title: Human induced pluripotent stem cell clone 2-4 cultured in mTeSR1 on Matrigel

status: Public on Mar 16 2008

city: Chuo-ku

first: Tetsuya

last: Ishikawa

state: Tokyo

address: 1-1, Tsukiji 5-chome

department: Research Institute

country: Japan

institute: Japanease National Cancer Center

description: RNA sample of Agilent array is the same as that of Affymetrix array (GSM257521).

hyb_protocol: Gene Expression Hybridization Kit

scan_protocol: Agilent microarray scanner

data_processing: Agilent Feature Extraction software (v.9.5.3); gProcessedSignal; processed Cy3 Signal

source_name: human induced pluripotent stem cells from fibroblast (5F0416) cultured in mTeSR1 on Matrigel

label_protocol: cRNA synthesis using Agilent low RNA input linear amplication kit and cyanine 3-CTP

growth_protocol: cultured in mTeSR1 on Matrigel

extract_protocol: RNeasy

treatment_protocol: preparation at passage 5 (102 days after 4 factor retroviral gene transfer)

tag: human embryonic stem cells like pluripotent stem cells (46XY)


title: Human induced pluripotent stem cell clone 3-2 cultured in mTeSR1 on Matrigel

type: RNA

description: RNA sample of Agilent array is the same as that of Affymetrix array (GSM257523).

molecule: total RNA

organism: Homo sapiens

source_name: human induced pluripotent stem cells from fibroblast (5F0438) cultured in mTeSR1 on Matrigel

treatment_protocol: preparation at passage 7 (80 days after 4 factor retroviral gene transfer)


title: Acetyl H4 IP 39 vs 30 set2

status: Public on Mar 17 2008

type: genomic

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

country: USA

institute: University of Texas at Austin

description: Immnoprecipitation of Acetyl H4 using anti Acetyl H4 antibody

hyb_protocol: The Cy3 and Cy5 labeled DNA were combined,5 ?g of tRNA, 10 ?g of polyA were added, 20x SSC was added to a final concentration of 3.5x and SDS was added to a final concentration of 0.25%. The mixture was denatured at 100°C for 2 min, cooled down to room temperature and hybridized onto microarrays for 6 hrs to over night at 65°C. Arrays were washed once each in wash solution I (0.57x SSC, 0.028% SDS) and wash solution II (0.057X SSC), dried by centrifuging at 600 rpm for 5 min at room temperature in a table top centrifuge.

scan_protocol: The arrays were scanned with the Axon 4000B scanner (Axon Instruments) and quantitated using GenePix Pro 5.1 software. The data was uploaded into Acuity microarray informatics software 4.037 (Axon Laboratory), and filtered to remove spots with bad signal intensity and passed though other quality control thresholds.

data_processing: normalized log2 ratio

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Acetyl H4 IP from heat shock cells

label_protocol: Cy5 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)

extract_protocol: Cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction.

tag: mid-log growth, heat shock for 15 min at 39 degree C

source_name: Acetyl H4 IP from unstressed cells

label_protocol: Cy3 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)

tag: mid-log growth at 30 degree C


title: Human induced pluripotent stem cell clone 1-8 cultured in mTeSR1 on Matrigel after freeze-thaw treatment

description: RNA sample of Agilent array is the same as that of Affymetrix array (GSM257520).

treatment_protocol: 4 factor retroviral gene transfer, see GSM257520.


title: hfq 04/07 vs. wt 04/07

status: Public on Mar 15 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Features were extracted with an image analysis tool version A.9.5.3 using the GE2-V5_95_Feb07 protocol (Agilent Technologies).

hyb_protocol: Labeled samples was mixed and hybridized to 15K custom-made microarray according to the supplier`s protocol (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Data analysis was carried out on the Rosetta Inpharmics platform Resolver Version 7.0. Ratio profiles were combined in an error-weighted fashion with Resolver to create ratio experiments. A two-fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.05), robust and reproducible.

organism: Synechocystis sp. PCC 6803

label_protocol: An amount of 3 µg total RNA was reverse transcribed with CyScribe post-labeling kit (GE Healthcare, Munich, Germany). An amount of 350µg first-strand cDNA probes were labeled by the 'post-labeling' (amino allyl) method with Cy3 and Cy5, respectively. Labeling efficiency and amount of labeled cDNA was determined with a Nanodrop ND-1000 spectrophotometer (Kisker, Steinfurt, Germany). The RNA samples were labeled vice versa with the two fluorescent dyes (fluorescence reversal). In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed.

extract_protocol: Exponentially growing Synechocystis 6803 liquid cultures (OD750 0.6 - 0.8) were collected by quenching on ice and immediate centrifugation at 0-4 °C. Cell pellets were resuspended in 1 mL TRIzol reagent (Invitrogen) per 20 mL aliquot and total RNA was isolated following the manufacturers instructions.

tag: Mutant

tag: The mutant strain of Synechocystis 6803 used in this study was ropagated on BG11 (Rippka et al., 1979) 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures were grown at 28°C in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 75 µmol of photons m–2 s–1 and a continuous stream of air. For the mutants described below, antibiotics were used at the following concentrations

value: chloramphenicol (Cm), 7 μg ml−1; kanamycin (Km), 40-80 μg ml−1.

tag: Wildtype

tag: The motile strain of Synechocystis 6803 used in this study was originally obtained from S. Shestakov (Moscow State University, Russia) and propagated on BG11 (Rippka et al., 1979) 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures of Synechocystis 6803 wild-type (WT)were grown at 28°C in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 75 µmol of photons m–2 s–1 and a continuous stream of air. For the mutants described below, antibiotics were used at the following concentrations


title: hfq 10/07 vs. wt 04/07


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 8-10wk

city: Madison

first: Mark

middle: Patrick

last: Keller

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin

description: Samples from liver, hypothalamus, pancreatic islets, adipose (gonadal fat pads) and muscle (soleus and gastrocnemius) were acquired from C56Bl/6 and Btbr male mice, bred from in-house colonies at the University of Wisconsin Biochemistry Department. Individuals from each strain were compared to a common pool created from equal portions of RNA from 20 conspecific samples.

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model

organism: Mus musculus

source_name: Soleus

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

tag: pool

tag: BTBRob 8-10wk


title: wt 04/07 vs. hfq 04/07


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 10-10wk, Male

tag: BTBRob 10-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 32-10wk, Male

tag: BTBR lean 32-10wk_Male


title: hfq 04/07 vs. wt 10/07

value: chloramphenicol (Cm), 7 μg ml−1; kanamycin (Km), 40-80 μg ml−1


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 10-4wk, Male

tag: B6ob 10-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 12-4wk, Male

tag: BTBRob 12-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 1751-10wk, Male

tag: B6ob 1751-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 13-4wk, Male

tag: BTBRob 13-4wk_Male


title: wt 04/07 vs. hfq 10/07

tag: Mutant


title: wt 10/07 vs. hfq 10/07

tag: The mutant strain of Synechocystis 6803 used in this study was ropagated on BG11 (Rippka et al., 1979) 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures were grown at 28°C in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 75 µmol of photons m–2 s–1 and a continuous stream of air. For the mutants described below, antibiotics were used at the following concentrations


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 11-4wk, Male

tag: BTBRob 11-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 1822-10wk, Male

tag: B6ob 1822-10wk_Male


title: hfq 10/07 vs. wt 10/07

tag: Wildtype

tag: The motile strain of Synechocystis 6803 used in this study was originally obtained from S. Shestakov (Moscow State University, Russia) and propagated on BG11 (Rippka et al., 1979) 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures of Synechocystis 6803 wild-type (WT)were grown at 28°C in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 75 µmol of photons m–2 s–1 and a continuous stream of air. For the mutants described below, antibiotics were used at the following concentrations


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 9-10wk, Male

tag: pool

tag: B6ob 9-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 48-10wk, Male

tag: B6 lean 48-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 5-4wk, Male

tag: B6ob 5-4wk_Male


title: wt 10/07 vs. hfq 04/07


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 7-4wk, Male

tag: B6ob 7-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 34-4wk, Male

tag: B6 lean 34-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 31-4wk, Male

tag: B6 lean 31-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 31-10wk, Male

tag: BTBR lean 31-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 35-4wk, Male

tag: B6 lean 35-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 37-4wk, Male

tag: BTBR lean 37-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 47-4wk, Male

tag: B6 lean 47-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 1823-10wk, Male

tag: B6ob 1823-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 30-10wk, Male

tag: BTBR lean 30-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 33-10wk, Male

tag: BTBR lean 33-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 45-4wk, Male

tag: B6 lean 45-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 42-4wk, Male

tag: pool

tag: BTBR lean 42-4wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 18-10wk, Male

tag: BTBRob 18-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 9-10wk, Male

tag: BTBRob 9-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 36-4wk, Male

tag: BTBR lean 36-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 11-4wk, Male

source_name: Hypo

tag: BTBRob 11-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 10-4wk, Male

tag: B6ob 10-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 41-4wk, Male

tag: BTBR lean 41-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Soleus, B6 Control Pool (n=20) vs. Soleus, B6 lean 23-10wk, Male

tag: B6 lean 23-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 5-10wk, Male

tag: BTBRob 5-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBR lean 26-10wk, Male

tag: BTBR lean 26-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 5-10wk, Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 23-10wk, Male


title: Soleus, BTBR Control Pool (n=20) vs. Soleus, BTBRob 15-4wk, Male

tag: BTBRob 15-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 33-10wk, Male

tag: pool

tag: BTBR lean 33-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 35-4wk, Male

tag: B6 lean 35-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 34-4wk, Male

tag: B6 lean 34-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 37-4wk, Male

tag: BTBR lean 37-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 7-4wk, Male

tag: B6ob 7-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 45-4wk, Male

tag: B6 lean 45-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 36-4wk, Male

tag: BTBR lean 36-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 42-4wk, Male

tag: BTBR lean 42-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 18-10wk, Male

tag: BTBRob 18-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 5-4wk, Male

tag: B6ob 5-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 47-4wk, Male

tag: B6 lean 47-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 41-4wk, Male

tag: BTBR lean 41-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 31-4wk, Male

tag: B6 lean 31-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 9-10wk, Male

tag: B6ob 9-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 1822-10wk, Male

tag: pool

tag: B6ob 1822-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 1823-10wk, Male

tag: B6ob 1823-10wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6ob 1751-10wk, Male

tag: B6ob 1751-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 12-4wk, Male

tag: BTBRob 12-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 4-10wk, Male

tag: BTBRob 4-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 15-4wk, Male

tag: BTBRob 15-4wk_Male


title: Hypo, B6 Control Pool (n=20) vs. Hypo, B6 lean 48-10wk, Male

tag: B6 lean 48-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 26-10wk, Male

tag: BTBR lean 26-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 26-10wk, Male

source_name: Gastroc


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 13-4wk, Male

tag: BTBRob 13-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 10-10wk, Male

tag: BTBRob 10-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 33-10wk, Male

tag: BTBR lean 33-10wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 30-10wk, Male

tag: BTBR lean 30-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 9-10wk, Male

tag: BTBRob 9-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 10-10wk, Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 32-10wk, Male

tag: BTBR lean 32-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 5-10wk, Male

tag: pool

tag: BTBRob 5-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 4-10wk, Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 9-10wk, Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 31-4wk, Male

tag: B6 lean 31-4wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 31-10wk, Male

tag: BTBR lean 31-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 32-10wk, Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 30-10wk, Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 41-4wk, Male

tag: BTBR lean 41-4wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 11-4wk, Male

tag: BTBRob 11-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 37-4wk, Male

source_name: Adipose

tag: BTBR lean 37-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBRob 13-4wk, Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 18-10wk, Male

tag: BTBRob 18-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: Hypo, BTBR Control Pool (n=20) vs. Hypo, BTBR lean 31-10wk, Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 42-4wk, Male

tag: BTBR lean 42-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 1822-10wk, Male

tag: B6ob 1822-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 15-4wk, Male

tag: BTBRob 15-4wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 1823-10wk, Male

tag: B6ob 1823-10wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBRob 12-4wk, Male

tag: BTBRob 12-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 9-10wk, Male

tag: B6ob 9-10wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 23-10wk, Male

tag: pool

tag: B6 lean 23-10wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 1751-10wk, Male

tag: B6ob 1751-10wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 34-4wk, Male

tag: B6 lean 34-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 5-4wk, Male

tag: B6ob 5-4wk_Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 37-4wk, Male

tag: BTBR lean 37-4wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 1822-10wk, Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 10-4wk, Male

tag: B6ob 10-4wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 1751-10wk, Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 35-4wk, Male

tag: B6 lean 35-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 1823-10wk, Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6ob 7-4wk, Male

tag: B6ob 7-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 47-4wk, Male

tag: B6 lean 47-4wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 9-10wk, Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 45-4wk, Male

tag: B6 lean 45-4wk_Male


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 10-4wk, Male

tag: pool


title: Gastroc, B6 Control Pool (n=20) vs. Gastroc, B6 lean 48-10wk, Male

tag: B6 lean 48-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 48-10wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 47-4wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 34-4wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 5-4wk, Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 5-10wk, Male

tag: BTBRob 5-10wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 4-10wk, Male

tag: BTBRob 4-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 7-4wk, Male


title: Gastroc, BTBR Control Pool (n=20) vs. Gastroc, BTBR lean 36-4wk, Male

tag: BTBR lean 36-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 9-10wk, Male

tag: BTBRob 9-10wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 42-4wk, Male

tag: BTBR lean 42-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 13-4wk, Male

tag: BTBRob 13-4wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 12-4wk, Male

tag: BTBRob 12-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 11-4wk, Male

tag: BTBRob 11-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 41-4wk, Male

tag: BTBR lean 41-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 15-4wk, Male

tag: BTBRob 15-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 8-10wk, Male

tag: BTBRob 8-10wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 36-4wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 31-4wk, Male

tag: B6 lean 31-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 32-10wk, Male

source_name: Liver

tag: pool

tag: BTBR lean 32-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 35-4wk, Male

tag: B6 lean 35-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 26-10wk, Male

tag: BTBR lean 26-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 18-10wk, Male

tag: BTBRob 18-10wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 33-10wk, Male

tag: BTBR lean 33-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 45-4wk, Male

tag: B6 lean 45-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 32-10wk, Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBRob 10-10wk, Male

tag: BTBRob 10-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 15-4wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 45-4wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 13-4wk, Male

tag: BTBRob 13-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 1774-10wk, Male

tag: BTBRob 1774-10wk_Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 23-10wk, Male

tag: B6 lean 23-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 26-10wk, Male


title: Adipose, B6 Control Pool (n=20) vs. Adipose, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 9-10wk, Male

tag: BTBRob 9-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 35-4wk, Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 31-10wk, Male

tag: BTBR lean 31-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 9-10wk, Male

tag: pool

tag: B6ob 9-10wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 31-10wk, Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 14-4wk, Male

tag: BTBRob 14-4wk_Male


title: Adipose, BTBRob Control Pool (n=20) vs. Adipose, BTBR lean 30-10wk, Male

tag: BTBR lean 30-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 7-4wk, Male

tag: B6ob 7-4wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 47-4wk, Male

tag: B6 lean 47-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 8-10wk, Male

tag: BTBRob 8-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 1822-10wk, Male

tag: B6ob 1822-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 1823-10wk, Male

tag: B6ob 1823-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 34-4wk, Male

tag: B6 lean 34-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 11-4wk, Male

tag: BTBRob 11-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 5-10wk, Male

tag: BTBRob 5-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 31-4wk, Male

tag: B6 lean 31-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 37-4wk, Male

tag: pool

tag: BTBR lean 37-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 30-10wk, Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 5-4wk, Male

tag: B6ob 5-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 42-4wk, Male

tag: BTBR lean 42-4wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 23-10wk, Male

tag: B6 lean 23-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 48-10wk, Male

tag: B6 lean 48-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 1751-10wk, Male

tag: B6ob 1751-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 36-4wk, Male

tag: BTBR lean 36-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 33-10wk, Male

tag: BTBR lean 33-10wk_Male


title: Liver, B6 Control Pool (n=20) vs. Liver, B6ob 10-4wk, Male

tag: B6ob 10-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 15-4wk, Male

source_name: Islets

tag: BTBRob 15-4wk_Male


title: Liver, BTBR Control Pool (n=19) vs. Liver, BTBR lean 41-4wk, Male

tag: BTBR lean 41-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 37-4wk, Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 5-10wk, Male

tag: BTBRob 5-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 26-10wk, Male

tag: pool

tag: BTBR lean 26-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 11-4wk, Male

tag: BTBRob 11-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 45-4wk, Male

tag: B6 lean 45-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 36-4wk, Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 41-4wk, Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 1822-10wk, Male

tag: B6ob 1822-10wk_Male


title: Control or Input Samples for MCF7 Cells (Replicate #3)

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

description: Chromatin immunoprecipitation on Affymetrix genomic tiling arrays 2.0R for the control sample or INPUT in MCF7 cells

hyb_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing: Tiling array data were normalized and analyzed as described (Cawley et al, 2004).  Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of ¡À250 bp was generated.  A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions.  Significantly enriched probes (p < 1e-5) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.

label: biotin

source_name: Chromatin Immunoprecipitated DNA

label_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.

extract_protocol: According to the standard chromatin extraction protocol (Shang et al., 2000).

treatment_protocol: ~5x10^6 MCF7 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: Sheared genomic DNA from MCF7 cells.


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 32-10wk, Male

tag: BTBR lean 32-10wk_Male


title: Control or Input Samples for MCF7 Cells (Replicate #2)

scan_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 34-4wk, Male

tag: B6 lean 34-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 9-10wk, Male

tag: BTBRob 9-10wk_Male


title: XBP1-S localization in MCF7 cells with anti-eGFP antibodies (Replicate #3)

description: Chromatin immunoprecipitation for XBP1-S in MCF7 BAC transgenic cells with anti-eGFP antibodies. The 4R array (including chromosomes 4, 15, 18, and 20) from Affymetrix GeneChip Human Tiling 2.0R Array Set was used.

data_processing: Tiling array data were normalized and analyzed as described (Cawley et al, 2004).  Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of ¡À250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions.  Significantly enriched probes (p < 1e-4) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.

tag: MCF7 cells. Anti-eGFP antibodies were used for ChIP.


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 47-4wk, Male

tag: B6 lean 47-4wk_Male


title: XBP1-S localization in MCF7 cells with anti-eGFP antibodies (Replicate #2)


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 18-10wk, Male

tag: BTBRob 18-10wk_Male


title: Control or Input Samples for MCF7 Cells (Replicate #1)


title: XBP1-S localization in MCF7 cells with antibodies against endogenous XBP1-S (Replicate #3)

description: Chromatin immunoprecipitation for XBP1-S in MCF7 BAC transgenic cells with antibodies against endogenous XBP1-S. The 4R array (including chromosomes 4, 15, 18, and 20) from Affymetrix GeneChip Human Tiling 2.0R Array Set was used.

tag: MCF7 cells. Anti-FOXA1 antibodies were used for ChIP.


title: XBP1-S localization in MCF7 cells with anti-eGFP antibodies (Replicate #1)


title: XBP1-S localization in MCF7 cells with antibodies against endogenous XBP1-S (Replicate #2)


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 42-4wk, Male

tag: BTBR lean 42-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 10-10wk, Male

tag: BTBRob 10-10wk_Male


title: XBP1-S localization in MCF7 cells with antibodies against endogenous XBP1-S (Replicate #1)


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 10-4wk, Male

tag: B6ob 10-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 22-10wk, Male

tag: B6 lean 22-10wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 31-4wk, Male

tag: pool

tag: B6 lean 31-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 11-4wk, Male

tag: B6ob 11-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 24-10wk, Male

tag: B6 lean 24-10wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 7-4wk, Male

tag: B6ob 7-4wk_Male


title: FOXA1 localization in MCF7 cells with anti-eGFP antibodies (Replicate #3)

description: Chromatin immunoprecipitation for FOXA1 in MCF7 BAC transgenic cells with anti-eGFP antibodies. The 4R array (including chromosomes 4, 15, 18, and 20) from Affymetrix GeneChip Human Tiling 2.0R Array Set was used.


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 33-10wk, Male

tag: BTBR lean 33-10wk_Male


title: FOXA1 localization in MCF7 cells with anti-eGFP antibodies (Replicate #1)


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 23-10wk, Male

tag: B6 lean 23-10wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 5-4wk, Male

tag: B6ob 5-4wk_Male


title: FOXA1 localization in MCF7 cells with anti-eGFP antibodies (Replicate #2)


title: FOXA1 localization in MCF7 cells with antibodies against endogenous FOXA1 (Replicate #2)

description: Chromatin immunoprecipitation for FOXA1 in MCF7 BAC transgenic cells with antibodies against endogenous FOXA1. The 4R array (including chromosomes 4, 15, 18, and 20) from Affymetrix GeneChip Human Tiling 2.0R Array Set was used.


title: FOXA1 localization in MCF7 cells with antibodies against endogenous FOXA1 (Replicate #3)


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 35-4wk, Male

tag: B6 lean 35-4wk_Male


title: FOXA1 localization in MCF7 cells with antibodies against endogenous FOXA1 (Replicate #1)


title: VDR localization in MCF7 cells with anti-eGFP antibodies (Replicate #3)

description: Chromatin immunoprecipitation for VDR in MCF7 BAC transgenic cells with anti-eGFP antibodies. The 4R array (including chromosomes 4, 15, 18, and 20) from Affymetrix GeneChip Human Tiling 2.0R Array Set was used.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to VD3 (20 nM) treatment, cells were changed to the media for 48 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were grown in the medium containing 10% charcoal-stripped calf serum for 2 days and then were treated with 20 nM the VDR ligand Vitamine D3 (VD3) for 1 hour at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: MCF7 cells. Anti-eGFP antibodies were used for ChIP.


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 31-10wk, Male

tag: BTBR lean 31-10wk_Male


title: VDR localization in MCF7 cells with anti-eGFP antibodies (Replicate #1)


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 14-4wk, Male

tag: B6ob 14-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 1823-10wk, Male

tag: B6ob 1823-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 4-10wk, Male

tag: BTBRob 4-10wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 20-10wk, Male

tag: B6 lean 20-10wk_Male


title: Control or Input Samples for MCF7 Cells (Whole Genome #2, Replicate #2)

status: Public on Mar 13 2008

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for the control sample or INPUT in MCF7 cells

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (E2 at 10 nM) or vehicle (100% EtOH) treatments, cells were changed to estrogen-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were E2-deprived for 3 days and then were treated with 10 nM E2 (45 minutes and 2 hours for mapping ER alpha and c-MYC binding sites, respectively) at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: Sheared genomic DNA from MCF7 cells.


title: Control or Input Samples for MCF7 Cells (Whole Genome #2, Replicate #3)


title: VDR localization in MCF7 cells with anti-eGFP antibodies (Replicate #2)


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 1751-10wk, Male

tag: B6ob 1751-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 30-10wk, Male

tag: pool

tag: BTBR lean 30-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 13-4wk, Male

tag: BTBRob 13-4wk_Male


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 1752-10wk, Male

tag: B6ob 1752-10wk_Male


title: c-MYC localization in MCF7 (Whole Genome #2, Replicate #2)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for transcription factor c-MYC in MCF7 cells (ChIP).

tag: MCF7 cells. Anti-MYC antibodies were used for ChIP.


title: Islets, B6 Control Pool (n=20) vs. Islet, B6ob 9-10wk, Male

tag: B6ob 9-10wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 12-4wk, Male

tag: BTBRob 12-4wk_Male


title: c-MYC localization in MCF7 (Whole Genome #2, Replicate #1)


title: ER alpha localization in MCF7 (Whole Genome #2, Replicate #3)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for transcription factor ER alpha in MCF7 cells (ChIP).

tag: MCF7 cells. Anti-ER alpha antibodies were used for ChIP.


title: ER alpha localization in MCF7 (Whole Genome #2, Replicate #2)


title: Control or Input Samples for MCF7 Cells (Whole Genome #2, Replicate #1)


title: ER alpha localization in MCF7 (Whole Genome #2, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #2, Replicate #3)


title: Control or Input Samples for MCF7 Cells (Whole Genome #3, Replicate #2)


title: Th17 polarized cells vs. Th0 polarized cells

city: Bethesda

first: Keith

last: Kerstann

state: MD

department: Surgery Branch

institute: National Institutes of Health

hyb_protocol: NCI Oligo Microarray Hybridization

scan_protocol: Axon 4000B Standard scan

data_processing: Genepix 5.1, Signal calculation: Mean Intensity minus Median Background Value definition:  Normalized Precalculated 50th Percentile (Median) average log ratio (test/reference)

source_name: Total RNA isolated from Th17-polarized lymphocytes from a TRP-1 mouse

label_protocol: 500ng of total RNA was used with Amino Allyl MessageAmp II reagents obtained from Ambion, Inc. following manufacture's protocols.

extract_protocol: Total RNA extracted using RNeasy column purification following manufacture's protocol.

source_name: Total RNA isolated from Th0-polarized lymphocytes from a TRP-1 mouse


title: Control or Input Samples for MCF7 Cells (Whole Genome #3, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #3, Replicate #3)


title: E. coli Hydrocortisone Treatment

status: Public on Mar 14 2008

city: Jefferson

first: Christopher

middle: A

last: Elkins

state: AR

address: 3900 NCTR Drive

department: Microbiology

institute: FDA National Center for Toxicological Research

description: Each microarray slide contains three full copies of the array design giving a total of at least 3 data points for each unique spot.

hyb_protocol: These differentially labeled cDNAs were hybridized together on Corning Epoxide slides containing the Operon E. coli Genome Oligo Set Version 1.0 printed by the Microarray and Proteomics Facility, Department of Biological Sciences, University of Alberta. The hybridizations were performed in a hybridization cassette (ArrayIt) in a water bath at 45ºC for 18 hours. The slides were then washed in pre-warmed washing buffer 2X SSC containing 0.1% SDS for 5 minutes, 1X SSC for 5 minutes, and 0.5X SSC for 5 minutes.

scan_protocol: The spun-dried hybridized slides were scanned with a GenePix 4000B scanner (Axon Instruments) at 10 µm resolution using appropriate photomultiplier tube gains to obtain the highest intensity with <0.1% saturated pixels. The resulting images were analyzed by measuring the fluorescence of all features on the slides using the GenePix Pro 6.0 software (Axon Instruments). The median fluorescence intensity of these pixels within each feature was taken as the intensity value for the whole feature.

data_processing: The analyzed data were imported to ArrayTrack (NCTR Center for Toxicoinformatics.  The raw data were normalized by using median channel (intensity) scaling with no background subtraction.

organism: Escherichia coli

source_name: Hydrocortisone Treatment

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy5.

growth_protocol: E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved hydrocortisone at 1 mM final culture concentration.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit.

tag: AG102 was previously derived from AG100 (K-12). AG102 is drug hyper-resistant due to a mutation in marR (marR1) which increases expression of MarA, a global regulator, which in turn results in overexpression of the AcrAB-TolC multidrug efflux system.

source_name: DMSO-Only Treatment

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy3.

growth_protocol: E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-only steroid carrier.


title: c-MYC localization in MCF7 (Whole Genome #3, Replicate #3)


title: C3H infected

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: C3H infected_2

hyb_protocol: Following fragmentation, 10 microg of cRNA 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.

source_name: mouse peritoneal cavity

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

growth_protocol: ex vivo

extract_protocol: peqGold TriFastTM (Peqlab)

treatment_protocol: infection with Streptococcus pyogenes

tag: genetic modification:

tag: tissue

value: peritoneal macrophages


title: E. coli Estradiol Treatment

source_name: Estradiol Treatment

growth_protocol: E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved estradiol at 1 mM final culture concentration.


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBR lean 45-4wk, Male

tag: BTBR lean 45-4wk_Male


title: Islets, BTBR Control Pool (n=20) vs. Islet, BTBRob 16-4wk, Male

tag: BTBRob 16-4wk_Male


title: C3H control

description: C3H control_2


title: E. coli Progesterone Treatment

source_name: Progesterone Treatment

growth_protocol: E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved progesterone at 1 mM final culture concentration.


title: E. coli Cholic Acid Treatment

source_name: Cholic Acid Treatment

growth_protocol: E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved cholic acid at 1 mM final culture concentration.


title: c-MYC localization in MCF7 (Whole Genome #3, Replicate #2)


title: c-MYC localization in MCF7 (Whole Genome #3, Replicate #1)


title: ER alpha localization in MCF7 (Whole Genome #3, Replicate #3)


title: ER alpha localization in MCF7 (Whole Genome #3, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #3, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #4, Replicate #3)


title: Control or Input Samples for MCF7 Cells (Whole Genome #4, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #4, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #4, Replicate #3)


title: Control or Input Samples for MCF7 Cells (Whole Genome #4, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #4, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #1, Replicate #3)


title: ER alpha localization in MCF7 (Whole Genome #4, Replicate #3)


title: Control or Input Samples for MCF7 Cells (Whole Genome #1, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #4, Replicate #2)


title: Control or Input Samples for MCF7 Cells (Whole Genome #1, Replicate #1)


title: Th1 polarized cells vs. Th0 polarized cells

source_name: Total RNA isolated from Th1-polarized lymphocytes from a TRP-1 mouse


title: c-MYC localization in MCF7 (Whole Genome #1, Replicate #3)


title: c-MYC localization in MCF7 (Whole Genome #1, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #1, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #1, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #1, Replicate #1)


title: ER alpha localization in MCF7 (Whole Genome #1, Replicate #3)


title: Control or Input Samples for MCF7 Cells (Whole Genome #7, Replicate #3)


title: c-MYC localization in MCF7 (Whole Genome #4, Replicate #2)


title: Control or Input Samples for MCF7 Cells (Whole Genome #7, Replicate #2)


title: c-MYC localization in MCF7 (Whole Genome #7, Replicate #2)


title: Control or Input Samples for MCF7 Cells (Whole Genome #6, Replicate #3)


title: ER alpha localization in MCF7 (Whole Genome #7, Replicate #3)


title: c-MYC localization in MCF7 (Whole Genome #7, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #6, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #7, Replicate #3)


title: HEEC_BPA-exposed_replicate 2

city: Uppsala

first: Carolina

last: Bredhult

address: Uppsala University Hospital

department: Women's and Children's Health

country: Sweden

institute: Uppsala University

description: Biological replicate 2 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.

hyb_protocol: Pre-hybridization buffer (5 x sodium chloride sodium citrate [SSC, VWR International AB, Stockholm, Sweden], 5 x Denhardt’s solution [Sigma-Aldrich Sweden AB, Stockholm, Sweden], 0.02 µg/µl tRNA [Invitrogen AB, Lidingö, Sweden], 0.5% sodiumdodecylsulfate [SDS, VWR International AB, Stockholm, Sweden] and 50% formamide [Sigma-Aldrich Sweden AB, Stockholm, Sweden]) was applied to each array under a hybrislip (22 x 60 mm, Sigma-Aldrich Sweden AB, Stockholm, Sweden). Incubation was performed in an Hybridization Cassette ArrayIt™ (TeleChem International Inc ArrayIt, Sunnyvale, CA, USA) at 42°C for 45 min at 100% humidity in a Heating Circulator model 8201 (PolyScience, Niles, Il, USA). Each array was then transferred to a 50 ml centrifugation tube containing double distilled water. The arrays were washed five times by repeatedly turning the tubes upside down for 30 seconds each time. Hybridization and post-hybridization washes of the slides were performed using the Pronto! Hybridization Kit (Corning Life Sciences, Noricon AB, Helsingborg, Sweden). The Hybridization Cassette ArrayIt™ and Erie Scientific Lifterslip (25 x 60 mm, Histolab, Västra Frölunda, Sweden) were used for hybridization of the slides at 42°C for 18-20 hours. After hybridization, the slides were washed in the three wash buffers described in the Pronto! Hybridization Kit.

scan_protocol: The slides were scanned in a ScanArray Express HT microarray scanner ([Packard BioScience] Perkin Elmer Life Sciences Inc, Boston, MA, USA). The scanning was performed at two different voltage values for the photo multiplier tube to get a wide dynamic range of signals (high or low). The laser value default was 99%. The tiff files from the scanned arrays were gridded using the software Spotreader v 1.3.1 (Niles Scientific, Portola Valley, CA, USA).

data_processing: The BioArray Software Environment BASE (Saal et al., 2002) and the Linnaeus Center of Bioinformatics Data Warehouse (LCB-DWH) (Ameur et al., 2006) were used for microarray data storage and analysis. Data was normalized within arrays using the print-tip lowess method (Yang et al., 2002).

source_name: Primary culture HEEC, obtained in proliferative phase, individual 2, BPA exposed 24 h

label_protocol: For each treatment and biological replicate, 500 ng isolated RNA was amplified and labelled using the Low RNA Input Linear Amplification Kit PLUS, Two-colour (Agilent Technologies Sweden AB, Kista, Sweden) and then purified using the RNeasy MinElute Cleanup Kit (Qiagen AB, Solna, Sweden). The amplification and labelling reactions were performed using the polymerase chain reaction (PCR) instrument model PTC-100 (MJ Research Inc, Waltham, MA, USA). Dye swaps were performed between the individuals to avoid dye bias between RNA from BPA treated and untreated HEEC. After the labelling reaction, the Nanodrop ND-1000 Spectrophotometer was used to measure the incorporation of Cy dye.

growth_protocol: HEEC were kept in 25 cm2 culture flasks (Fischer Scientific GTF, Västra Frölunda, Sweden) and grown in Microvascular Endothelial Cell Medium-2 (EGM™-2MV Bulletkit®; In vitro Sweden AB, Stockholm, Sweden) at 37ºC in an atmosphere of 5% CO2 in humidified air. Four culture flask per treatment alternative and culture (biological replicate) were used.

extract_protocol: Total RNA extracted using RNeasy Mini Kit spin protocol (Qiagen AB, Solna, Sweden) and QiaShredder homogenizers (Qiagen AB, Solna, Sweden) according to manufacturer's instructions.

treatment_protocol: At subconfluency in passage 2, HEEC in four culture flasks per culture (biological replicate) were exposed to 50 µM BPA for 24h. Control HEEC in four culture flasks per culture were exposed to fresh culture medium containing 0.21% DMSO.

tag: Female of fertile age

tag: Tissue

value: endometrium

tag: Cells

value: endothelial cells

tag: Menstrual cycle phase

value: proliferative

source_name: Primary culture HEEC, obtained in proliferative phase, individual 2, control exposed 24 h


title: ER alpha localization in MCF7 (Whole Genome #7, Replicate #2)


title: c-MYC localization in MCF7 (Whole Genome #6, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #7, Replicate #1)


title: c-MYC localization in MCF7 (Whole Genome #6, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #5, Replicate #3)

tag: Sheared genomic DNA from MCF7 cells.


title: Control or Input Samples for MCF7 Cells (Whole Genome #5, Replicate #2)


title: Control or Input Samples for MCF7 Cells (Whole Genome #5, Replicate #1)


title: Control or Input Samples for MCF7 Cells (Whole Genome #6, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #6, Replicate #3)


title: HEEC_BPA-exposed_replicate 4

description: Biological replicate 4 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 4, BPA exposed 24 h

source_name: Primary culture HEEC, obtained in proliferative phase, individual 4, control exposed 24 h


title: c-MYC localization in MCF7 (Whole Genome #6, Replicate #3)


title: HEEC_BPA-exposed_replicate 1

description: Biological replicate 1 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 1, BPA exposed 24 h

source_name: Primary culture HEEC, obtained in proliferative phase, individual 1, control exposed 24 h


title: Control or Input Samples for MCF7 Cells (Whole Genome #7, Replicate #1)


title: ER alpha localization in MCF7 (Whole Genome #6, Replicate #1)


title: HEEC_BPA-exposed_replicate 3

description: Biological replicate 3 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 3, BPA exposed 24 h

source_name: Primary culture HEEC, obtained in proliferative phase, individual 3, control exposed 24 h


title: c-MYC localization in MCF7 (Whole Genome #5, Replicate #2)

source_name: Chromatin Immunoprecipitated DNA


title: c-MYC localization in MCF7 (Whole Genome #5, Replicate #1)


title: HEEC_BPA-exposed_replicate 5

description: Biological replicate 5 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 5, BPA exposed 24 h

source_name: Primary culture HEEC, obtained in proliferative phase, individual 5, control exposed 24 h


title: Islets, B6 Control Pool (n=20) vs. Islet, B6 lean 48-10wk, Male

source_name: Islets

tag: pool

tag: B6 lean 48-10wk_Male


title: ER alpha localization in MCF7 (Whole Genome #5, Replicate #2)


title: ER alpha localization in MCF7 (Whole Genome #5, Replicate #3)


title: c-MYC localization in MCF7 (Whole Genome #5, Replicate #3)


title: ER alpha localization in MCF7 (Whole Genome #5, Replicate #1)


title: Normal-1 - mAdbID:91503

first: Thomas

last: Wadlmann

address: 10 Center Drive

department: Metabolism Branch

institute: NCI/NIH

description: mAdb experiment ID: 91503

hyb_protocol: Hybridization Protocol Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 40 ul of 2X F-hyb buffer and 20ul water to samples. Load 80 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 790;; 670 ScanPower: 100;; 100 LaserPower: 1.19;; 2.51 Temperature: 36.38

data_processing:
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

source_name: Universal Human Reference RNA - Cy3

label_protocol:
Cy3 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: Other

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

label_protocol:
Invitrogen cDNA Labeling Kit - cy5
Other: Labeled sample with Cy5 using a NHS-ester coupling reaction following the manufacturer's cDNA Labeling Kit protocol (Invitrogen).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was prepared using RNAeasy kit (Qiagen, Valencia, CA).

value: blood

tag: Cell type

value: monocytes

tag: Disease state

value: Normal


title: Normal-3 - mAdbID:91658

description: mAdb experiment ID: 91658

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 660;; 650 ScanPower: 100;; 100 LaserPower: 1.17008;; 2.47444 Temperature: 33.9784


title: ATL-3 - mAdbID:91660

description: mAdb experiment ID: 91660

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 760;; 650 ScanPower: 100;; 100 LaserPower: 1.11;; 2.48 Temperature: 33.18

value: smodering ATL


title: Normal-2 - mAdbID:91659

description: mAdb experiment ID: 91659

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 710;; 650 ScanPower: 100;; 100 LaserPower: 1.11;; 2.46 Temperature: 33.62


title: ATL-2 - mAdbID:91502

description: mAdb experiment ID: 91502

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 750;; 700 ScanPower: 100;; 100 LaserPower: 1.24;; 2.27 Temperature: 36.04


title: 12990943 - Wt_root vs nrt2.4_root

status: Public on Mar 12 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Transcriptome of the AtNRT2.4 mutant

hyb_protocol: nrt2.4_root Cy5 / Wt_root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: root - 2mM nitrate 8h day/16h night

tag: Arabidopsis thaliana (columbia)  mutant (nrt2.4) - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13366292 - MF1 vs M1

description: Which gene are upregulated in a hypomethylated mutant?

hyb_protocol: M1 Cy5 / MF1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

growth_protocol: leaf - Media : soil hygrometry : 60% Temperature : 20 C Light : 8 hours light/ 16 hours night

tag: Arabidopsis thaliana (columbia)  mutant (M) - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (columbia)  mutant (MF) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13371029 - FWA vs Ler

hyb_protocol: Ler Cy5 / FWA Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler

tag: Arabidopsis thaliana (landsberg erecta)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: FWA

tag: Arabidopsis thaliana (landsberg erecta)  mutant (fwa) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 12990941 - Wt_leaf vs nrt2.4_leaf

description: Transcriptome of the AtNRT2.4 mutant

hyb_protocol: nrt2.4_leaf Cy5 / Wt_leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - 2mM nitrate 8h day/16h night


title: 13001245 - nrt2.4_leaf vs Wt_leaf

description: Transcriptome of the AtNRT2.4 mutant

hyb_protocol: Wt_leaf Cy5 / nrt2.4_leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ATL-1 - mAdbID:91501

description: mAdb experiment ID: 91501

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 780;; 680 ScanPower: 100;; 100 LaserPower: 1.18;; 2.6 Temperature: 35.69


title: 13366294 - M2 vs MF2

hyb_protocol: MF2 Cy5 / M2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366296 - MF2 vs M2

hyb_protocol: M2 Cy5 / MF2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366288 - MF1 vs Col

hyb_protocol: Col Cy5 / MF1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col


title: 13366290 - MF2 vs Col

hyb_protocol: Col Cy5 / MF2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366287 - Col vs MF1

hyb_protocol: MF1 Cy5 / Col Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366289 - Col vs MF2

hyb_protocol: MF2 Cy5 / Col Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366291 - M1 vs MF1

hyb_protocol: MF1 Cy5 / M1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12990942 - nrt2.4_root vs Wt_root

description: Transcriptome of the AtNRT2.4 mutant

hyb_protocol: Wt_root Cy5 / nrt2.4_root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488723 - N509-9-1-P vs Col-1-P

description: What are the consequences of knocking out a nodulin-like gene?

hyb_protocol: Col-1-P Cy5 / N509-9-1-P Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: plantlet - Media 		MS hygrometry 	40% Temperature	25°C Light 		D 16h/N 8h

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):seedling

tag: Arabidopsis thaliana (columbia)  mutant (N509.9) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13488966 - Col-2-P vs N509-9-2-P

hyb_protocol: N509-9-2-P Cy5 / Col-2-P Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: plantlet - Media 		Soil hygrometry 	70% Temperature 	D 22°C/N 20°C Light 		D 16h/N 8h


title: 13488981 - N509-9-2-P vs Col-2-P

hyb_protocol: Col-2-P Cy5 / N509-9-2-P Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488721 - N509-9-2-H vs Col-2-H

hyb_protocol: Col-2-H Cy5 / N509-9-2-H Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: stem - Media 		Soil hygrometry 	70% Temperature 	D 22°C/N 20°C Light 		D 16h/N 8h


title: 13489207 - Col-2-H vs N509-9-2-H

hyb_protocol: N509-9-2-H Cy5 / Col-2-H Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366248 - Ler vs FWA

hyb_protocol: FWA Cy5 / Ler Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488722 - Col-1-P vs N509-9-1-P

hyb_protocol: N509-9-1-P Cy5 / Col-1-P Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488714 - Col-1-H vs N509-9-1-H

hyb_protocol: N509-9-1-H Cy5 / Col-1-H Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488715 - N509-9-1-H vs Col-1-H

hyb_protocol: Col-1-H Cy5 / N509-9-1-H Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13372748 - PI1 vs I1

description: Does Stifenia elicitor pretreatment prime defense genes?

hyb_protocol: I1 Cy5 / PI1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - 10 days on agar, 4°C, 8h then 20 days on soil, 22°C, 8h

treatment_protocol: Name:Fusarium - compound+pathogen,pathogen - elicitor+pathogen infection,pathogen infection,fusarium:. Fusarium oxysporum pv rafani sprayed at 10^6 spores/ml.

treatment_protocol: Name:Stifenia+Fusarium - compound+pathogen - elicitor+pathogen infection,stifenia+fusarium:. Stifenia sprayed at 10 g/L. Fusarium oxysporum infection: 10^6 spores/ml one day later.


title: 13372745 - PI1 vs P1

hyb_protocol: P1 Cy5 / PI1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Stifenia - compound based treatment - compound addition,stifenia:. Stifenia sprayed at 10 g/L.


title: 13372746 - I1 vs PI1

hyb_protocol: PI1 Cy5 / I1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13372767 - PP2 vs PI2

hyb_protocol: PI2 Cy5 / PP2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Stifeniax2 - compound based treatment - compound addition,stifenia:. Stifenia sprayed and another Stifenia sprayed one day later at 10 g/L.


title: Hela AS350-2

city: Pamplona

first: Rafael

last: Aldabe

state: Navarra

address: Av Pio XII 55

department: Hepatology and Gene Therapy

country: Spain

institute: FIMA

description: The Hela cells were cultured in a 94/16 mm plate and infected with adenovirus AdAS350 for 56 hours before harvesting them. This adenovirus expresses a siRNA control.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: The data were condensed with Affymetrix GCOS 1.2 software. The normalization target was set to 200.

source_name: Tissue culture experiment with Adenovirus infection expressing siRNA 350

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: Hela cells


title: 13372765 - P2 vs PI2

hyb_protocol: PI2 Cy5 / P2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.