title: WT_P0_whole_Vestibule_3

type: other

city: Tel Aviv

first: Karen

middle: B

last: Avraham

address: Levanon St.

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

hyb_protocol: Each spotted microarray was hybridized with two RNA samples that were labeled with different dyes, using the buffers and instructions of the mirVana miRNA Bioarray Essentials Kit (Ambion), according to the manufacturer's protocol.

scan_protocol: The microarray was scanned by an Affymetrix 428 array scanner and quantified using the ImaGene (version 5.1) software (BioDiscovery).

data_processing: Intensities, as calculated by ImaGene v5.1, were averaged for each probe (4 spots per each probe).

molecule: other

source_name: Newborn mouse P0 whole vestibules

label_protocol: Small <40 nt RNAs were labeled with Cy3 fluorescent dye (Post-Labeling Reactive CyDyes, GE Healthcare), using the mirVana miRNA Labeling Kit (Ambion), according to the manufacturer's protocol.

growth_protocol: Normal conditions

extract_protocol:
Inner ears were dissected from wild type newborn C57BL/6 mice. From inner ears, cochleae and vestibules were separated, with meticulous separation of saccules from cochleae.
The mirVana miRNA Isolation Kit (Ambion, Applied Biosystems) was used for isolation of small (<200 nt) RNAs, following the manufacturer's instructions. The quality and integrity of the small RNAs were evaluated by denaturing polyacrylamide gel electrophoresis (PAGE: 15% polyacrylamide/8M urea gels in TBE buffer) and ethidium bromide staining of the gels. Tiny (<40 nt) RNAs were isolated from the small (<200 nt) RNA fraction, using flashPAGE Fractionator (Ambion), according to the manufacturer's instructions. The <40 nt RNA fractions, which are expected to include mature RNAs without pre-miRNAs, were precipitated overnight at -20oC with a linear acrylamide carrier (Ambion) in the presence of 0.06M sodium acetate and 80% ethanol. After this stage, the RNA amount was about 1% of the <200 nt sample amount.

value: mixed (both males and females)

value: newborns

value: whole vestibules

tag: Small RNAs (<40 nt) from at least 20 vestibules were pooled and hybridized


title: 25whole_flies_Df(3L)ED4543_5

status: Public on Apr 03 2009

type: RNA

city: Johnson City

first: Lev

last: Yampolsky

state: TN

address: ETSU

department: Biological Sciences

country: USA

institute: East Tennessee State University

hyb_protocol: See Neal, S.J., Gibson, M.L., So, A.K. & Westwood, J.T. Genome 46, 879-892. (2003)

data_processing: Background subtracted, repeated intensities for multiple probes averaged by gene, data normalized by ANOVA normalization with arrays and channels as factors. AutoBlank subtracted from each observation.

molecule: total RNA

organism: Drosophila melanogaster

source_name: 25 whole flies

label_protocol: Lines Df(3L)ED4475 and Df(3L)ED4543 alternated for Cy3 and Cy5. For details see Neal, S.J., Gibson, M.L., So, A.K. & Westwood, J.T. Genome 46, 879-892. (2003)

growth_protocol: Standard SCY Drosophila medium, 26oC

extract_protocol: Twenty five adult flies 2-5 days after eclosion frozen in liquid nitrogen immediately prior to extraction by Trizol method (Invitrogen ®, Carlsbad, CA)

treatment_protocol: the two lines compared are heterozygous for different long deletions in chromosome 3L

tag: isogenic line


title: Null glnR_ 48h_A

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: delta-glnR_ 48h_A

hyb_protocol: Following fragmentation, 4 microg of cDNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

organism: Mycobacterium tuberculosis H37Rv

source_name: Null glnR_ 48h_A

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Prokaryotic Expression Analysis, Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: minimal medium with nitrate; incubated for 48 hours

extract_protocol: RNeasy (Qiagen)

tag: genetic modification

value: deletion of glnR (Rv0818)


title: BDEneu Tumor at Day 25, biological rep3

status: Public on Apr 02 2009

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

description: Gene expression data from BDEneu Tumor at Day 25 from rat# 9

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner.

data_processing: The data were analyzed using the Robust Multiarray Analysis (RMA) method.

organism: Rattus norvegicus

source_name: BDEneu Tumor, Day 25

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

growth_protocol: Tissues were snap-frozen immediately after extirpation from the animal.

extract_protocol: Trizol extraction of total RNA was performed followed by a Qiagen cleanup step, according to manufacturers' instructions.

tag: rat number

tag: tissue

value: intrahepatic cholangiocarcinoma

tag: strain

value: Fischer 344

tag: gender

value: male

tag: age

value: Young adult


title: WT_P0_whole_Vestibule_1

organism: Mus musculus

treatment_protocol: no treatment


title: WT_P0_whole_Cochlea_3_V4

description: A different array template (diffrent date of printing) than the other samples. Therefore, this array was not included in the analysis.

data_processing: Intensities, as calculated by ImaGene v5.1, were averaged for each probe (4 or 8 spots per each probe).

source_name: Newborn mouse P0 whole cochleae

value: whole cochleae

tag: Small RNAs (<40 nt) from at least 20 cochleae were pooled and hybridized


title: 11HUVEC_scrambled_24h_rep3

city: Frankfurt

first: Carmen

last: Urbich

institute: Molecular Cardiology

description: Gene expression data 24h after HDAC5 siRNA treatment

hyb_protocol: Fifteen micrograms fragmented, biotinylated cRNA was hybridized to an HG-U133 Plus 2.0 microarray (Affymetrix) for 16 hours at 45°C with constant rotation at 60 rpm, according to the Affymetrix protocol.

scan_protocol: After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and was scanned with an Fluorescence intensity normalized to the average fluorescence for the entire microarray.

data_processing: GeneChip image analysis was performed using the Microarray Analysis Suites 5.0 (Affymetrix). Data analysis was performed with the GeneSpring software version 4.2 (Silicon Genetics, San Carlos, CA). Normalization of gene expression data was performed in a two step way. First, data of any gene on each microarray was normalized to 1. Second, data for each gene from any microarray was normalized to 1 as well.

organism: Homo sapiens

source_name: SCRAM transfected HUVEC 24h

label_protocol: To assay 10 µg total RNA, the standard Affymetrix target amplification protocol was used for synthesis of the biotinylated cRNA.

growth_protocol: Pooled human umbilical vein endothelial cells (HUVECs) were purchased from Cambrex (Verviers, Belgium) and cultured in endothelial basal medium (EBM; Cambrex) supplemented with hydrocortisone, bovine brain extract, gentamicin, amphotericin B, epidermal growth factor, and 10% fetal calf serum (FCS; Gibco, Karlsruhe, Germany) until the third passage. After detachment with trypsin, cells were grown in 6-cm culture dishes for at least 18 hours.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen). Ten microgram of total RNA was processed for hybridization to the HG U133 Plus 2.0 microarray (Affymetrix, Inc.)

treatment_protocol: For siRNA-mediated silencing, HUVECs were grown to 60% to 70% confluence and transfected with GeneTrans II (MoBiTec, Göttingen, Germany) for 24h according to the manufacturer's protocol.

tag: cell type

value: HUVEC


title: BDEneu Tumor at Day 15, biological rep1

description: Gene expression data from BDEneu Tumor at Day 15 from rat# 4

source_name: BDEneu Tumor, Day 15


title: BDEneu Tumor at Day 10, biological rep3

description: Gene expression data from BDEneu Tumor at Day 10 from rat# 3

source_name: BDEneu Tumor, Day 10


title: 12HUVEC_HDAC5_siRNA_24h_rep3

source_name: siHDAC5 transfected HUVEC 24h


title: WT_P0_whole_Cochlea_2

label_protocol: Small <40 nt RNAs were labeled with Cy5 fluorescent dye (Post-Labeling Reactive CyDyes, GE Healthcare), using the mirVana miRNA Labeling Kit (Ambion), according to the manufacturer's protocol.


title: 9HUVEC_scrambled_24h_rep2

description: Gene expression data 24h after SCRAM siRNA treatment


title: BDEneu Tumor at Day 25, biological rep1

description: Gene expression data from BDEneu Tumor at Day 25 from rat# 7


title: BDEneu Tumor at Day 25, biological rep2

description: Gene expression data from BDEneu Tumor at Day 25 from rat# 8


title: BDEneu Tumor at Day 10, biological rep2

description: Gene expression data from BDEneu Tumor at Day 10 from rat# 2


title: 10HUVEC_HDAC5_siRNA_24h_rep2


title: WT_P0_whole_Vestibule_2


title: 7HUVEC_scrambled_24h_rep1


title: WT_P0_whole_Cochlea_1


title: Nod mouse 3

city: Boston

first: Andrea

last: Vergani

state: MA

address: 300 Longwood Ave

institute: Children's Hospital Harvard Medical School

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mesenchymal stem cells derived from Bone Marrow

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

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

value: NOD


title: BDEneu Tumor at Day 15, biological rep2

description: Gene expression data from BDEneu Tumor at Day 15 from rat# 5


title: Nod mouse 4

description: replicate 4


title: Nod mouse 1

description: replicate 1


title: Nod mouse 2

description: replicate 2


title: Balb mouse 4

description: replicate 4

value: BALB/c


title: Balb mouse 2

description: replicate 2


title: BDEneu Tumor at Day 15, biological rep3

description: Gene expression data from BDEneu Tumor at Day 15 from rat# 6


title: Balb mouse 3

description: replicate 3


title: delta crzA time 10 min vs wild type time 10 min upon 200 mM CaCl2

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

description: This hybridization used the wild type RNA from a 16 hours culture plus 10 minutes upon calcium chloride (200 mM) treatment as reference. The test RNA was obtained from a delta crzA mutant strain 16 hours culture treated for 10 minutes with 200 mM calcium chloride.

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2x SSC 0,5% SDS, 0,5x SSC and 0.05x SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation

scan_protocol: Slides were dried by centrifugation and subjected to fluorescent detection with a GMS 418 Array Scanner (Affymetrix Inc., Santa Clara, CA).

data_processing: TIFF images generated were analyzed using TIGR Spotfinder (http://www.tigr.org/software/) to obtain relative transcript levels. Spotfinder uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels. This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio). Spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses. Data was normalized using a local regression technique LOWESS (LOcally WEighted Scatterplot Smoothing) for hybridizations with RNA-based samples and SD regularization of the Cy5/Cy3 ratio across all sectors (blocks) of the array using a software tool MIDAS (http://www.tigr.org/softlab). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS and the union of all genes identified at each time point were considered significant in this experiment. The resulting data were organized and visualized based on similar expression vectors in genes using Euclidean distance and hierarchical clustering with average linkage clustering method to view the whole data set and k-means to group the genes in clusters with TIGR MEV (multi experiment viewer), also available at http://www.tigr.org/software.

organism: Aspergillus fumigatus

source_name: delta crzA conidia grown for 16 hours plus 10 min upon 200 mM CaCl2

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNeasy kit (Qiagen, Germany) and directly labelled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript III (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.

extract_protocol: At each time point the micelia was harvested by centrifugation and quickly frozen in liquid nitrogen. For total RNA isolation, the micelia weas disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 2.2 M formaldehyde, 1.2% agarose gel, stained with ethidium bromide, and then visualized with UV-light. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

treatment_protocol: For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus delta crzA strain were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures from the wild type and mutant strains were added by calcium chloride (200 mM) and incubated for 10 and 30 more minutes before centrifugation and RNA extraction.

tag: genotype/variation

value: delta crzA

tag: agent

tag: time

value: 10 minutes

source_name: wild type conidia grown for 16 hours plus 10 min upon 200 mM CaCl2

treatment_protocol: For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type (CEA17 DakuBKU80) strain were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures from the wild type and mutant strains were added by calcium chloride (200 mM) and incubated for 10 and 30 more minutes before centrifugation and RNA extraction.

value: wild type


title: 8HUVEC_HDAC5_siRNA_24h_rep1


title: delta crzA time 30 min vs wild type time 30 min upon 200 mM CaCl2 dye swap

description: This hybridization used the wild type RNA from a 16 hours culture plus 30 minutes upon calcium chloride (200 mM) treatment as reference. The test RNA was obtained from a delta crzA mutant strain 16 hours culture treated for 30 minutes with 200 mM calcium chloride.

source_name: delta crzA conidia grown for 16 hours plus 30 min upon 200 mM CaCl2

growth_protocol: For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus delta crzA strain were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C.

value: 30 minutes

source_name: wild type conidia grown for 16 hours plus 30 min upon 200 mM CaCl2

growth_protocol: For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type (CEA17 DakuBKU80) strain were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C.


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 12

status: Public on Apr 01 2009

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays.

hyb_protocol: From each paired sample, 1.5 μg of labeled cDNA was combined, dried-down, resuspended in 60 μl Pronto! cDNA/long oligonucleotide hybridization solution (Corning), incubated at 95°C for 5 min and centrifuged at 13,000 × g for 2 min at room temperature. This solution was then pipetted on a freshly pre-hybridized microarray slide, covered with a 22 x 60 mm HybriSlip (Grace Bio Labs, Bend, OR), placed in a Corning hybridization chamber, and incubated in a 42°C water bath for 12 to 16 h. Array pre-hybridization was conducted using sodium borohydride as previously described (Raghavachari, et al., 2003). Slides were washed according to Corning’s UltraGAPS protocol and dried by centrifugation.

scan_protocol: Scanning, image segmentation, and normalization were conducted as previously described (Madsen, et al., 2006).

data_processing: Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples. [mean log transformed median centered lowess normalized signal intensity]

label: Cy 3

organism: Escherichia coli

source_name: Escherichia coli O157:H7 EDL933 control

label_protocol: Targets were generated from 10 µg of DNase treated total RNA as follows. Ten µg of total RNA was combined with 1 μl of 10 µg/μl random hexamers (Integrated DNA Technologies) and ddH20 was added to bring the total reaction volume to 15.5 μl. Samples were incubated at 70°C for 10 min followed by 10 min incubation on ice. After incubation, 14.5 μl of a reaction mix (6 μl of 5x First Strand Buffer, 1.2 μl of 25x aa-dUTP/dNTP mix (Fermentas, Glen Burnie, MD), 3 μl 0.1M DTT, 2 μl Superscript III 200U/ μl (Invitrogen Corp., Carlsbad, CA), 2.4 μl RNase-free water) was added and reactions were incubated at 42°C for at least 2 hrs. After incubation, RNA was immediately hydrolyzed by incubation with 3 μl 0.1 M ETDA and 3.5 μl 0.1 M NaOH at 65°C for 10 min. The pH was neutralized with the addition of 36.5 μl of 500 mM HEPES (pH 7.0). Reactions were purified using the Mo Bio UltraClean PCR Clean-Up Kit (MO BIO Laboratories, Inc., Carlsbad, CA), quantified using the ND-1000 spectrophotometer, dried-down, and resuspended in 10 μl RNase-free water and 1.5 μl sodium bicarbonate (pH 8.7). After 10 min, 6 μl of Cy 3 (catalog number PA25001) or Cy 5 (catalog number PA23001) (GE Healthcare, Piscataway, NJ) were added according the microarray experimental design, and samples were incubated at room temperature for 3 h. Dyes were prepared by resuspending a single tube of dye in 72 μl of DMSO and storing in 6 μl aliquots at -70°C until use. Dye coupled reactions were purified in the same manner as cDNA synthesis reactions. Frequency of dye incorporation and yield was determined using the ND-1000 spectrophotometer.

extract_protocol: RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR.

tag: Escherichia coli O157:H7 EDL933

label: Cy 5

source_name: Escherichia coli O157:H7 EDL933 heat shock


title: Balb mouse 1

description: replicate 1


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 10


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 11


title: delta crzA time 10 min vs wild type time 10 min upon 200 mM CaCl2 dye swap


title: delta crzA time 30 min vs wild type time 30 min upon 200 mM CaCl2


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 6


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 8


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 9


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 3


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 4


title: BDEneu Tumor at Day 10, biological rep1

description: Gene expression data from BDEneu Tumor at Day 10 from rat# 1


title: Fushi taratzu ChIP data; Ftz ChIP; slide 24617

type: genomic

city: Chicago

first: Kevin

last: White

state: IL

address: 400 CLSC

institute: University of Chicago

hyb_protocol: 65 degrees Celsius overnight hybridization. After hybridization, slides were washed in subsequent steps with washing solutions with decreasing SSC concentration.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Axon 4000B laser scanner) at 5 µm resolution and intensity data were extracted with NimbleScan software (NimbleGen Systems).

data_processing: High density oligonucleotide tiling arrays used in this study contain 187,023 unique 36-nucleotide probe (or 36-mers) spanning the entire euchromatic genome of Drosophila melanogaster and 4,000 negative control probes. The negative control probes, joined by three randomly selected non-existing 12-mers (with at least one mismatch in Drosophila genome), were designed to estimate the hybridization background due to non-specific binding. Locally weighted linear regression (LOWESS) analysis (10) was performed to normalize the ChIP-on-Chip datasets within and across the slides. For each probe, we calculated an intensity P value based on the normalized intensities of all negative control probes which follow an approximately gamma distribution. Intensity dependent Z scores (11) were calculated to identify those probes in which ChIP experiments with protein-specific antibodies were significantly greater than mock experiments. All probes with the p-value < 0.01 were considered significant.

molecule: genomic DNA

source_name: 2 hour embryo (after egg lay)

label_protocol: 1μg of both control and IP samples for each experimental condition were labeled with Cy3 and Cy5 using the Bioprime labeling kit.

extract_protocol: Flies were grown at 25ºC on a standard medium and then the egg laying was made on plates filled with standard Agar-grape medium. Flies were given 2 h egg lay period and the eggs were aged for additional 2 h after which they were collected in EWB (Embryo Wash Buffer: 0.03% Triton X100, 0.4% NaCl). The ChIP method was an adaptation of a previously published protocol [Chanas G, Lavrov S, Iral F, Cavalli G, Maschat F (2004) Engrailed and polyhomeotic maintain posterior cell identity through cubitus-interruptus regulation. Dev Biol 272: 522–535.]. For each ChIP, a reference sample named Mock corresponds to a ChIP performed at the same time without the addition of the specific antibody. Formaldehyde, at a final concentration of 1.8% in buffer A1, i.e., 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 15 mM HEPES (pH 7.6), 0.5% Triton X-100, 0.5 mM DTT, 10 mM sodium butyrate, protease inhibitor cocktail (Roche, Basel, Switzerland), was used for crosslinking while crushing the embryos for 15 min at room temperature. After blocking the reaction with glycine and after three washes (5 min each, at 4 8C with buffer A1), the crushed material was then filtered through Centricon Y-100 columns to recover chromatin. Subsequent steps were performed as previously described [Chanas G, Lavrov S, Iral F, Cavalli G, Maschat F (2004) Engrailed and polyhomeotic maintain posterior cell identity through cubitus-interruptus regulation. Dev Biol 272: 522–535.]. Sheared chromatin had an average length of 500 bp. The polyclonal antibodies for IP were diluted at 1:100 for both FTZ and EVE.

tag: embryos


title: Fushi taratzu ChIP data; Mock ChIP; slide 24617


title: Even skipped ChIP data; Eve ChIP; slide 24615

source_name: 2 to 4 hour embryo (after egg lay)


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 2


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 1

data_processing: Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the  RNA samples. [mean log transformed median centered lowess normalized signal intensity]


title: Even skipped ChIP data; Eve ChIP; slide 24602


title: Even skipped ChIP data; MockChIP; slide 24615

tag: embryo


title: Fushi taratzu ChIP data; Mock ChIP; slide 24559

hyb_protocol: 65 degrees Celsius overnight hybridization.  After hybridization, slides were washed in subsequent steps with washing solutions with decreasing SSC concentration.

data_processing: High density oligonucleotide tiling arrays used in this study contain 187,023 unique 36-nucleotide probe (or 36-mers) spanning the entire euchromatic genome of Drosophila melanogaster and 4,000 negative control probes.  The negative control probes, joined by three randomly selected non-existing 12-mers (with at least one mismatch in Drosophila genome), were designed to estimate the hybridization background due to non-specific binding.  Locally weighted linear regression (LOWESS) analysis (10) was performed to normalize the ChIP-on-Chip datasets within and across the slides.  For each probe, we calculated an intensity P value based on the normalized intensities of all negative control probes which follow an approximately gamma distribution.  Intensity dependent Z scores (11) were calculated to identify those probes in which ChIP experiments with protein-specific antibodies were significantly greater than mock experiments. All probes with the p-value < 0.01 were considered significant.


title: Even skipped ChIP data; MockChIP; slide 24602


title: Even skipped ChIP data; MockChIP; slide 24599


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 5


title: Fushi taratzu ChIP data; Ftz ChIP; slide 24559


title: Even skipped ChIP data; Eve ChIP; slide 24599


title: Escherichia coli O157:H7 EDL933 Heat Shock vs. Control Slide 7


title: t80kd_tnf_1

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

description: stimulated Trap-80 knock-down fibroblasts, biological replicate 1

hyb_protocol: according to Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling manual (version 4)

data_processing: RMA algorithm

source_name: Trap-80 knock-down 3T3 fibroblasts, stimulated with TNF-alpha

extract_protocol: Qiaquick

treatment_protocol: stimulated 1hr with 5ng/ml TNF-alpha

tag: transduced with shRNA targeting Trap-80 in pSuper-retro-puro


title: wt_tnf_1

description: stimulated wild-type fibroblasts, biological replicate 1

scan_protocol: according to Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling manual (version 4)

source_name: wt 3T3 fibroblasts, stimulated with TNF-alpha

tag: transduced with scrambled shRNA in pSuper-retro-puro


title: wt_tnf_2

description: stimulated wild-type fibroblasts, biological replicate 2

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling


title: wt_tnf_3

description: stimulated wild-type fibroblasts, biological replicate 3


title: t80kd_tnf_3

description: stimulated Trap-80 knock-down fibroblasts, biological replicate 3


title: t80kd_tnf_2

description: stimulated Trap-80 knock-down fibroblasts, biological replicate 2


title: CR3_N

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR3_N_Mapping250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0

source_name: periferal blood cells from leukemic patient at complete remission

label_protocol: Affymetrix standard protocol

extract_protocol: standard DNA extraction

tag: blood at complete remission


title: mammary_epithelial_cells_50days_LFS_animal866

city: RTP

first: Johannes

middle: M

last: Freudenberg

state: NC

address: 111 TW Alexander Dr

department: Biostatistics Branch

institute: NIEHS

description: mammary epithelial cells,50days,LFS

hyb_protocol: Rat Genome 230 2.0 Array  GeneChips were hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing are carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols.  The arrays are hybridized for 16 hr at 45oC using Affymetrix Hybridization Oven 640 (P/N 800139).  FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS and software and Affymetrix preset settings.

data_processing: Data was processed separately for 21 days and 50 days data.  Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 10 (Dai et al. (2005); Nucl Acids Res 33: e175).  Batch effects were factored out by fitting a two-way ANOVA model with the batch designation and the diet type as the explanatory variables, any by subtracting the batch effect estimate from each gene expression measurement.  Finally, log-scale data was further normalized by 1) setting the per-sample median to 7 and 2) subtracting the per-gene median.

source_name: mammary epithelial cells,50days,LFS

label_protocol: Total RNA samples of 1 μg or greater are amplified one round, and the amplified RNA (aRNA) biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.  Samples of 10-100 ng including those extracted from LCM samples are amplified two rounds using Ambion’s Message Amp II Kit (#1751, Ambion, Austin, Texas) followed by the Biotin-Enhanced Message Amp II Kit following manufacturer’s protocols.

growth_protocol: Female, virgin Spraque-Dawley rats were obtained from Taconic Farms (Germantown, NY) at approximately 7 weeks of age and placed on one of 9 pelleted purified diets (Research Diets, New Brunswick, NJ) for one month. Animals were housed individually in a temperature- and humidity-controlled room in the AALAC approved University of Cincinnati facility under a 12-h light-dark cycle. All rats were provided food and tap water ad libitum and animals were housed on Sani-chips bedding (P.J. Murphy Forest Products Corp. Montville, NJ). Bedding is consistently made from hardwoods (no pine or cedar or other softwoods) within closed manufacturing and shipping systems to yield non-contaminated wood chips. All animal procedures were approved by the Institutional Animal Care and Use Committee and the experiments were performed following the guidelines of the National Institutes of Health for the proper and humane use of animals in biomedical research. After one month of diet exposure, female rats were bred with male Sprague-Dawley rats of approximately 3 months of age in stainless steel hanging cages. Mating plugs were noted and recorded as gestational day 1 and females were returned to single housing during the remainder of the gestational period. Males were used to sire only 2 litters from different diets; dams were used for only one litter. Females which did not become pregnant following mating were mated again. If females successfully mated and appeared to successfully become pregnant but did not deliver live pups were euthanized along with any females which never mated successfully. Hence each litter was the first pregnancy for all dams. Litters were culled to 8 pups within 2nd day of gestation (Day of Life DOL 2); keeping all female pups and sufficient males to balance. Litters were weighed and monitored throughout gestational period. Pups had access to dam’s milk as well as tap water and food throughout gestation. Pups were weaned at DOL 21 and individually housed on Sani-chips bedding with tap water and diets ad libitum. Offspring raised for morphological measurements were placed on appropriate diets and tap water ad libitum at DOW (day of weaning). Rats were killed by CO2 asphyxiation and decapitated at the following two ages, DOW (DOL21) and DOL 50 with no other treatments.

extract_protocol: The mammary glands were dissected and the fresh tissue specimens were embedded using Tissue-Tek OCT compound (Sakura Fineteck USA, Torrance, CA) snap-frozen and stored at – 80oC. The frozen mammary tissue was sectioned to 10m thickness using a cryostat (Leica Bannockburn, Ill), and stored at -80oC until use.  The tissue sections were stained with H&E and immediately laser capture micro-dissection (LCM) was performed using the PixCell II, Arcturus LCM system (Arcturus Sunnyvale Cal). Mammary ductal epithelial cells were captured at a total of 10-12000 hits were collected for each sample. RNA was isolated using TRI Reagent according to manufacture protocol (#TR118, Molecular Research Center Inc., Cincinnati).

treatment_protocol: Female rat pups from in-house breeding consumed high fat (39% of kcal) or low fat (10% of kcals) versions of one of these diets, or reference diet (17% of kcal from fat). 10% and 39% fat by kcal reflects a minimum and maximum fat contents consumed in the western diet. The mothers of the pups consumed the same diet before and throughout gestation and lactation. We evaluated pups at key time points in their lifetime, weaning (21 days) and the end of puberty (50 days), which correspond to important milestones in human mammary development and maturation. Studies detailed here evaluate the effects of AIN-93G based formulated diets containing primarily one specific dietary fatty acid (olive, safflower or butter) on the mammary development  in young and pubescent offspring consuming the same diets as their mothers. Diet formulations (Research Diets -New Brunswick, NJ) appear in Table S1. Diets reflect a mixture of fatty acids as found in the typical diet. The fatty acids in these diets primarily consisted of n-9 monounsaturated fatty acids (oleic acid-olive oil), n-6 polyunsaturated fatty acids (linoleic acid-safflower), saturated acids (palmitic-acid-butter), or a reference diet (soy oil).  Diets (Research Diets-New Brunswick,NJ) were controlled for caloric content, vitamins, salts, and protein but varied in fat and carbohydrate content and therefore density.  AIN-93G with a soy oil base, a widely used diet for mammary studies, was used here as the reference diet.  A basal amount of soy oil was added to each of the diets to provide essential fatty acids lacking in some of the diets.

tag: diet

value: Low fat safflower

value: 50 days

tag: batch


title: wt_ns_3

description: non-stimulated wild-type fibroblasts, biological replicate 3

source_name: wt 3T3 fibroblasts, non-stimulated


title: CR19_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR19_N_Mapping250K_Nsp


title: CR2_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR2_N_Mapping250K_Nsp


title: wt_ns_2

description: non-stimulated wild-type fibroblasts, biological replicate 2


title: wt_ns_1

description: non-stimulated wild-type fibroblasts, biological replicate 1


title: APL64_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL64_N_Mapping250K_Nsp

source_name: leukemic cell obtained from acute lymphoblastic leukemia patient

tag: leukemia


title: mammary_epithelial_cells_50days_LFS_animal864

description: mammary epithelial cells,50days,LFS


title: APL65_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL65_N_Mapping250K_Nsp


title: CR18_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR18_N_Mapping250K_Nsp


title: CR38_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR38_N_Mapping250K_Nsp


title: CR50_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR50_N_Mapping250K_Nsp


title: CR39_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
CR39_N_Mapping250K_Nsp


title: mammary_epithelial_cells_50days_LFS_animal865

description: mammary epithelial cells,50days,LFS


title: mammary_epithelial_cells_50days_LFS_animal329

description: mammary epithelial cells,50days,LFS


title: APL62_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL62_N_Mapping250K_Nsp


title: APL63_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL63_N_Mapping250K_Nsp


title: APL57_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL57_N_Mapping250K_Nsp


title: mammary_epithelial_cells_50days_LFS_animal326

description: mammary epithelial cells,50days,LFS


title: mammary_epithelial_cells_50days_LFO_animal3172

description: mammary epithelial cells,50days,LFO

source_name: mammary epithelial cells,50days,LFO

value: Low fat olive oil


title: APL56_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL56_N_Mapping250K_Nsp


title: mammary_epithelial_cells_50days_LFO_animal319

description: mammary epithelial cells,50days,LFO


title: mammary_epithelial_cells_50days_LFB_animal3373

description: mammary epithelial cells,50days,LFB

source_name: mammary epithelial cells,50days,LFB

value: Low fat butter


title: mammary_epithelial_cells_50days_LFO_animal3170

description: mammary epithelial cells,50days,LFO


title: mammary_epithelial_cells_50days_LFO_animal3151

description: mammary epithelial cells,50days,LFO


title: mammary_epithelial_cells_50days_LFB_animal3370

description: mammary epithelial cells,50days,LFB


title: APL58_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL58_N_Mapping250K_Nsp


title: APL60_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL60_N_Mapping250K_Nsp


title: APL52_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL52_N_Mapping250K_Nsp


title: APL51_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL51_N_Mapping250K_Nsp


title: APL66_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL66_N_Mapping250K_Nsp


title: APL55_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL55_N_Mapping250K_Nsp


title: APL61_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL61_N_Mapping250K_Nsp


title: APL53_N

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
APL53_N_Mapping250K_Nsp


title: mammary_epithelial_cells_50days_LFB_animal337

description: mammary epithelial cells,50days,LFB


title: mammary_epithelial_cells_50days_LFO_animal317

description: mammary epithelial cells,50days,LFO


title: mammary_epithelial_cells_50days_LFB_animal868

description: mammary epithelial cells,50days,LFB


title: mammary_epithelial_cells_50days_HFS_animal862

description: mammary epithelial cells,50days,HFS

source_name: mammary epithelial cells,50days,HFS

value: High fat safflower


title: mammary_epithelial_cells_50days_HFO_animal7084

description: mammary epithelial cells,50days,HFO

source_name: mammary epithelial cells,50days,HFO

value: High fat olive oil


title: mammary_epithelial_cells_50days_HFS_animal323

description: mammary epithelial cells,50days,HFS


title: mammary_epithelial_cells_50days_HFS_animal861

description: mammary epithelial cells,50days,HFS


title: mammary_epithelial_cells_50days_HFO_animal1153

description: mammary epithelial cells,50days,HFO


title: mammary_epithelial_cells_50days_HFS_animal322

description: mammary epithelial cells,50days,HFS


title: mammary_epithelial_cells_50days_HFS_animal860

description: mammary epithelial cells,50days,HFS


title: mammary_epithelial_cells_50days_HFO_animal312

description: mammary epithelial cells,50days,HFO


title: mammary_epithelial_cells_50days_HFO_animal3130

description: mammary epithelial cells,50days,HFO


title: mammary_epithelial_cells_50days_HFO_animal859

description: mammary epithelial cells,50days,HFO


title: mammary_epithelial_cells_50days_HFO_animal311

description: mammary epithelial cells,50days,HFO


title: mammary_epithelial_cells_50days_HFB_animal897

description: mammary epithelial cells,50days,HFB

source_name: mammary epithelial cells,50days,HFB

value: High fat butter


title: mammary_epithelial_cells_50days_HFB_animal333

description: mammary epithelial cells,50days,HFB


title: mammary_epithelial_cells_50days_AIN_animal892

description: mammary epithelial cells,50days,AIN

source_name: mammary epithelial cells,50days,AIN

value: AIN-93G (soy oil)


title: mammary_epithelial_cells_50days_HFB_animal330

description: mammary epithelial cells,50days,HFB


title: mammary_epithelial_cells_50days_HFB_animal332

description: mammary epithelial cells,50days,HFB


title: mammary_epithelial_cells_50days_HFB_animal3311

description: mammary epithelial cells,50days,HFB


title: mammary_epithelial_cells_50days_AIN_animal894

description: mammary epithelial cells,50days,AIN


title: mammary_epithelial_cells_50days_AIN_animal399

description: mammary epithelial cells,50days,AIN


title: mammary_epithelial_cells_50days_AIN_animal891

description: mammary epithelial cells,50days,AIN


title: mammary_epithelial_cells_21days_LFS_animal3780

description: mammary epithelial cells,21days,LFS

source_name: mammary epithelial cells,21days,LFS

value: 21 days


title: mammary_epithelial_cells_50days_AIN_animal398

description: mammary epithelial cells,50days,AIN


title: mammary_epithelial_cells_21days_LFS_animal827

description: mammary epithelial cells,21days,LFS


title: mammary_epithelial_cells_50days_HFB_animal331

description: mammary epithelial cells,50days,HFB


title: mammary_epithelial_cells_21days_LFS_animal6220

description: mammary epithelial cells,21days,LFS


title: mammary_epithelial_cells_21days_LFS_animal376

description: mammary epithelial cells,21days,LFS


title: mammary_epithelial_cells_21days_LFO_animal369

description: mammary epithelial cells,21days,LFO

source_name: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFS_animal377

description: mammary epithelial cells,21days,LFS


title: mammary_epithelial_cells_21days_LFO_animal1121

description: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFO_animal816

description: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFO_animal368

description: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFO_animal817

description: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFB_animal837

description: mammary epithelial cells,21days,LFB

source_name: mammary epithelial cells,21days,LFB


title: mammary_epithelial_cells_21days_LFB_animal1141

description: mammary epithelial cells,21days,LFB


title: mammary_epithelial_cells_21days_LFB_animal389

description: mammary epithelial cells,21days,LFB


title: mammary_epithelial_cells_21days_LFO_animal366

description: mammary epithelial cells,21days,LFO


title: mammary_epithelial_cells_21days_LFB_animal386

description: mammary epithelial cells,21days,LFB


title: mammary_epithelial_cells_21days_HFS_animal822

description: mammary epithelial cells,21days,HFS

source_name: mammary epithelial cells,21days,HFS


title: mammary_epithelial_cells_21days_LFB_animal385

description: mammary epithelial cells,21days,LFB


title: mammary_epithelial_cells_21days_HFS_animal371

description: mammary epithelial cells,21days,HFS


title: mammary_epithelial_cells_21days_HFS_animal821

description: mammary epithelial cells,21days,HFS


title: mammary_epithelial_cells_21days_HFO_animal813

description: mammary epithelial cells,21days,HFO

source_name: mammary epithelial cells,21days,HFO


title: mammary_epithelial_cells_21days_HFO_animal1116

description: mammary epithelial cells,21days,HFO


title: mammary_epithelial_cells_21days_HFB_animal1361

description: mammary epithelial cells,21days,HFB

source_name: mammary epithelial cells,21days,HFB


title: mammary_epithelial_cells_21days_AIN_animal1147

description: mammary epithelial cells,21days,AIN

source_name: mammary epithelial cells,21days,AIN


title: mammary_epithelial_cells_21days_HFS_animal374

description: mammary epithelial cells,21days,HFS


title: mammary_epithelial_cells_21days_HFO_animal811

description: mammary epithelial cells,21days,HFO


title: mammary_epithelial_cells_21days_HFB_animal1358

description: mammary epithelial cells,21days,HFB


title: mammary_epithelial_cells_21days_HFO_animal810

description: mammary epithelial cells,21days,HFO


title: mammary_epithelial_cells_21days_HFO_animal363

description: mammary epithelial cells,21days,HFO


title: mammary_epithelial_cells_21days_HFB_animal834

description: mammary epithelial cells,21days,HFB


title: mammary_epithelial_cells_50days_LFB_animal3371

description: mammary epithelial cells,50days,LFB


title: mammary_epithelial_cells_21days_HFB_animal380

description: mammary epithelial cells,21days,HFB


title: mammary_epithelial_cells_21days_AIN_animal843

description: mammary epithelial cells,21days,AIN


title: mammary_epithelial_cells_21days_AIN_animal1146

description: mammary epithelial cells,21days,AIN


title: mammary_epithelial_cells_21days_AIN_animal390

description: mammary epithelial cells,21days,AIN


title: mammary_epithelial_cells_21days_HFB_animal830

description: mammary epithelial cells,21days,HFB


title: mammary_epithelial_cells_21days_AIN_animal392

description: mammary epithelial cells,21days,AIN


title: 15_17_50_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_50_X_Mapping50K_Xba240


title: mammary_epithelial_cells_21days_HFS_animal824

description: mammary epithelial cells,21days,HFS


title: 15_17_46_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_46_X_Mapping50K_Xba240


title: 15_17_43_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_43_X_Mapping50K_Xba240


title: 15_17_48_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_48_X_Mapping50K_Xba240


title: 15_17_42_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_42_X_Mapping50K_Xba240


title: 15_17_40_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_40_X_Mapping50K_Xba240


title: 15_17_39_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_39_X_Mapping50K_Xba240


title: 15_17_38_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_38_X_Mapping50K_Xba240


title: 15_17_37_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_37_X_Mapping50K_Xba240


title: 15_17_35_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_35_X_Mapping50K_Xba240


title: 15_17_33_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_33_X_Mapping50K_Xba240


title: 15.17-3_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-3_X_Mapping50K_Xba240


title: 15.17-2_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-2_X_Mapping50K_Xba240


title: 15_17_28_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_28_X_Mapping50K_Xba240


title: 15_17_29_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15_17_29_X_Mapping50K_Xba240


title: 15.17-24_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-24_X_Mapping50K_Xba240


title: 15-17-9_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-9_X_Mapping50K_Xba240


title: 15.17-5_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-5_X_Mapping50K_Xba240


title: 15.17-20_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-20_X_Mapping50K_Xba240


title: 15.17-4_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-4_X_Mapping50K_Xba240


title: 15.17-23_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-23_X_Mapping50K_Xba240


title: 15-17-13_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-13_X_Mapping50K_Xba240


title: 15-17-8_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-8_X_Mapping50K_Xba240


title: 15.17-1_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-1_X_Mapping50K_Xba240


title: 15.17-19_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-19_X_Mapping50K_Xba240


title: 15.17-17_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-17_X_Mapping50K_Xba240


title: 15-17-14_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-14_X_Mapping50K_Xba240


title: intestine_C57BL/6J_EPA/DHA_pool

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Male 4-month-old C57BL/6J mice were maintained for 4 weeks on semisynthetic high-fat (20% wt/wt) diets differing in the composition of n-3 PUFA. Two isocaloric diets were used (n=12): control sHFf diet which contained flax-seed oil (rich in ALA) as the only lipid source, or the sHFf-F2 diet, which had the same composition except that 44 % of the lipids were replaced by a n-3 PUFA concentrate (EPA&DHA) containing 6 % EPA and 51 % DHA (EPAX 1050TG; EPAX AS, Lysaker, Norway). Quality control of RNA samples showed that four samples did not pass quality thresholds, and these samples were excluded from array analysis (two control small intestine samples and one EPA&DHA small intestine sample). The remaining RNA samples were pooled per tissue per diet group. Thus; the flax-seed (control) array was hybridized with RNA pooled from of 10 mice, the PUFA array was hybridized with RNA pooled from 11 mice.

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: MAS5 expression values

label: Biotin

source_name: small intestine complete,  4 weeks on diet

label_protocol: Affymetrix One-cycle Target Labeling Assay. Five μg of total RNA was labelled using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

extract_protocol: Small intestines were excised, homogenized in TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns.

tag: C57BL/6J, male


title: 15.17-21_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-21_X_Mapping50K_Xba240


title: 15.17-6_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-6_X_Mapping50K_Xba240


title: 15-17-7_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-7_X_Mapping50K_Xba240


title: 15-17-11_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-11_X_Mapping50K_Xba240


title: 15.17-18_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15.17-18_X_Mapping50K_Xba240


title: intestine_C57BL/6J_flaxseed_pool

source_name: small intestine complete, 4 weeks on diet

tag: C57BL/6J, male, adult


title: adipocytes Forskolin 2hrs

status: Public on Mar 03 2009

city: La Jolla

first: Marc

last: Montminy

state: CA

address: 10010 N. Torrey Pines Rd.

institute: The Salk Institute

hyb_protocol: Followed standard Affymetrix protocols

scan_protocol: Followed standard Affymetrix protocols

data_processing: Scanned images were analyzed using DCHIP software.

source_name: cultured adipocytes

label_protocol: Followed standard Affymetrix protocols

extract_protocol: RNA extractions were performed with Trizol followed by purification over a Qiaeasy RNA column.

tag: C57/Bl6 male


title: 15-17-12_X

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
15-17-12_X_Mapping50K_Xba240

source_name: leukemic cell obtained from acute lymphoblastic leukemia patient


title: white adipose normal chow

source_name: white adipose tissue

tag: c57/Bl6 male


title: H1_ES sample1

status: Public on Feb 17 2009

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: cell pellet in Trizol

data_processing:
Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

pgf-file = HuEx-1_0-st-v2.r2.pgf
clf-file = HuEx-1_0-st-v2.r2.clf
bgp-file = HuEx-1_0-st-v2.r2.antigenomic.bgp
meta-ps-file = HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

growth_protocol:
http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#Cell_phenotype_study
Human H1 human male ES cells cultured on TESR/Matrigel and split one to six using dispase. Karyotypically normal, 95% Oct4 positive, differentiable into mesodermal, endodermal and ectodermal lineages

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol

treatment_protocol: cells were supplied as pellets in trizol

tag: cell type

value: embryonic stem (H1_ES)


title: adipocytes DMSO 2hrs


title: Hippocampus, Aged animals, BDNF treated, biological rep2

status: Public on Jan 23 2009

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: Gene expression data in brain regions after lentiviral infusion of BDNF, eGFP vs. control in Young and Aged animals

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA-normalized, log2 transformed data

source_name: Rat brains 4 weeks after lentiviral infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Young and aged rats

extract_protocol: Entorhinal cortices and hippocampi were rapidly dissected from experimental subjects and snap frozen to -80oC.

treatment_protocol: Aged entorhinal cortex and hippocampus were examined one month after entorhinal administration of BDNF lentivirus and compared to controls.

tag: Region

value: Hippocampus

tag: Age

value: Aged

tag: treatment

value: BDNF


title: Hippocampus, Aged animals, control, biological rep1

value: Cntr


title: Hippocampus, Aged animals, control, biological rep4


title: Hippocampus, Aged animals, BDNF treated, biological rep1


title: Hippocampus, Young animals, control, biological rep4

value: Young


title: Hippocampus, Young animals, control, biological rep3


title: Hippocampus, Aged animals, eGFP treated, biological rep2

value: eGFP


title: Hippocampus, Young animals, control, biological rep2


title: Hippocampus, Aged animals, control, biological rep3


title: Entorhinal cortex, Aged animals, control, biological rep1

value: EntCortex


title: Hippocampus, Aged animals, eGFP treated, biological rep1


title: Hippocampus, Young animals, control, biological rep1


title: Entorhinal cortex, Aged animals, BDNF treated, biological rep3


title: Hippocampus, Aged animals, control, biological rep2


title: Entorhinal cortex, Aged animals, BDNF treated, biological rep2


title: Entorhinal cortex, Aged animals, eGFP treated, biological rep2


title: Entorhinal cortex, Aged animals, control, biological rep4


title: Entorhinal cortex, Young animals, control, biological rep4


title: Entorhinal cortex, Aged animals, eGFP treated, biological rep3


title: Entorhinal cortex, Aged animals, control, biological rep3


title: Entorhinal cortex, Aged animals, BDNF treated, biological rep4


title: Entorhinal cortex, Young animals, control, biological rep2


title: Entorhinal cortex, Aged animals, BDNF treated, biological rep1


title: Entorhinal cortex, Young animals, control, biological rep3


title: Entorhinal cortex, Young animals, control, biological rep1


title: Entorhinal cortex, Aged animals, control, biological rep2


title: white adipose high fat diet


title: Post MCF10AT-MSCV A

status: Public on Oct 31 2008

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

description: Probeset RMA summarized expression data from post-polysomal fraction mRNA MCF10AT-MSCV cells, biological replicate A

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Genetrix software used for data processing. First the data was normalized using RMA sketch quantile normalization on PSRs with CORE level annotation (~283K PSRs) generating both summarized gene-level and individual normalized PSR-level expression matrices. Gene-level summarized expression data was determined using CORE annotation level PSRs only using the core-mapping file that maps HuExon 1.0 st exon probesets to HG-U133 2.0 probesets (see Series supplementary file).

source_name: MCF10AT-MSCV fraction 3

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Low-passage MCF10AT (also known as MCF10AT1k.cl2) cell lines were provided by Dr. S.J. Kim (National Cancer Institute, Bethesda) and cultured on tissue culture plastic (Falcon) or on Matrigel-coated plates in defined medium, as previously described (Debnath et al., 2003; Janda et al., 2002; Roskelley et al., 1994).

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

treatment_protocol: Total cell extracts from monolayer cultured cells were prepared using the NP-40 lysis buffer containing 20 mM Hepes-KOH, pH 7.6, 100 mM KCl, 5 mM MgCl2, 2 mM dithiothreitol, 0.25% Nonidet P-40, 2 ug/ml leupeptin, 2 ug/ml pepstatin and 10 ug/ml cycloheximide. Cell fractionation, purification of polysomal and post-polysomal mRNA fractions using differential centrifugation on sucrose gradients.

tag: female; breast cancer cell line MCF10-AT

tag: post-polysomal fraction mRNA


title: Post MCF10AT-YB-1 B

description: Probeset RMA summarized expression data from post-polysomal fraction mRNA MCF10AT-YB-1 cells, biological replicate B

source_name: MCF10AT-YB-1 fraction 3


title: Poly MCF10AT-YB-1 B

description: Probeset RMA summarized expression data from polysomal fraction mRNA MCF10AT-YB-1 cells, biological replicate B

source_name: MCF10AT-YB-1 fraction 2

tag: polysomal fraction mRNA


title: Post MCF10AT-YB-1 A

description: Probeset RMA summarized expression data from post-polysomal fraction mRNA MCF10AT-YB-1 cells, biological replicate A


title: Post MCF10AT-MSCV B

description: Probeset RMA summarized expression data from post-polysomal fraction mRNA MCF10AT-MSCV cells, biological replicate B


title: Poly MCF10AT-MSCV B

description: Probeset RMA summarized expression data from polysomal fraction mRNA MCF10AT-MSCV cells, biological replicate B

source_name: MCF10AT-MSCV fraction 2


title: Poly MCF10AT-MSCV A

description: Probeset RMA summarized expression data from polysomal fraction mRNA MCF10AT-MSCV cells, biological replicate A


title: Entorhinal cortex, Aged animals, eGFP treated, biological rep1


title: Total MCF10AT-MSCV-1

description: Probeset RMA summarized expression data from total mRNA MCF10AT-MSCV cells

source_name: MCF10AT-MSCV fraction 1

tag: total mRNA


title: Poly MCF10AT-YB-1 A

description: Probeset RMA summarized expression data from polysomal fraction mRNA MCF10AT-YB-1 cells, biological replicate A


title: 3405

status: Public on Oct 17 2008

city: Bethesda

first: Liqiang

last: Xi

state: MD

address: 10 Center Dr. Bldg 10 Rm 2N110

department: Lab of Pathology

institute: NIH/NCI

hyb_protocol: Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human Exon 1.0 ST arrays.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: All exon array data was analyzed using tools in Partek Genomic Suite 6.4 software (Partek Inc., St. Louis, MO). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (exon-level) intensity analysis .

source_name: Snap frozen lung tissue specimen

label_protocol: 2 µg of total RNA from each of 20 tumor/normal paired specimens (n=40) was labeled with reagents from Affymetrix according to the manufacturers instructions.

extract_protocol: Forty, 5-micron sections from each tissue block were cut and placed immediately in Qiagen RNA lysis buffer.  RNA was isolated using Qiagen kits with on-column DNAse treatment to remove genomic DNA followed by precipitation.

tag: PatientID

tag: Histology

value: adeno

tag: N Stage

tag: Stage

value: I

tag: Sex

value: female

tag: Race

value: White

tag: Chemo

tag: Radiation


title: H1_ES sample2

description: cell pellet in Trizol

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

data_processing:
Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG
pgf-file = HuEx-1_0-st-v2.r2.pgf
clf-file = HuEx-1_0-st-v2.r2.clf
bgp-file = HuEx-1_0-st-v2.r2.antigenomic.bgp
meta-ps-file = HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: MS855

value: normal

value: III


title: 3402


title: MS857

value: male


title: MS861


title: 3403


title: MS859


title: MS16B


title: MS852


title: 3397


title: MS860


title: 3398


title: 3407


title: 3400


title: MS854


title: MS847


title: MS15B


title: MS848


title: MS843

value: Black


title: MS14B


title: MS840


title: 3115


title: MS846


title: MS19B


title: 2785

value: II


title: MS839


title: MS838


title: MS836


title: 3111


title: MS849


title: 3123


title: 3125


title: MS837


title: 2784


title: 3112


title: MS850


title: hESC-derived cardiac precursors, day 40 of differentiation, biological rep1

status: Public on Oct 24 2008

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Raw probeset RMA expression values for all probesets from H9 human embryonic stem cells differentiated to day 40 cardiomyocyte precursors.
Biological replicate 1 of 3.

hyb_protocol: According to manufacturer's (Affymetrix) recommendations.

data_processing: Probeset intensity values for the Affymetrix Human Exon 1.0 ST CEL files were obtained using the RMA algorithm in the Affymetrix ExpressionConsole application.

source_name: Differentiated cardiac precursor, day 40

growth_protocol: Differentiated H9 ESCs for 40 days.

extract_protocol: RNA was fractionated with the Invitrogen Purelink MicroRNA Isolation kit (selecting for >200nt fraction) following Trizol/chloroform extraction.

treatment_protocol: H9 ESCs were transduced with a lentiviral preparation that encoded two drug selection cassettes from the same construct: a neomycin-resistance gene under the control of the REX-1 promoter (Rex-neo_resistance) and a puromycin-resistance gene under the control of the alpha-MHC promoter (aMHC-puro_resistance). Stable clonal lines were created through subsequent neo selection of a homogenous population of undifferentiated hESCs (day 0) and then differentiated for 40 days with selection of cardiac precursors using puromyocin selection.

tag: Differentiated H9 human embryonic stem cells, day 40, cardiomyocytes, alpha_MHC-puromyocin resistant (puromyocin selected).


title: MS835


title: MS834


title: subject 26 Liver Rejector

status: Public on Sep 15 2008

city: Pittsburgh

first: Rakesh

last: Sindhi

state: PA

address: 3705 Fifth Avenue

department: Hillman Center for Pediatric Transplantation

institute: Children’s Hospital of Pittsburgh

description: Exon array data from child <20 yrs

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

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

data_processing: The data were analyzed with Affy Power Tools (APT) using rma-sketch normalization method.

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: hESC-derived cardiac precursors, day 40 of differentiation, biological rep3

description:
Raw probeset RMA expression values for all probesets from H9 human embryonic stem cells differentiated to day 40 cardiomyocyte precursors.
Biological replicate 3 of 3.

scan_protocol: According to manufacturer's (Affymetrix) recommendations.


title: 3109


title: Rex+ H9 ESCs, day 0, biological rep3

description:
Raw probeset RMA expression values for all probesets from undifferentiated H9 human embryonic stem cells day 0, Rex-neomyocin resistant (neomyocin selected).
Biological replicate 3 of 3.

label_protocol: According to manufacturer's (Affymetrix) recommendations.

growth_protocol: Undifferentiated H9 ESCs.

treatment_protocol: H9 ESCs were transduced with a lentiviral preparation that encoded two drug selection cassettes from the same construct: a neomycin-resistance gene under the control of the REX-1 promoter (Rex-neo_resistance) and a puromycin-resistance gene under the control of the alpha-MHC promoter (aMHC-puro_resistance). Stable clonal lines were created through subsequent neo selection of a homogenous population of undifferentiated hESCs (day 0).

tag: Undifferentiated H9 human embryonic stem cells, day 0, Rex-neomyocin resistant (neomyocin selected).


title: subject 24 Liver Non-rejector

description: Exon array data from child <20 yrs


title: Rex+ H9 ESCs, day 0, biological rep1

description:
Raw probeset RMA expression values for all probesets from undifferentiated H9 human embryonic stem cells day 0, Rex-neomyocin resistant (neomyocin selected).
Biological replicate 1 of 3.

source_name: Undifferentiated H9 human embryonic stem cells, day 0


title: Rex+ H9 ESCs, day 0, biological rep2

description:
Raw probeset RMA expression values for all probesets from undifferentiated H9 human embryonic stem cells day 0, Rex-neomyocin resistant (neomyocin selected).
Biological replicate 2 of 3.


title: subject 20 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 23 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 22 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 15 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 18 Liver Non-rejector

description: Exon array data from child <20 yrs


title: 2777


title: subject 12 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 14 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 17 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 21 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 25 Liver Non-rejector

description: Exon array data from child <20 yrs


title: hESC-derived cardiac precursors, day 40 of differentiation, biological rep2

description:
Raw probeset RMA expression values for all probesets from H9 human embryonic stem cells differentiated to day 40 cardiomyocyte precursors.
Biological replicate 2 of 3.


title: subject 16 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 19 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 8 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 11 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 13 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 7 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 9 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 6 Liver Non-rejector

description: Exon array data from child <20 yrs


title: NoCAD_replicate50

status: Public on Aug 31 2008

city: Bern

first: Pascal

last: Meier

address: Freiburgstrasse

department: Cardîology

country: Switzerland

institute: University Hospital

description: Gene expression data from an individual without coronary artery disease

hyb_protocol: Gene expression was analyzed using Affymetrix HG-U133A 2.0 arrays. : Starting with 1µg of total RNA, complementary RNA (cRNA) was generated. Double stranded complementary DNA (cDNA) was synthesized in two steps according to the manufacturer's protocol (Superscript ds cDNA Synthesis Kit, Invitrogen). cDNA cleanup was performed by phenol chloroform extraction. Biotinylated cRNA was synthesized by in vitro transcription using T7 polymerase (GeneChip Expression 3'-Amplification IVT labeling kit; Affymetrix). The resulting cRNA was purified using RNeasy kit (Qiagen), quantitated and quality was assessed before fragmentation at 94°C for 35 min. A total of 7 g cRNA was hybridized to the Affymetrix U133A 2.0 gene chip for 16h at 45°C. Washing, staining and scanning procedures were carried out according to the protocol of the manufacturer.

scan_protocol: The GeneChips were processed with a Affymetrix GeneChip® Scanner 3000 7G (Affymetrix) by using the current default settings. DAT image files of the microarrays were generated using GeneChip Operating Software (GCOS 1.4; Affymetrix).

data_processing: Microarray quality was assessed with the R software, in particular with the affyPLM package in Bioconductor 12 and its model based quality assessment methods 13. For each batch of microarrays the following procedures were performed: First, homogeneity of the probe intensity distributions was checked across arrays in a batch. Chips with aberrant distributions were marked for exclusion. Second, the probe level intensities for each Affymetrix probe set were fitted with robust weighted regressions in which the intensities are explained by a linear model with gene chip effects and probe effects. If the probes of a probe set behave consistently, the residuals of the fit are small. Outlier probe intensities result in larger absolute residuals and low weights. These are symptomatic for intensity measurements from regions of a gene chip that provide low quality data. Chips with extended areas of large absolute residuals were marked for exclusion. Third, we used the normalized un-scaled standard errors (NUSE) of the probe effects on each array.  We found that excluding the arrays with a median NUSE of 1.05 or more was a good criterion summarizing the observations from all three procedures and so these arrays were excluded from further statistical analyses

source_name: Human monocytes from individuals  without coronary artery disease

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Monocytes were separated from whole blood immediately after completion of the invasive study protocol. Following an erythrocyte lysis step (erythrocyte lysis buffer, Qiagen, Hilden, Germany), peripheral blood monocytes were isolated from leukocytes by the magnetic activated cell separation bead selection method (MACS, CD14 antibody linked to paramagnetic beads; Dynal AG, Oslo, Norway). RNA from monocytes was extracted immediately after their isolation using a membrane based system (RNeasy mini, Qiagen)

tag: Collateral flow index


title: subject 4 Liver Rejector

description: Exon array data from child <20 yrs


title: subject 5 Liver Rejector

description: Exon array data from child <20 yrs


title: NoCAD_replicate42


title: NoCAD_replicate41


title: subject 3 Liver Rejector

description: Exon array data from child <20 yrs


title: CAD_replicate77

description: Gene expression data from an individual with coronary artery disease

source_name: Human monocytes from individuals  with coronary artery disease


title: NoCAD_replicate40


title: subject 2 Liver Non-rejector

description: Exon array data from child <20 yrs


title: subject 1 Liver Rejector

description: Exon array data from child <20 yrs


title: NoCAD_replicate39


title: CAD_replicate78


title: CAD_replicate75


title: CAD_replicate74


title: NoCAD_replicate36


title: CAD_replicate79


title: NoCAD_replicate38


title: CAD_replicate76


title: NoCAD_replicate43


title: CAD_replicate110


title: CAD_replicate73


title: NoCAD_replicate35


title: NoCAD_replicate49


title: NoCAD_replicate34


title: CAD_replicate72


title: CAD_replicate109


title: CAD_replicate70


title: CAD_replicate108


title: subject 10 Liver Non-rejector

description: Exon array data from child <20 yrs


title: CAD_replicate67


title: CAD_replicate107


title: CAD_replicate71


title: CAD_replicate68


title: NoCAD_replicate31


title: CAD_replicate105


title: NoCAD_replicate33


title: NoCAD_replicate32


title: CAD_replicate66


title: CAD_replicate69


title: CAD_replicate61


title: NoCAD_replicate37


title: CAD_replicate62


title: NoCAD_replicate30


title: CAD_replicate104


title: CAD_replicate65


title: NoCAD_replicate29


title: CAD_replicate64


title: CAD_replicate103


title: CAD_replicate106


title: NoCAD_replicate27


title: NoCAD_replicate28


title: NoCAD_replicate44


title: CAD_replicate63


title: CAD_replicate60


title: CAD_replicate59


title: CAD_replicate57


title: CAD_replicate58


title: CAD_replicate102


title: CAD_replicate56


title: CAD_replicate55


title: CAD_replicate54


title: CAD_replicate48


title: CAD_replicate49


title: CAD_replicate53


title: CAD_replicate100


title: CAD_replicate52


title: NoCAD_replicate26


title: CAD_replicate47


title: CAD_replicate44


title: CAD_replicate46


title: CAD_replicate101


title: CAD_replicate40


title: CAD_replicate50


title: CAD_replicate42


title: CAD_replicate51


title: NoCAD_replicate47


title: CAD_replicate99


title: CAD_replicate45


title: CAD_replicate43


title: CAD_replicate39


title: CAD_replicate41


title: CAD_replicate37


title: CAD_replicate38


title: CAD_replicate36


title: CAD_replicate35


title: CAD_replicate31


title: CAD_replicate30


title: CAD_replicate28


title: CAD_replicate32


title: NoCAD_replicate24


title: NoCAD_replicate25


title: CAD_replicate27


title: CAD_replicate33


title: CAD_replicate97


title: CAD_replicate24


title: CAD_replicate29


title: CAD_replicate26


title: CAD_replicate22


title: NoCAD_replicate21


title: CAD_replicate98


title: CAD_replicate25


title: CAD_replicate34


title: NoCAD_replicate22


title: CAD_replicate21


title: CAD_replicate19


title: CAD_replicate20


title: NoCAD_replicate23


title: CAD_replicate17


title: NoCAD_replicate19


title: CAD_replicate23


title: NoCAD_replicate20


title: CAD_replicate18


title: NoCAD_replicate17


title: NoCAD_replicate18


title: CAD_replicate14


title: CAD_replicate96


title: CAD_replicate95


title: CAD_replicate15


title: CAD_replicate16


title: NoCAD_replicate16


title: CAD_replicate94


title: CAD_replicate92


title: NoCAD_replicate48


title: CAD_replicate93


title: CAD_replicate13


title: CAD_replicate12


title: CAD_replicate91


title: CAD_replicate11


title: CAD_replicate90


title: CAD_replicate8


title: CAD_replicate10


title: NoCAD_replicate15


title: NoCAD_replicate14


title: NoCAD_replicate13


title: CAD_replicate9


title: NoCAD_replicate12


title: CAD_replicate6


title: CAD_replicate87


title: CAD_replicate88


title: CAD_replicate89


title: CAD_replicate7


title: NoCAD_replicate9


title: NoCAD_replicate11


title: NoCAD_replicate8


title: CAD_replicate85


title: CAD_replicate86


title: NoCAD_replicate6


title: CAD_replicate5


title: NoCAD_replicate7


title: NoCAD_replicate5


title: NoCAD_replicate10


title: CAD_replicate4


title: NoCAD_replicate46


title: CAD_replicate83


title: NoCAD_replicate4


title: CAD_replicate2


title: CAD_replicate82


title: CAD_replicate1


title: NoCAD_replicate45


title: CAD_replicate3


title: CAD_replicate84


title: CAD_replicate80


title: NoCAD_replicate2


title: NoCAD_replicate1


title: CAD_replicate81


title: NoCAD_replicate3


title: WGACON-273

status: Public on Nov 04 2007

city: Miami

first: Amanda

last: Myers

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

description: Human Cortex from neurologically normal control, Caucasian, female.

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract, log10 transformation before analysis

source_name: neuropathologically normal frozen temporal cortex

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)


title: WGACON-264


title: WGACON-268


title: WGACON-270

description: Human Cortex from neurologically normal control, Caucasian, male.


title: WGACON-265


title: WGACON-259


title: WGACON-252

source_name: neuropathologically normal frozen frontal cortex


title: WGACON-256


title: WGACON-274

source_name: neuropathologically normal frozen parietal cortex


title: WGACON-261


title: WGACON-260


title: WGACON-257


title: WGACON-255


title: WGACON-249


title: WGACON-246

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal DNA: biotin labeled as per Affymetrix protocol for cat # 900753/900754


title: WGACON-277


title: WGACON-242


title: WGACON-253


title: WGACON-243


title: WGACON-245


title: WGACON-251


title: WGACON-241


title: WGACON-244


title: WGACON-263

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254), genomic DNA (Qiagen Dneasy kit cat # 69504)


title: WGACON-235

source_name: neuropathologically normal frozen unknown region cortex


title: WGACON-254


title: WGACON-250


title: WGACON-234


title: WGACON-237


title: WGACON-233


title: WGACON-232


title: WGACON-231

source_name: neuropathologically normal frozen unknown cortex


title: WGACON-236


title: WGACON-267


title: WGACON-240


title: WGACON-230


title: WGACON-228


title: WGACON-226

source_name: neuropathologically normal frozen frontal temporal cortex


title: WGACON-208


title: WGACON-223


title: WGACON-207


title: WGACON-202


title: WGACON-210


title: WGACON-218


title: WGACON-221


title: WGACON-199


title: WGACON-217


title: WGACON-204


title: WGACON-213


title: WGACON-196

extract_protocol:
total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat
# 79254)


title: WGACON-205


title: WGACON-206


title: WGACON-225


title: WGACON-214


title: WGACON-189


title: WGACON-219


title: WGACON-201


title: WGACON-188

description:
RNA: Illumina Beadstation
DNA: Genechip Scanner 3000


title: WGACON-198


title: WGACON-193


title: WGACON-190


title: WGACON-191


title: WGACON-203


title: HGDP-608

status: Public on Feb 05 2008

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland)

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC3/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: GCOS MAS 5

label: C-Bio and A-DNP

source_name: lymphoblastoid cell lines

label_protocol: Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturer’s protocol (Illumina Inc., San Diego, CA, www.illumina.com). 1000ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted at the Foundation Jean Dausset (CEPH) in Paris using standard protocols.

tag: Population

value: Bedouin

tag: Country

value: Israel-Negev

tag: Region

tag: Gender

value: Male


title: WGACON-175


title: WGACON-186


title: WGACON-178


title: WGACON-179


title: WGACON-176


title: HGDP-607

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland) .

value: Female


title: WGACON-172


title: WGACON-173


title: WGACON-163

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837);DNA: Allele Specific Hybridization, Affymetrix Mapping 500K Assay Manual (Affymetrix P/N 701930 Rev. 3)

scan_protocol: RNA: Illumina Beadstation; DNA: Genechip Scanner 3000


title: WGACON-154


title: WGACON-181


title: WGACON-177


title: WGACON-162


title: WGACON-180


title: WGACON-153


title: WGACON-156


title: WGACON-155

scan_protocol: RNA: Illumina Beadstation; DNA: Genechip Scanner 3000a


title: WGACON-158


title: WGACON-161


title: WGACON-174


title: WGACON-147


title: WGACON-160


title: WGACON-145


title: WGACON-151


title: WGACON-148


title: WGACON-150


title: WGACON-142


title: WGACON-143


title: WGACON-139


title: WGACON-140


title: WGACON-115


title: WGACON-137


title: WGACON-141


title: WGACON-136


title: WGACON-130


title: WGACON-109


title: WGACON-113


title: WGACON-134


title: WGACON-124


title: WGACON-122


title: WGACON-128


title: WGACON-135


title: WGACON-112


title: WGACON-127


title: WGACON-111


title: WGACON-114


title: WGACON-119


title: WGACON-117


title: WGACON-106


title: WGACON-118


title: WGACON-131


title: WGACON-125


title: WGACON-123


title: WGACON-98


title: WGACON-103


title: WGACON-104


title: WGACON-97


title: WGACON-99


title: WGACON-77


title: WGACON-96


title: WGACON-90


title: WGACON-82


title: WGACON-102


title: WGACON-83


title: WGACON-100


title: WGACON-79


title: WGACON-87


title: WGACON-94


title: WGACON-84


title: WGACON-89


title: WGACON-91


title: WGACON-95


title: WGACON-75


title: WGACON-70


title: WGACON-80


title: WGACON-85


title: WGACON-73


title: WGACON-86


title: WGACON-72


title: WGACON-68


title: WGACON-62


title: WGACON-67


title: WGACON-61


title: WGACON-65


title: WGACON-50


title: WGACON-37


title: WGACON-45


title: WGACON-48


title: WGACON-58


title: WGACON-64


title: WGACON-52


title: WGACON-57


title: WGACON-49

hyb_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

label_protocol: Illumina TotalPrep RNA Amplification Kit From Ambion, Inc. (catalogue # L-1755).


title: WGACON-55


title: WGACON-54


title: WGACON-56


title: WGACON-47


title: WGACON-42


title: WGACON-44


title: WGACON-43


title: WGACON-60


title: WGACON-51


title: WGACON-38


title: WGACON-36


title: WGACON-35


title: WGACON-33


title: WGACON-40


title: WGACON-34


title: WGACON-31


title: WGACON-29


title: WGACON-26


title: WGACON-18


title: WGACON-32


title: WGACON-30


title: WGACON-22


title: WGACON-25


title: WGACON-9


title: Zinc-limited Anaerobic chemostat culture-1

status: Public on Oct 16 2007

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description:
LH12
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

scan_protocol: Affymetrix Scanner 3000

data_processing: GCOS

organism: Saccharomyces cerevisiae

source_name: chemostat culture

label_protocol:
EukGE-ws2v4
Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x

growth_protocol:
Chemostat cultivation
Steady-state chemostat cultures of S. cerevisiae CEN.PK113-7D strain were performed in a 2-liter fermenter (Applikon) with a working volume of 1 liter (van den Berg et al 1996) . These cultures were fed with synthetic medium (see below) which limited growth by carbon, nitrogen or zinc with all other growth requirements in excess and at constant residual concentration (Boer et al 2003). The dilution rate was set at 0.1 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set at 800 rpm. Anaerobic conditions were maintained by sparging the medium reservoir (0.05 liter.min-1) and the fermenter with pure nitrogen gas (0.5 liter.min-1). Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures (Visser et al 1990). The off-gas was cooled by a condenser connected to a cryostat set at 2 °C. Oxygen and carbon dioxide were measured off-line with an NGA 2000 Rosemont gas analyzer. Cultures were assumed to be in steady-state when, after 4 to 5 volume changes, culture dry-weight, glucose concentration, carbon-dioxide production rate and oxygen consumption rate varied by less than 2 % during one volume change (Ferea et al, 1999; Jansen etal 2004). Steady-state samples were taken after 10 generations at the latest to avoid strain adaptation due to long-term cultivation. Each cultivation condition was performed in triplicate.
Growth media
The synthetic media composition was based on that described by Verduyn (1992). In all chemostats except for those limited by carbon, residual glucose concentration was targeted to 17 g.liter-1 in order to sustain glucose repression at the same level. For anaerobic cultivations, Tween 80 (420 mg.l-1) and ergosterol (10 mg.l-1) were supplemented to the media as described previously (Verduyn et al, 1990) to compensate for the inability of S. cerevisiae to synthesise fatty acids in the absence of oxygen. These media contained the following components: for zinc-limited cultivation, 5.0 g.liter-1 (NH4)2SO4, 3.0 g.liter-1 KH2PO4, 0.5 g.liter-1 MgSO4•7H2O and 58 g.liter-1 glucose. ZnSO4•7H2O was omitted from the anaerobic zinc-limited media.
	van den Berg, M. A., P. de Jong-Gubbels, C. J. Kortland, J. P. van Dijken, J. T. Pronk, and H. Y. Steensma. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J. Biol. Chem. 271:28953-28959.
van Dijken, J. P., J. Bauer, L. Brambilla, P. Duboc, J. M. Francois, C. Gancedo, M. L. Giuseppin, J. J. Heijnen, M. Hoare, H. C. Lange, E. A. Madden, P. Niederberger, J. Nielsen, J. L. Parrou, T. Petit, D. Porro, M. Reuss, R. N. van, M. Rizzi, H. Y. Steensma, C. T. Verrips, J. Vindelov, and J. T. Pronk. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb. Technol. 26:706-714.
Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1990. Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J. Gen. Microbiol. 136:405-412.
Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8:501-517.
Visser, W., W. A. Scheffers, Batenburg-van der Vegte WH, and J. P. van Dijken. 1990. Oxygen requirements of yeasts. Appl. Environ. Microbiol. 56:3785-3792.
Boer, V. M., J. H. de Winde, J. T. Pronk, and M. D. Piper. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278:3265-3274.
	Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U. S. A 96:9721-9726.
	Jansen, M. L., P. Daran-Lapujade, J. H. de Winde, M. D. Piper, and J. T. Pronk. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl. Environ. Microbiol. 70:1956-1963.

treatment_protocol: Liquid nitrogen

tag: The haploid prototrophic S. cerevisiae strain CEN.PK 113-7D (MATa) was obtained from Dr. P. Kötter, Frankfurt, Germany. Zinc-depleted cells were obtained by four serial transfers of yeast cells in shake flasks containing synthetic medium from which zinc was omitted, and subsequently mixed with glycerol (final concentration 20%), aliquoted and stored at -80 °C.


title: WGACON-15


title: Zinc-limited Anaerobic chemostat culture-3

description:
LH16
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

hyb_protocol: Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates. Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x

source_name: Chemostat culture


title: WGACON-11


title: WGACON-20


title: Zinc-limited Anaerobic chemostat culture-2

description:
LH13
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

extract_protocol:
Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x