for Cy3- and Cy5-labeled probes were extracted by ImaGene software package version 4.2 using default settings and auto image segmentation.  Mean and median intensities for signal and background as well quality characteristics (“empty” or “poor”) of the spots were obtained at this time.

organism: Mus musculus

source_name: GATA6 (-/-) RW-4 ES cells

label_protocol: Fifteen micrograms of this DNase-treated RNA were reverse transcribed and amino allyl dUTP was incorporated in a reaction containing 500 ng oligo (dT) primers, 1x first strand buffer (Invitrogen, Carlsbad, CA), 0.01 M DTT, 500 µM each of dATP, dCTP, dGTP, and dTTP/aadUTP (2:3 ratio) 40 Units of rRNasin (Promega, Madison, WI) and 200Units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).  After brief denaturation and annealing of the primers at 70˚C for 8 mins, the reaction was incubated at 42˚C for 2 hours, followed by alkali hydrolysis of RNA and cDNA purification using Microcon-30 columns (Millipore, Bedford, MA) according to the manufacturer’s instructions.  The cDNA was then labeled with Cy5 by a coupling reaction using FluoroLink TM monofunctional dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacture’s specifications.  Probes were then purified using StrataPrep PCR Purification Kit (Stratagene, La Jolla, CA).

extract_protocol: Total RNA was isolated from 60-80% confluent ES cell cultures.  Total RNA was isolated using the guanidinium/isothiocyanate/phenol/chloroform method as previously described (Schultz).  Total RNA was DNase treated using “DNA free” kit (Ambion, Austin, TX) according to manufacturer’s specifications.

tag: GATA6 (-/-) RW-4 ES cells, untreated

label_protocol: Fifteen micrograms of this DNase-treated RNA were reverse transcribed and amino allyl dUTP was incorporated in a reaction containing 500 ng oligo (dT) primers, 1x first strand buffer (Invitrogen, Carlsbad, CA), 0.01 M DTT, 500 µM each of dATP, dCTP, dGTP, and dTTP/aadUTP (2:3 ratio) 40 Units of rRNasin (Promega, Madison, WI) and 200Units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).  After brief denaturation and annealing of the primers at 70˚C for 8 mins, the reaction was incubated at 42˚C for 2 hours, followed by alkali hydrolysis of RNA and cDNA purification using Microcon-30 columns (Millipore, Bedford, MA) according to the manufacturer’s instructions.  The cDNA was then labeled with Cy3 by a coupling reaction using FluoroLink TM monofunctional dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacture’s specifications.  Probes were then purified using StrataPrep PCR Purification Kit (Stratagene, La Jolla, CA).

tag: GATA6 (-/-) RW-4 ES cells, treated with retinoic acid


title: Normal Female rd vs Normal Male grn sld5

source_name: Genomic Female DNA(Genomic Female Blood DNA)

tag: gender

value: female

source_name: Genomic Male DNA(Genomic Male blood DNA)


title: SRF replicate 2, array a, Be(2)-C cells

type: other

city: Stanford

first: Sara

last: Cooper

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: followed agilent hybridization and wash conditions for Array CGH

data_processing: Feature Extraction 8.5 Agilent

label: Alexa Fluor 647

molecule: other

source_name: SRF ChIP DNA from Be(2)-C

extract_protocol: ChIP enriched DNA

tag: SRF ChIP enriched DNA Santa Cruz Antibody sc-335

label: Alexa fluor 555

source_name: Mock IP DNA Be(2)-Ccells

extract_protocol: sheared genomic DNA

tag: Mock IP, no antibody control, be(2)-c


title: SRF replicate 3, array a, Be(2)-C cells

tag: ChIP enriched DNA SRF antibody Santa Cruz sc-335

tag: mock IP DNA, no antibody control, sheared genomic DNA


title: Normal Female rd vs Normal Male grn sld4

tag: tissue type


title: SRF replicate 1, array b, Be(2)-C cells

tag: ChIP enriched DNA, from Be(2)-C, neuronal cell line

tag: Mock IP, no antibody control, sheared genomic DNA


title: LVHeart_Normal153_16wks, biological rep4


title: LVHeart_Normal060_16wks, biological rep3


title: GATA5 (-/-) -RA vs +RA

source_name: GATA5 (-/-) RW-4 ES cells

tag: GATA5 (-/-) RW-4 ES cells, untreated

tag: GATA5 (-/-) RW-4 ES cells, treated with retinoic acid


title: SRF No Treatment, replicate 2, array a Jurkat cells

source_name: SRF ChIP DNA from Jurkat, no treatment

tag: ChIP enriched DNA from Jurkat  cells, Antibody :Santa Cruz sc-335

source_name: mock IP DNA Jurkat cells


title: SRF 24 hour serum induction, replicate 2, array a Jurkat

source_name: sRF, ChIP enriched DNA, 24hr serum induction Jurkat

tag: ChIP enriched DNA Antibody

value: Santa Cruz sc-335

source_name: Mock IP DNA Jurkat cells

tag: Sheared Genomic DNA, no antibody Mock IP control


title: LVHeart_Normal030_16wks, biological rep2


title: Normal Female rd vs Normal Male grn sld3


title: GATA4 (-/-) -RA vs +RA

source_name: GATA4 (-/-) RW-4 ES cells

tag: GATA4 (-/-) RW-4 ES cells, untreated

tag: GATA4 (-/-) RW-4 ES cells, treated with retinoic acid (RA)


title: SRF No Treatment, replicate 1, array a Jurkat cells

source_name: SRF ChIP DNA from Jurkat

tag: anti-SRF antibody sc-335, Jurkat Cells

tag: No treatment, Mock IP, no antibody, sheared genomic DNA


title: SRF replicate a, array a, Be(2)-C cells

source_name: Be(2)-C cells, ChIP enriched DNA

tag: antibody

source_name: mock IP DNA Be(2)-Ccells


title: SRF replicate 1, array a, CRL-1999 cells

description: Agilent Array CGH hybridization and wash buffers, following protocol as directed.

data_processing: Agilent Feature Extraction 8.5

label: alexa Fluor 647

source_name: SRF ChIP DNA from CRL-1999 Smooth Muscle Cells

tag: Chip enriched. SRF antbody Santa Cruz sc-335

source_name: Mock IP DNA CRL-199 cells


title: Normal Female rd vs Normal Male grn sld2

tag: gender


title: SRF replicate 2, array a, CRL-1999 cells

tag: SRF ChIP enriched using Santa Cruz antibody sc-335

source_name: mock IP DNA CRL-1999 cells


title: SRF replicate 2, array b, CRL-1999 cells

tag: ChIP enriched DNA Santa Cruz antibody sc-335

source_name: Mock IP DNA CRL-1999 cells


title: Wild-type -RA vs +RA

source_name: Wt RW-4 ES cells

tag: Wt RW-4 ES cells, untreated

tag: Wt RW-4 ES cells, treated with retinoic acid (RA)


title: Normal Female rd vs Normal Male grn sld1

hyb_protocol: Slides were rinsed in 4 x SSPE and 10mM EDTA, transferred to a fresh wash solution (4 x SSPE, 10mM EDTA) and gently agitated until the cover slip detached, and then in a third wash solution (4 x SSPE, 10mM EDTA) for 1 minute, all solution were pre warmed to 42ºC. Slides were then transferred a 42ºC wash containing 6 x SSPE and 50% formamide for 5 – 15 seconds, and finally washed for 30 seconds each in 2 x SSPE and 10mM EDTA, and 0.1 x SSPE. Finally slides were rinsed in HPLC grade water and excess solution removed with canned air.

source_name: Genomic Female DNA(Genomic Female Blood DNA)

tag: tissue type

source_name: Genomic Male DNA(Genomic Male blood DNA)


title: LVHeart_Normal195_16wks, biological rep1

source_name: control (no diabetes), left ventricle (LV) heart tissue, 16wks

tag: Wistar, control animal, saline injection, left ventricle heart tissue


title: control_c

status: Public on Oct 30 2006

city: gainesville

first: jean noel

last: gouze

state: FL

address: 1600 SW archer rd

department: orthopaedics

institute: university of florida

description: Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine

hyb_protocol: Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.

scan_protocol: GeneChips were scanned using the Genearray Scanner, Agilent Technologies

data_processing: Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.

label: streptavidin-phycoerythryn

source_name: rat chondrocyte control

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

growth_protocol: Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in complete DMEM (n=3/group).

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

treatment_protocol: Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin  at 37°C in a humidified atmosphere containing 5% CO2.

tag: Genotype

value: Rattus norvegicus

tag: Age

value: 2 months


title: SRF No Treatment, replicate 1, array b Jurkat cells

source_name: SRF ChIP DNA from Jurkat, no treatment

tag: ChIP enriched sample Antibody

value: SRF Santa Cruz sc-335 From Jurkat cells

tag: Mock IP, no antibody, Sheared genomic DNA


title: control_b


title: SRF 24 hour serum induction, replicate 3, array a Jurkat cells

source_name: srF, ChIP enriched DNA, 24hr serum induction Jurkat

tag: ChIP enriched DNA anti-SRF antibody

source_name: mock IP DNA Jurkat cells

tag: Mock IP, no antibody control, sheared genomic dna


title: control_a


title: SRF 24 hour serum induction, replicate 2, array b Jurkat

source_name: SRF, ChIP enriched DNA, 24hr serum induction Jurkat

tag: SRF enriched ChIP DNA Antibody

source_name: Mock IP DNA Jurkat cells

tag: Mock IP, No antibody control. sheared genomic DNA


title: IL-1 beta treatment_d

source_name: rat chondrocyte cultured in presence of IL-1

growth_protocol: Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of  IL-1 beta for 14 hours (10ng/ml) (n=4/group).


title: IL-1 beta treatment_c


title: SRF 24 hour serum induction, replicate 3, array b Jurkat cells

source_name: srf, ChIP enriched DNA, 24hr serum induction Jurkat

tag: ChIp enriched DNA, Santa Cruz antibody sc-335

tag: Mock IP, no treatment, sheared genomic DNA


title: SRF 24 hour serum induction, replicate 1, array b Jurkat

tag: ChIP enriched DNA, SRF antibody

tag: sheared genomic DNA, no antibody control


title: IL-1 beta treatment_b


title: SRF replicate 1, array b, CRL-1999 cells

tag: SRF ChIP enriched Santa Cruz Antibody sc-335

tag: Mock IP, no antibody control, sheared genomic DNA


title: SRF replicate 3, array b, Be(2)-C cells

source_name: SRF ChIP DNA from Be(2)-C

tag: SRF ChIP enriched, antibody Santa cruz sc-335, Neuronal Be(2)-C cells

source_name: Mock IP DNA Be(2)-Ccells

tag: mock IP, no antibody control, sheared genomic DNA


title: SRF No Treatment, replicate 2, array b Jurkat cells

tag: SRF ChIP enriched Antibody Santa Cruz sc-335


title: SRF replicate 2, array b, Be(2)-C cells

tag: ChIP enriched DNA antibody


title: Serum Response Factor ChIP tiling array

source_name: Jurkat Cells, Serum Treated 24 hours, anti SRF chip enriched

tag: antibody

tag: Mock Immunoprecipitation no antibody control


title: IL-1 beta treatment_a

tag: Genotype

tag: Age


title: cDNA microarray on 2days wild type mouse islets

city: University Park

first: YULIN

last: LI

address: 113 life sciences building

institute: Penn State

description: Affymetrix

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: GCOS 1.02

source_name: neonatal mouse islets

label_protocol: Ambion cRNA kit

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Collagenase P digestion to isolate islets.

tag: strains

value: Mixed

value: two days after birth

tag: Gender

value: mixed


title: Glucosamine treatment_b

source_name: rat chondrocyte cultured in presence of glucosamine

growth_protocol: Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 20 hours (n=2/group).


title: islet microarry on 2 days old PERK knockout mice

description: Affymetrix

label: Biotin

source_name: mouse islets

label_protocol: Ambion cRNA

extract_protocol: Qiagen RNeasy

treatment_protocol: Collagenase P islotation

tag: Strain mixed

tag: gender mixed

tag: age

value: 2days after birth


title: Glucosamine and IL-1 beta treatment_b

source_name: rat chondrocyte cultured in presence of glucosamine and IL-1

growth_protocol: Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 6 hours then stimulated with IL-1 beta for 14 hours (10ng/ml) (n=4/group).


title: Glucosamine and IL-1 beta treatment_d


title: Glucosamine and IL-1 beta treatment_c


title: Glucosamine and IL-1 beta treatment_a


title: k LNcapgrn vs male bld rd DNA slide 1 13 12 01

status: Public on Oct 28 2006

description: Slides were pre-hybed at 65C overnight, then washed and dried.  Labelled samples were hybridised overnight at 65C.

hyb_protocol: The microarray grids were denatured by submerging in 70% (v/v) deionised formamide/2x SSC (pH 7) at 65°C for 1 min. Slides were then washed sequentially with 70%, 80%, and 100% (v/v) ethanol, blow-dried with canned air (RS Components, Corby, UK), and prewarmed to 37°C in a hybridisation chamber (BDH Precision Engineers, Cambridge, UK) for 30-60 min. Labeled samples (made from 1.5 ug of genomic DNA or 2.5 ug of total RNA) in 40 ul of hybridisation mix (0.1%, v/v) Tween 20, 6x SSPE (pH 7.4), and 12.5 mM EDTA (pH 8.0) were heated to 99°C for 2 min, 65°C for 10 min, and 37°C for 10 min; pipetted onto a microarray slide; and covered with a Hybrislip (22 x 60 mm; Sigma). A 150 ul aliquot of 0.5x SSPE was pipetted underneath the slide, and the hybridisation chamber was sealed and incubated at 65°C overnight. The slides were soaked in 2x SSC at 32°C until the coverslip detached, and then washed with 2x SSC 32°C for 2 min, 1x SSC/50 mM EDTA (pH 8.0) at RT for 1 min, and 0.05x SSC at RT for 1 min. Excess wash solution was removed with canned air.

scan_protocol: Hybridised microarray slides were scanned in a GenePix 4000B scanner (Axon Instruments, Foster City, CA). Slides were scanned at PMT (photomultiplier tube) voltage levels that provided an average Cy5:Cy3 hybridisation ratio across the slide of 1.0. Fluorescence intensity ratios (I = Cy5:Cy3) for individual cDNAs were then determined after subtraction of background using the GenePix Pro 3.0 software (Axon Instruments).

data_processing: Data were filtered for quality by automated spot flagging and manual inspection in GenePix software and the normalised using a lowess algorithm.

source_name: LNCaP(LNCaP Genomic DNA)

label_protocol: For CGH experiments, labeled DNA was generated using a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions, except that 2 ug of DNA was labeled in a 50 ul reaction with 60 uM Cy5-dCTP (or Cy3-dCTP) [NEN, Boston, MA], plus 60 uM dCTP, and 120 uM dGTP, dATP, dTTP. Total cellular RNA (8 ug) was reverse transcribed overnight at 37°C with 1,200 units Superscript II (Invitrogen) in 40 ul of reaction buffer supplemented with 500 uM dGTP, dATP, and dTTP, 200 uM dCTP, 100 uM DTT, 100 uM Cy5- or Cy3-labeled dCTP, and 100uM excess random primer (5'-IIINNNNNN-3', where I is inosine). Labeling reactions were stopped by the addition of EDTA (pH 8.0) to 90 mM. Cot-1 DNA (25 ug; Invitrogen) was added and unincorporated nucleotides were removed using a Sephadex ProbeQuant G-50 column (Amersham-Pharmacia Biotech, Little Chalfont, UK). Samples were heated to 70°C for 10 min in 80 mM NaOH, then neutralised by addition of HCl to 80 mM. A 400 ul aliquot of 0.5x SSPE (Sigma) was added and the sample was filtered through a 0.1 uM ultra free-MC filter column (Millipore Ltd., Watford, UK). The volume was then reduced to 30 ul using a Microcon YM-30 filtration unit (Millipore).

extract_protocol: DNA from these specimens was prepared using standard methods ie. cell lysis, proteinase K digestion, phenol extraction followed by precipitation (Sambrook and Russell,2001).  RNA from these specimens was prepared using TRIzols reagent (Invitrogen, Paisley, UK) according to the manufacturer’s guidelines with the additional step of a second chloroform extraction before precipitation. RNA from normal prostate and other normal human tissues were obtained from BD Biosciences (Oxford, UK), Ambion (Huntingdon, UK) and Stratagene (La Jolla, CA, USA).

tag: gender

tag: tissue type

source_name: Male Genomic DNA(Male Genomic DNA)


title: k PC3grn vs male bld rd DNA slide 2 14 12 01

description: Slides were pre-hybed at 65C overnight, then washed and dried. Labelled samples were hybridised overnight at 65C.

source_name: PC3(PC3 cell line DNA)


title: k PC3grn vs male bld rd DNA slide 1 14 12 01


title: k DU145grn vs male bld rd 1ug DNA  slide2 10 12 01

source_name: DU145(DU145 Genomic Cell line DNA)


title: 32K 5637 E2F3 si3_0002

description: Slides were incubated at 651C for 1 h and then transferred to 42C for 72 h.

hyb_protocol: The hybridisation was carried out in triplicate.  Labelled samples were hybridised in a 50 micro l hybridisation mixture.  Samples were heated to 99C for 2 minutes, cooled to 37C and pipetted on to a microarray slide and covered with a Hybridslip (22x60 mm), placed in the hybridisation chamber with 150 micro l of 0.5 x SSPE pippeped underneath the slide.  Slides were incubated at 65C for 1 h and then transferred to 42C for 72 h.  Slides were rinsed in 4 x SSPE and 10mM EDTA, transferred to a fresh wash solution (4 x SSPE, 10mM EDTA) and gently agitated until the cover slip detached, and then in a third wash solution (4 x SSPE, 10mM EDTA) for 1 minute, all solution were pre warmed to 42C. Slides were then transferred a 42C wash containing 6 x SSPE and 50% formamide for 5 – 15 seconds, and finally washed for 30 seconds each in 2 x SSPE and 10mM EDTA, and 0.1 x SSPE.  Finally slides were rinsed in HPLC grade water and excess solution removed with air.

scan_protocol: The signals were detected and visualized by GenePix 4000B scanner and software (Axon Instruments, Foster City, CA, USA), and data were filtered for quality by automated spot flagging and manual inspection, and analysed in Genespring (Silicon Genetics, Redwood City, CA, USA), using per spot and per chip intensity–dependent Lowess normalisation.  The gene list of differentially expressed genes was uploaded into the Ingenuity pathway analysis (Ingenuity, Mountain View, CA, USA). A score was computed for each networkaccording to the fit of the original set of significant genes. This score reflects the negative logarithm of the P-value, which indicates the likelihood of the focus genes in a network being found together as a result of random chance.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 5637_E2F3_si3_knockdown(Bladder Cell line 5637 treated with E2F3 siRNA#3)

label_protocol: The Amersham first strand cDNA post-labelling kit was used to label 5 mg of total RNA, according to the manufacturer’s recommendations.  The control samples were labelled with Cy3 and the test samples with Cy5, and hybridized to CRUK Human Whole Genome-wide Array v1.0.0 (30K) cDNA microarray slides (http://www.crukdmf.icr.ac.uk/) coated with poly-L-lysine.

extract_protocol: Total RNA was extracted from growing cells using either a cytoplasmic lysis method, according to Wilkinson (1988), or Trizol (Invitrogen) according to the manufacturer’s instructions.

value: unknown

source_name: 5637_E2F3_si_scrambled(Bladder Cell line 5637 treated with a scrambled siRNA)


title: 32K 5637 E2F3 si3_0003


title: k DU145grn vs male bld rd 1ug DNA  slide1 10 12 01


title: 32K 5637 E2F3 si3_0001 #2


title: LNCaP 3x15plt thymus cy5 vs PNT2 cy3 RNA 181102

hyb_protocol: The microarray grids were denatured by submerging in 70% (v/v) deionized formamide/2x SSC (pH 7) at 65°C for 1 min. Slides were then washed sequentially with 70%, 80%, and 100% (v/v) ethanol, blow-dried with canned air (RS Components, Corby, UK), and prewarmed to 37°C in a hybridisation chamber (BDH Precision Engineers, Cambridge, UK) for 30-60 min. Labeled samples (made from 1.5 ug of genomic DNA or 2.5 ug of total RNA) in 40 ul of hybridisation mix (0.1%, v/v) Tween 20, 6x SSPE (pH 7.4), and 12.5 mM EDTA (pH 8.0) were heated to 99°C for 2 min, 65°C for 10 min, and 37°C for 10 min; pipetted onto a microarray slide; and covered with a Hybrislip (22 x 60 mm; Sigma). A 150 ul aliquot of 0.5x SSPE was pipetted underneath the slide, and the hybridisation chamber was sealed and incubated at 65°C overnight. The slides were soaked in 2x SSC at 32°C until the coverslip detached, and then washed with 2x SSC 32°C for 2 min, 1x SSC/50 mM EDTA (pH 8.0) at RT for 1 min, and 0.05x SSC at RT for 1 min. Excess wash solution was removed with canned air.

data_processing: The data given are red (635)/green (532) ratios normalised to the median after removing all bad (mitochondrial), "not found" data and weak spots (signal intensity <1.4 in both channels)

source_name: Thymus(Commercial Thymus RNA)

label_protocol: Total cellular RNA (8ug) was reverse transcribed overnight at 37°C with 1,200 units Superscript II (Invitrogen) in 40 ul of reaction buffer supplemented with 500 uM dGTP, dATP, and dTTP, 200 uM dCTP, 100 uM DTT, 100 uM Cy5- or Cy3-labeled dCTP, and 100uM excess random primer (5'-IIINNNNNN-3', where I is inosine). Labeling reactions were stopped by the addition of EDTA (pH 8.0) to 90 mM. Cot-1 DNA (25 ug; Invitrogen) was added and unincorporated nucleotides were removed using a Sephadex ProbeQuant G-50 column (Amersham-Pharmacia Biotech, Little Chalfont, UK). Samples were heated to 70°C for 10 min in 80 mM NaOH, then neutralized by addition of HCl to 80 mM. A 400 ul aliquot of 0.5x SSPE (Sigma) was added and the sample was filtered through a 0.1 uM ultra free-MC filter column (Millipore Ltd., Watford, UK). The volume was then reduced to 30 ul using a Microcon YM-30 filtration unit (Millipore).

extract_protocol: RNA from these specimens was prepared using TRIzols reagent (Invitrogen,Paisley, UK) according to the manufacturer’s guidelines with the additional step of a second chloroform extraction before precipitation. RNA from normal prostate and other normal human tissues were obtained from BD Biosciences (Oxford, UK), Ambion (Huntingdon, UK) and Stratagene (La Jolla, CA, USA).

source_name: PNT2(Normal prostate cell line)


title: K 2xfBLDrd v 2xmBLDgrn 3days47 43Cwsh sld1 11 01 02

source_name: Female Genomic DNA(Female Genomic DNA)


title: LNCaP 3x15plt thyroid cy5 vs PNT2 cy3 RNA 160802

source_name: Thyroid(Commercial Thyroid RNA)


title: LNCaP 3x15plt breast cy5 vs PNT2 cy3 RNA 190802

source_name: Breast(Commercial Breast RNA)


title: LNCaP 3x15plt testis cy5 vs PNT2 cy3 RNA 150802

source_name: Testis(Commercial Testis RNA)


title: LNCaP 3x15plt liver cy5 vs PNT2 cy3 RNA 071002

source_name: Liver(Commercial Liver RNA)


title: K 2xfBLDrd v 2xmBLDgrn 3days47 43Cwsh sld2 11 01 02


title: ABI_A2780_TRT_6h_rep3

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description:
Human Ovarian cell line A2780 was obtained from ECACC (Cat no.93112519) and cells were untreated or exposed to 3 micromolar of a cell cycle inhibitor for 6hrs.  Three biological replicates were performed for each treatment. Only attached cells were harvested. RNA was purified using a Qiagen RNA purification kit. RNA was quantitated using a spectrophotometer and the quality of the RNA was assessed using a Bioanalyser.
Biological replicates were pooled to obtain a unique sample for each treatment, which was then divided to generate three aliquots for each condition (technical replicates).

hyb_protocol: 10micrograms of the labeled cRNA was hybridized to ABI Human Genome Survey Microarray v 1.0 accordingly to ABI’s protocol.

scan_protocol: Following hybridization and washing steps, chemiluminescent detection and image acquisition was performed using Applied Biosystems 1700 Chemiluminescent Microarrays Analyzer, following manufacturer’s protocol.

data_processing: Global median normalization was applied

label: Digoxigenin-UTP

source_name: A2780 ovarian carcinoma cell line

label_protocol: 2 micrograms of each RNA sample was labeled with Digoxigenin-UTP using the ABI Chemiluminescent RT-IVT Labeling Kit v 1.0 accordingly to manufacturer’s protocol.

growth_protocol: A2780 was grown in RMPI 1640 + 10% FCS +2mM Glutamine and maintained at 37C in an atmosphere of 5% CO2 and 95% room air. Cells were plated at 2 x 106 cell/ml and after 24hrs were exposed to 3 micromolar of the inhibitor for 6hrs.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy Mini kit 74106 following manufacturers instructions.

treatment_protocol: Human Ovarian cell line A2780 was untreated or exposed to 3 micromolar of a cell cycle inhibitor for 6hrs

tag: A2780 ovarian carcinoma cell line


title: ABI_A2780_TRT_6h_rep1


title: LNCaP 3x15plt lung cy5 vs PNT2 cy3 RNA 190802

source_name: Lung(Commercial Lung RNA)


title: LNCaP 3x15plt kidney cy5 vs PNT2 cy3 RNA 190802

source_name: Kidney(Commercial Kidney RNA)


title: LNCaP 3x15plt sk muscle cy5 vs PNT2 cy3 RNA 160802

source_name: Skeletal Muscle(Commercial Skeletal Muscle RNA)


title: ABI_A2780_TRT_6h_rep2


title: LNCaP 3x15plt bladder cy5 vs PNT2 cy3 RNA 071002

source_name: Bladder(Commercial Bladder RNA)


title: ABI_A2780_6h_rep2


title: LNCaP 3x15plt 9A cy5 vs PNT2 cy3 RNA 200902

source_name: 9A_PT37(primary prostate tumour sample)


title: LNCaP 3x15plt bonemarrow cy5 vs PNT2 cy3 RNA 071002

source_name: Bone Marrow(Commercial Bone Marrow RNA)


title: LNCaP 3x15plt colon cy5 vs PNT2 cy3 RNA 190802

source_name: Colon(Commercial Colon RNA)


title: LNCaP 3x15plt 8A cy5 vs PNT2 cy3 RNA 270902

source_name: 8A_PT35(primary prostate tumour sample)


title: ABI_A2780_6h_rep1


title: LNCaP 3x15plt 6A cy5 vs PNT2 cy3 RNA 270902

source_name: 6A_PT30(primary prostate tumour sample)


title: LNCaP 3x15plt 5B cy5 vs PNT2 cy3 RNA 230902

source_name: 5B_PT28(primary prostate tumour sample)


title: LNCaP 3x15plt 7A cy5 vs PNT2 cy3 RNA 270902

source_name: 7A_PT33(primary prostate tumour sample )

source_name: PNT2(Normal prostate cell line)


title: Slide 2 TIGR4 wild-type vs delta-rr09

city: Glasgow

first: Tim

last: Mitchell

address: 120 University Place

department: IBLS

institute: University of Glasgow

description: see Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent.

data_processing: BlueFuse

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae TIGR4 wild-type

tag: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae TIGR4 delta-rr09


title: LNCaP 3x15plt 5A cy5 vs PNT2 cy3 RNA 230902

source_name: 5A_PT27(primary prostate tumour sample )


title: Slide 4 D39 wild-type vs delta-rr09

hyb_protocol: see Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent.

source_name: Streptococcus pneumoniae D39 wilde-type

source_name: Streptococcus pneumoniae D39 delta-rr09


title: ABI_A2780_6h_rep3

source_name: A2780 ovarian carcinoma cell line


title: WT2562

city: New York

first: Chi-Ming

last: Li

state: NY

address: 1130 St Nicholas Ave, rm607

department: ICG

institute: Columbia University

description: Sporadic Wilms tumor

hyb_protocol: affymetrix standard protocol

scan_protocol: affymetrix scanner

source_name: Class I Wilms tumor

label_protocol: one cycle labelling

extract_protocol: Trizol extraction

tag: Class I Wilms tumor


title: Slide 1 TIGR4 wild-type vs delta-rr09

scan_protocol: see Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent.


title: WT2769

description: Sporadic Wilms tumor


title: LNCaP 3x15plt 11A cy5 vs PNT2 cy3 RNA 230902

source_name: 11A_PT4(primary prostate tumour sample)


title: LNCaP 3x15plt 4A cy5 vs PNT2 cy3 RNA 200902

source_name: 4A_PT23(primary prostate tumour sample)


title: LNCaP 3x15plt 3A cy5 vs PNT2 cy3 RNA 270902

source_name: 3A_PT19(primary prostate tumour sample)


title: WT2409B

description: Sporadic Wilms tumor


title: Slide 1 D39 wild-type vs delta-rr09

label_protocol: see Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent.


title: WT2113B

description: Sporadic Wilms tumor


title: WT2767

description: Sporadic Wilms tumor


title: FKi2551

description: fetal kidney

source_name: fetal kidney

tag: fetal kidney


title: LNCaP 3x15plt 1A cy5 vs PNT2 cy3 RNA 200902

source_name: 1A_PT14(primary prostate tumour sample)


title: FKi3124

description: fetal kidney


title: Tuberculosis Pool_vs_TB_1086

status: Public on Oct 27 2006

city: Berlin

first: Marc

last: Jacobsen

address: Chariteplatz 1

department: Immunology

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: no

hyb_protocol: After photometric quantification of cRNA and determination of labeling efficiency, 2 µg of samples were fragmented and hybridized for 20 h on custom designed oligonucleotide microarrays (AMADID 011412; Agilent Technologies) containing 8,033 human genes.

scan_protocol: Microarrays were processed according to manufacturer’s instructions and scanned at 5 µm resolution using an Agilent scanner. Image analysis was performed with feature extraction software (Feature Extractor Version 6.1.1., Agilent Technologies) using default settings and global background normalization.

source_name: PBMC

label_protocol: Total RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

growth_protocol: no

extract_protocol: PBMC were immediately mixed with TRIzol® reagent (Invitrogen, Carlsbad, CA) and frozen at −80 °C until RNA was extracted according to manufacturer’s instructions. RNA content, purity, and integrity were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Forster City, CA).

treatment_protocol: no


title: FKi2799

description: fetal kidney


title: WT2345B

description: Sporadic Wilms tumor


title: Tuberculosis Pool_vs_TB_1072

description: no

data_processing: Image analysis was performed with feature extraction software (Feature Extractor Version 6.1.1., Agilent Technologies) using default settings and global background normalization.


title: Tuberculosis TB_1053_vs_Pool

description: no


title: Healthy infected Pool_vs_LTBI_1074

description: no


title: Slide 2 D39 wild-type vs delta-rr09

extract_protocol: see Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent.


title: LNCaP 3x15plt 10A cy5 vs PNT2 cy3 RNA 230902

source_name: 10A_PT3(primary prostate tumour sample)


title: Glucosamine treatment_a

source_name: rat chondrocyte cultured in presence of glucosamine


title: Tuberculosis Pool_vs_TB_1058

description: no


title: Tuberculosis Pool_vs_TB_1053

description: no


title: Tuberculosis Pool_vs_TB_1049

description: no


title: Healthy infected Pool_vs_LTBI_1048

description: no


title: Tuberculosis Pool_vs_TB_1043

description: no


title: Healthy infected Pool_vs_LTBI_1055

description: no


title: Healthy infected Pool_vs_LTBI_1056

description: no


title: Slide 3 D39 wild-type vs delta-rr09


title: Healthy infected Pool_vs_LTBI_1041

description: no


title: Healthy infected Pool_vs_LTBI_1040

description: no


title: Tuberculosis Pool_vs_TB_1024

description: no


title: Tuberculosis Pool_vs_TB_1030

description: no


title: Healthy infected Pool_vs_LTBI_1051

description: no


title: Tuberculosis Pool_vs_TB_1067

description: no


title: GM2-1

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: GM6990 cell lines

hyb_protocol: See manuscript

scan_protocol: See manuscript

data_processing: RMA normalized, log2 intensity

label_protocol: See manuscript


title: Healthy infected Pool_vs_LTBI_1016

description: no


title: k LNcapgrn vs male bld rd DNA slide 2 13 12 01

source_name: LNCaP(LNCaP Genomic DNA)

source_name: Male Genomic DNA(Male Genomic DNA)


title: Tuberculosis TB_1072_vs_Pool

description: no


title: Tuberculosis TB_1086_vs_Pool

description: no


title: NA-CD4-1815

description: CD4 cells isolated from a normal individual, number 1815

extract_protocol: CD4+ T-cells purified using negative selection


title: GM2-2

description: GM6990 cell lines


title: NA-CD4-1813

description: CD4 cells isolated from a normal individual, number 1813


title: GM-2

description: GM6990 cell lines


title: Healthy infected Pool_vs_LTBI_1006

description: no


title: GM-1

description: GM6990 cell lines


title: CD4-2

description: CD4 cells isolated from a normal individual, number 1615


title: Healthy infected LTBI_1055_vs_Pool

description: no


title: Tuberculosis TB_1058_vs_Pool

description: no


title: Healthy infected LTBI_1074_vs_Pool

description: no


title: CD4-1


title: Healthy infected LTBI_1051_vs_Pool

description: no


title: Healthy infected LTBI_1056_vs_Pool

description: no


title: GS MGII T63 Rd V's sgima male Grn merged 160802

description: 65C for 1 hour, 42C 3 nights, custom made buffer

hyb_protocol: Labelled samples were hybridised in a 50 micro l hybridisation mixture containing 6x SSPE, 12.5mM EDTA (pH 7.4), 0.1% v/v Tween 20 and 50% deionised Formamide. Samples were heated to 70C (CGH) for 2 minutes, cooled to 37C and pipetted on to a microarray slide and covered with a Hybridslip (22x60 mm), placed in the hybridisation chamber with 150 micro l of 0.5 x SSPE pippeped underneath the slide. The slide chamber was sealed and incubated at 65C for 1 hour, and then transferred to 47C incubator for 1-3 days.  Slides were rinsed in 4 x SSPE and 10mM EDTA, transferred to a fresh wash solution (4 x SSPE, 10mM EDTA) and gently agitated until the cover slip detached, and then in a third wash solution (4 x SSPE, 10mM EDTA) for 1 minute, all solution were pre warmed to 42C. Slides were then transferred a 42C wash containing 6 x SSPE and 50% formamide for 5 – 15 seconds, and finally washed for 30 seconds each in 2 x SSPE and 10mM EDTA, and 0.1 x SSPE. Finally slides were rinsed in HPLC grade water and excess solution removed with canned air.

scan_protocol: Hybridised microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments), and images visualised by GenePix software (version 3). Slides were scanned with laser power levels at 100% PMT (Photomultiplyer Tube) voltage levels were altered in order to provide an average Cy5:Cy3 hybridisation ratio across the slide of 1:1.  Individual fluoresce intensities rations (Cy5:Cy3) for each cDNA were determined by the software, with the hybridisation signal for each clone being calculated as the median fluorescence of pixels within an defined area of array spot.  Spots from cDNA clones representing mitochondrial sequences and spots, which didn’t respond, were removed at this point of data analysis.  Data was normalised using Lowess Normalisation.

source_name: T63(Primary Bladder Tumour DNA)

label_protocol: For CGH experiments, labeled DNA was generated using a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions, except that 2 ug of DNA was labeled in a 40 ul reaction with 75 uM Cy5-dCTP (or Cy3-dCTP) [NEN, Boston, MA], plus 60 uM dCTP, and 120 uM dGTP, dATP, dTTP and 40units of Klenow large fragment DNA polymerase. Samples were then incubated over night at 37C.  The labelling reaction was terminated by the addition of 90mM EDTA, unincorporated nucleotides were removed by the addition of 32 micrograms of COT-1 DNA and 80mM NaOH and heated to 70C for 10 minutes. Samples were clean up and volume reduced by first adding 0.5 x SSPE (5mM Phosphate, pH 7.4, 0.5mM EDTA) to a total volume of 500 microl, this was then filtered through a 0.1 micro m Ultrafree-MC filter column (Millipore) and centrifuged 6500rpm. The volume was then reduced to 3 micro l/2 micro g of labelled sample by filtering through a Microcon YM-30 filtration unit (Millipore) at 13K rpm.

extract_protocol: Cell line DNA was prepared using standard methods ie. cell lysis, proteinase K digestion, phenol extraction followed by precipitation (Sambrook and Russell,2001).  Tumour samples were ground in a pestle and mortar and extracted as per Cell line DNA.

source_name: Sigma Genomic Male(Commercial Genomic Male DNA)


title: Tuberculosis TB_1048_vs_Pool

description: no


title: Tuberculosis TB_1067_vs_Pool

description: no


title: GS MGII HT-1376 Rd v's sigma male Grn (1)  020802

source_name: HT1376(HT1376 Genomic Cell line DNA)


title: Healthy infected LTBI_1041_vs_Pool

description: no


title: GS MGII T110 Rd V's sgima male Grn merged. 160802

source_name: T110(Primary Bladder Tumour DNA)


title: GS MGII NEW HT-1197 Rd v's sigma male Grn (1)  merged 020802

source_name: HT1197(HT1197 Genomic Cell line DNA)


title: Tuberculosis TB_1049_vs_Pool

description: no


title: lung_E18_sftpc-nmyc_rep1

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

scan_protocol: affymetrix

data_processing: signal intensity values for each probe set derived from the Affymetrix Microarray Analysis Suite (v5.0) software; noralized to target value of 150

source_name: whole lung E18 sftpc-nmyc

label_protocol: Affymetrix kit

extract_protocol: RNeasy kit from QIagen

tag: lungs were over expressing nmyc-gfp fusion protein using the lung surfactant  c promoter.


title: Tuberculosis TB_1043_vs_Pool

description: no


title: Healthy infected PBMC_1016_vs_Pool

description: no


title: GS MGII NEW 5637  Rd v's sigma male Grn (1) 020802

source_name: 5637(Genomic Cell line DNA)


title: lung_E18_sftpc-nmyc_rep2

tag: whole lungs overexpressing an nmyc-gfp fusion protein via the lung surfactant c promoter


title: K 5637 Rd v's Male musc Grn (2)251101

source_name: Male Muscle DNA(Genomic Male Muscle DNA)


title: Tuberculosis TB_1040_vs_Pool

description: no


title: lung_E18_wildtype_rep2

source_name: whole lung E18 normal

tag: normal lung


title: K TCCSUP Rd v's sigma male Grn (1) 240602

source_name: TCCSUP(TCCSUP Genomic Cell line DNA)


title: K HT-1376 Rd v's Male musc Grn 251101


title: Tuberculosis TB_1024_vs_Pool

description: no


title: Healthy infected PBMC 1006 vs. PBMC Pool

description: no


title: Tuberculosis TB_1030_vs_Pool

description: no


title: GS MGII NEW TCCSUP Rd v's sigma male Grn (1) 020802


title: K TCCSUP Rd V's Male blood Grn 101101


title: congenic brain rep3

status: Public on Oct 26 2006

city: Davis

first: Kyoungmi

last: Kim

address: One Shields Avenue

department: Rowe Program in Human Genetics

institute: University of California-Davis

description: We previously constructed a congenic mouse, B6.S-D2Mit194-D2Mit311 (B6.S-2) with SPRET/Ei donor DNA on distal chromosome 2 in a C57BL/6J background that captured an obesity quantitative trait locus (QTL). Mice homozygous for SPRET/Ei alleles at the donor region had decreased body weight and obesity related phenotypes. The B6.S-2 congenic donor region spanned a minimum of 26 Mb. In this study, we constructed five overlapping subcongenics with smaller SPRET/Ei donor regions to fine map the underlying gene(s). One of the five subcongenic lines derived from the B6.S-2 founding congenic, B6.S-2A, captures most of the body weight and adiposity phenotypes in a donor region with a maximum size of 7.4 Mb. Homozygous SPRET/Ei donor alleles in both the founding congenic and the derived B6.S-2A subcongenic exhibit significant decreases in body weight, multiple fat pad weights with the greatest decrease in mesenteric fat pad weight, and Adiposity Index (total fat pad weight divided by body weight). Interval specific microarray analysis in four tissues for donor region genes from the founding B6.S-2 congenic identified several differentially expressed genes mapping to the B6.S-2A subcongenic donor region, including prohormone convertase 2 (PC2). Quantitative real-time PCR confirmed a modest decrease of PC2 expression in whole brains of mice homozygous for SPRET/Ei donor alleles. Analysis of the relative levels of mRNA for B6 and SPRET/Ei in heterozygous congenic mice showed differentially higher expression of the C57BL/6J allele over the SPRET/Ei allele indicating a cis regulation of differential expression. Using subcongenic mapping, we have successfully narrowed a body weight and obesity QTL interval and identified PC2 as a positional candidate gene.

hyb_protocol: cRNA was then hybridized according to the NimbleGen protocol

scan_protocol: Maskless Array Synthesizer (MAS) technology (Nuwaysir, Huang et al. 2002)

data_processing: RMA

source_name: congenic brain rep3

label_protocol: cDNA was transcribed into cRNA using the MEGAscript T7 Kit (Ambion, Austin, TX) with biotin labeled CTP and UTP followed by purification with RNeasy (QIAGEN, Valencia, CA).

growth_protocol: At weaning, F2 mice were group housed with ad libitum access to water and a standard chow diet (Purina Rodent Chow 5001, Dean’s Animal Feed) with approximately 12% energy from fat (Research Diets D12492, Research Diets, New Brunswick, NJ). One group of male B6.S-2 congenic mice were also fed a purified high fat diet with 60% energy from fat.

extract_protocol: Total RNA from whole brain, epididymal white adipose tissue, gastrocnemius skeletal muscle, and liver were isolated using TRIzol reagent (Gibco/BRl, Grand Island, NY) followed by further purification with QIAGEN RNeasy kit (QIAGEN Inc., Valencia, CA) using the RNA cleanup protocol. cRNA was then hybridized to a custom NimbleScreen 12-well array platform.

treatment_protocol: congenic mouse

tag: congenic brain rep3


title: congenic liver rep3

source_name: congenic liver rep3

tag: congenic liver rep3


title: congenic liver rep2.

source_name: congenic liver rep2.

tag: congenic liver rep2.


title: B6 adipose rep1

source_name: B6 adipose rep1

tag: B6 adipose rep1


title: B6 adipose rep2

source_name: B6 adipose rep2

tag: B6 adipose rep2


title: B6 adipose rep3

source_name: B6 adipose rep3

tag: B6 adipose rep3


title: congenic liver rep1.

source_name: congenic liver rep1.

tag: congenic liver rep1.


title: congenic adipose rep2

source_name: congenic adipose rep2

tag: congenic adipose rep2


title: congenic brain rep2.

source_name: congenic brain rep2.

tag: congenic brain rep2.


title: congenic muscle rep2

source_name: congenic muscle rep2

extract_protocol: Total RNA from whole brain, epididymal white adipose tissue, gastrocnemius skeletal muscle, and liver were isolated using TRIzol reagent (Gibco/BRl, Grand Island, NY) followed by further purification with QIAGEN RNeasy kit (QIAGEN Inc., Valencia, CA) using the RNA cleanup protocol. cRNA was then hybridized to a custom NimbleScreen 12-well array platform

tag: congenic muscle rep2


title: congenic muscle rep3

source_name: congenic muscle rep3

tag: congenic muscle rep3


title: congenic muscle rep1

source_name: congenic muscle rep1

tag: congenic muscle rep1


title: lung_E18_wildtype_rep1

tag: normal embryonic day 18 lungs


title: B6 muscle rep3

source_name: B6 muscle rep3

tag: B6 muscle rep3


title: congenic brain rep1

source_name: congenic brain rep1

tag: congenic brain rep1


title: FoxP3-transduced activated T cells - control vector-transduced activated T cells 1_5972

city: Cambridge

first: James

last: Smith

address: Tennis Court Road

department: Gurdon Institute

institute: Cambridge University

description: See materials and methods in originating publication

data_processing: Data is unnormalized due to high variablility in adjusting small datasets.

source_name: 72hr control vector-transduced activated T cells

source_name: 72hr FoxP3-transduced activated T cells

tag: 72hr FoxP3-transduced activated T cells


title: FoxP3-transduced activated T cells - control vector-transduced activated T cells 3_6030

source_name: 96hr control vector-transduced activated T cells

source_name: 96hr FoxP3-transduced activated T cells

tag: 96hr FoxP3-transduced activated T cells


title: FoxP3-transduced activated T cells - control vector-transduced activated T cells 4_6031

tag: 96hr control vector-transduced activated T cells


title: congenic adipose rep3

source_name: congenic adipose rep3

tag: congenic adipose rep3


title: congenic adipose rep1

source_name: congenic adipose rep1

tag: congenic adipose rep1


title: B6 muscle rep2

source_name: B6 muscle rep2

tag: B6 muscle rep2


title: B6_liver_rep1


title: LNCaP 3x15plt brain cy5 vs PNT2 cy3 RNA 071002

source_name: Brain(Commercial Brain RNA)

tag: gender

tag: tissue type

source_name: PNT2(Normal prostate cell line)


title: B6 muscle rep1

source_name: B6 muscle rep1

tag: B6 muscle rep1


title: Activated - Normal T cell comparison 5_6033

source_name: 10 day activated CD4+25- T cell

tag: 10 day activated CD4+25- T cell

source_name: CD4+25- T cell

tag: CD4+25- T cell


title: B6_liver_rep2


title: B6_liver_rep3


title: B6_Brian_rep3


title: Activated - Normal T cell comparison 4


title: Activated - Normal T cell comparison 2

source_name: 3day activated CD4+25- T cell

tag: 3day activated CD4+25- T cell


title: Activated - Normal T cell comparison 3_6027


title: FoxP3-transduced activated T cells - control vector-transduced activated T cells 2_5973

tag: 72hr control vector-transduced activated T cells


title: Activated - Normal T cell comparison 1_5946

source_name: overnight activated CD4+25- T cell

tag: overnight activated CD4+25- T cell


title: T Cell - T reg comparison 5_5966


title: T Cell - T reg comparison 6_5967


title: T Cell - T reg comparison 4_5965


title: T Cell - T reg comparison 2_5963


title: Proximal colon whey 3

city: Little Rock

first: Rijin

last: Xiao

state: AR

address: 2020 Marshall Street

institute: Nutrition Center, Arkansas Chidren's Hospital

description: Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.

hyb_protocol: Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.

data_processing: To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.

source_name: Rat Proximal colon

label_protocol: Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.

extract_protocol: TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.

tag: Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon


title: Proximal colon whey 1


title: Proximal colon soy 1


title: Proximal colon casein 3


title: Proximal colon soy 2


title: Proximal colon soy 3


title: Proximal colon whey 2


title: Rap1 wt 37 C rep2

status: Public on Oct 24 2006

city: Albany

first: Randall

middle: Heywood

last: Morse

institute: Wadsworth Center

description: Nothing else

hyb_protocol: Affymetrix protocol

scan_protocol: Standard Affy protocol

organism: Saccharomyces cerevisiae

source_name: Rap1 wild type control 37 C

label_protocol: Affymetrix protocol

growth_protocol: Growth in YPD at 37 C for one hour

extract_protocol: Masterpure RNA purification kit (Epicenter Technology, Madison WI, USA)

tag: Rap1 wild type control (W303a derived), 1 hr at 37 C


title: T Cell - T reg comparison 3_5964


title: Proximal colon casein 2


title: Proximal colon casein 1

tag: Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet(CAS), proximal colon


title: B6_Brain_rep2


title: Rap1 ts 37 C rep3

description: Nothing else

source_name: Rap1 ts mutant 37 C

tag: Rap1 ts mutant, 1 hr at 37 C


title: Rap1 ts 37 C rep1

description: Nothing else


title: T Cell - T reg comparison 1_5962


title: Rap1 wt 37 C rep3

description: Nothing else


title: Rap1 wt 37 C rep1

description: Nothing else


title: Abf1 wt 37C rep3

description: Nothing else

source_name: Abf1 wild type control

growth_protocol: Growth at 37 C for one hour

tag: Abf1 wild type control (W303a derived), 1 hr at 37 C


title: Rap1 ts 37 C rep2

description: Nothing else


title: Abf1 ts 37 C rep3

description: Nothing else

source_name: Abf1 ts mutant

tag: Abf1 ts mutant (W303a derived), 1 hr at 37 C


title: Abf1 ts 37 C rep2

description: Nothing else


title: Abf1 ts 37 C rep1

description: Nothing else

tag: Abf1 ts mutant, 1 hr at 37 C


title: Abf1 wt 37 C rep2

description: Nothing else

tag: Abf1 wild type control, replicate 2


title: shma-HepG2 24h 1 BaP B

city: Sutton

first: Ian

last: Giddings

address: 15 Cotswold Road

institute: Institute of Cancer Research

description: 50% formamide, amersham hyb buffer, 3 nights, 42 degrees

data_processing: Regions were used for normalizing samples 1-96. To account for dye swap, the signal channel and control channel measurements for sample(s) 43, 47, 49, 53, 59, 61, 65, 67, 71, 73, 77, 79, 83, 85, 89, 91, 95 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: sh-HepG2 24h DMSO B(hepg2 24h dmso)

source_name: sh-HepG2 24hr 1uM BaP B(hepg2 24h 1 bap)


title: Abf1 wt 37 C rep1

description: Nothing else

tag: Abf1 wild type control (W303a derivative) 37 C for one hour, replicate 1


title: shma-MCF7 24h 1 BaP A

source_name: sh-MCF7 24h DMSO A(mcf7 24h dmso )

source_name: sh-MCF7 24hr 1uM BaP A(mcf7 24h 1um bap )


title: shma-HepG2 48h 1 BaP A

source_name: sh-HepG2 48h DMSO A(hepg2 48h dmso)

source_name: sh-HepG2 48hr 1uM BaP A(hepg2 48h 1 bap)


title: shma-HepG2 48h 0.25 BaP B

source_name: sh-HepG2 48h DMSO B(hepg2 48h dmso)

source_name: sh-HepG2 48hr 0.25uM BaP B(hepg2 48h 0.25 bap)


title: shma-HepG2 48h 1 BaP B

source_name: sh-HepG2 48hr 1uM BaP B(hepg2 48h 1 bap)


title: shma-HepG2 6h 0.25 BaP A #2

source_name: sh-HepG2 6h DMSO A(hepg2 6h dmso)

source_name: sh-HepG2 6hr 0.25uM BaP A(hepg2 6h 0.25um bap)


title: shma-HepG2 24h 2.5 BaP A #2

source_name: sh-HepG2 24h DMSO A(hepg2 24h dmso)

source_name: sh-HepG2 24hr 2.5uM BaP A(hepg2 24h 2.5 bap)


title: shma-MCF7 6h 0.25 BeP A

source_name: sh-MCF7 6h DMSO A(mcf7 6h dmso)

source_name: sh-MCF7 6hr 0.25uM BeP A(mcf7 6h 0.25 bep)


title: shma-HepG2 24h 0.25 BaP A

source_name: sh-HepG2 24hr 0.25uM BaP A(24h 0.25 bap)


title: shma-HepG2 24h 2.5 BaP B

source_name: sh-HepG2 24hr 2.5uM BaP B(hepg2 24h 2.5 bap)


title: shma-HepG2 24h 1 BaP A

source_name: sh-HepG2 24hr 1uM BaP A(hepg2 24h 1 bap)


title: shma-HepG2 48h 0.25 BaP A

source_name: sh-HepG2 48hr 0.25uM BaP A(hepg2 48h 0.25 bap)


title: shma-HepG2 24h 0.25 BaP B

source_name: sh-HepG2 24h DMSO B(hepg2 24h dmso)

source_name: sh-HepG2 24hr 0.25uM BaP B(hepg2 24h 0.25 bap)


title: shma-HepG2 6h 1 BaP A

source_name: sh-HepG2 6hr 1uM BaP A(hepg2 6h 1um bap)


title: shma-HepG2 6h 1 BaP B

source_name: sh-HepG2 6h DMSO B(hepg2 6h dmso )

source_name: sh-HepG2 6hr 1uM BaP B(hepg2 6h 1um bap)


title: shma-HepG2 48h 2.5 BaP A

source_name: sh-HepG2 48h DMSO A(hepg2 48h dmso)

source_name: sh-HepG2 48hr 2.5uM BaP A(hepg2 48h 2.5 bap)


title: shma-HepG2 6h 2.5 BaP A

source_name: sh-HepG2 6h DMSO A(hepg2 6h dmso)

source_name: sh-HepG2 6hr 2.5uM BaP A(hepg2 6h 2.5 bap)


title: shma-MCF7 24h 0.25 BaP A

source_name: sh-MCF7 24h DMSO A(mcf7 24h dmso )

source_name: sh-MCF7 24hr 0.25uM BaP A(mcf7 24 0.25um bap)


title: shma-HepG2 48h 2.5 BaP B

source_name: sh-HepG2 48h DMSO B(hepg2 48h dmso)

source_name: sh-HepG2 48hr 2.5uM BaP B(hepg2 48h 2.5 bap)


title: shma-HepG2 6h 0.25 BaP B

source_name: sh-HepG2 6hr 0.25uM BaP B(hepg2 6h 0.25um bap)


title: shma-6K-HepG2 24h 2.5 BaP A

source_name: sh-HepG2 24h DMSO A(hepg2 24h dmso)

source_name: sh-HepG2 24hr 2.5uM BaP A(hepg2 24h 2.5 bap)


title: shma-6K-HepG2 6h 5 BaP A #2

source_name: sh-HepG2 6h DMSO C(hepg2 6h dmso)

source_name: sh-HepG2 6hr 5uM BaP A(hepg2 6h 5 bap)


title: shma-MCF7 24h 0.25 BaP B

source_name: sh-MCF7 24h DMSO B(mcf7 24h dmso)

source_name: sh-MCF7 24hr 0.25uM BaP B(mcf7 24h 0.25um bap)


title: shma-6k HepG2 48h 5 BaP C

description: 50% formamide, amersham hyb buffer, 42C o/n

source_name: sh-HepG2 48hr 5uM BaP B(hepg2 48h 5 bap)

source_name: sh-HepG2 48h DMSO D(hepg2 48h dmso)


title: shma-HepG2 6h 2.5 BaP B

source_name: sh-HepG2 6h DMSO B(hepg2 6h dmso )

source_name: sh-HepG2 6hr 2.5uM BaP B(hepg2 6h 2.5um bap )


title: shma-6k HepG2 24h 5 BaP C

description: 50% formamide, Amersham hyb buffer, 42C o/n

source_name: sh-HepG2 24hr 5uM BaP B(hepg2 24h 5 bap)

source_name: sh-HepG2 24h DMSO D(hepg2 24h dmso)


title: shma-MCF7 24h 1 BeP A

source_name: sh-MCF7 24h DMSO A(mcf7 24h dmso )

source_name: sh-MCF7 24hr 1uM BeP A(mcf7 24h 1um bep)


title: shma-6K-HepG2 24h 2.5 BaP B

source_name: sh-HepG2 24h DMSO B(hepg2 24h dmso)

source_name: sh-HepG2 24hr 2.5uM BaP B(hepg2 24h 2.5 bap)


title: shma-MCF7 24h 1 BeP B

source_name: sh-MCF7 24hr 1uM BeP B(mcf7 24h 1um bep)


title: shma-MCF7 24h 0.25 BeP A

source_name: sh-MCF7 24hr 0.25uM BeP A(mcf-7 24h 0.25um bep)


title: shma-MCF7 24h 0.25 BeP B

source_name: sh-MCF7 24hr 0.25uM BeP B(mcf7 24h 0.25um bep)


title: shma-MCF7 24h 2.5 BaP B

source_name: sh-MCF7 24hr 2.5uM BaP B(mcf7 24h 2.5um bap)


title: shma-6K-HepG2 24h 5 BaP A

source_name: sh-HepG2 24h DMSO C(hepg2 24h dmso)

source_name: sh-HepG2 24hr 5uM BaP A(hepg2 24h 5 bap)


title: shma-6K-HepG2 24h 5 BaP B


title: shma-MCF7 24h 2.5 BeP B

description: shma-MCF7 24h 2.5 BeP B  50% formamide, amersham hyb buffer, 3 nights, 42 degrees

source_name: sh-MCF7 24h DMSO B(mcf7 24h dmso)

source_name: sh-MCF7 24hr 2.5uM BeP B(mcf7 24h 2.5um bep)


title: shma-MCF7 24h 1 BaP B

source_name: sh-MCF7 24hr 1uM BaP B(mcf7 24h 1um bap)


title: shma-6K-HepG2 48h 2.5 BaP A

source_name: sh-HepG2 48h DMSO A(hepg2 48h dmso)

source_name: sh-HepG2 48hr 2.5uM BaP A(hepg2 48h 2.5 bap)


title: shma-MCF7 24h 2.5 BaP A

source_name: sh-MCF7 24hr 2.5uM BaP A(mcf7 24h 2.5um bap)


title: shma-MCF7 24h 2.5 BeP A

source_name: sh-MCF7 24hr 2.5uM BeP A(mcf7 24h 2.5um bep)


title: shma-MCF7 48h 0.25 BaP A

source_name: sh-MCF7 48h DMSO A(mcf7 48h dmso)

source_name: sh-MCF7 48hr 0.25uM BaP A(mcf7 48h 0.25um bap)


title: shma-6K-HepG2 48h 5 BaP A

source_name: sh-HepG2 48h DMSO C(hepg2 48h dmso)

source_name: sh-HepG2 48hr 5uM BaP A(hepg2 48h 5 bap)


title: shma-MCF7 48h 1 BaP B

source_name: sh-MCF7 48h DMSO B(mcf7 48h dmso)

source_name: sh-MCF7 48hr 1uM BaP B(mcf7 48h 1um bap)


title: shma-MCF7 48h 1 BaP A

source_name: sh-MCF7 48hr 1uM BaP A(mcf7 48h 1um bap)


title: shma-MCF7 48h 1 BeP B

source_name: sh-MCF7 48hr 1uM BeP B(mcf7 48h 1um bep)


title: shma-MCF7 48h 0.25 BeP A

source_name: sh-MCF7 48hr 0.25uM BeP A(mcf7 48h 0.25um bep)


title: shma-6K-HepG2 48h 2.5 BaP B

source_name: sh-HepG2 48h DMSO B(hepg2 48h dmso)

source_name: sh-HepG2 48hr 2.5uM BaP B(hepg2 48h 2.5 bap)


title: shma-MCF7 48h 0.25 BaP B

source_name: sh-MCF7 48hr 0.25uM BaP B(mcf7 48h 0.25um bap )


title: shma-MCF7 48h 2.5 BaP A

source_name: sh-MCF7 48hr 2.5uM BaP A(mcf7 48h 2.5um bap)


title: shma-6K-HepG2 6h 2.5 BaP A

source_name: sh-HepG2 6h DMSO A(hepg2 6h dmso)

source_name: sh-HepG2 6hr 2.5uM BaP A(hepg2 6h 2.5 bap)


title: shma-MCF7 48h 2.5 BaP B

source_name: sh-MCF7 48hr 2.5uM BaP B(mcf7 48h 2.5um bap)


title: shma-MCF7 48h 1 BeP A

source_name: sh-MCF7 48hr 1uM BeP A(mcf7 48h 1um bep)


title: shma-MCF7 48h 2.5 BeP B

source_name: sh-MCF7 48hr 2.5uM BeP B(mcf7 48h 2.5um bep)


title: shma-MCF7 48h 0.25 BeP B

source_name: sh-MCF7 48hr 0.25uM BeP B(mcf7 48h 0.25um bep)


title: shma-6K-HepG2 48h 5 BaP B

source_name: sh-HepG2 48h DMSO D(hepg2 48h dmso)

source_name: sh-HepG2 48hr 5uM BaP B(hepg2 48h 5 bap)


title: shma-6K-HepG2 6h 2.5 BaP B

source_name: sh-HepG2 6h DMSO B(hepg2 6h dmso )

source_name: sh-HepG2 6hr 2.5uM BaP B(hepg2 6h 2.5um bap )


title: shma-MCF7 48h 2.5 BeP A

source_name: sh-MCF7 48h DMSO A(mcf7 48h dmso)

source_name: sh-MCF7 48hr 2.5uM BeP A(mcf7 48h 2.5um bep)


title: shma-MCF7 6h 1 BeP A

source_name: sh-MCF7 6h DMSO A(mcf7 6h dmso)

source_name: sh-MCF7 6hr 1uM BeP A(mcf7 6h 1um bep)


title: shma-MCF7 6h 1 BaP B

source_name: sh-MCF7 6h DMSO B(mcf7 6h dmso)

source_name: sh-MCF7 6hr 1uM BaP B(mcf7 6h 1um bap)


title: shma-MCF7 6h 1 BaP A

description: amersham hyb buffer, 3 nights, 42 degrees

source_name: sh-MCF7 6hr 1uM BaP A(mcf7 6h 1um bap)


title: shma-MCF7 6h 0.25 BaP A

source_name: sh-MCF7 6hr 0.25uM BaP A(mcf7 6h 0.25 uM BaP)


title: shma-6K-HepG2 6h 5 BaP B

source_name: sh-HepG2 6h DMSO D(hepg2 6h dmso)

source_name: sh-HepG2 6hr 5uM BaP B(hepg2 6h 5 bap)


title: shma-6K-MCF7 24h 2.5 BaP A

source_name: sh-MCF7 24h DMSO A(mcf7 24h dmso )

source_name: sh-MCF7 24hr 2.5uM BaP A(mcf7 24h 2.5um bap)


title: shma-MCF7 6h 0.25 BaP B

source_name: sh-MCF7 6hr 0.25uM BaP B(mcf7 6h 0.25 bap)


title: shma-MCF7 6h 2.5 BaP B

source_name: sh-MCF7 6hr 2.5uM BaP B(mcf7 6h 2.5 bap)


title: shma-MCF7 6h 2.5 BaP A

source_name: sh-MCF7 6hr 2.5uM BaP A(mcf7 6h 2.5um bap)


title: shma-MCF7 6h 0.25 BeP B

source_name: sh-MCF7 6hr 0.25uM BeP B(mcf7 6h 0.25 bep)


title: shma-MCF7 6h 2.5 BeP A

source_name: sh-MCF7 6hr 2.5uM BeP A(mcf7 6h 2.5um bep)


title: shma-MCF7 6h 2.5 BeP B

source_name: sh-MCF7 6hr 2.5uM BeP B(mcf7 6h 2.5um bep)


title: shma-MCF7 6h 1 BeP B

source_name: sh-MCF7 6hr 1uM BeP B(mcf7 6h 1 um bep)


title: shma-HepG2 24h 5 BaP A

source_name: sh-HepG2 24hr 5uM BaP A(hepg2 24h 5 bap)

source_name: sh-HepG2 24h DMSO C(hepg2 24h dmso)


title: shma-6K-MCF7 48h 2.5 BaP A

source_name: sh-MCF7 48h DMSO A(mcf7 48h dmso)

source_name: sh-MCF7 48hr 2.5uM BaP A(mcf7 48h 2.5um bap)


title: shma-HepG2 24h 5 BaP B

source_name: sh-HepG2 24hr 5uM BaP B(hepg2 24h 5 bap)

source_name: sh-HepG2 24h DMSO D(hepg2 24h dmso)


title: shma-6K-MCF7 24h 2.5 BaP B

source_name: sh-MCF7 24h DMSO B(mcf7 24h dmso)

source_name: sh-MCF7 24hr 2.5uM BaP B(mcf7 24h 2.5um bap)


title: shma-6K-MCF7 24h 5 BaP A

source_name: sh-MCF7 24h DMSO C(mcf7 24h dmso)

source_name: sh-MCF7 24hr 5uM BaP A(mcf7 24h 5um bap)


title: shma-HepG2 6h 5 BaP A

source_name: sh-HepG2 6h DMSO C(hepg2 6h dmso)

source_name: sh-HepG2 6hr 5uM BaP A(hepg2 6h 5 bap)


title: shma-HepG2 48h 5 BaP A

source_name: sh-HepG2 48h DMSO C(hepg2 48h dmso)

source_name: sh-HepG2 48hr 5uM BaP A(hepg2 48h 5 bap)


title: shma-6K-MCF7 24h 5 BaP B

source_name: sh-MCF7 24h DMSO D(mcf7 24h dmso)

source_name: sh-MCF7 24hr 5uM BaP B(mcf7 24h 5um bap)


title: shma-HepG2 6h 5 BaP B

source_name: sh-HepG2 6h DMSO D(hepg2 6h dmso)

source_name: sh-HepG2 6hr 5uM BaP B(hepg2 6h 5 bap)


title: shma-MCF7 24h 5 BaP A


title: shma-HepG2 48h 5 BaP B

source_name: sh-HepG2 48h DMSO D(hepg2 48h dmso)

source_name: sh-HepG2 48hr 5uM BaP B(hepg2 48h 5 bap)


title: shma-6K-MCF7 48h 2.5 BaP B

source_name: sh-MCF7 48h DMSO B(mcf7 48h dmso)

source_name: sh-MCF7 48hr 2.5uM BaP B(mcf7 48h 2.5um bap)


title: shma-6k-MCF7 48h 5 BaP A

source_name: sh-MCF7 48h DMSO C(mcf7 48h dmso)

source_name: sh-MCF7 48hr 5uM BaP A(mcf7 48h 5um bap)


title: shma-MCF7 24h 5 BaP B


title: shma-MCF7 48h 5 BaP A


title: shma-HepG2 6h 5 BeP A

source_name: sh-HepG2 6h DMSO A(hepg2 6h dmso)

source_name: sh-HepG2 6hr 5uM BeP A(hepg2 6h 5 bep)


title: shma-MCF7 48h 5 BaP B

source_name: sh-MCF7 48h DMSO D(mcf7 48h dmso)

source_name: sh-MCF7 48hr 5uM BaP B(mcf7 48h 5um bap)


title: shma-MCF7 6h 5 BaP B

source_name: sh-MCF7 6h DMSO D(mcf7 6h dmso)

source_name: sh-MCF7 6hr 5uM BaP B(mcf7 5h 5um bap)


title: shma-6K-MCF7 48h 5 BaP B


title: shma-HepG2 24h 5 BeP B

source_name: sh-HepG2 24h DMSO B(hepg2 24h dmso)

source_name: sh-HepG2 24hr 5uM BeP B(hepg2 24h 5 bep)


title: E. coli K12 BW25113 w/t suspension after 15 hr of culturing

status: Public on Oct 23 2006

city: College Station

first: Thomas

middle: K.

last: Wood

state: TX

address: 220 Jack E. Brown Building

department: Artie McFerrin Department of Chemical Engineering

institute: Texas A & M University

description: RNA extracted from suspenion cells of E. coli K12 wild type after 15 hours of growth in LB

hyb_protocol: Affimetrix Protocol

scan_protocol: Affimetrix Protocol

data_processing: MAS 5.0 Expression Analysis Default Settings

organism: Escherichia coli

source_name: E. coli suspension

label_protocol: Affimetrix Protocol


title: shma-MCF7 6h 5 BaP A

source_name: sh-MCF7 6h DMSO C(mcf7 6h dmso)

source_name: sh-MCF7 6hr 5uM BaP A(mcf76h 5um bap)


title: shma-HepG2 6h 5 BeP B

source_name: sh-HepG2 6h DMSO B(hepg2 6h dmso )

source_name: sh-HepG2 6hr 5uM BeP B(hepg2 6h 5 bep)


title: shma-6K-MCF7 6h 5 BaP B


title: E. coli K12 BW25113 w/t suspension after 24 hr of culturing

description: RNA extracted from suspenion cells of E. coli K12 wild type after 24 hours of growth in LB

data_processing: AfMAS 5.0 Expression Analysis Default Settings


title: shma-6K-MCF7 6h 2.5 BaP B

source_name: sh-MCF7 6h DMSO B(mcf7 6h dmso)

source_name: sh-MCF7 6hr 2.5uM BaP B(mcf7 6h 2.5 bap)


title: shma-6K-MCF7 6h 5 BaP A


title: shma-HepG2 24h 5 BeP A

source_name: sh-HepG2 24h DMSO A(hepg2 24h dmso)

source_name: sh-HepG2 24hr 5uM BeP A(hepg2 24h 5 bep)


title: E. coli K12 BW25113 w/t suspension after 7 hr of culturing

description: RNA extracted from suspenion cells of E. coli K12 wild type after 7 hours of growth in LB


title: E. coli K12 BW25113 w/t suspension after 4 hr of culturing

description: RNA extracted from suspenion cells of E. coli K12 wild type after 4 hours of growth in LB


title: E. coli K12 BW25113 w/t biofilm after 24 hr of culturing

description: RNA extracted from biofilm cells of E. coli K12 wild type after 24 hours of growth in LB

source_name: E. coli biofilm


title: E. coli K12 BW25113 w/t biofilm after 15 hr of culturing

description: RNA extracted from biofilm cells of E. coli K12 wild type after 15 hours of growth in LB


title: sea urchin tiling array urchin4 (BC459)

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

description: A High-Resolution Transcriptome Map of the Sea Urchin Embryo

hyb_protocol: Protocol is described in V. Stolc et al., Proc. Nat. Acad. Sci. USA 102, 4453 (2005).

scan_protocol: Features were scanned using Nimblescan software.

data_processing: Custom softwares were used for data processing. Normalization was performed to make the distribution of the common control probes identical in all arrays.

molecule: polyA RNA

organism: Strongylocentrotus purpuratus

source_name: Poly-A RNA from egg, early blastula (15hr.), early gastrula (30hr.) and late gastrula stage (45hr.) embryos of sea urchin.

label_protocol: Samples were mixed in equal quantities, reverse transcribed and fluorescently labeled.

extract_protocol: protocol is described in V. Stolc et al., Proc. Nat. Acad. Sci. USA 102, 4453 (2005).

tag: RNA pooled from four early stages of sea urchin embryo


title: sea urchin tiling array urchin21 (BC467)


title: sea urchin tiling array urchin13 (BC468)


title: sea urchin tiling array urchin20 (BC454)


title: sea urchin tiling array urchin2 (BC442)


title: sea urchin tiling array urchin19 (BC466)


title: sea urchin tiling array urchin27 (BC464)


title: E. coli K12 BW25113 w/t biofilm after 7 hr of culturing

description: RNA extracted from biofilm cells of E. coli K12 wild type after 7 hours of growth in LB


title: sea urchin tiling array urchin1 (BC456)


title: sea urchin tiling array urchin3 (BC457)


title: sea urchin tiling array urchin26 (BC443)


title: sea urchin tiling array urchin24 (BC453)


title: E. coli K12 BW25113 w/t biofilm after 4 hr of culturing

description: RNA extracted from biofilm cells of E. coli K12 wild type after 4 hours of growth in LB

label_protocol:
1. RNA Extraction
2. Random priming cDNA synthesis
3. RNA degradation with NaOH
4. cDNA column purification
5. cDNA fragmentation and terminal labeling with biotinylated GeneChip® DNA Labeling Reagent


title: sea urchin tiling array urchin25 (BC449)


title: sea urchin tiling array urchin23 (BC447)


title: sea urchin tiling array urchin14 (BC465)


title: shma-6K-MCF7 6h 2.5 BaP A

source_name: sh-MCF7 6h DMSO A(mcf7 6h dmso)

tag: tissue type

source_name: sh-MCF7 6hr 2.5uM BaP A(mcf7 6h 2.5um bap)


title: sea urchin tiling array urchin18 (BC445)


title: Comparing baseline and galactose-induced yeast expression using a double-tiled array

status: Public on Oct 22 2006

city: Baltimore

first: Sarah

last: Wheelan

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

description: See above.

hyb_protocol: hybridized overnight in a humid chamber at 65C.

data_processing: the value given is simply the log2 of the ratio of the subtracted intensities.

source_name: galactose-grown yeast RNA

label_protocol: Yeast RNA was processed using a modification of the Agilent Low RNA Input Fluorescent Linear Amplification protocol (Agilent Technologies Kit, Protocol version 3.3, July 2005)

extract_protocol: Cells were pelleted, snap frozen, and later thawed on ice and resuspended in 400 microliters TES; 400 microliters acid phenol/chloroform was added and the extracts were incubated at 65 C for 60 minute with brief, occasional vortexing. The samples were then extracted twice with acid phenol/chloroform, and RNA was precipitated with ethanol and 40 microliters 3M sodium acetate, pH 5.3 at -80 C overnight. The pellet was washed in 70% ethanol, resuspended, and the RNA was further purified using a Qiagen RNeasy kit. Finally, the RNA was treated with DNaseI according to standard protocol. All solutions were DEPC-treated or otherwise certified RNase-free.

tag: RNA prepared from yeast cultures grown first in raffinose and then switched to galactose, harvested at OD600 = 0.6.

source_name: glucose-grown yeast RNA

label_protocol: as for ch1, except using Cy3

extract_protocol: see protocol for ch1

tag: RNA prepared from yeast cultures grown first in raffinose and then switched to glucose, harvested at OD600 = 0.6.


title: Comparing baseline and galactose-induced yeast expression using a double-tiled array, replicate

description: See above.


title: sea urchin tiling array urchin12 (BC451)


title: Demonstration of double tiling with a simple yeast plasmid sample, #2

description: See above.

data_processing: the value given is simply the log2 of the difference between F635 and B635

source_name: yeast plasmid DNA

label_protocol: Each plasmid was digested in three parallel reactions with AluI, MspI, and HpyCH4V. The resulting fragments were heat-inactivated, pooled and labeled for hybridization to the microarray as follows: 200 ng DNA was incubated with 36 micrograms random hexamer in a 23 microliter reaction at 100C for 2 minutes, then 4C for 4 minutes. The labeling reaction then proceeded with the addition of 5 microliters 10x dNTP (8 mM dATP, dCTP, dGTP, 4 mM dUTP), 5 microliters 10x Klenow buffer, 7 microliters  Klenow (exo-) fragment (5U/microliter/), 7 microliters H2O, and 2 microliters Cy5 dUTP, and was incubated at 37C for 2 hours. The reaction was stopped with 5 microliters  0.5 M EDTA pH 8.0. The products were mixed with 450 microliters TE and concentrated on a Microcon YM-30 (Amicon catalog #42410) column. The products were washed again with 450 microliters TE and 10 microliters sheared salmon sperm DNA (10 mg/ml), and concentrated again on a Microcon column. The resulting volume was adjusted to 26 microliters with the addition of H2O, and SDS and SSC were added to final concentrations of 3x SSC and 0.3% SDS, in a total volume of 32.5 microliters. After incubation at 100C for 90 seconds and then 37C for 30 minutes, the products were spotted onto microarrays and covered with VWR 22x60mm cover slips.

extract_protocol: standard yeast plasmid DNA preparation

tag: HIS3, HIS4, Ty1 plasmids also with URA3 and GAL1 promoter


title: Demonstration of double tiling with a simple yeast plasmid sample, #1

description: See above.

data_processing: the value reported is simply the log2 of the difference between F635 and B635


title: sea urchin tiling array urchin15 (BC463)


title: NRMRL test replicate03, EPA1UVHK batch072104 430B chip

status: Public on Oct 21 2006

city: Cincinnati

first: Samuel

last: Hayes

state: OH

address: 26 W. Martin Luther King Dr.

institute: United States Environmental Protection Agency

hyb_protocol: MAS 5.0 software EukGE-WS1

scan_protocol: MAS 5.0 with model 4500 scanner

data_processing: Microarray Suite (MAS) 5.0 software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065; Tau 0.015; Gamma1L and 1H 0.0045; Gamma 2L and 2H 0.06; and Pertubation 1.1.

label: Streptavidin Phycoerythrin (SAPE)

source_name: mouse small intestinal cell culture, 5 hour infection

label_protocol: Affymetrix SOP, EukGE-WS2

extract_protocol: TriZol procedure

tag: MICcl2 cell line


title: NRMRL test replicate02, EPA1UVHK batch072104 430B chip


title: NRMRL test replicate04, EPA1UVHK batch072104 430B chip


title: NRMRL test replicate01, EPA1UVHK batch072104 430B chip


title: sea urchin tiling array urchin17 (BC444)


title: NRMRL test replicate05, EPA1UVHK batch072104 430B chip


title: sea urchin tiling array urchin11 (BC452)


title: sea urchin tiling array urchin22 (BC450)


title: NRMRL control replicate05, uninfected batch072104 430B chip

source_name: mouse small intestinal cell culture, 5 hours


title: Comparing baseline and galactose-induced yeast expression for comparison with the double-tiled array

description: See above.


title: sea urchin tiling array urchin9 (BC446)


title: Comparing baseline and galactose-induced yeast expression for comparison with the double-tiled array, replicate

description: See above.


title: sea urchin tiling array urchin7 (BC460)


title: sea urchin tiling array urchin6 (BC458)


title: sea urchin tiling array urchin16 (BC462)


title: sea urchin tiling array urchin5 (BC455)


title: NRMRL control replicate04, uninfected batch072104 430B chip


title: NRMRL test replicate05, EPA73 batch072104 430B chip


title: NRMRL control replicate01, uninfected batch072104 430B chip


title: sea urchin tiling array urchin8 (BC461)


title: sea urchin tiling array urchin10 (BC448)


title: NRMRL control replicate02, uninfected batch072104 430B chip


title: NRMRL test replicate04, EPA73 batch072104 430B chip


title: NRMRL test replicate01, EPA73 batch072104 430B chip


title: NRMRL test replicate05, EPA100 batch072104 430B chip


title: NRMRL test replicate01, EPA100 batch072104 430B chip

source_name: mouse smalll intestinal cell culture, 5 hour infection


title: NRMRL test replicate03, EPA100 batch072104 430B chip


title: NRMRL test replicate04, EPA100 batch072104 430B chip


title: NRMRL control replicate05, uninfected batch022304 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hours

tag: Swiss Webster neonate, 5 days old


title: NRMRL test replicate03, EPA73 batch072104 430B chip


title: NRMRL control replicate03, uninfected batch022304 430B chip


title: NRMRL test replicate04, EPA1 batch022304 430B chip

source_name: neonatal mouse small intestinal sample, 5 hour infection


title: NRMRL test replicate02, EPA1 batch022304 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hours infection


title: NRMRL test replicate02, EPA100 batch072104 430B chip


title: NRMRL control replicate01, uninfected batch022304 430B chip


title: NRMRL control replicate04, uninfected batch022304 430B chip


title: NRMRL test replicate03, EPA1 batch022304 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate05, EPA1 batch022304 430B chip


title: NRMRL control replicate02, uninfected batch022304 430B chip

source_name: neonatal mouse small intestinal tissue


title: NRMRL test replicate02, EPA2 batch022304 430B chip


title: NRMRL test replicate01, EPA1 batch022304 430B chip


title: NRMRL test replicate04, EPA2 batch022304 430B chip


title: NRMRL test replicate01, EPA2 batch022304 430B chip


title: NRMRL control replicate02, uninfected batch092303 430B chip

source_name: neonatal small intestinal tissue, 5 hours


title: NRMRL control replicate03, uninfected batch092303 430B chip

source_name: noenatal mouse small intestinal tissue, 5 houors


title: NRMRL test replicate03, EPA5 batch092303 430B chip


title: NRMRL test replicate01, EPA5 batch092303 430B chip


title: NRMRL control replicate01, uninfected batch092303 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hour


title: NRMRL test replicate03, EPA2 batch022304 430B chip


title: NRMRL test replicate02, EPA71 batch052704 430B chip


title: NRMRL test replicate02, EPA5 batch092303 430B chip


title: NRMRL test replicate03, EPA71 batch052704 430B chip


title: NRMRL test replicate04, EPA71 batch052704 430B chip


title: NRMRL test replicate05, EPA71 batch052704 430B chip


title: NRMRL test replicate03, EPA73 batch052704 430B chip


title: NRMRL control replicate03, uninfected batch072104 430B chip

tag: MICcl2 cell culture


title: NRMRL test replicate05, EPA73 batch052704 430B chip


title: NRMRL test replicate04, EPA73 batch052704 430B chip


title: NRMRL test replicate05, EPA100 batch052704 430B chip


title: NRMRL test replciate04, EPA72 batch052704 430B chip


title: NRMRL test replicate03, EPA100 batch052704 430B chip

source_name: noenatal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate04, EPA0100 batch052704 430B chip


title: NRMRL test replicate01, EPA72 batch052704 430B chip

data_processing: MAS 5.0 software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065; Tau 0.015; Gamma1L and 1H 0.0045; Gamma 2L and 2H 0.06; and Pertubation 1.1.


title: NRMRL test replicate01, EPA71 batch052704 430B chip


title: NRMRL test replicate03, EPA1HK batch052704 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hour treatment


title: NRMRL test replicate02, EPA72 batch052704 430B chip


title: NRMRL test replicate05, EPA1HK batch052704 430B chip

tag: Swiss Webster noenate, 5 days old


title: NRMRL test replicate01, EPA100 batch052704 430B chip


title: NRMRL test replicate04, EPA1HK batch052704 430B chip


title: NRMRL test replicate02, EPA73 batch052704 430B chip


title: NRMRL test replicate03, EPA72 batch052704 430B chip


title: NRMRL test replicate02, EPA73 batch072104 430B chip


title: NRMRL test replicate02, EPA100 batch052704 430B chip


title: NRMRL test replicate05, EPA72 batch052704 430B chip


title: NRMRL control replicate04, uninfected batch052704 430B chip


title: NRMRL test replicate02, EPA1HK batch052704 430B chip


title: NRMRL control replicate03, uninfected batch052704 430B chip


title: NRMRL control replicate05, uninfected batch052704 430B chip


title: NRMRL control replicate02, uninfected batch052704 430B chip


title: NRMRL control replicate03, uninfected batch092304 430B chip


title: NRMRL test replicate01, EPA73 batch052704 430B chip

source_name: neonatal mouse small intestinal tissue, 5 hour infeection


title: NRMRL control replicate02, uninfected batch092304 430B chip


title: NRMRL control replicate01, uninfected batch092304 430B chip


title: NRMRL test replicate01, EPA1HK batch052704 430B chip


title: NRMRL test replicate05, EPA1UVHK batch072104 430A chip


title: NRMRL test replicate04, EPA63 batch092304 430B chip


title: NRMRL test replicate05, EPA63 batch092304 430B chip


title: NRMRL control replicate04, uninfected batch092304 430B chip


title: NRMRL control replicate01, uninfected batch052704 430B chip


title: NRMRL test replicate04, EPA61 batch092304 430B chip


title: NRMRL test replicate03, EPA61 batch092304 430B chip


title: NRMRL test replicate01, EPA63 batch092304 430B chip


title: NRMRL test replicate04, EPA1UVHK batch072104 430A chip


title: NRMRL test replicate03, EPA1UVHK batch072104 430A chip


title: NRMRL test replicate02, EPA63 batch092304 430B chip


title: NRMRL test replicate03, EPA63 batch092304 430B chip


title: NRMRL test replicate05, EPA61 batch092304 430B chip


title: NRMRL test replicate02, EPA61 batch092304 430B chip


title: NRMRL test replicate02, EPA1UVHK batch072104 430A chip


title: NRMRL test replicate01, EPA1UVHK, batch072104 430A chip


title: NRMRL control replicate01, uninfected batch072104 430A chip


title: NRMRL control replicate04, uninfected batch072104 430A chip


title: NRMRL test replicate05, EPA73 batch072104 430A chip


title: NRMRL control replicate03, uninfected batch072104 430A chip

source_name: mouse small intestinal call culture, 5 hours


title: NRMRL control replicate02, uninfected batch072104 430A chip


title: NRMRL test replicate05, EPA100 batch072104 430A chip


title: NRMRL test replicate03, EPA73 batch072104 430A chip


title: NRMRL control replicate05, uninfected batch072104 430A chip


title: NRMRL test replicate04, EPA73 batch072104 430A chip


title: NRMRL test replicate04, EPA100 batch072104 430A chip


title: NRMRL test replicate02, EPA100 batch072104 430A chip


title: NRMRL test replicate05, EPA1 batch022304 430A chip

source_name: neonatal mouose small intestinal tissue, 5 hour infection


title: NRMRL test replicate01, EPA1 batch022304 430A chip

source_name: neonatal small intestinal tissue, 5 hour infection


title: NRMRL control replicate05, uninfected batch022304 430A chip


title: NRMRL control replicate02, uninfected batch022304 430A chip


title: NRMRL test replicate03, EPA100 batch072104 430A chip

source_name: mouse small intestinal cell culture, 5 hour infection


title: NRMRL test replicate01, EPA61 batch092304 430B chip


title: NRMRL test replicate04, EPA1 batch022304 430A chip

source_name: neonatal mouse small intestinal tissue, 5 houor infection


title: NRMRL control replicate04, uninfected batch022304 430A chip


title: NRMRL control replicate03, uninfected batch022304 430A chip


title: NRMRL test replicate03, EPA2 batch022304 430A chip


title: NRMRL test replicate03, EPA1 batch022304 430A chip


title: NRMRL test replicate01, EPA73 batch072104 430A chip


title: NRMRL test replicate04, EPA2 batch022304 430A chip


title: NRMRL control replicate01, unifected batch022304 430A chip


title: NRMRL test replicate02, EPA1 batch022304 430A chip


title: NRMRL test replicate01, EPA2 batch022304 430A chip


title: NRMRL test replicate03, EPA5 batch092303 430A chip


title: NRMRL test replicate02, EPA2 batch022304 430A chip


title: NRMRL test replicate01, EPA5 batch092303 430A chip

source_name: neontal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate01, EPA100 batch072104 430A chip

source_name: mouse small intestinal cell cuture, 5 hour infection


title: NRMRL test replicate02, EPA5 batch092303 430A chip


title: NRMRL test replicate05, EPA71 batch052704 430A chip


title: NRMRL test replicate04, EPA73 batch052704 430A chip


title: NRMRL test replicate03, EPA73 batch052704 430A chip


title: NRMRL test replicate04, EPA71 batch052704 430A chip


title: NRMRL test replicate05, EPA73 batch052704 430A chip


title: NRMRL control replicate02, uninfected batch092303 430A chip


title: NRMRL control replicate03, uninfected batch092303 430A chip

source_name: neonatal mouse small intestinal tissue, 5 hours