title: KO-MEFs_TNFalfa 100 ng/ml 45’_Rep2

status: Public on Sep 29 2010

type: RNA

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

description: KO-MEFs_TNFalfa 100 ng/ml 45’_Rep2

hyb_protocol: All procedures of hybridization, slide and image processing were carried out according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis protocol). In each experiment, 825 ng of contrasting cRNA samples were fragmented at 60°C for 30 min and hybridized at 65ºC for 17hr.

scan_protocol: The slides were scanned at a 10 µm resolution with Agilent G2565BA Microarray Scanner (Agilent Technologies).

data_processing: Signal quantification was carried out with Feature Extraction 9.1 software (Agilent Technologies) by using default analysis parameters for 44K gene expression arrays (feature extraction protocol 44K). Data normalization was then performed by importing raw data in GeneSpring GX 7.3 Software by using the enhanced Agilent Feature Extraction Import setting.

molecule: total RNA

organism: Mus musculus

source_name: MAPK p38alfa knock out MEFs-TNFa-0.75h

label_protocol: RNA amplification and labelling was carried out by using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent Technologies). Briefly, for each sample 2 µg of total RNA input were amplified in two rounds of amplification by following manufacturer’s instructions. The first strand cDNA syntheses and amplification reactions were carried out by using random and T7 primers, respectively. During the 2hr in vitro transcription, Cy3- or Cy5-labeled CTP was incorporated in each amplified RNA (cRNA) from Reference and pooled samples respectively. Products of the reaction were then purified using RNAeasy mini spin column (Qiagen, Dusseldorf, Germany).

growth_protocol: Wild type and p38 alpha knock out immortalised mouse embryonic fibroblasts (MEFs) were maintained in Dulbecco’s modified Eagle’s medium (Biological Industries) containing 10% fetal calf serum (Sigma) and supplemented with 1 mM sodium pyruvate, 2mM L-glutamine, 100 U/ml Penicilin and 100 µg/ml Streptomycin (GibCO) and cultured in a 5% CO2 humidified incubator at 37ºC.

extract_protocol: Total RNA was extracted from MEFs cells samples using the RNeasy Mini Kit (Quiagen Inc., Hilden, Germany). Quality of the RNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Carlsbad, CA) and RNA amount was established by using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Exponentially growing MEFs were stressed with either 100 mM NaCl for 45’, 2h and 8h, 25 ng/ml anisomycin (Sigma) for 45’ or 100 ng TNF alpha (Preprotech) for 45’. When indicated cells were treated with 10 µM SB203580 (Calbiochem) for 30 minutes prior to stressing the cells.

tag: culture phase

value: exponentially growing cells

tag: genotype

value: MAPK p38alfa knock out

tag: cell type

value: mouse embryonic fibroblast

tag: agent

value: TNFa

source_name: Pool of two untreated WT MEFs

value: Exponentially growing cells

tag: reference

value: Pool of two untreated WT MEFs


title: KO-MEFs_Untreated_Rep2

source_name: MAPK p38alfa knock out MEF untreated


title: KO-MEFs_Untreated_Rep1


title: KO-MEFs_TNFalfa 100 ng/ml 45’_Rep1

description: KO-MEFs_TNFalfa 100 ng/ml 45’_Rep1


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 2h_Rep1

source_name: Wild type MEFs-SB+NaCl-2h

value: wild type


title: KO-MEFs_Anisomycin 25 ng/ml 45’_Rep2

description: KO-MEFs_Anisomycin 25 ng/ml 45’_Rep2

source_name: MAPK p38alfa knock out MEFs-sAn-0.75h

value: Anisomycin


title: KO-MEFs_NaCl 100 mM 2h_Rep2

description: KO-MEFs_NaCl 100 mM 2h_Rep2

source_name: MAPK p38alfa knock out MEFs-NaCl-2h

value: NaCl


title: KO-MEFs_NaCl 100 mM 2h_Rep1

description: KO-MEFs_NaCl 100 mM 2h_Rep1


title: KO-MEFs_Anisomycin 25 ng/ml 45’_Rep1

description: KO-MEFs_Anisomycin 25 ng/ml 45’_Rep1


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 2h_Rep2


title: WT-MEFs_SB 203580 10 mM 2h_Rep2

description: WT-MEFs_SB 203580 10 mM 2h_Rep2

source_name: Wild type MEFs-SB-2h


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 8h_Rep1

source_name: Wild type MEFs-SB+NaCl-8h


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 45’_Rep2

source_name: Wild type MEFs-SB+NaCl-0.75h


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 8h_Rep2


title: WT-MEFs_SB 203580 10 mM 2h + NaCl 100 mM 45’_Rep1


title: WT-MEFs_SB 203580 10 mM 2h + Anisomycin 25 ng/ml 45’_Rep1

source_name: Wild type MEFs-SB+sAn-0.75h

value: SB 203580 + Anisomycin


title: WT-MEFs_SB 203580 10 mM 2h + TNFalfa 100 ng/ml 45’_Rep2

source_name: Wild type MEFs-SB+TNFa-0.75h


title: WT-MEFs_SB 203580 10 mM 2h + TNFalfa 100 ng/ml 45’_Rep1


title: WT-MEFs_SB 203580 10 mM 2h_Rep1

description: WT-MEFs_SB 203580 10 mM 2h_Rep1


title: WT-MEFs_NaCl 100 mM 8h_Rep1

description: WT-MEFs_NaCl 100 mM 8h_Rep1

source_name: Wild type MEFs-NaCl-8h


title: WT-MEFs_SB 203580 10 mM 2h + Anisomycin 25 ng/ml 45’_Rep2


title: WT-MEFs_NaCl 100 mM 8h_Rep2

description: WT-MEFs_NaCl 100 mM 8h_Rep2


title: WT-MEFs_NaCl 100 mM 2h_Rep2

description: WT-MEFs_NaCl 100 mM 2h_Rep2

source_name: Wild type MEFs-NaCl-2h


title: WT-MEFs_TNFalfa 100 ng/ml 45’_Rep2

description: WT-MEFs_TNFalfa 100 ng/ml 45’_Rep2

source_name: Wild type MEFs-TNFa-0.75h


title: WT-MEFs_NaCl 100 mM 2h_Rep1

description: WT-MEFs_NaCl 100 mM 2h_Rep1


title: WT-MEFs_TNFalfa 100 ng/ml 45’_Rep1

description: WT-MEFs_TNFalfa 100 ng/ml 45’_Rep1


title: WT-MEFs_NaCl 100 mM 45’_Rep2

description: WT-MEFs_NaCl 100 mM 45’_Rep2

source_name: Wild type MEFs-NaCl-0.75h


title: WT-MEFs_NaCl 100 mM 45’_Rep1

description: WT-MEFs_NaCl 100 mM 45’_Rep1


title: WT-MEFs_Anisomycin 25 ng/ml 45’_Rep2

description: WT-MEFs_Anisomycin 25 ng/ml 45’_Rep2

source_name: Wild type MEFs-sAn-0.75h


title: WT-MEFs_Anisomycin 25 ng/ml 45’_Rep1

description: WT-MEFs_Anisomycin 25 ng/ml 45’_Rep1


title: an3-4 leaf primordia rep2

status: Public on Sep 28 2010

city: Tokyo

first: Gorou

last: Horiguchi

address: 3-34-1, Nishi-Ikebukuro, Toshima-ku

department: College of Science, Faculty of Life Science

country: Japan

institute: Rikkyo University

description: Gene expression data of the first set of leaf primorida harvested 7 days after sowing.

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

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.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf primordia

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

growth_protocol: Plants were grown at 22C under continuous light.

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Leaf primordia were transferred to liquid nitrogen before RNA extraction

tag: ecotype

tag: phenotype

value: an3-4 mutants


title: an3-4 leaf primordia rep1


title: WT leaf primordia rep1

source_name: Leaf primordia


title: Losartan-treated aortic media Replicate 3

status: Public on Sep 23 2010

city: Paris

first: Sophie

last: Nadaud

address: 91 Bd de l'hopital

country: France

institute: INSERM

description: Biological replicate 3 of 5. rats bred in normal conditions and treated with Losartan 20mg/d in the drinking water for 9 months

hyb_protocol: Microarrays were hybridized with 750ng of labelled amplified RNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization and washing were performed according to manufacturer's instructions

scan_protocol: All slides were all scanned with an Axon 4000B scanner with the same settings and analyzed using Genepix 5 (Molecular Devices, Sunnyvale, USA).

data_processing: LOWESS normalization was performed using VARAN (Golfier et al, Bioinformatics. 2004;20(10):1641-3). With this normalization, the new Cy3 values can calculated to be above the maximal scanning value of ~65500. Therefore all the normalized values above this limit were set to 65500. For the normalization, all spots called BAD or control spots (NA, eQC, Brightcorner, Negative control, E1A) were not used.

organism: Rattus norvegicus

source_name: Rat aortic media, Losartan 20mg/d, 9 months

label_protocol: Total RNA (1µg) from 5 samples of each group was amplified (one-round amplification) using MessageAmp amplification kit (Applied Biosystems, Courtaboeuf, France). Amplified RNA (1.5µg) was labelled with Cy5 dyes (Cyscribe direct mRNA labelling kit, GE Healthcare, Orsay, France) following the manufacturer’s instructions, purified with RNeasy Mini columns (Qiagen, Courtaboeuf, France) and the RNA quality was evaluated using Agilent 2100 Bioanalyzer. CyScribe Direct mRNA Labeling Kit provides a one-step non-enzymatic, non-destructive method of covalently labeling the original substrate nucleic acids. The Cy™ Direct labeling reagents modify guanine residues in RNA at a site that does not interfere with subsequent base pairing.

growth_protocol: One month-old female WAG/Rij rats (Harlan, Gannat, France) of 50-80g were bred under normal conditions for 10 months in the specific pathogen-free husbandry of the Faculté de Médecine Pitié-Salpétrière (Paris, France). One group of animals was not treated and animals of the other group received Losartan (20mg/kg/d) within the drinking water for 9 months. Water consumption was carefully controlled and used to adapt losartan concentrations.

extract_protocol: Rats were sacrificed under pentobarbital anaesthesia (pentobarbital sodium 50mg/kg ip), abdominal and thoracic aortas were rapidly excised and the media was extruded by dissociating it mechanically from the adventitia  and immediately frozen in liquid nitrogen. Frozen medias (usually 50-150 mg) were crushed in ice in 1ml Trizol (Invitrogen) and then total RNA was prepared using RNeasy columns (Qiagen) according to the manufacturer’s instructions. To avoid any genomic contamination, each RNA was treated during the puirification on the column with rDNase I. RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France). RNA quality was assayed using RNA nano LabChip ® and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). Only samples with a RNA Integrity number greater than 7 (determined by the Bioanalyzer) and a 28S/18S value greater than 1.5 were selected for the following studies.

tag: strain

value: Wag/Rij

tag: gender

value: female

tag: age

value: 10 months

source_name: pooled rat aortic media RNA from control and losartan-treated animals

tag: tissue


title: Control aortic media Replicate 4

description: Biological replicate 4 of 5. Control rats bred in normal conditions for 9 months

source_name: Rat aortic media, control, 9 months


title: WT leaf primordia rep2


title: Allograft vs. Isograft, biological replicate 1

status: Public on Sep 24 2010

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

description: Biological replicate 1

hyb_protocol: Hybridization was performed at 60°C over-night on Agilent G4131A rat whole genome microarrays (Agilent Technologies, Böblingen, Germany) as indicated by the supplier.

scan_protocol: Slides were scanned using the GenePix 4100A scanner , scanned with the Genepix A4100 scanner (MDS Analytical Technologies, Ismaning, Germany) and analyzed with GenePix software V5.0 (MDS).

data_processing: MA data was calculated from the Genepix data and lowess-nomalized using R (http://www.R-project.org)

source_name: Isograft

label_protocol: Total RNA (40-50 µg) was incubated at 65° C with 1.5 µg oligo-dT (15-20) primers, at 20° C and on ice for 10 min each. Reverse transcription was performed in 40 µl Superscript II reaction buffer (Superscript II kit, Invitrogen, Karlsruhe, Germany) containing 0.5 mM of each dATP, dTTP, dGTP, 0.2 mM dCTP, 0.1 mM Cy-dCTP (PerkinElmer, Waltham, USA), 10 mM DTT, and 300 U Superscript II at 39°C for 180 min, terminated by adding 10 µl 1 M NaOH and heating to 65°C, and neutralized with 10 µl 1 M HCl and 200 µl TE buffer. Labeled cDNA was purified using the PCR Purification Kit (Qiagen) and eluted in 50 µl water.

growth_protocol: LEW (RT1l) and F344 (RT1lv1) male rats from Harlan Winkelmann (Borchen, Germany) were kept under conventional conditions. Animal care and animal experiments were performed following the current version of the German Law on the Protection of Animals as well as the NIH Principles of laboratory animal care.

extract_protocol: RNA was extracted using the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Transplantation was performed in rats weighing 270-300 g. For allogeneic transplantation, F344 rats were used as donors and LEW rats as recipients. This rat strain combination is characterized by a minor difference in the MHC class I locus. LEW rats were used for isogeneic transplantation and as healthy untreated controls.  Animals were anaesthetized with 60 mg/kg sodium pentobarbital i.p. (Narcoren, Merial, Hallbergmoos, Germany). Kidneys were transplanted orthotopically to totally nephrectomized recipients as described (Fabre et al. 1971) except that the ureter was anastomozed end-to-end. Before organ procurement, donors obtained 1000 IU/kg Heparin i.v. (Ratiopharm, Ulm, Germany), recipients obtained 30 µg ampicillin i.p. after surgery (Ratiopharm). Total ischemic times remained below 30 min. No immunosuppression was given. Graft recipients dying within 4 days after transplantation (less than 20%) were excluded from the study. None of the recipients died thereafter.  Graft recipients and healthy control animals were anaesthetized and heparinized. Perfusion of the renal blood vessels was performed as described (Grau et al. 2001). Percoll (1.082 g/l) isopycnic density gradient centrifugation was carried out to deplete granulocytes and erythrocytes from leukocyte samples as described (Scriba et al. 1996). Mononuclear leukocytes were harvested and further analyzed by flow cytometry or snap frozen and stored for RNA isolation.

value: intravascular mononuclear leukocytes

tag: iso/allo

value: iso

value: male

source_name: Allograft

value: allo


title: Losartan-treated aortic media Replicate 5

description: Biological replicate 5 of 5. rats bred in normal conditions and treated with Losartan 20mg/d in the drinking water for 9 months


title: Allograft vs. Isograft, biological replicate 3

description: Biological replicate 3


title: Losartan-treated aortic media Replicate 2

description: Biological replicate 2 of 5. rats bred in normal conditions and treated with Losartan 20mg/d in the drinking water for 9 months


title: Control aortic media Replicate 5

description: Biological replicate 5 of 5. Control rats bred in normal conditions for 9 months


title: Human-HK-2 cells

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

description: HK-2 cells are derived from an immortalized proximal tubule epithelial cell line from normal adult human kidney.

hyb_protocol: Standard Phalanx protocol

scan_protocol: Arrays were scanned using Genepix 4.1 software (Molecular Devices).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed using the Genepix 4.1 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the surrounding area. Control probes were filtered out to measure the background-corrected signal intensity of each spot. Spots were then normalized using the Limma package of the R program.

organism: Homo sapiens

source_name: HK-2 cells were cultivated on 25-T flask for 24 h.

label_protocol: Standard MessageAmp aRNA kit (Ambion) protocol

growth_protocol: HK-2 cells were grown in keratinocyte serum-free basal medium (Gibco) supplemented with 5 ng/ml of recombinant epidermal growth factor and 50 μg/ml of bovine pituitary extract without antibiotics in 5 % CO2 at 370C. Aristolochic acid sodium salt, a mixture of AA I (41%) and AA II (56%) (Sigma, St. Louis, MO, USA) was dissolved in double-distilled water. HK-2 cells were seeded in 25-T flasks and incubated for 24 h before AA treatment. Aristolochic acid (10 μM) were added to HK-2 cells for 24 h.

extract_protocol: Standard RNeasy kit (Qiagen) protocol

value: HK-2 cells


title: Allograft vs. Isograft, biological replicate 2

description: Biological replicate 2


title: Allograft vs. Isograft, biological replicate 5

description: Biological replicate 5


title: Allograft vs. Isograft, biological replicate 4

description: Biological replicate 4


title: Losartan-treated aortic media Replicate 4

description: Biological replicate 4 of 5. rats bred in normal conditions and treated with Losartan 20mg/d in the drinking water for 9 months


title: Control aortic media Replicate 3

description: Biological replicate 3 of 5. Control rats bred in normal conditions for 9 months


title: Human-aristolochic acid-10 uM

description: HK-2 cells are derived from an immortalized proximal tubule epithelial cell line from normal adult human kidney

source_name: HK-2 cells were treated with aristolochic acid (10 uM) for 24 h

growth_protocol: HK-2 cells were grown in keratinocyte serum-free basal medium (Gibco) supplemented with 5 ng/ml of recombinant epidermal growth factor and 50 μg/ml of bovine pituitary extract without antibiotics in 5 % CO2 at 370C. Aristolochic acid sodium salt, a mixture of AA I (41%) and AA II (56%) (Sigma, St. Louis, MO, USA) was dissolved in double-distilled water. HK-2 cells were seeded in 25-T flasks and incubated for 24 h before aristolochic acid treatment. Aristolochic acid (10 μM) were added to HK-2 cells for 24 h.

value: Aristolochic acid sodium salt (a mixture of AA I (41%) and AA II (56%))


title: Control aortic media Replicate 2

description: Biological replicate 2 of 5. Control rats bred in normal conditions for 9 months


title: Control aortic media Replicate 1

description: Biological replicate 1 of 5. Control rats bred in normal conditions for 9 months


title: Losartan-treated aortic media Replicate 1

description: Biological replicate 1 of 5. rats bred in normal conditions and treated with Losartan 20mg/d in the drinking water for 9 months


title: Dmocrz1_CaCl2_30m_rep1

status: Public on Sep 17 2010

city: Columbus

first: Soonok

last: Kim

state: OH

address: 2021 Coffey Rd.

department: Plant Pathology

country: USA

institute: The Ohio State University

description: Gene expression in delta-mocrz1 mutant after CaCl2 treatment

hyb_protocol: Cy3-labeled cRNA (1.65 ug) from each sample was hybridized to Magnaporthe grisea 2.0 4x44k Microarrays.

scan_protocol: The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: An error-weighted average signal intensity of two probes within a chip was used for normalization with Lowess normalization module implanted in JMP Genomics software. An average expression of all probes among 16 data sets was used as the baseline.

organism: Pyricularia oryzae

label_protocol: Five hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol: Mycelial blocks from actively growing margin of colony were inoculated into complete media (CM) liquid media at 25C by shaking for 3 days.

extract_protocol: Total RNA was isolated from frozen mycelial powder using an Easy-Spin RNA extraction kit (iNtRON Biotechnology, Seoul, Korea).

treatment_protocol: After thorough washing with sterile distilled water, the mycelia were treated with 200mM CaCl2 with or without 10ug/ml FK506 for 30m with shaking.

value: mycelia

tag: developmental stage

value: young

tag: genome/variation


title: KJ201_Control_30m_rep3

description: Gene expression in wild type mycelia in water


title: Dmocrz1_CaCl2_30m_rep3


title: Dmocrz1_CaCl2_30m_rep4


title: Dmocrz1_CaCl2_30m_rep2


title: KJ201_Control_30m_rep2


title: KJ201_CaCl2/FK506_30m_rep1

description: Gene expression in wild type mycelia after CaCl2/FK506 treatment


title: KJ201_Control_30m_rep4


title: KJ201_CaCl2_30m_rep4

description: Gene expression in wild type mycelia after CaCl2 treatment


title: KJ201_Control_30m_rep1


title: KJ201_CaCl2/FK506_30m_rep4


title: KJ201_CaCl2_30m_rep2


title: KJ201_CaCl2/FK506_30m_rep3


title: KJ201_CaCl2/FK506_30m_rep2


title: KJ201_CaCl2_30m_rep3


title: KJ201_CaCl2_30m_rep1


title: 8287-8296-Cy3

status: Public on Sep 14 2010

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Purified and dye-labeled sample and reference cDNA (Human Reference RNA, Stratagene, LaJolla, USA) was pooled an mixed with 520 µl hybridisation buffer (4x SSC, 50perc formamide, 2perc SDS), agitated for 60 min at 60C, heated for 10 min at 70C on a thermo mixer and subsequently applied to preheated (60C) microarrays mounted in hybridisation chambers. Hybridisations were performed for 23 h at 42C and a rotation speed of 4 rpm in an Agilent DNA Microarray Hybridisation Oven (Agilent, Santa Clara, USA). The arrays were washed at 35C with (i) 0.5x SSC, 0.1perc SDS for 4 min; (ii) 0.05x SSC, 0.1perc SDS for 4 min; (iii) 0.05x SSC for 2 min; (iv) 0.05x SSC, 0.05perc Tween for 30 sec. Immediately thereafter, slides were dried by centrifugation in 50 ml Falcon tubes at 2500 rpm for 5 min.

scan_protocol: Hybridized microarrays were scanned at 5 µm resolution in a two-color Agilent Scanner G25505B (Agilent, Santa Clara, USA) with automatically adjusted PMT voltages according to manufacturer’s specification. Array raw data were generated from scanned images using Axon GenePixPro Software (v6.1.0.2)

data_processing: Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).

label_protocol: Samples were amplified and labeled using TAcKLE Protocol [PMID: 15718295]

extract_protocol: 2ug universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)

value: Universal Human Reference Total RNA

extract_protocol: RNA were prepared from fresh frozen tumor tissue using ultracentrifugation [PMID: 12937144]

tag: sex

value: unknown

value: sample

value: normal-brain

tag: ageatsampling

tag: chemotherapy

value: no data


title: 4388-8234-Cy3

value: M

value: pGBIV

value: no

value: yes


title: 4392-8272-Cy3

value: F


title: Ca treated 1

type: genomic

description: ChIP-chip Ca treated 1 ChIP DNA/input DNA

hyb_protocol: Labeled DNA was hybridized according to NimbleGen's protocol.

scan_protocol: Arrays were scanned per Nimblegen's standard protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: Ca treated 1 ChIP DNA

label_protocol: DNA was then labeled with Cy3 or Cy5 fluorescent dyes for input or immunoprecipitated DNA, respectively, according to the NimbleGen's protocol.

growth_protocol: Fungal mycelia were grown in CM for 2 days.

extract_protocol: Mycelia were cross-linked with 1% formaldehyde in buffer A (0.4M sucrose, 10mM Tris-HCl, pH 8.0, 1 mM EDTA, 1 mM phenylmethylsulfonyl fluoride, and 1% formaldehyde) for cross-linking for 20min. Mycelia were harvested with excess amount of distilled water after stopping cross-link with 0.1M glycine for 10 min, frozen in liquid nitrogen, ground into a fine powder in a chilled mortar and pestle, and stored at -80C until used. Nuclear DNA was then isolated from cross-linked mycelia with Plant Nuclear Isolation Kit (Sigma, St. Louis, MO) and sheared into fragments by sonication to 200- to 1,000-bp with an average size of 500bp. Sonication was conducted on ice with an amplitude of 10% using 30× 30s pulses (30s between bursts) using Biorupter (Cosmo Bio, Tokyo, Japan). After pre-clearing nuclear lysates with Salmon sperm/protein A agarose (Upstate, Temecula, CA) for 4 hours at 4C, immunoprecipitations were performed with either 1 µg of rabbit control IgG (ab46540-1, Abcam, Cambridge, MA) or 0.5µl of antiGFP antibody (ab290, Abcam) for overnight at 4C. A small aliquot of DNA (30%) was saved for input DNA (input). Immunoprecipitated DNA was captured with proteinA agarose beads (Upstate, Temecula, CA) for 4 hours, and then washed twice with LNDET buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA) and twice with TE buffer. The DNAs were reverse-cross linked at 65C overnight in elution buffer (1% SDS and 0.1 M NaHCO3) containing 1 mg/ml proteinase K, and purified using PCR purification kit (Qiagen).

treatment_protocol: Fresh mycelia were incubated in 200mM CaCl2 solution for 1 hour with shaking.

tag: organism structure

value: nuclear MoCRZ1

source_name: Ca treated 1 input DNA


title: Ca treated 4

description: ChIP-chip Ca treated 4 ChIP DNA/input DNA

source_name: Ca treated 4 ChIP DNA

source_name: Ca treated 4 input DNA


title: 4381-8062-Cy3


title: CaCl2 + FK506

description: ChIP-chip Ca + FK506 treated 1 ChIP DNA/input DNA

source_name: Ca + FK506 treated 1 ChIP DNA

treatment_protocol: Fresh mycelia were incubated in 200mM CaCl2 + 10ug/ml FK506 solution for 1 hour with shaking.

value: MoCRZ1 without nuclear localization

source_name: Ca + FK506 treated 1 input DNA


title: 4356-8395-Cy3


title: 4408-8182-Cy3


title: 8679-8681-Cy5

value: Pooled


title: 4584-8179-Cy3

value: sGBIV


title: 4252-8237-Cy5

value: AII


title: 4369-8253-Cy5


title: 4242-8394-Cy3

value: AAIII


title: 4529-8242-Cy5


title: 4263-8398-Cy3


title: 8284-8295-Cy5


title: 4378-8071-Cy3


title: 4249-8678-Cy3


title: 4368-8161-Cy5


title: 4380-8152-Cy5


title: 4261-8151-Cy3


title: 4396-8275-Cy3


title: 4246-8259-Cy3


title: 4245-8262-Cy3


title: 8287-8296-Cy5


title: 4406-8255-Cy5


title: 4251-8278-Cy3


title: 4259-8246-Cy5


title: 4521-8396-Cy5


title: 4391-8270-Cy5


title: 4385-8233-Cy5


title: 4361-8061-Cy3


title: 4263-8398-Cy5


title: 4389-8267-Cy3


title: 4258-8245-Cy5


title: 4518-8389-Cy5


title: 4247-8260-Cy5


title: 8281-8291-Cy3


title: 4393-8268-Cy5


title: 4376-8064-Cy5


title: 4359-8251-Cy5


title: 4381-8062-Cy5


title: 4252-8237-Cy3


title: 4375-8263-Cy3


title: 4527-8240-Cy5


title: 4368-8161-Cy3


title: 4529-8242-Cy3


title: 4516-8384-Cy5


title: 4522-8393-Cy5


title: 4256-8248-Cy3


title: 4364-8172-Cy3


title: 4264-8383-Cy3


title: 4371-8407-Cy5

value: RZ-GBIV


title: 4402-8277-Cy3

value: Universal Human Reference Total RNA


title: 4367-8173-Cy5


title: 4527-8240-Cy3


title: 4258-8245-Cy3


title: 4394-8269-Cy3


title: 4361-8061-Cy5


title: 8679-8681-Cy3


title: 4380-8152-Cy3


title: 4247-8260-Cy3


title: 4383-8235-Cy5


title: 4404-8153-Cy3


title: 4523-8068-Cy3


title: 4521-8396-Cy3


title: 4386-8264-Cy3


title: 4383-8235-Cy3


title: 4585-8163-Cy5


title: 4370-8252-Cy3


title: 4356-8395-Cy5


title: 8286-8297-Cy5

value: unknown


title: 4586-8408-Cy3

value: sample


title: 4358-8176-Cy5


title: 4373-8391-Cy3


title: 4528-8247-Cy3


title: 4242-8394-Cy5


title: 4395-8257-Cy3


title: 4256-8248-Cy5


title: 4367-8173-Cy3


title: 4249-8678-Cy5


title: 4401-8399-Cy3


title: 6282-8170-Cy5


title: 4392-8272-Cy5


title: 4388-8234-Cy5


title: 4257-8070-Cy5


title: 4390-8271-Cy5


title: 4360-8060-Cy5


title: 4585-8163-Cy3


title: 8281-8291-Cy5

value: normal-brain


title: 4519-8405-Cy5

value: no data


title: 4516-8384-Cy3


title: 6290-8169-Cy3

value: M


title: 4355-8390-Cy3


title: 4357-8250-Cy3


title: 4259-8246-Cy3


title: 4365-8177-Cy5


title: 4403-8276-Cy3

value: pGBIV


title: 4407-8254-Cy3


title: 4261-8151-Cy5


title: 4371-8407-Cy3


title: 4402-8277-Cy5

value: no


title: 4523-8068-Cy5

value: yes


title: 4375-8263-Cy5

value: F


title: 4377-8063-Cy5


title: 4253-8241-Cy5


title: 4390-8271-Cy3


title: 8286-8297-Cy3


title: 4382-8249-Cy3


title: 4400-8388-Cy5


title: 4251-8278-Cy5


title: 4357-8250-Cy5


title: 4519-8405-Cy3


title: 4406-8255-Cy3


title: 4405-8181-Cy5


title: 4405-8181-Cy3


title: 4376-8064-Cy3


title: 4391-8270-Cy3


title: 4393-8268-Cy3


title: 4400-8388-Cy3


title: 4407-8254-Cy5


title: 4404-8153-Cy5


title: 4382-8249-Cy5


title: 4377-8063-Cy3


title: 4264-8383-Cy5


title: 4370-8252-Cy5


title: 4528-8247-Cy5


title: 4385-8233-Cy3


title: 4364-8172-Cy5


title: 4373-8391-Cy5


title: 4586-8408-Cy5


title: 4408-8182-Cy5


title: 4245-8262-Cy5


title: 4396-8275-Cy5


title: 4373-1038-Cy3

hyb_protocol: Ten micrograms of tumor and reference DNA were combined with 300 mg of human Cot-1 DNA (Roche Diagnostics, Mannheim, Germany) and suspended in 125 ml of UltrahybTM hybridization buffer (Ambion, Bad Soden, Germany). Denaturation of combined DNA was performed at 75C for 10 min, followed by preannealing at 37C for 30 min. Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37C.

data_processing: Spot replicates were averaged. Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the printtip loess normalization function of limma.

label_protocol: Cy3-/ Cy5-conjugated dCTP by use of BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany)

extract_protocol: DNA extraction from peripheral blood leukocytes was performed according to standard protocol

value: control

extract_protocol: DNA were prepared from fresh frozen tumor tissue using ultracentrifugation [PMID: 12937144]


title: 4518-8389-Cy3


title: 4367-1032-Cy3


title: 4521-1186-Cy3


title: 4386-8264-Cy5


title: 4359-1024-Cy3


title: 4355-8390-Cy5


title: 4371-1036-Cy3


title: 4397-1062-Cy3


title: 4357-1022-Cy3


title: 5979-2671-Cy3


title: 4387-1052-Cy3


title: 4377-1042-Cy3


title: 4369-1034-Cy3


title: 4257-922-Cy3


title: 4372-8401-Cy3


title: 4401-1066-Cy3


title: 4365-8177-Cy3


title: 4391-1056-Cy3


title: 4375-1040-Cy3


title: 6308-3005-Cy3


title: 4243-908-Cy3


title: 6301-3034-Cy3


title: 5974-2666-Cy3


title: 8285-8293-Cy5


title: 6302-2999-Cy3


title: 4354-1019-Cy3


title: 4246-911-Cy3


title: 4393-1058-Cy3


title: 4385-1050-Cy3


title: 4364-1029-Cy3


title: 4379-1044-Cy3


title: 4259-924-Cy3


title: 4388-1053-Cy3


title: 4361-1026-Cy3


title: 4242-907-Cy3


title: 4379-8072-Cy3


title: 4261-926-Cy3


title: 4372-1037-Cy3


title: 5980-2672-Cy3


title: 4524-1281-Cy3


title: 4247-912-Cy3


title: 6282-2979-Cy3


title: 5972-2664-Cy3


title: 4516-1181-Cy3


title: 4515-1282-Cy3


title: 4380-1045-Cy3


title: 4526-1191-Cy3


title: 4363-1028-Cy3


title: 6295-2992-Cy3


title: 5976-2668-Cy3


title: 4517-1182-Cy3


title: 6307-3004-Cy3


title: 4245-910-Cy3


title: 6290-2987-Cy3


title: 4389-1054-Cy3


title: 5971-2663-Cy3


title: 4398-1063-Cy3


title: 4520-1185-Cy3


title: 6309-3006-Cy3


title: 6292-2989-Cy3


title: 6289-2986-Cy3


title: 4244-909-Cy3


title: 4407-1072-Cy3


title: 6293-2990-Cy3


title: 4408-1073-Cy3


title: 4399-1064-Cy3


title: 4400-1065-Cy3


title: 4370-1035-Cy3


title: 4381-1046-Cy3


title: 4585-1250-Cy3


title: 6299-2996-Cy3


title: 4249-914-Cy3


title: 4402-1067-Cy3


title: 6281-2978-Cy3


title: 6287-2984-Cy3


title: 4355-1020-Cy3


title: 4529-1194-Cy3


title: 5982-2674-Cy3


title: 6283-2980-Cy3


title: 4252-917-Cy3


title: 5981-2673-Cy3


title: 4366-1031-Cy3


title: 6296-2993-Cy3


title: 4253-918-Cy3


title: 4406-1071-Cy3


title: 4392-1057-Cy3


title: 5973-2665-Cy3


title: 6300-2997-Cy3


title: 6294-3031-Cy3


title: 6291-3030-Cy3


title: 4390-1055-Cy3


title: 4518-1183-Cy3


title: 6288-2985-Cy3


title: 6303-3000-Cy3


title: 4396-1061-Cy3


title: 4382-1047-Cy3


title: 5975-2667-Cy3


title: 4251-916-Cy3


title: 4519-1184-Cy3


title: 4263-928-Cy3


title: 6304-3001-Cy3


title: 6297-2994-Cy3


title: 4255-920-Cy3


title: 6305-3002-Cy3


title: 4404-1069-Cy3


title: 4386-1051-Cy3


title: 4262-927-Cy3


title: 4365-1030-Cy3


title: 4264-929-Cy3


title: 4383-1048-Cy3


title: 4523-1188-Cy3


title: 4525-1190-Cy3


title: 4358-1023-Cy3


title: 4405-1070-Cy3


title: 4376-1041-Cy3


title: 4362-3029-Cy3


title: 5977-2669-Cy3


title: 4522-1187-Cy3


title: 4360-1025-Cy3


title: 6298-3032-Cy3


title: 4256-921-Cy3


title: 4394-1059-Cy3


title: 4403-1068-Cy3


title: 4586-1251-Cy3


title: 4528-1193-Cy3


title: 4384-1049-Cy3


title: 4254-919-Cy3


title: 4378-1043-Cy3


title: 4374-1039-Cy3


title: 4527-1192-Cy3


title: 4258-923-Cy3


title: 4584-1249-Cy3


title: 5978-2670-Cy3


title: 4395-1060-Cy3


title: 4409-1074-Cy3


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate21

status: Public on Sep 10 2010

city: Waurn Ponds

first: Sean

last: McGee

state: Victoria

address: 75 Pigdons Rd

department: Metolic Research Unit, School of Medicine

country: Australia

institute: Deakin University

description: To capture the biological variability, replicates were collected over 6 independent days with MTT cellular viability analysis, and 5 different passage numbers of 3T3-L1 adipocytes

hyb_protocol: The hybridization solution (40 µl) was then applied to coverslips and mounted onto the array slide. Hybridization was conducted in humid hybridization chambers in a hybridization oven at 65°C for 16-20 h.

scan_protocol: Microarray slides were scanned using the GenePix 4000B scanner (Molecular Devices)

data_processing: Data was extracted using GenePix Pro 5.1 software (Molecular Devices) with Normalisation (ratio based)  and primary microarray data analysis performed using Acuity 4 software (Molecular Devices). The data used for normalisation had to meet the following filtering criteria ('% > B532+2SD' > 55) AND ('% > B635+2SD' > 55) AND ('F532 % Sat.' < 3) AND ('F635 % Sat.' < 3) AND ('Sum of Medians (635/532)' > 200) AND ('Rgn R² (635/532)' > 0.5) AND ('Flags' >= 0).

source_name: 3T3-L1 adipocyte treated with TNF (3 ng/ml, 48 h, 37°C), then 5 mM ASA and 10 µM TGZ for a further 24 h

label_protocol: Fluorescently labelled cDNA was prepared from 20 µg total RNA using an indirect labelling method. cDNA synthesis was performed in a 30 µl reaction containing 2 µg oligo-dT primer, 200 U Superscript III, 1 x first-strand buffer, 5 mM DTT, 0.5mM dNTP mix and 1.3 µg/µl RNaseOUT (Invitrogen). Synthesis was conducted in a GeneAmp PCR System 9700 (PE Applied Systems) at 46°C for 2 h.

growth_protocol: 3T3-L1 fibroblasts were cultured and differentiated as described previously Konstantopoulos, Endocrinology 148(1):374-85, 2007. Adipocytes were used for experiments 8-12 days after initiation of differentiation.

extract_protocol: Total RNA was extracted from 3T3-L1 adipocytes using TRIzol reagent and purified using RNA clean-up columns as per manufacturer’s instructions

treatment_protocol:
Treated with TNFα (3 ng/ml; Peprotech) for 48 h in D-MEM containing 10% (v/v) heat-inactivated FBS (Invitrogen) followed by co-treatment for a further 24 h with ASA (5 mM; Sigma) and TGZ (10 µM; Sigma)
Treatments were replenished every 24 h.

tag: cell line

value: Fully differentiated 3T3-L1 adipocytes

source_name: Total RNA from pooled differentiated 3T3-L1 cells (untreated)


title: 4356-1021-Cy3

value: Pooled


title: 4368-1033-Cy3

value: sGBIV


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate20


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate16


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate12


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate17


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate19


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate14


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate13


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate18


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate5


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate15


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate7


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate11


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate8


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate9


title: 3T3-L1 adipocyte_TNF-treated_replicate20

source_name: 3T3-L1 adipocyte treated with TNFα (3 ng/ml, 48 h, 37°C), then 3 ng/ml of TNFα for a further 24 h

treatment_protocol:
Treated with TNFα (3 ng/ml; Peprotech) for 48 h in D-MEM containing 10% (v/v) heat-inactivated FBS (Invitrogen) followed by co-treatment for a further 24 h with TNFα (3 ng/ml)
Treatments were replenished every 24 h.


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate10


title: FTO in interstitial 16q duplication

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: The nomalized data were analyzed using CGH Analytics 3.5.14 with the annotation build 18 of the human genome. A filter with a minimum of three probes in a region and a minimum average absolute log2 ratio for the region of 0.3. Checked whether the chromosomal regions showing gain or loss in the patient overlapped with genomic imbalances reported in healthy individuals in the database of genomic variants (http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg18 ; using human genome build 36). Two additional databases were inspected if this database did not report any CNVs in the region: USCS (http://genome.ucsc.edu/cgi-bin/hgTracks) and ensembl (http://www.ensembl.org/). We used NCBI’s Map Viewer (http://www.ncbi.nlm.nih.gov/ projects/mapview/) to inspect the genes in the chromosomal regions showing gain or loss plus

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent

data_processing: Image analysis was performed using feature extraction software (version 9.1, Agilent Technologies, Palo Alto, USA). The Agilent CGH-v4_95_Feb07 protocol was applied using default settings. The normalized log2ratios were calculated with global median normalization.

source_name: FTO in interstitial 16q duplication

label_protocol: Labeling of genomic DNA was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer’s instructions (Enzo Life Sciences, Farmingdale, NY, USA)

extract_protocol: Genomic DNA was extracted from peripheral blood as previously described (Stratakis et al., 2000)

tag: FTO in interstitial 16q duplication

source_name: Normal reference (XX-mix).

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: DNA isolated from blood obtained from eighteen healthy females was mixed for the use as a normal reference (XX-mix).


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate4


title: 3T3-L1 adipocyte_TNF-treated_replicate21


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate6


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate3


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate1


title: 3T3-L1 adipocyte_TNF+ASA+TGZ-treated_replicate2


title: 3T3-L1 adipocyte_TNF-treated_replicate19


title: 3T3-L1 adipocyte_TNF-treated_replicate11


title: 3T3-L1 adipocyte_TNF-treated_replicate12


title: 3T3-L1 adipocyte_TNF-treated_replicate18


title: 3T3-L1 adipocyte_TNF-treated_replicate5


title: 3T3-L1 adipocyte_TNF-treated_replicate9


title: 3T3-L1 adipocyte_TNF-treated_replicate6


title: 3T3-L1 adipocyte_TNF-treated_replicate7


title: 3T3-L1 adipocyte_TNF-treated_replicate14


title: 3T3-L1 adipocyte_vehicle_replicate21

source_name: 3T3-L1 adipocyte treated with TNFα (3 ng/ml, 48 h, 37°C), then D-MEM containing 0.2% (w/v) BSA for a further 24 h

treatment_protocol:
Treated with TNFα (3 ng/ml; Peprotech) for 48 h in D-MEM containing 10% (v/v) heat-inactivated FBS (Invitrogen) followed by co-treatment for a further 24 h with D-MEM containing 0.2% (w/v) BSA (Sigma)
Treatments were replenished every 24 h.


title: 3T3-L1 adipocyte_TNF-treated_replicate1


title: 3T3-L1 adipocyte_TNF-treated_replicate13


title: 3T3-L1 adipocyte_TNF-treated_replicate10


title: 3T3-L1 adipocyte_TNF-treated_replicate2


title: 3T3-L1 adipocyte_TNF-treated_replicate17


title: 3T3-L1 adipocyte_TNF-treated_replicate16


title: 3T3-L1 adipocyte_TNF-treated_replicate15


title: 3T3-L1 adipocyte_TNF-treated_replicate8


title: 3T3-L1 adipocyte_TNF-treated_replicate4


title: 3T3-L1 adipocyte_TNF-treated_replicate3


title: 3T3-L1 adipocyte_vehicle_replicate22


title: 3T3-L1 adipocyte_vehicle_replicate17


title: 3T3-L1 adipocyte_vehicle_replicate20


title: 3T3-L1 adipocyte_vehicle_replicate15


title: 3T3-L1 adipocyte_vehicle_replicate12


title: 3T3-L1 adipocyte_vehicle_replicate13


title: 3T3-L1 adipocyte_vehicle_replicate19


title: 3T3-L1 adipocyte_vehicle_replicate4


title: 3T3-L1 adipocyte_vehicle_replicate16


title: 3T3-L1 adipocyte_vehicle_replicate18


title: 3T3-L1 adipocyte_vehicle_replicate5


title: 3T3-L1 adipocyte_vehicle_replicate6


title: 3T3-L1 adipocyte_vehicle_replicate7


title: 3T3-L1 adipocyte_vehicle_replicate9


title: 3T3-L1 adipocyte_vehicle_replicate10


title: 3T3-L1 adipocyte_vehicle_replicate8


title: 3T3-L1 adipocyte_vehicle_replicate11


title: 3T3-L1 adipocyte_vehicle_replicate14


title: NOV-R-M-0 PSU-BA-207

city: Beaverton

first: Maria

last: Smit

state: OR

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 207

hyb_protocol: Hybridization of CustomArray™ microarrays was performed as recommended by the manufacturer (http://www.combimatrix.com/docs/PTL005_00_4x2K_Hyb_Imaging.pdf), using the single-color experimental scheme. The microarrays were hybridized at 46˚C for 16 hours, using Cy5-labeled cDNA targets, 1.5-2 mg per sector for the 4X2K format.

scan_protocol: Hybridization images were obtained using a ScanArray 4000 fluorescent scanner (PerkinElmer, Waltham, MA) at 5 micron.

data_processing: Quantification was done with Microarray Imager software (CombiMatrix). Data normalization based on the quantile algorithm was done using the Probe Weaver software from CombiMatrix. Data QC was done with scatter plot analysis of duplicate hybridizations, and calculation of pair-wise correlation coefficients among samples using NCI-supported software BRB-ArrayTools (http://linus.nci.nih.gov/pilot/index.html). Then the duplicate samples were used to calculate average normalized signal intensities for each probe in each sample.

organism: uncultured prokaryote

source_name: filtered environmental water sample, BA

label_protocol: Total RNA samples were converted into cDNA using the Superscript III Reverse Transcriptase Kit with random hexamer primers, and then RNA was removed with RNase H, as described by the kit manufacturer (Invitrogen, Carlsbad, CA). The cDNA samples were purified using QIAQuick Nucleotide Removal Kit (Qiagen), and fluorescently labeled using LabelIT uArray Cy5 Kit (Mirus Bio, Madison WI) as described by the manufacturer. The Cy5-labeled cDNA samples were purified using Illustra ProbeQuant G-50 Micro Columns (GE Healthcare, Piscataway, NJ), dried in a SpeedVac centrifuge and applied for microarray hybridization.

growth_protocol: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms.

extract_protocol: Total RNA was isolated using a protocol described in Griffiths et al. (Griffiths et al, 2000), and modified for working with Sterivex filters in the following manner:  Each filter was removed from the holder, cut longitudinally into 5 mm strips and placed into 2 ml screw-top eppendorf tubes containing CTAB extraction buffer (5% CTAB, 0.8 M NaCl in 0.1 M phosphate buffer, pH 8.0) and 0.5 mL zirconia/silica beads (1:1 mixture of 0.1 and 1 mm, BioSpec Products, Bartlesville, OK). Bead beating for microbial cell disruption was performed for 1 min using a FastPrep FP120 machine (Thermo Fisher Scientific, Waltham, MA), and the extract was collected after 3 min centrifugation at maximum speed. The filter strips were re-extracted 3 times to maximize RNA yield, after which the extracts were pooled together and supplemented with an equal volume of 1:1 mixture of phenol:chloroform,  and 0.1 volume each of 10%  SDS, and 10% Sodium Lauryl Sarcosine.  The sample extracts were further incubated for 20 min at room temperature with intense shaking, followed by standard phenol:chloroform purification and isopropanol precipitation. The extracted RNA was treated with DNase using the RNase-free DNase Set (Qiagen, Germantown, MD), and then purified using the RNeasy Kit (Qiagen) as recommended by the manufacturer. The RNA content was measured spectrophotometrically with a Nanodrop 3300 instrument (Thermo Fisher Scientific  ), and RNA quality was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: After filtration, samples were preserved in RNAlater and stored at -80oC.

tag: location

value: BA

tag: date

tag: salinity (psu)

tag: depth (m)

tag: temperature (c)

tag: oxygen (mg/l)

tag: silicic acid (um)

tag: nitrate (um)

tag: phosphate (um)

tag: ammonium (um)

tag: chlorophyll a content (ug/l)

tag: pheophytin content (ug/l)

tag: bacterial production (mg c/l*h)

tag: rna (ug/l)

tag: dissolved organic carbon (mg/l)


title: NOV-O-S-31 PSU-CR7-219

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 219

source_name: filtered environmental water sample, CR7


title: NOV-R-M-22 PSU-AST-201

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 201

source_name: filtered environmental water sample, AST

value: AST


title: NOV-O-S-33 PSU-NH3-168

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 168

source_name: filtered environmental water sample, NH3


title: NOV-R-S-3 PSU-AST-200

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 200


title: NOV-O-S-30 PSU-CR15-159

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 159

source_name: filtered environmental water sample, CR15


title: 3T3-L1 adipocyte_vehicle_replicate3

tag: cell line


title: NOV-O-S-32 PSU-CR30-162

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 162

source_name: filtered environmental water sample, CR30


title: NOV-R-S-6 PSU-HAM-198

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 198

source_name: filtered environmental water sample, HAM

value: HAM


title: 3T3-L1 adipocyte_vehicle_replicate1


title: 3T3-L1 adipocyte_vehicle_replicate2


title: NOV-O-S-32 PSU-CR40-165

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 165

source_name: filtered environmental water sample, CR40


title: NOV-R-M-28 PSU-HAM-199

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 199

data_processing: Quantification was done with Microarray Imager software (CombiMatrix). Data normalization based on the quantile algorithm was done using the Probe Weaver software from CombiMatrix. Then normalized signal intensities were calculated for each probe in the sample.


title: NOV-R-M-9 PSU-HAM-152

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 152


title: NOV-R-M-15 PSU-AST-154

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 154


title: AUG-R-S-6 PSU-AST-104

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 104


title: AUG-R-S-0 PSU-UP-002

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 002

source_name: filtered environmental water sample, UP

value: UP


title: NOV-R-S-12 PSU-HAM-149

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 149


title: AUG-R-M-12 PSU-AST-132

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 132


title: AUG-R-S-20 PSU-HAM-102

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 102


title: NOV-R-S-1 PSU-AST-153

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 153


title: AUG-R-S-0 PSU-TID-96

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 96

source_name: filtered environmental water sample, TID

value: TID


title: AUG-R-S-10 PSU-HAM-100

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 100


title: AUG-R-M-0 PSU-TID-95

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 95


title: NOV-O-S-24 PSU-CR7-157

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 157


title: AUG-R-S-0 PSU-BA-006

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 006


title: AUG-O-S-32 PSU-CR40-50

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 50


title: AUG-O-S-25 PSU-CR15-66

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 66


title: AUG-R-M-6 PSU-AST-125

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 125


title: AUG-R-M-15 PSU-HAM-99

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 99


title: JUN-O-S-27 PSU-CR15-354

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 354


title: JUN-R-M-30 PSU-HAM-344

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 344


title: JUN-R-S-0 PSU-BA-347

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 347


title: AUG-O-M-32 PSU-CR15-43

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 43


title: JUN-O-M-32 PSU-CR7-350

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 350


title: AUG-O-S-28 PSU-CR7-41

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 41


title: JUN-O-S-10 PSU-CR7-351

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 351


title: JUN-R-S-0.5 PSU-AST-339

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 339


title: JUN-R-S-0 PSU-AST-338

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 338


title: JUN-O-M-32 PSU-CR40-336

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 336


title: JUN-O-S-31 PSU-CR30-334

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 334


title: JUN-R-M-25 PSU-HAM-342

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 342


title: JUN-O-M-32 PSU-CR15-330

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 330


title: JUN-R-M-16 PSU-AST-340

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 340


title: JUN-O-S-31 PSU-CR7-328

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 328


title: JUN-O-S-18 PSU-CR15-331

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 331


title: JUN-O-M-32 PSU-CR7-327

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 327


title: JUN-O-S-34 PSU-NH5-310

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 310

data_processing: Quantification was done with Microarray Imager software (CombiMatrix). Data normalization based on the quantile algorithm was done using the Probe Weaver software from CombiMatrix. Data QC was done with scatter plot analysis of replicate hybridizations, and calculation of pair-wise correlation coefficients among samples using NCI-supported software BRB-ArrayTools (http://linus.nci.nih.gov/pilot/index.html). Then the triplicate samples were used to calculate average normalized signal intensities for each probe in each sample.

source_name: filtered environmental water sample, NH5

value: n/d


title: APR-O-S-32 PSU-CR40-291

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 291


title: APR-O-M-31 PSU-CR30-287

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 287


title: APR-O-S-30 PSU-CR30-288

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 288


title: APR-O-S-24 PSU-CR15-285

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 285


title: APR-O-S-27 PSU-CR15-278

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 278


title: APR-O-S-18 PSU-CR7-274

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 274


title: APR-O-M-30 PSU-CR15-277

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 277


title: APR-O-M-30 PSU-CR7-273

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 273


title: APR-O-S-30 PSU-CR7-282

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 282


title: APR-R-M-0 PSU-BA-268

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 268


title: APR-R-S-0 PSU-BA-270

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 270


title: APR-R-M-10 PSU-AST-266

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 266


title: APR-R-M-1 PSU-AST-267

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 267


title: APR-R-S-0 PSU-AST-264

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 264


title: APR-R-M-24 PSU-AST-265

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 265


title: APR-R-S-1 PSU-AST-263

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 263


title: APR-R-M-14 PSU-AST-262

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 262


title: APR-O-S-31 PSU-NH3-248

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 248


title: Monocyte_patient50_time7

status: Public on Sep 09 2010

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

description: Gene expression data (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

hyb_protocol: GeneCip IVT hyb. Affymetrix EukGE-WSv5 wash and stain protocol

scan_protocol: Affymetrix GeneChip using GCOS.

data_processing: The data were analyzed with RMA using default analysis settings and log2 scaling.

source_name: Monocyte

label_protocol: Affymetrix GeneChip IVT labeling

growth_protocol: Samples from each patient were enriched using a previously described (monocyte or Neutrophil) enrichment protocol or Buffy coat protocol.

extract_protocol: Modiefied Qiagen Rneasy protocol


title: Monocyte_patient50_time1


title: Monocyte_patient51_time5


title: Monocyte_patient51_time9


title: LB vs low iron array #3

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

description: This array compared the P. mirabilis transcriptome during logarithmic-phase growth in LB broth to logarithmic-phase growth in iron-restricted LB broth. This is array #3 of 5.

hyb_protocol: Labeled cDNA was mixed and hybridized to an array slide using TIGR SOP#M008 (ftp://ftp.jcvi.org/pub/data/PFGRC/pdf_files/protocols/M008.pdf).

scan_protocol: The microarray was scanned using a ScanArray Express microarray scanner (Perkin Elmer) at 10 μm resolution and quantified using the ScanArray Express software.

data_processing: The LOWESS normalization algorithm (ScanArray Express, Perkin Elmer) was used to normalize microarray data. Median spot values for each triplicate probe were extracted using MIDAS (TIGR). A gene was considered differentially regulated if it was greater than 2-fold changed in LB compared to LB + Desferal.

organism: Proteus mirabilis HI4320

source_name: LB

label_protocol: RNA (4 μg), obtained from cultured P. mirabilis, was used as a template for cDNA synthesis and was labeled with Cyanine 5 (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: Cultured in LB broth at 37C (mid-log).

extract_protocol: 1 ml of culture was added to 2 ml RNA Protect. RNA was isolated using the RNEasy kit (Qiagen) according to the manufacturer’s instructions, except that 3 mg/ml lysozyme was added to cells for 15 min. DNA was digested using Turbo-DNAfree DNase (Ambion).

tag: strain

tag: medium

value: LB broth

source_name: low iron

label_protocol: RNA (4 μg), obtained from cultured P. mirabilis, was used as a template for cDNA synthesis and was labeled with Cyanine 3 (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: Cultured in LB broth + 15uM Desferal at 37C (mid-log).

value: LB broth + Desferal


title: LB vs low iron array #5

description: This array compared the P. mirabilis transcriptome during logarithmic-phase growth in LB broth to logarithmic-phase growth in iron-restricted LB broth. This is array #5 of 5.


title: Monocyte_patient50_time5


title: LB vs low iron array #4

description: This array compared the P. mirabilis transcriptome during logarithmic-phase growth in LB broth to logarithmic-phase growth in iron-restricted LB broth. This is array #4 of 5.


title: Monocyte_patient41_time7


title: Monocyte_patient45_time5


title: LB vs low iron array #1

description: This array compared the P. mirabilis transcriptome during logarithmic-phase growth in LB broth to logarithmic-phase growth in iron-restricted LB broth. This is array #1 of 5.

label_protocol: RNA (4 μg) was used as a template for cDNA synthesis and was labeled with Cyanine 5 (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: Cultured in LB broth at 37C to OD600 = 0.744 (mid-log).

label_protocol: RNA (4 μg) was used as a template for cDNA synthesis and was labeled with Cyanine 3 (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: Cultured in LB broth + 15uM Desferal at 37C to OD600 = 0.604 (mid-log).


title: Monocyte_patient50_time9


title: Buffycoat_patient51_time7

source_name: Buffycoat


title: Monocyte_patient51_time7


title: Monocyte_patient50_time3


title: Buffycoat_patient50_time9


title: LB vs low iron array #2

description: This array compared the P. mirabilis transcriptome during logarithmic-phase growth in LB broth to logarithmic-phase growth in iron-restricted LB broth. This is array #2 of 5.


title: Monocyte_patient45_time7


title: Buffycoat_patient50_time7


title: Monocyte_patient41_time1


title: Monocyte_patient45_time1


title: Monocyte_patient41_time11


title: Monocyte_patient45_time3


title: Monocyte_patient45_time9


title: Buffycoat_patient51_time9


title: Monocyte_patient41_time9


title: Monocyte_patient41_time3


title: Buffycoat_patient51_time5


title: Buffycoat_patient45_time7


title: Buffycoat_patient50_time11


title: Buffycoat_patient51_time1


title: Buffycoat_patient50_time5


title: Buffycoat_patient51_time3


title: Buffycoat_patient50_time1


title: Buffycoat_patient45_time5


title: Buffycoat_patient50_time3


title: Buffycoat_patient45_time9


title: Buffycoat_patient45_time3


title: Buffycoat_patient45_time1


title: Buffycoat_patient41_time7


title: Buffycoat_patient41_time11


title: Buffycoat_patient41_time5


title: Buffycoat_patient41_time9


title: ES Differentiation HD day 4_withLIF

city: Stanford

first: Nesanet

last: Mitiku

state: CA

address: 300 Pasteur Drive Alway M313

department: Genetics

institute: Stanford University

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74157.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 4 d

hyb_protocol: see channel 2 labeling protocol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.78; Parameter Scan Time = 23:30:41; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 26682; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.08; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.78; Parameter Scan Time = 23:30:41; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 25404; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.12; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: REF

label_protocol: see channel 2 labeling protocol

extract_protocol: Reference RNA extraction: The common reference used in this work was comprised of a mixture of maternal brain, E17.5 embryo, E17.5 placenta, and CGR8 ES cells.  All tissues used in the reference RNA pool, with the exception of CGR8 ES cells, were ground via mortar and pestle in the presence of liquid nitrogen.  The resulting powder was put through one acid phenol extraction, two Trizol (Invitrogen) extractions, DNAse I (Ambion) treated, and then re-purified over RNAqueous Midi columns (Ambion).  The ES cell component of the reference pool was purified similarly beginning with the acid phenol extraction.  In lieu of mortar and pestle grinding, ES cells were spun down and directly resuspended in solution D.  Total RNA from all four sources was combined at a proportion of 1:1.5:2:2.5 (brain:placenta:ES cells:E17.5 embryos, according to mass) and linearly amplified (mMessageAmp, Ambion).  All reference amplification reactions were then pooled. This reference aRNA pool was used for all hybridizations.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku

tag: REF

source_name: EXP

label_protocol:
Linear Amplification; RNA  Linear Amplification  As sample quantity and, as a result, RNA quantity was limiting , purified total RNA samples were linearly amplified (Eberwine 1996).  1000ng of total RNA were used in each amplification reaction using the mMessageAmp kit (Ambion).  First strand synthesis was carried out for 2 hours at 42degC with a heated lid (47degC) in an Eppendorf thermocycler.  Immediately after first strand synthesis, a denaturing step was carried out for 10 minutes at 70degC with the thermocycler lid heated to 80degC.  Samples were then quickly spun down and placed on ice while preparations were made for the second strand synthesis reaction.  Second strand synthesis was carried out for 2 hours at 16degC without a heated lid.  cDNA template purification was carried out per the manufacturer?s recommendations.  Synthesis of amplified RNA (aRNA) from the resulting purified cDNA template mix was carried out at 37degC for 10 hours.   aRNA samples were then treated with DNAse for 45 minutes and further purified according to manufacturer instructions.  5 mcL of the final aRNA product was examined for both sample integrity and assessment of amplification efficiency via agarose gel electrophoresis.; Protocol Type = Amplification; Performer: Nesanet,,Mitiku
Sample Labeling; Microarray Methods: Labeling and Hybridization Each labeling reaction was carried out using 4 mcg of aRNA , 10 mcg of pDN6 (Amersham), 0.6 mcL 50X dNTPs (Invitrogen), 3 mcL 0.1M DTT, 3 mcL Cy3 or Cy5 dUTP and 2mcL Superscript II (Invitrogen) reverse transcriptase in the supplied buffer.  Samples were incubated at 42°C for 2 hours in an Eppendorf cycler with the lid heated to 47°C.  Each labeling reaction was stopped via the addition of 15 mcL of 0.1N NaOH + 2mM EDTA followed by incubation at 70°C for 10 min.  15 mcL of 0.1N HCL was added to neutralize each sample.  Cy3 and Cy5 samples for a single hybridization were combined.  Labeled aRNA samples were then purified over Microcon YM-30 columns (Millipore); samples were washed 5X with TE buffer and suspended in a volume of 10.14 mcl TE by the end of purification.; Protocol Type = Labeling; Performer: Nesanet,,Mitiku

extract_protocol:
ES Cell Differentiation with LIF --> Culture conditions; Passage 13 CGR8 ES cells were grown in GMEM-based cell media (500 mL GMEM, 5 mL 200mM Glutamine, 5 mL 100mM MEM Sodium Pyruvate, 5 mL 100mM MEM Non Essential Amino Acids, 50 mL Characterized FBS (Hyclone), 50 mcL Leukemia Inhibitory factor (ESGro, Chemicon), 0.56 mL 1000X Beta-mercaptoethanol stock) in an incubator with 6% carbon dioxide at 37°C.  Sub-confluent monolayer cultures were split 1:10 every other day using trypsin.  Briefly, used growth media was removed, cells were washed once in phosphate buffered saline (Gibco BRL), trypsin solution was applied at a volume appropriate to the current flask size (25cm2 flask = 1mL; 75cm2 flask = 3mL; 150cm2 flask = 5mL), and cells were incubated in trypsin solution for 2 minutes at 37°C followed by further dissociation via pipetting.  Trypsin activity was terminated by the addition of 9 volumes of ES cell media.  The cells were then spun down at 1200g for 3 minutes swing bucket table top, diluted in fresh ES cell media, and plated on an appropriate gelatin-coated surface.  On intervening days, old growth media was exchanged for fresh pre-warmed ES cell media. In preparation for differentiation, sub-confluent ES cells were split 1:15 two days prior to the start of the differentiation timecourse.  This resulted in 70% confluence on day 0 of the differentiation timecourse.  Cells were released from the flask surface by trypsinization as described above.  Differentiation media was identical to the standard ES cell media.  Cell counts were assessed twice in preparation for hanging drop cultures: once of the stock resulting from trypsin inactivation and once of a 1:10 dilution of that stock.  The average of the two calculations was used as the final post-trypsinization cell concentration.  The ES cells were then diluted in media in order to achieve a concentration approximately 880 cells per 25 mcL volume.  Forty drops of 25 mcL cell suspension were applied to the lid of each 10cm Petri dish.  Each lid was then carefully inverted and placed over its corresponding Petri dish bottom.  The cell suspension drops were thus ?hanging drops.?  Each Petri dish bottom contained 10mL of prewarmed (37°C) PBS in order to keep the drops adequately hydrated.  Within each drop, resident cells move toward the lowest point and aggregate, forming embryoid bodies (EBs) within the first day of suspension culture.   After two days in hanging drop culture, EBs were transferred to ordinary suspension culture.  For this purpose, the appropriate number of 6 well Costar low adhesion plates (Corning) were pre-incubated with fresh prewarmed differentiation media for greater than 20 minutes at 37°C.  Subsequently, 20 EBs were transferred to each well of a 6-well plate.; Protocol Type = Growth Conditions; Performer: Nesanet,,Mitiku
Sample Extraction: Experimental Sample RNA Isolation  Total RNA was prepared using a variation on the acid phenol method of Chomczynski et al(Chomczynski and N. 1987).  The method of sample homogenization in solution D (4M guanidinium thiocyanate, 100mM NaOAc, 0.5% Sarkosyl, 0.1M beta-mercaptoethanol)  varied according to the composition of the sample from which RNA was being extracted.  Suspension growth embryoid bodies (EBs) were transferred into microfuge tubes, washed twice with phosphate buffered saline, and then resuspended in solution D; homogenization was achieved through pipetting.  Adherent cells were washed twice with phosphate buffered saline, lysed on the plate with solution D, scraped vigorously with a cell scraper, passed 2-3times through a 27 gauge needle, and then transferred to a microfuge tube.  Homogenized samples were stored at -80degC until RNA isolation.   On the day of RNA isolation, solution D-homogenized samples were defrosted and vortexed to ensure complete mixing.  As the initial volume of lysate was in accordance to the initial sample quantity, lysate volumes were variable, and solution volumes throughout the RNA isolation were adjusted for the initial lysate volume.  Initial lysate volumes were one of the following: 650 mcL/400 mcL/300 mcL/100 mcL.  Lysates were stored at -80degC.  Phase Lock Gel-Heavy (PLGH) tubes were prespun at 1500g for 30sec in order to collect the gel at the bottom of the microfuge tube.  65 mcL/40 mcL/30 mcL/10 mcL NaOAc pH 4.0 was added to each defrosted sample, followed by 400mcL H20-saturated phenol.  The lysate-NaOAc-phenol mix was added to the PLGH tubes and incubated for 5 minutes at room temperature.  487.5 mcL/300 mcL/225 mcL/75 mcL chloroform:isoamyl alcohol was added to each differentiation timecourse sample.  Each tube was shaken vigorously for 15 seconds and then less vigorously for 2 minutes.  Samples were incubated for 15 minutes at room temperature and the centrifuged at 12000g for 15 minutes at room temperature.  The clear aqueous phase above the Phase Lock Gel layer was carefully removed and transferred into a fresh nuclease-free tube.  In order to precipitate the RNA, the following were added to each sample: 1/10th vol 5mcL linear acrylamide (Ambion), and 1X vol isopropanol.  Samples were then incubated on dry ice or -80degC for a minimum of 1 hour.  After defrosting, 1/10th vol NaOAc pH 4.0 was added to each sample, followed by 1X vol mcL H20-saturated phenol.  1/5th vol of chloroform:isoamyl alcohol was added to each sample.  Samples were mixed via inversion then incubated on ice for 15 minutes.  After this incubation, samples were centrifuged at 20817g for 15 minutes at room temperature.  The top phase of each sample was removed and deposited in a fresh nuclease-free tube.  Samples were then precipitated at -80degC using 1/10th vol NaOAc, 5 mcL linear acrylamide (Ambion), and 1X vol isopropanol.   Prior to starting the second round of purification, the samples were defrosted on ice, and centrifuged at 20817g for 30 minutes at room temperature.  After removal o f all isopropanol, the resulting pellet was resuspended in sample lysis buffer (RNAqueous Mini kit, Ambion).  During this step, the provided silica-based filter cartridges were assembled in microfuge tubes.  Following dissolution of the pellet, 400mcL of 64% ethanol was added.  Mixing was achieved through pipeting 2-3 times.  The resulting mixture was immediately applied to the previously prepared filter cartridges.  After centrifugation at 13000g for 1 minute, the flow-through was discarded.  Subsequently, each cartridge was washed once with 700mcL of Wash Solution #1 and twice with 500 mcL of Wash Solution #2.  Cartridges were spun for 1 minute in the absence of wash solution in order to remove any residual ethanol.  Purified RNA was eluted into a fresh nuclease free tube with nuclease-free H20 preheated to 75degC.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku

tag: EXP


title: Buffycoat_patient41_time1


title: Buffycoat_patient41_time3


title: ES Differentiation HD day 13_withLIF

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74165.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 13 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.51; Parameter Scan Time = 01:23:07; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 26806; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 1.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.51; Parameter Scan Time = 01:23:07; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 25528; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.16; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 13_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74149.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 13 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.74; Parameter Scan Time = 00:00:25; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-18; Parameter Pixel Size = 10; Parameter Laser on time = 25270; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.74; Parameter Scan Time = 00:00:25; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-18; Parameter Pixel Size = 10; Parameter Laser on time = 23991; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 2_withLIF

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74154.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 2 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.08; Parameter Scan Time = 22:35:33; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 26639; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.08; Parameter Scan Time = 22:35:33; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 25360; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 9_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74147.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 9 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.50; Parameter Scan Time = 23:30:05; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 25240; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.50; Parameter Scan Time = 23:30:05; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 23961; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 3_withLIF

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74156.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 3 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.47; Parameter Scan Time = 23:03:36; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 26663; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.26; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.47; Parameter Scan Time = 23:03:36; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-08; Parameter Pixel Size = 10; Parameter Laser on time = 25385; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 11_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74148.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 11 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.59; Parameter Scan Time = 23:43:58; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 25253; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.59; Parameter Scan Time = 23:43:58; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 23974; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 1_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74139.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 1 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.97; Parameter Scan Time = 22:02:41; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-01; Parameter Pixel Size = 10; Parameter Laser on time = 26046; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.03; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.97; Parameter Scan Time = 22:02:41; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-01; Parameter Pixel Size = 10; Parameter Laser on time = 24767; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 6_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74144.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 6 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.98; Parameter Scan Time = 22:45:15; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 25195; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.98; Parameter Scan Time = 22:45:15; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-17; Parameter Pixel Size = 10; Parameter Laser on time = 23916; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 8_withLIF

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74161.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 8 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.30; Parameter Scan Time = 00:39:31; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 26763; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.30; Parameter Scan Time = 00:39:31; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 25484; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 17_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74136.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 17 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.30; Parameter Scan Time = 01:52:40; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-25; Parameter Pixel Size = 10; Parameter Laser on time = 25749; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.30; Parameter Scan Time = 01:52:40; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-25; Parameter Pixel Size = 10; Parameter Laser on time = 24470; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 7_withLIF

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74160.gif
Measurement: concentration(absolute) 0.1 volume/volume_percent
Measurement: time(absolute) 7 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 7040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 00:24:39; Parameter PMT Volts = 540; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 26748; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 00:24:39; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-09; Parameter Pixel Size = 10; Parameter Laser on time = 25470; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.14; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku


title: ES Differentiation HD day 3_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74126.gif
Measurement: concentration(absolute) 0 volume/volume_percent
Measurement: time(absolute) 3 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.94; Parameter Scan Time = 22:39:47; Parameter PMT Volts = 540; Parameter Scan Date = 2005-04-24; Parameter Pixel Size = 10; Parameter Laser on time = 25556; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.24; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.94; Parameter Scan Time = 22:39:47; Parameter PMT Volts = 660; Parameter Scan Date = 2005-04-24; Parameter Pixel Size = 10; Parameter Laser on time = 24277; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku