title: Control for non-specific binding for GFP antibody (Whole Genome # 4, Replicate # 1)


title: Control for non-specific binding for GFP antibody (Whole Genome # 4, Replicate # 3)

status: Public on Mar 16 2009

type: genomic

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

country: USA

institute: MD Anderson Cancer Center

description: Chromatin immunoprecipitation control experiments on Affymetrix whole genome tiling arrays 2.0R with GFP antibodies  in MCF7 cells (ChIP).

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

data_processing: Tiling array data were normalized and analyzed as described (Cawley et al, 2004).  Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions.  Significantly enriched probes (p < 1e-4) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin Immunoprecipitated DNA

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

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

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

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

tag: cell type

value: wild type MCF7 cells

tag: antibody

value: Goat anti-eGFP


title: 7041

city: Boston

first: Cheng

last: Li

state: MA

address: 44 Binney St

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: High molecular weight DNA from DLBCLs and sex-matched normal control DNAs (Stratagene) were differentially labeled with Cy3 and Cy5  and co-hybridization to the array CGH platform, as recommended by the manufacturer (Agilent Technologies).

scan_protocol: The arrays were scanned and the intensity of the hybridization signals obtained using the Feature Extraction software (Agilent Technologies).

data_processing: The log10 data of the 44K CGH probes (LogRatio column in the  individual text files) of all array CGH samples were organized into a single data file. The  data were read into to the dChip software (www.dchip.org, version 6/7/08) and the log10  ratios were converted to log2 ratios. The probe chromosome and position information  were used to visualize the data in dChip according to probe genome positions. Data  quality check. We inspected the sample quality visually according the log2 ratio curves  and excluded 13 samples with noisy or very low signals throughout the genome. The 77  remaining samples were used in the following analyses. First, for each probe, we  computed the median log2 ratio across all samples and subtracted this median value from  all samples. This step removed regional systematic gain or loss patterns, which are likely  due to the bias in the hybridization process or the control channel sample. Second, data  quality verification was performed for the each probe included in the array. We observed  the existence of “spike probes”, which showed significantly outlying higher or lower  signals comparing to their neighboring probes in multiple samples (defined as absolute  value of log 2 ratio >= 1 in more than 20% of samples). Thus, we computed a correlation  score across all samples between each probe data vector and the average data vector of all  “spike probes”; a threshold >0.5 was then used to exclude these underperforming probes  (n= 4158) from the downstream analysis. Thus, the actual number of probes in miRTile is  37113 and its resolution (mean probe spacing) in the focally covered areas is 319bp.  Obtaining the miRNA-level data. To obtain the miRNA genes copy number data we first  organized the probes into miRNA regions. Each region extends the positions of the  precursor miRNAs by ~ 17 Kb in the upstream and downstream directions to include all  the CGH probes in that region; two or more such extended areas could be merged into  one miRNA region (due to the common clustering of miRNA genes) containing multiple  miRNA genes. The log2 ratio values of all the probes in a region were averaged to obtain  the miRNA region-level log2 ratios and copy number summary plots displayed the  proportion of the samples that have copy number gain (>=2.5) or loss (<=1.5) for all  miRNA regions.

source_name: Frozen DLBCL sample

growth_protocol: Primary tumors were flash frozen after excision. Cell lines were grown in RPMI 10% serum prior to DNA isolation

extract_protocol: High molecular weight genomic DNA was isolated from the frozen DLBCL samples and DLBCL cell lines using the Blood & Cell Culture DNA Maxi Kit from Qiagen. DNA quality was verified by spectrophotometry and gel electrophoresis.

tag: cell line

value: DLBCL

tag: tumor site

value: Lymph Node

tag: cell of origin classifiction defined by ihc

value: Non-GCB

tag: infiltrating t-cells

source_name: sex-matched normal control DNA

tag: tissue

value: normal


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

description: Input DNA from MCF-7 cells hybridized on Affymetrix whole genome tiling arrays 2.0R.

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

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with nuclear receptor ligand or vehicle at 80% confluence.

value: MCF7 cells


title: 7089

label_protocol: High molecular weight DNA from DLBCLs and sex-matched normal control DNAs (Stratagene) were differentially labeled with Cy3 and Cy5  and co-hybridization to the array CGH platform, as recommended by the manufacturer (Agilent Technologies).

value: GCB


title: GATA3 localization in MCF7 (Whole Genome # 4, Replicate # 3)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for GATA3 in MCF7 cells (ChIP).

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

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with vehicle at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: transgenic MCF7 cells

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing green fluorescent protein (GFP)

value: Goat anti-GFP


title: GATA3 localization in MCF7 (Whole Genome # 4, Replicate # 1)


title: Control for non-specific binding for GFP antibody (Whole Genome # 4, Replicate # 2)


title: GATA3 localization in MCF7 (Whole Genome # 4, Replicate # 2)


title: FoxA1 localization in MCF7 (Whole Genome # 4, Replicate # 3)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for FoxA1 in MCF7 cells (ChIP).

value: goat anti-foxa1 (abcam:ab5089)


title: 6614


title: 6902


title: FoxA1 localization in MCF7 (Whole Genome # 4, Replicate # 2)


title: 5935


title: 7119


title: 5782


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

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

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (CD437 at 100 nM) or vehicle (100% DMSO) treatments, cells were changed to hormone-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM CD437 at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: RARG


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


title: FoxA1 localization in MCF7 (Whole Genome # 4, Replicate # 1)


title: 6290


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


title: 5028

value: Extra-nodal


title: 5081


title: 5485


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

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

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (AM580 at 100 nM) or vehicle (100% DMSO) treatments, cells were changed to hormone-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM AM580 at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: RARA


title: 4470


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


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


title: 5186


title: 4554


title: 4522


title: 4494


title: Control for non-specific binding for GFP antibody (Whole Genome # 2, Replicate # 3)


title: 4450


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


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


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


title: 4021


title: Control for non-specific binding for GFP antibody (Whole Genome # 2, Replicate # 1)


title: 4221


title: 4236


title: Control for non-specific binding for GFP antibody (Whole Genome # 2, Replicate # 2)


title: 4350


title: 3832


title: 3466


title: 3717


title: GATA3 localization in MCF7 (Whole Genome # 2, Replicate # 3)


title: FoxA1 localization in MCF7 (Whole Genome # 2, Replicate # 3)


title: 3279


title: FoxA1 localization in MCF7 (Whole Genome # 2, Replicate # 1)


title: 3409


title: GATA3 localization in MCF7 (Whole Genome # 2, Replicate # 1)


title: FoxA1 localization in MCF7 (Whole Genome # 2, Replicate # 2)


title: 3122


title: 2633


title: PDGF-BB stimulation for 24h_replicate2

type: RNA

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: 24h PDGF-BB stimulation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5 (GCOS) : the scaling factor using all probe sets was set to 100 and the normalization factor was set to 1

label: Biotin

molecule: total RNA

source_name: AG01518 forskin human fibroblasts

label_protocol: Standard Affymetrix protocol

growth_protocol: Human foreskin fibroblasts (AG01518) were cultured (1.5E6 cells/10 cm dish) in MEM medium with 10% fetal calf serum and glutamine for 24h, then washed and incubated for 47h in serum-free medium. Cells were stimulated for 1h by PDGF-BB (25ng/ml) or b-FGF (10ng/ml, + heparine 50 microg/ml). Alternatively, cells were incubated for 24h in starvation medium and treated for 24h with growth factors, or left untreated for 48h in serum-free medium (control treatment).

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Cells were stimulated for 24h or 1h by PDGF-BB (25 ng/ml) or b-FGF (10 ng/ml + heparine 50 microg/ml)

tag: Normal Fibroblasts


title: 3271


title: 3002


title: 2202


title: 1650


title: PDGF-BB stimulation for 1h_replicate2

description: 1h PDGF-BB stimulation


title: 1750


title: 1423


title: 1326


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


title: b-FGF stimulation for 24h_replicate2

description: 24h b-FGF stimulation


title: Unstimulated Control_replicate2

description: Unstimulated Control

treatment_protocol: Cells left untreated for 48h in serum-free medium (control treatment).


title: GATA3 localization in MCF7 (Whole Genome # 2, Replicate # 2)


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


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


title: 3416


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


title: 1143


title: 1309


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


title: 1320


title: Unstimulated Control_replicate1

description: Unstimulated Control


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


title: Control for non-specific binding for GFP antibody (Whole Genome # 5, Replicate # 3)


title: b-FGF stimulation for 1h_replicate1

description: 1h b-FGF stimulation


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


title: 642


title: PDGF-BB stimulation for 1h_replicate1

description: 1h PDGF-BB stimulation


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


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


title: 559


title: PDGF-BB stimulation for 24h_replicate1

description: 24h PDGF-BB stimulation


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


title: Control for non-specific binding for GFP antibody (Whole Genome # 5, Replicate # 1)


title: 865


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


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


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


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


title: GATA3 localization in MCF7 (Whole Genome # 5, Replicate # 2)


title: FoxA1 localization in MCF7 (Whole Genome # 5, Replicate # 3)


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


title: FoxA1 localization in MCF7 (Whole Genome # 5, Replicate # 2)


title: 517


title: b-FGF stimulation for 24h_replicate1

description: 24h b-FGF stimulation


title: FoxA1 localization in MCF7 (Whole Genome # 5, Replicate # 1)


title: GATA3 localization in MCF7 (Whole Genome # 5, Replicate # 1)


title: Control for non-specific binding for GFP antibody (Whole Genome # 6, Replicate # 3)


title: Control for non-specific binding for GFP antibody (Whole Genome # 3, Replicate # 3)


title: Control for non-specific binding for GFP antibody (Whole Genome # 6, Replicate # 2)


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


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


title: Control for non-specific binding for GFP antibody (Whole Genome # 6, Replicate # 1)


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


title: Control for non-specific binding for GFP antibody (Whole Genome # 3, Replicate # 2)


title: Control for non-specific binding for GFP antibody (Whole Genome # 3, Replicate # 1)


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


title: GATA3 localization in MCF7 (Whole Genome # 3, Replicate # 3)


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


title: GATA3 localization in MCF7 (Whole Genome # 6, Replicate # 3)


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


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


title: GATA3 localization in MCF7 (Whole Genome # 3, Replicate # 2)


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


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


title: GATA3 localization in MCF7 (Whole Genome # 6, Replicate # 2)


title: GATA3 localization in MCF7 (Whole Genome # 6, Replicate # 1)


title: GATA3 localization in MCF7 (Whole Genome # 3, Replicate # 1)


title: Control for non-specific binding for GFP antibody (Whole Genome # 7, Replicate # 3)


title: FoxA1 localization in MCF7 (Whole Genome # 6, Replicate # 3)


title: Control for non-specific binding for GFP antibody (Whole Genome # 7, Replicate # 2)


title: Control for non-specific binding for GFP antibody (Whole Genome # 7, Replicate # 1)


title: FoxA1 localization in MCF7 (Whole Genome # 6, Replicate # 2)


title: FoxA1 localization in MCF7 (Whole Genome # 3, Replicate # 3)


title: Control for non-specific binding for GFP antibody (Whole Genome # 5, Replicate # 2)


title: GATA3 localization in MCF7 (Whole Genome # 7, Replicate # 2)


title: FoxA1 localization in MCF7 (Whole Genome # 6, Replicate # 1)


title: GATA3 localization in MCF7 (Whole Genome # 7, Replicate # 1)


title: FoxA1 localization in MCF7 (Whole Genome # 3, Replicate # 1)


title: FoxA1 localization in MCF7 (Whole Genome # 7, Replicate # 3)


title: FoxA1 localization in MCF7 (Whole Genome # 7, Replicate # 2)


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


title: FoxA1 localization in MCF7 (Whole Genome # 7, Replicate # 1)


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


title: b-FGF stimulation for 1h_replicate2

description: 1h b-FGF stimulation


title: GATA3 localization in MCF7 (Whole Genome # 7, Replicate # 3)


title: RARG localization in MCF7 (Whole Genome # 6, Replicate # 2)


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


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


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


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


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


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


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


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


title: RARA localization in MCF7 (Whole Genome # 6, Replicate # 2)


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


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


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


title: Rac1+/- vs. Rac1+/+, rep. S67

city: Cambridge

first: Naoki

last: Sawada

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

description: Rac1+/- and Rac1+/+ mice were littermates and used at 12 weeks. Genetic background: 129SV backcrossed to C57/Bl6 8 times

hyb_protocol: Hybridization was performed at 46˚C overnight.

scan_protocol: Images were acquired using Axon (Molecular Devices) 4000B 2-color single-slide scanner.

data_processing: Filtering and normalization of the raw data were conducted using BASE software. All spots were sequentially subjected to background subtraction, Lowess normalization, and brightness filtering that removed spots with intensities less than 200. This processing resulted in 12,089 reporters (gene features) comprising 45,311 spots from the 4 slides.

organism: Mus musculus

source_name: Steady-state, continuously cultured Rac1+/- ECs

label_protocol: Fluorescent dye labeling was performed using the Atlas Powerscript Fluorescent Labeling Kit (Clontech). Isolated total RNA (8 µg) was reverse transcribed into amine modified cDNA using random hexamers and oligo (dT) primers. The cDNA was labeled via a coupling reaction to the Cy3 or Cy5 dye, then purified and concentrated.

growth_protocol: Mouse primary ECs were isolated from the heart by an affinity selection method using Dynabeads sheep anti-rat IgG (Invitrogen) and anti-PECAM1 antibody (BD Biosciences). The cells were cultivated in DMEM containing 20% FCS, heparin (100 ｵg/ml), penicillin (100 U/ml), streptomycin (100 ｵg/ml) and endothelial cell growth factor (ECGF, 50 ｵg/ml), and grown on dishes coated with 0.1% gelatin. After 8 days, the cells were trypsinized and underwent the second selection using Dynabeads plus anti-ICAM2 antibody (BD Biosciences). The cells were continuously grown and passaged. Total RNA was isolated from subconfluent cells at passage 4.

extract_protocol: High quality total RNA was prepared by 2-step purification through the sequential use of Trizol reagent (Invitrogen) and RNeasy columns (Qiagen) according to the manufacturerﾕs instructions. The quality control of RNA was conducted by measuring the 28S/18S rRNA ratio using Agilent 2100 BioAnalyzer.

treatment_protocol: Cells grown under static condition in the growth medium described in growth protocol were used for total RNA isolation.

tag: strain

source_name: Steady-state, continuously cultured Rac1+/+ ECs


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


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


title: Rac1+/- vs. Rac1+/+, rep. S70


title: Rac1+/- vs. Rac1+/+, rep. S63


title: Human_TK40T_clinically isolated tissue

status: Public on Mar 14 2009

city: Itabashi

first: shinobu

last: Masuda

state: Tokyo

address: 30-1 Ohyaguchikami-cho

department: pathology

country: Japan

institute: Nihon Univeristy School of Medicine

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: According to standard Affymetrix protocol. 15ug of cRNA was fragmented, fragmented product was checked on gel(average size 100nt), Hybridization cocktail added and hybed on HG_U133A arrays. Washed with non-stringent wash buffer (A) and stained with SAPE solution.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human breast cancer

label_protocol: Enzo Biotin labeling

growth_protocol: not received any pre-operative adjuvant hormone or chemotherapy

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Tissues were surgically isolated and were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was extracted using the Sepasol-I (WAKO)

tag: clinical isolate, flash-frozen


title: Human_TK39T_clinically isolated tissue


title: Human_TK43T_clinically isolated tissue


title: Human_TK38T_clinically isolated tissue


title: FoxA1 localization in MCF7 (Whole Genome # 3, Replicate # 2)


title: Human_TK41T_clinically isolated tissue


title: Rac1+/- vs. Rac1+/+, rep. S66


title: Human_TK34T_clinically isolated tissue


title: Human_TK35T_clinically isolated tissue


title: Human_TK37T_clinically isolated tissue


title: Human_TK42T_clinically isolated tissue


title: Human_TK33T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_05

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

hyb_protocol: The cRNA (1.5 µg) was mixed with hybridization buffer and added to the BeadChips for hybridization at 58°C for 18 hours according to the manufacturer's protocol. BeadChips were then washed, blocked, and stained with streptavidin-Cy3, before they were washed again and dried by centrifugation.

scan_protocol: The BeadChips were scanned on the Illumina BeadStation according to the manufacturer's protocol

data_processing: Raw signal intensities were log2 transformed and cubic spline normalized in BeadStudio software v 3.2

source_name: Peripheral Blood Mononuclear Cells from patients cured with no malaria symptons

label_protocol: 300 ng of total RNA was reverse transcribed and in vitro transcribed to cRNA using the Illumina TotalPrep RNA Amplification Kit (Illumina) according to the manufacturer's protocol

growth_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were isolated from undiluted whole blood on Ficoll-paque Plus (GE Healthcare) per the manufacturer’s recommendations. After isolation, PBMCs were washed in PBS and frozen as described below.

extract_protocol: Total RNA was extracted from PBMCs using an RNeasy kit (Qiagen) following the manufacturer’s recommendations. RNA integrity and purity was analyzed with an Experion Automated Electrophoresis System (Bio-Rad) and a ND-1000 spectrophotometer (NanoDrop Technologies Inc.).

treatment_protocol: Cells were immediately frozen at -80°C in RNeasy extraction buffer (Qiagen).

tag: gender

value: Female

tag: age

tag: symptoms

value: PBMC 3-4 weeks after treatment; individual cured and without symptoms.


title: PBMCs_cured_no_symptoms_patient_11

value: Male


title: PBMCs_with_malaria_symptoms_patient_01

source_name: Peripheral Blood Mononuclear Cells from patients with malaria symptons

value: PBMC in parasitemic, symptomatic (fever, headache, etc) individual prior to treatment


title: Human_TK31T_clinically isolated tissue


title: Human_TK36T_clinically isolated tissue


title: Human_TK30T_clinically isolated tissue


title: Human_TK32T_clinically isolated tissue


title: Human_TK29T_clinically isolated tissue


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


title: Human_TK28T_clinically isolated tissue


title: Human_TK27T_clinically isolated tissue


title: T+L24h rep2

city: Madrid

first: Eduardo

last: Lopez-Collazo

address: Paseo de la Castellana, 261

country: Spain

institute: Research Unit, Hospital La Paz

description: Human monocyte exposure to LPS 8h. Wash and leaving at incubator for 16 h. After that, the cells were re-stimulated with 10 ng/ml LPS 24h

hyb_protocol: According to Illumina Protocol

scan_protocol: Illumina BeadScan

data_processing: Data were normalized with cross-correlation method and differential expression was based on the mean of the log2 fold changes.

source_name: Endotoxin-tolerant human monocytes re-stimulated with LPS 24h

label_protocol: According to Illumina Protocol

growth_protocol: For microarray transcriptome profiling of LPS tolerized human monocytes restimulated with LPS for 3, 6 and 24h.  Human monocytes were isolated from buffy coats and cultured in DMEM media containing antibiotics (100IU/ml penicillin and 100ug/ml streptomycin; Invitrogen) for 2h. Non-adherant cells were removed by washing and cells were thereafter cultured in DMEM media containing antibiotics (100IU/ml penicillin and 100ug/ml streptomycin; Invitrogen) and 10% heat inactivated fetal calf serum (Pasching, Austria). These cells were used for all subsequent treatments described above.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and column-purified with RNeasy kits (Qiagen).

value: Human monocyte


title: T+L24h rep1


title: PBMCs_with_malaria_symptoms_patient_04


title: PBMCs_cured_no_symptoms_patient_06


title: PBMCs_cured_no_symptoms_patient_02


title: GATA3 localization in MCF7 (Whole Genome # 5, Replicate # 3)


title: Human_TK25T_clinically isolated tissue


title: Human_TK24T_clinically isolated tissue


title: Human_TK26T_clinically isolated tissue


title: T+L6h rep2

description: Human monocyte exposure to LPS 8h. Wash and leaving at incubator for 16 h. After that, the cells were re-stimulated with 10 ng/ml LPS 6h

source_name: Endotoxin-tolerant human monocytes re-stimulated with LPS 6h


title: PBMCs_cured_no_symptoms_patient_13


title: Human_TK23T_clinically isolated tissue


title: T+L6h rep1


title: Human_TK22T_clinically isolated tissue


title: Human_TK20T_clinically isolated tissue


title: Human_TK19T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_14


title: T+L3h rep1

description: Human monocyte exposure to LPS 8h. Wash and leaving at incubator for 16 h. After that, the cells were re-stimulated with 10 ng/ml LPS 3h

source_name: Endotoxin-tolerant human monocytes re-stimulated with LPS 3h


title: T+L3h rep2


title: Human_TK16T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_07


title: PBMCs_cured_no_symptoms_patient_12


title: PBMCs_cured_no_symptoms_patient_08


title: PBMCs_cured_no_symptoms_patient_03


title: Tol rep2

description: Human monocyte exposure to LPS 8h. Wash and leaving at incubator for 16 h.

source_name: Endotoxin-tolerant human monocytes control


title: Human_TK18T_clinically isolated tissue


title: Tol rep1


title: Human_TK14T_clinically isolated tissue


title: Human_TK15T_clinically isolated tissue


title: Human_TK17T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_09


title: L24h rep2

description: Human monocyte exposure to 10 ng/m of LPS 24h

source_name: Human monocyte exposure to LPS 24h


title: L24h rep1


title: Human_TK13T_clinically isolated tissue


title: Human_TK12T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_04


title: Human_TK21T_clinically isolated tissue


title: Human_TK9T_clinically isolated tissue


title: Human_TK11T_clinically isolated tissue


title: PBMCs_cured_no_symptoms_patient_10


title: PBMCs_cured_no_symptoms_patient_01


title: Human_TK4T_clinically isolated tissue


title: Human_TK10T_clinically isolated tissue


title: L6h rep2

description: Human monocyte exposure to 10 ng/m of LPS 6h

source_name: Human monocyte exposure to LPS 6h


title: Human_TK5T_clinically isolated tissue


title: PBMCs_with_malaria_symptoms_patient_11


title: L3h rep2

description: Human monocyte exposure to 10 ng/m of LPS 3h

source_name: Human monocyte exposure to LPS 3h


title: Human_TK6T_clinically isolated tissue


title: L6h rep1


title: Human_TK3T_clinically isolated tissue


title: L3h rep1


title: Control rep2

description: Human monocyte control

source_name: Human monocyte control


title: PBMCs_with_malaria_symptoms_patient_05


title: PBMCs_with_malaria_symptoms_patient_13


title: Human_TK2T_clinically isolated tissue


title: bcl6 in OCI-LY7 replicate3

city: new york

first: weimin

last: ci

state: NY

address: 1300 York ave

department: medicine

institute: weill cornell college of medicine

description: chip-on-chip is performing in OCI-LY7 DLBCL cell line by BCL6 antibody.

hyb_protocol: described in www.nimblegen.com

scan_protocol: described in www.nimblegen.com

data_processing: Take all the probes in the promoter region and do Log2 transformed IP/INPUT(Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter

source_name: genomic DNA (input)

label_protocol: described in www.nimblegen.com

extract_protocol: sonicated genomic DNA, then purify by qiagen column

tag: type

value: Input

extract_protocol: chromatinIP products which are genomic regions bound by BCL6, then purify by qiagen column.

value: DLBCL

value: ChIP


title: PBMCs_with_malaria_symptoms_patient_02


title: PBMCs_with_malaria_symptoms_patient_08


title: Control rep1

description: Human monocyte control


title: bcl6 in OCI-LY1 replicate3

description: chip-on-chip is performing in OCI-LY1 DLBCL cell line by BCL6 antibody.

data_processing: Take all the probes in the promoter region and do Log2 transformed IP/INPUT(Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter.

extract_protocol: sonicated genomic DNA, then purify by qiagen column.

source_name: chromatinIP products which are genomic regions bound by BCL6


title: bcl6 in OCI-LY1 replicate1


title: valve at H, biological rep3

city: STARKVILLE

first: CAROL

middle: ANDREA

last: PREGONERO

state: MS

address: 130 Creelman Street

department: AG & BIO ENGINEERING

institute: MISSISSIPPI STATE UNIVERSITY

description: Gene expression data from aortic valve interstitial cells

hyb_protocol: Microarray hybridizations were performed in triplicate for each of the  experimental groups using Affymetrix Porcine Chips as described by the  manufacturer (Affymetrix Santa Clara, CA).

scan_protocol: The chips were then washed and stained with  streptavidin/phycoerythrin (SAPE) antibody solution using an Affymetrix FS-450 fluidics  station. GeneChips were scanned using the Affymetrix GeneChip scanner 3300.

data_processing: Images were processed with the Affymetrix GeneChip® Operating Software  (GCOS) and expression quantified with MAS 5.0, which also provides information on  signal, detection and calculated the detection p-value. Signal information is a numeric  value indicating transcript abundance for a particular probe set. Detection information  indicates whether the transcript is detected (P, present), undetected (A, absent), or if it is  at the limit of detection (M, marginal).The RAW signal intensities for all probes in of each microarray were normalized and log transformed. The t test with the option of unequal variance was used to calculate P values for each gene. The fold change and Q values for each gene were calculated with SAM program with permutation of 500 (57). A p value< 0.05 was considered statistically significant.

organism: Sus scrofa

source_name: Valve leaflets exposed to cyclic hypertensive pressure (0-120mmHg)

label_protocol: 70 ng total RNA from each sample was used for linear, two-cycle amplification by in vitro transcription and a total of 10 µg of single stranded cRNA was hybridized to GeneChip® Porcine Genome Array following the manufacturer’s set protocol (Affymetrix). The MEGAscript® T7 Kit (Ambion, Inc.) was used  for the first in vitro transcription (IVT). GeneChip IVT Labeling Kit was used for the  second IVT and labelling of RNA. Complementary RNA (cRNA) was fragmented and 10  μg of fragmented cRNA were hybridized to the Genechips in a Hybridization Oven, set to  45°C and rotations of 60 rpm for 16 hours

growth_protocol: Aortic valve leaflets were excised from adult female pigs (Sansing Meat Services, Maben, MS) and rinsed in ice-cold sterile PBS (Sigma, St Louis, MO). Endothelium was removed from leaflets using collagenase II solution (2 ug/ml, Worthington Biochemical Corp.). Leaflets were incubated overnight in DMEM supplemented with 10% FBS (Hyclone, Logan UT), and 1% ABAM (Sigma)

extract_protocol: Total RNA from six valve leaflets samples ( leaflets exposed to normotensive pressure as well as exposed to hypertensive pressure) was extracted using the Qiagen RNeasy Mini kit  following the manufacturer’s instructions and stored at -80 OC.  The quality and concentration of RNA was determined by Agilent Bioanalyzer.

treatment_protocol: Valve leaflets were placed in 6-well tissue culture plates in 3ml of DMEM supplemented with 10% Fetal Bovine Serum (FBS; Hyclone, Logan UT), and 1% antibiotic/anti-mycotic solution (Sigma)within a custom designed pressure bioreactor. Valve leaflets (n=3) were exposed to normotensive (0-80 mm Hg) and to hypertensive cyclic pressure (0-120 mmHg) at frequency of 1 Hz for 24 hours. Upon completion of experiments each leaflet was rinsed twice with sterile PBS, submerged in 1 ml of RNAlater RNA Stabilization Reagent (Qiagen, Valencia, CA) to avoid changes in RNA expression.

value: aortic valve leaflet

value: female


title: PBMCs_with_malaria_symptoms_patient_06


title: PBMCs_with_malaria_symptoms_patient_03


title: PBMCs_with_malaria_symptoms_patient_07


title: valve at H, biological rep2


title: bcl6 in OCI-LY7 replicate2

description: chip-on-chip is performing in OCI-LY7 DLBCL cell line by BCL6 antibody


title: bcl6 in OCI-LY7 replicate1


title: bcl6 in OCI-LY1 replicate2

description: chip-on-chip is performing in OCI-LY1 DLBCL cell line by BCL6 antibody


title: PBMCs_with_malaria_symptoms_patient_14


title: bcl6 in germinal center cells replicate3

description: chip-on-chip is performing in germinal center cells by BCL6 antibody.

value: germinal center cells


title: valve at H, biological rep1


title: bcl6 in germinal center cells replicate1


title: PBMCs_with_malaria_symptoms_patient_10


title: PBMCs_with_malaria_symptoms_patient_09


title: bcl6 in germinal center cells replicate2


title: valve at N, biological rep2

source_name: Valve leaflets exposed to cyclic normotensive pressure (0-80mmHg)


title: valve at N, biological rep1


title: valve at N, biological rep3


title: Hippocampus_Soman_168h_rep3

status: Public on Mar 13 2009

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description: Individually housed; controlled temperature and humidity;12h light/12h dark cycle; food and water ad libitum.

hyb_protocol: Spike controls were added to 15 µg fragmented cRNA before hybridization (36h) using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

scan_protocol: After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.

data_processing: Raw signal intensities were imported into Partek Genomics Solutions v6.3 (Partek, St. Louis, MO) and normalized using the robust multi-array averaging (RMA) algorithm (Irizarry et al., 2003)

organism: Rattus norvegicus

source_name: Hippocampus, soman, 168h

label_protocol: 10 µg of mRNA was used to generate first-strand cDNA using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Kits from Affymetrix).

extract_protocol: Frozen tissue was homogenized in Tri Reagent (Sigma Chemical Company, St. Louis, MO) and the RNA extracted according to the manufacturer's protocol. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). The quality and amount of RNA was monitored throughout processing with an Agilent Bioanalyzer (Agilent, Palo Alto, CA) and a NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, DE).

treatment_protocol: The soman exposure paradigm utilized in this study was based on the model developed by Shih et al. (1991) and McDonough et al. (1998).  Animals were pretreated with the oxime HI-6 (125 mg/kg, ip, obtained from the Walter Reed Army Institute of Research, Rockville, MD) 30 min prior to challenge with soman (180 μg/kg, sc; diluted with 0.9% sodium chloride; soman was obtained from the Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD). One minute after soman challenge, animals were treated with atropine methyl nitrate (2.0 mg/kg, im, Sigma-Aldrich, St. Louis, MO). Vehicle control animals (n=4; 2 euthanized at 1h, 1 euthanized at 12h, and 1 euthanized at 24h) received an equivalent volume of vehicle (0.9% sodium chloride), HI-6 and atropine. Naïve animals (n=3) were also included in the study and received no treatments.

tag: Sprague Dawley rats

tag: Gender

value: male

tag: Weight


title: Hippocampus_Soman_96h_rep3

source_name: Hippocampus, soman, 96h


title: 12wk BDC_1_rep2

city: Stanford

first: Hugh

middle: O

last: McDevitt

state: CA

department: Departments of Microbiology and Immunology and Medicine

institute: Stanford University School of Medicine

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68831.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1330, 5890; Software: type: feature extraction; Performer: Qing,,Li

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: NOD 2 wk old Pancreatic LN CD4 cells

label_protocol: Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA  1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul:    mRNA 3-4ug  pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL  2. Heat to 65oC for 10 min and cool on ice.   3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture  5X first-strand buffer 6.0uL  0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL   4. Incubate at 42oC for 1 hr.   5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr.   6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min.   7. Neutralize by addition of 15uL of 0.1N HCl.  8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column.  Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon.  9. WASH 1: Spin 7-8 min. at 14,000g (=RCF).  Remove flow through and save to a separate tube.  10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube.  11.  WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL  polyA RNA (Sigma, #P9403) 2 uL 10ug/uL  tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane.  Make sure not to dry the membrane completely!  12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Qing,,Li

extract_protocol:
Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases.  Keep the samples cold or on ice as much as possible to prevent RNA degradation.   Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment.  2. Add 1mL of Trizol to the frozen PBMC pellet.   3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes.  4. Vortex and transfer to 1.5ml microfuge tubes if not already in them.  5. Add 0.2 mls chloroform per 1 ml Trizol.  Vortex or shake vigorously and incubate at room temp. for 2-3 minutes.  6. Centrifuge at 12,000g for 15 minutes at 4C.  7. Transfer the aqueous phase to a fresh tube.  (The volume will be about 60% of the volume of Trizol.)  Note:  If isolating DNA, save the organic phase.  Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low.  8. Add 0.5 mLs of isopropanol per 1 ml Trizol used.  Incubate at room temp. for 10 minutes.   9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C.    10. The RNA pellet will be visible at the bottom of the tube.  Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  11. WASH 1: Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  13. WASH 2:  Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes).  Do not overdry!  16. Resuspend the pellet in 20uls of DEPC H2O.  Store at ?80C.  17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Qing,,Li
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug  Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water  70oC for 10 min in a thermocycler with lid on, but not clamped down.   Centrifuge briefly.   Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly.  Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes.   Add to the master mix: Amount Reagent 1uL Reverse Transcriptase  Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting.   42oC for 2 hours in thermocycler with lid on, but not clamped down.   Centrifuge briefly, place on ice, and immediately proceed to next step  SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  16oC for 2 hours in thermocycler with lid completely off.    DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min.  Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through.  Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol.  Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column.   Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g.   Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat.   Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC.  IN VITRO TRANSCRIPTION  Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 6 hours in hybridization oven.  Add to each reaction: Amount Reagent 2uL DNaseI  Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 30min in hybridization oven   aRNA PURIFICATION  Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes.  Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min.  Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL.   Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing.  Apply entire sample to the equilibrated filter cartridge.  Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube.  Add 650uL aRNA Wash Buffer to each filter.   Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube.  Elute aRNA by adding 50uL preheated (50oC) water to center of column.  Incubate at room temperature for 2 min.  Centrifuge for 1 minute at 10,000 x g.  Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g.   Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Qing,,Li

tag: cell type

value: NOD 2 wk old Pancreatic LN CD4 cells

source_name: 12wk BDC_1_rep2 Pancreatic LN CD4 cells

value: 12wk BDC_1_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_168h_rep1


title: 6wk_1_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68176.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 5120; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 291500; Parameter Laser Power = 1.40; Parameter Scan Time = 13:01:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.22; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656410; Parameter Laser Power = 2.08; Parameter Scan Time = 13:01:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.22; Performer: Qing,,Li

source_name: BDC2.5 6wk_1 old Pancreatic LN CD4 cells


title: 12wk NOD_1_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68835.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1270, 6340; Software: type: feature extraction; Performer: Qing,,Li

source_name: 12wk NOD_1_rep2 Pancreatic LN CD4 cells

value: 12wk NOD_1_rep2 Pancreatic LN CD4 cells


title: 6wk_2_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68177.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 5120; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 291515; Parameter Laser Power = 1.39; Parameter Scan Time = 13:16:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.28; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656425; Parameter Laser Power = 2.09; Parameter Scan Time = 13:16:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.28; Performer: Qing,,Li

source_name: BDC2.5 6wk_2 old Pancreatic LN CD4 cells


title: 12wk_1_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68178.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 5120; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 291533; Parameter Laser Power = 1.39; Parameter Scan Time = 13:35:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.34; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656443; Parameter Laser Power = 2.10; Parameter Scan Time = 13:35:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.34; Performer: Qing,,Li

source_name: BDC2.5 12wk_1 old Pancreatic LN CD4 cells


title: 6wk BDC_2_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68830.gif

source_name: 6wk BDC_2_rep2 Pancreatic LN CD4 cells

value: 6wk BDC_2_rep2 Pancreatic LN CD4 cells


title: 12wk_2_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68174.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 5120; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 291547; Parameter Laser Power = 1.39; Parameter Scan Time = 13:48:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.37; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656457; Parameter Laser Power = 2.10; Parameter Scan Time = 13:48:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.37; Performer: Qing,,Li

source_name: BDC2.5 12wk_2 old Pancreatic LN CD4 cells


title: 6wk NOD_1_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68833.gif

source_name: 6wk NOD_1_rep2 Pancreatic LN CD4 cells

value: 6wk NOD_1_rep2 Pancreatic LN CD4 cells


title: 6wk NOD_2_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68834.gif

source_name: 6wk NOD_2_rep2 Pancreatic LN CD4 cells

value: 6wk NOD_2_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_168h_rep2


title: 2wk BDC_1_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68827.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1330, 6010; Software: type: feature extraction; Performer: Qing,,Li

source_name: 2wk BDC_1_rep2 Pancreatic LN CD4 cells

value: 2wk BDC_1_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_96h_rep2


title: 12wk BDC_2_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68832.gif

source_name: 12wk BDC_2_rep2 Pancreatic LN CD4 cells

value: 12wk BDC_2_rep2 Pancreatic LN CD4 cells


title: 2wk_2_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68175.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1090, 5990; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 291481; Parameter Laser Power = 1.40; Parameter Scan Time = 12:42:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.16; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656391; Parameter Laser Power = 2.07; Parameter Scan Time = 12:42:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.16; Performer: Qing,,Li

source_name: BDC2.5 2wk_2 old Pancreatic LN CD4 cells


title: 12wk NOD_2_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68836.gif

source_name: 12wk NOD_2_rep2 Pancreatic LN CD4 cells

value: 12wk NOD_2_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_96h_rep1


title: Hippocampus_Soman_72h_rep4

source_name: Hippocampus, soman, 72h


title: 2wk BDC_2_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68828.gif

source_name: 2wk BDC_2_rep2 Pancreatic LN CD4 cells

value: 2wk BDC_2_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_72h_rep3


title: Hippocampus_VehicleControl_rep3

source_name: Hippocampus, vehicle control


title: Hippocampus_Soman_72h_rep1


title: Hippocampus_Soman_72h_rep2


title: Hippocampus_Soman_48h_rep2

source_name: Hippocampus, soman, 48h


title: Hippocampus_Soman_24h_rep3

source_name: Hippocampus, soman, 24h


title: Hippocampus_Soman_48h_rep1


title: Hippocampus_Soman_24h_rep1


title: Hippocampus_Soman_12h_rep3

source_name: Hippocampus, soman, 12h


title: Hippocampus_VehicleControl_rep4


title: 6wk BDC_1_rep2

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68829.gif

source_name: NOD 2 wk old Pancreatic LN CD4 cells

source_name: 6wk BDC_1_rep2 Pancreatic LN CD4 cells

value: 6wk BDC_1_rep2 Pancreatic LN CD4 cells


title: Hippocampus_Soman_48h_rep3


title: Hippocampus_Soman_24h_rep2


title: PBMCs_with_malaria_symptoms_patient_12

source_name: Peripheral Blood Mononuclear Cells from patients with malaria symptons

value: Male

value: PBMC in parasitemic, symptomatic (fever, headache, etc) individual prior to treatment


title: Hippocampus_Soman_12h_rep1


title: Hippocampus_Soman_6h_rep3

source_name: Hippocampus, soman, 6h


title: TOV21G, untreated mock pool from all timepoints vs. TOV21G, 200nM doxorubicin, 12hr

status: Public on Apr 01 2009

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

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

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

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

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

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: conditions

tag: cell line

tag: time

value: all time points

value: TOV21G, 200nM doxorubicin, 12hr

tag: agent

value: doxorubicin


title: Hippocampus_Soman_6h_rep2

description: Individually housed; controlled temperature and humidity;12h light/12h dark cycle; food and water ad libitum.

value: male


title: Hippocampus_Soman_12h_rep2


title: Hippocampus_Soman_3h_rep5

source_name: Hippocampus, soman, 3h


title: Hippocampus_Soman_3h_rep6


title: Hippocampus_Soman_3h_rep2


title: Hippocampus_VehicleControl_rep2


title: Hippocampus_NaiveControl_rep3

source_name: Hippocampus, naïve control


title: Hippocampus_Soman_3h_rep3


title: Hippocampus_NaiveControl_rep1


title: Hippocampus_Soman_1h_rep1

source_name: Hippocampus, soman, 1h


title: Hippocampus_VehicleControl_rep1


title: Hippocampus_Soman_3h_rep1


title: Hippocampus_Soman_1h_rep3


title: Hippocampus_Soman_3h_rep4


title: Hippocampus_NaiveControl_rep2


title: Liver_18mgRDX_48hr_rep2

description: pair-housed; one week acclimatization period; 12/12 light/dark cycle; food and water provided ad libitum.

hyb_protocol: Spike controls were added to 15 µg fragmented cRNA before overnight (16hr) hybridization using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

data_processing: Data was imported into Gensifter  (VizX Laboratories, Seattle, WA) (www.gensifter.net) and normalized using Robust Multiarray Averaging (RMA).  Data was also imported into Partek Genomics Solutions (Partet, St. Louis, MO), normalized using RMA, and visualized using principal component analysis (PCA).

source_name: liver, 18 mg RDX, 48 hr

treatment_protocol: Dosing capsules were filled by weighing pure RDX into size 9 gel capsules (Torpac, Fairfield, NJ).  Capsules were then individually stored in dark glass sample bottles for up to two days in a refrigerator until required for dosing.  At the time of dosing animals weighing 300-400 g were administered a one time dose of pure RDX in a gel capsule according to the manufacturer's instructions.  Doses were calculated, based on previous work, so as not to induce seizure, and animals were observed over the first hour to confirm lack of seizure.

tag: Sprague Dawley rats, male, 300-400 g


title: Hippocampus_Soman_1h_rep2


title: Cortex_18mgRDX_48hr_rep2

source_name: cortex, 18 mg RDX, 48 hr


title: Liver_18mgRDX_48hr_rep3


title: Liver_18mgRDX_24hr_rep3

source_name: liver, 18 mg RDX, 24 hr


title: Hippocampus_Soman_6h_rep1


title: Liver_18mgRDX_24hr_rep2


title: Cortex_18mgRDX_24hr_rep3

source_name: cortex, 18 mg RDX, 24 hr


title: Liver_18mgRDX_48hr_rep1


title: Cortex_18mgRDX_48hr_rep1


title: 2wk_1_T1D_in_BDC

description:
Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68173.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1090, 5990; Software: type: feature extraction; Performer: Qing,,Li Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 291466; Parameter Laser Power = 1.40; Parameter Scan Time = 12:28:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.12; Performer: Qing,,Li Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 656376; Parameter Laser Power = 2.07; Parameter Scan Time = 12:28:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.12; Performer: Qing,,Li

value: NOD 2 wk old Pancreatic LN CD4 cells

source_name: BDC2.5 2wk_1 old Pancreatic LN CD4 cells


title: Liver_18mgRDX_24hr_rep1


title: Cortex_18mgRDX_24hr_rep2


title: Cortex_18mgRDX_4hr_rep2

source_name: cortex, 18 mg RDX, 4 hr


title: Liver_18mgRDX_4hr_rep2

source_name: liver, 18 mg RDX, 4 hr


title: Cortex_18mgRDX_4hr_rep3


title: Liver_18mgRDX_0hr_rep3

source_name: liver, 18 mg RDX, 0 hr


title: Liver_18mgRDX_4hr_rep3


title: Liver_18mgRDX_4hr_rep1


title: Cortex_18mgRDX_24hr_rep1


title: Cortex_18mgRDX_4hr_rep1


title: Liver_18mgRDX_0hr_rep2


title: Cortex_18mgRDX_0hr_rep2

source_name: cortex, 18 mg RDX, 0 hr


title: Liver_3mgRDX_48hr_rep2

source_name: liver, 3 mg RDX, 48 hr


title: Cortex_3mgRDX_48hr_rep3

source_name: cortex, 3 mg RDX, 48 hr


title: Liver_3mgRDX_48hr_rep3


title: Liver_18mgRDX_0hr_rep1


title: Cortex_3mgRDX_48hr_rep1


title: Cortex_3mgRDX_48hr_rep2


title: Cortex_18mgRDX_0hr_rep3


title: Cortex_18mgRDX_0hr_rep1


title: Cortex_3mgRDX_24hr_rep3

source_name: cortex, 3 mg RDX, 24 hr


title: Liver_3mgRDX_4hr_rep3

source_name: liver, 3 mg RDX, 4 hr


title: Liver_3mgRDX_48hr_rep1


title: Cortex_3mgRDX_24hr_rep1


title: Liver_3mgRDX_24hr_rep2

source_name: liver, 3 mg RDX, 24 hr


title: Cortex_3mgRDX_4hr_rep3

source_name: cortex, 3 mg RDX, 4 hr


title: Liver_3mgRDX_4hr_rep1


title: Cortex_3mgRDX_4hr_rep2


title: Cortex_3mgRDX_24hr_rep2


title: Liver_3mgRDX_24hr_rep1


title: sorted_Lgr5_high_vs_low_cells_sort_2

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

description: total RNA isolated from sorted cells expressing Lgr5 at a high level hybridized against sorted cells expressing Lgr5 at a low level (sort2), dyeswap

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies). All data analyses were performed using ArrayAssist (5.5.1, Stratagene Inc, La Jolla, CA, USA) and Microsoft Excel (Microsoft Corporation, Redmond, WA, USA). Raw signal intensities were corrected by subtracting local background. Negative values were changed into a positive value close to zero (standard deviation of the local background) in order to allow calculation of ratios between intensities for features only present in one sample (GFPhi or GFPlo) or (Ah-Cre/Ascl2floxed/wt or Ah-Cre/Ascl2floxed/floxed). Data were filtered if both (GFPhi and GFPlo) or (Ah-Cre/Ascl2floxed/wt or Ah-Cre/Ascl2floxed/floxed)  intensities were changed or if both intensities were less than two times the background signal and normalized using the Loess algorithm.

source_name: sorted intestinal epithelial cells expressing Lgr5 at a high level  (sort2)

label_protocol: 500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

extract_protocol: RNA was isolated using Trizol (Invitrogen)

treatment_protocol: For the stem cell signature we used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlo). For the analysis of Ascl2 target genes RNA was isolated from intestinal epithelial cells of Ah-Cre/Ascl2floxed/floxed animals and Ah-Cre/Ascl2floxed/wt control animals 3 and 5 days post induction

tag: FACS sorted epithelial intestinal cells from Lgr5-EGFP-ires-CreERT2 mice

source_name: sorted intestinal epithelial cells expressing Lgr5 at a low level  (sort2)

tag: FACS sorted epithelial intestinal cells cells from Lgr5-EGFP-ires-CreERT2 mice


title: sorted_Lgr5_high_vs_low_cells_sort_1

description: total RNA isolated from sorted cells expressing Lgr5 at a high level hybridized against sorted cells expressing Lgr5 at a low level (sort1), dyeswap

source_name: sorted intestinal epithelial cells expressing Lgr5 at a high level  (sort1)

source_name: sorted intestinal epithelial cells expressing Lgr5 at a low level  (sort1)


title: Cortex_18mgRDX_48hr_rep3

source_name: cortex, 18 mg RDX, 48 hr


title: sorted_Lgr5_low_vs_high_cells_sort_2

description: total RNA isolated from sorted cells expressing Lgr5 at a high level hybridized against sorted cells expressing Lgr5 at a low level (sort2)


title: Cortex_3mgRDX_4hr_rep1


title: Liver_3mgRDX_4hr_rep2


title: sorted_Lgr5_low_vs_high_cells_sort_1

description: total RNA isolated from sorted cells expressing Lgr5 at a high level hybridized against sorted cells expressing Lgr5 at a low level (sort1)


title: Liver_3mgRDX_0hr_rep3

source_name: liver, 3 mg RDX, 0 hr


title: small_intestine_3days_after_conditional_Ascl2_deletion_ko_vs_wildtype

description: total RNA isolated from small intestine 3 days after conditional knockout of Ascl2 hybridized against wildtype tissue, dyeswap

source_name: epithelial cells from small intestine

tag: epithelial intestinal cells of Ah-Cre/Ascl2floxed/wt control animals

source_name: epithelial cells from small intestine 3 days after conditional knockout of Ascl2

tag: epithelial intestinal cells from Ah-Cre/Ascl2floxed/floxed animals


title: Cortex_3mgRDX_0hr_rep3

source_name: cortex, 3 mg RDX, 0 hr


title: Liver_3mgRDX_0hr_rep2


title: Liver_3mgRDX_24hr_rep3


title: small_intestine_5days_after_conditional_Ascl2_deletion_wildtype_vs_ko

description: total RNA isolated from small intestine 5 days after conditional knockout of Ascl2 hybridized against wildtype tissue, dyeswap

source_name: epithelial cells from small intestine 5 days after conditional knockout of Ascl2


title: small_intestine_5days_after_conditional_Ascl2_deletion_ko_vs_wildtype

description: total RNA isolated from small intestine 5 days after conditional knockout of Ascl2 hybridized against wildtype tissue


title: Liver_3mgRDX_0hr_rep1


title: small_intestine_3days_after_conditional_Ascl2_deletion_wildtype_vs_ko

description: total RNA isolated from small intestine 3 days after conditional knockout of Ascl2 hybridized against wildtype tissue


title: Cortex_3mgRDX_0hr_rep1


title: RAD24A

first: Federico

middle: A

last: Monzon

state: TX

address: 6565 Fannin St., MS205

department: Pathology

institute: The Methodist Hospital Research Institute

description: RenalCellCarcinoma_Unclassified_FFPE_33_sarcomatoid_component

scan_protocol: Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0

label: Biotinilated - Fragmented PCR products

source_name: Renal Cell Carcinoma, Unclassified, DNA from Paraffin Embedded Tissue

label_protocol: Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)

extract_protocol: Deparaffinization followed by Qiagen DNeasy Blood and Tissue kit by manufacturer's instructions

tag: Sex

tag: AgeDecade

tag: Tumor Size

tag: Furhman Nuclear Grade

tag: TNM Stage

tag: LymphoVascular Invasion


title: SARC01

value: F

value: FALSE


title: Cortex_3mgRDX_0hr_rep2


title: MRCC28


title: RAD24B

description: RenalCellCarcinoma_Unclassified_FFPE_33_clearcell_component

value: M


title: MRCC21


title: MRCC16


title: MRCC13Cs

description: RenalCellCarcinoma_Unclassified_FFPE_28_sarcomatoid_component


title: MRCC13Cc

description: RenalCellCarcinoma_Unclassified_FFPE_28_clearcell_component


title: MRCC13Cp

description: RenalCellCarcinoma_Unclassified_FFPE_28_papillary_component


title: MRCC13A


title: MRCC054

scan_protocol: Affymetrix Mapping 250K Nsp Assay with an Affymetrix GeneChip 3000 7G scanner

source_name: Renal Oncocytoma, DNA from Paraffin Embedded Tissue

label_protocol: Standard labeling protocol for FFPE tissue based on Affymetrix Mapping 250K Nsp Assay. Startup DNA amount is 1ug


title: MRCC057


title: MRCC06P

description: RenalCellCarcinoma_Unclassified_FFPE_26_papillary_component


title: MRCC17B

source_name: Renal Cell Carcinoma, Mucinous Tubular and Spindle Cell Type, DNA from Paraffin Embedded Tissue


title: MRCC055


title: MRCC050

source_name: Renal Cell Carcinoma, Papillary Type 1, DNA from Paraffin Embedded Tissue


title: MRCC051A


title: MRCC06C

description: RenalCellCarcinoma_Unclassified_FFPE_26_chromophobe_component


title: MRCC19


title: MRCC049A


title: MRCC048


title: MRCC074


title: MRCC46A

source_name: Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue


title: MRCC064


title: RAD03B


title: DESM26


title: MRCC063C


title: Endometrium day18 SCNT rep8

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: intercaruncular endometrial tissue sample collected at day 18 of pregnancy after transfer of 2 somatic cell nuclear transfer embryos at day 7 of the estrous cycle

hyb_protocol: Pre-hybridization was done for five arrays together in one 15 cm glass hybridization bottle, respectively: 2 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 85 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 1 x 10 ml 1 x PBS / 10 % SDS at room temperature. Hybridization was done in plastic vials (Poly-Q vials, 18 ml; Beckmann Coulter, Munich, Germany) in 2,5 ml 1 x PBS / 10 % SDS for 47 h at 65 °C. Subsequently, the hybridization solution was decanted and the vials filled immediately with 1 x PBS / 10 % SDS. For washing five arrays were put together in 15 cm glass hybridization bottles, respectively, and processed as follows: 3 x 5 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 65 °C; 3 x 5 min 10 ml 1 x PBS / 1 % SDS / 2 mM EDTA at 30 °C. Membranes were dried by baking at 80 °C for 20 min.

scan_protocol: The arrays were exposed to an imaging plate BAS-SR (Fuji Photo Film Co) for 16 to 30 hrs. Imaging plates were scanned with a phosphor imager (Typhoon Imager, GE Healthcare Life Sciences).

data_processing: Array evaluation was done using AIDA Image Analyzer (Version 4.15, Raytest, Straubenhardt, Germany), backround was subtracted with the 'Lowest Grid Dot' function. Raw data (integral minus background) were normalized with vsn (vsn; BioConductor).

organism: Bos taurus

source_name: endometrium, day 18, SCNT

label_protocol: 33P-labelled cDNA probes were generated from ds cDNA corresponding to 7.5-15 µg total RNA. cDNA was heat-denatured for 10 min at 96 °C and then chilled on ice. High Prime reaction mixture (Roche), dNTP mixture (dCTP final concentration 10 pmol/µl, dATP, dGTP and dTTP final concentration each 100 pmol/µl)and 90 µCi [a-33P] dCTP were added to a final colume of 20 µl. Reactions were incubated for 1 h at 37 °C and subsequently purified with ProbeQuant G-50 Micro Columns (GE Healthcare, Buckinghamshire, UK) to remove unincorporated nucleotides and to estimate labeling efficiency.

extract_protocol: Tissue samples of the caudal part of the ipsilateral uterine horn were carefully cut from the lamina propria of the intercaruncular endometrium with a scalpel and conserved in RNAlater (Ambion, Huntingdon, Cambridgeshire, UK). Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufactorer's recommendations. The quantity and quality of total RNA were determined by spectrometry and agarose gel electrophoresis respectively.

tag: Gender

value: female

tag: Breed

value: Simmental

tag: Localization

value: ipsilateral, caudal


title: MRCC056


title: Endometrium day18 SCNT rep9


title: MRCC08

source_name: Renal Cell Carcinoma, Papillary Type 2, DNA from Paraffin Embedded Tissue

value: TRUE


title: MRCC25


title: MRCC30A


title: KR006-A


title: KR008-A


title: LYNCH001A


title: MRCC15


title: Endometrium day18 SCNT rep7


title: Endometrium day18 SCNT rep6


title: MRCC065


title: Endometrium day18 SCNT rep5


title: DESM16A


title: Endometrium day18 SCNT rep4


title: MRCC061

source_name: Renal Cell Carcinoma, Chromophobe Type, DNA from Paraffin Embedded Tissue


title: Endometrium day18 SCNT rep2


title: MRCC22


title: Endometrium day18 SCNT rep1


title: MRCC20


title: RADM018A


title: RAD05


title: Endometrium day18 IVP rep10

description: intercaruncular endometrial tissue sample collected at day 18 of pregnancy after transfer of 2 in vitro produced embryos at day 7 of the estrous cycle

source_name: endometrium, day 18, IVP


title: MRCC47A


title: Endometrium day18 IVP rep9


title: Endometrium day18 IVP rep8


title: MRCC059


title: MRCC060A


title: RADM019


title: Endometrium day18 IVP rep7


title: MRCC05


title: Endometrium day18 IVP rep6


title: KR005-A


title: MRCC04


title: MRCC058


title: DESM10


title: MRCC24A


title: DES17A


title: Endometrium day18 IVP rep3


title: DES06A


title: Endometrium day18 IVP rep4


title: DESM16B


title: Endometrium day18 IVP rep2


title: Endometrium day18 IVP rep1


title: Endometrium day18 SCNT rep3


title: MRCC27

source_name: Metastatic Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue


title: P43 Hair Germ RFP(-) GFP(+) CD34(-) Pcad Hi

status: Public on Mar 12 2009

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description: Gene expression data from mouse hair germ at early telogen phase

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to mouse genome array MOE430A2.0 (Affymetrix, Santa Clara, California, United States).

scan_protocol: Processed chips were read by an argon-ion laser confocal scanner (Genomics Core Facility, Sloan Kettering Cancer Center, New York, New York, United States).

data_processing: Scanned microarray images were imported into Gene Chip Operating Software (GCOS, Affymetrix) to generate signal values and absent/present calls.For each probe-set using the MAS 5.0 statistical expression algorithm (.chp files). Each array was scaled to a target signal of 500 using all probe-sets and default analysis parameters. Signature gene lists for isolated hair germ and bulge cells at all 3 time points were compiled containing probesets that are > 2-fold increased or < 2-fold decreased. For functional gene annotation probeset lists were uploaded to the “Database for Annotation, Visualization and Integrated Discovery” (DAVID 2008) Web tool.

source_name: Female CD1 hair follicle from early telogen postnatal day 43

label_protocol: Two rounds of amplification/labeling were performed on 20 nanogram to obtain biotinylated cRNA (MessageAmp aRNA kit; Ambion, Austin, Texas, United States).

growth_protocol: CD1 Lef1RFP/K14H2BGFP female mice are weaned at day 21 and grown as virgins until the different days of analysis.

extract_protocol:
Supernatant 1 is FACS sorted on the basis of RFP+GFP-CD45-CD117-Itgα7- to isolate Dermal Papilla cells. Supernatant 2 is s FACS sorted on the basis of RFP(-) GFP(+) CD34(-) Pcad Hi to isolate Hair Germ cells, and RFP(-) GFP(+) CD34(+) Pcad low to isolate Bulge cells
Total RNAs from FACS cells are purified using the Absolutely RNA Microprep kit (Stratagene,La Jolla, California, United States), and quantified (Nanodrop, United States). Quality was assessed by RNA 6000 Pico Assay (Agilent Technologies, Palo Alto, California, United States).

treatment_protocol: Back skin of telogen mice are first treated with collagenase creating a Dermal Papilla enriched cell suspension (Supernatant 1). The remaining skin is further treated with trypsin (Supernatant 2).

tag: tissue

value: Enzymatically treated mouse skin

tag: genotype

tag: age

value: Postnatal day 43


title: P56 Dermal Papilla GFP(-) RFP(+) CD45/CD117/CD34/itga7(-)

description: Gene expression data from mouse dermal papilla at middle telogen phase

source_name: Female CD1 hair follicle from middle telogen postnatal day 56

value: Postnatal day 56


title: P69 Dermal Papilla GFP(-) RFP(+) CD45/CD117/CD34/itga7(-)

description: Gene expression data from mouse dermal papillaat late telogen phase

source_name: Female CD1 hair follicle from late telogen postnatal day 69

value: Postnatal day 69


title: MRCC26


title: P69 Hair Germ RFP(-) GFP(+) CD34(-) Pcad Hi

description: Gene expression data from mouse hair germ at late telogen phase


title: KR007-A


title: P69 Bulge RFP(-) GFP(+) CD34(+) Pcad low

description: Gene expression data from mouse bulge at late telogen phase


title: P56 Hair Germ RFP(-) GFP(+) CD34(-) Pcad Hi

description: Gene expression data from mouse hair germ at middle telogen phase


title: ATG5-/- Bcl-2 iBMK tumor expressing p62-EGFP 2

city: New Brunswick

first: Robin

last: Mathew

state: NJ

address: 195 Little Albany Street

department: CINJ

institute: Cancer Institute of New Jersey

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GPL339 Affymetrix GeneChip  Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array).

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

data_processing: MAS 5.  In addition, we used a feature selection algorithm called USE-Fold in the  Genes@Work software (IBM) to compare cases to cases and controls to  cases to determine  the expected error distribution for each gene expression value in  these controls and can use it to identify significantly over-expressed  or under-expressed genes

source_name: ATG5-/- Bcl-2 iBMK cells expressing p62-EGFP

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

growth_protocol: All cell lines were maintained in DMEM (Gibco/InVitrogen) containing 10% fetal bovine serum (FBS). 10 million cells were injected subcutaneously in nude (NCR Nu/Nu) mice to generate tumors.

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

treatment_protocol: No treatment.

tag: genoytpe

tag: cell line

value: iBMK


title: ATG5-/- Bcl-2 iBMK tumor expressing p62-EGFP 1


title: P56 Bulge RFP(-) GFP(+) CD34(+) Pcad low

description: Gene expression data from mouse bulge at middle telogen phase


title: ATG5-/- Bcl-2 iBMK tumor expressing EGFP 1

source_name: ATG5-/- Bcl-2 iBMK cells expressing EGFP


title: P43 Dermal Papilla GFP(-) RFP(+) CD45/CD117/CD34/itga7(-)

description: Gene expression data from mouse dermal papilla at early telogen phase


title: ATG5-/- Bcl-2 iBMK tumor expressing EGFP 2


title: P43 Bulge RFP(-) GFP(+) CD34(+) Pcad low

description: Gene expression data from mouse bulge at early telogen phase


title: VUMC_HNSCC_50

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: as described by S.J.Smeets et al. Oncogene 2006, 25(17):2558-64

hyb_protocol: Hybridisations were performed as described by Snijders et al, Nat Genetics, volumn 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 - Perkin Elmer Life Sciences).

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalized by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.

source_name: Carcinoma

label_protocol: as described by Snijders et al, Nat Genetics, volume 29, p263-4

extract_protocol: Frozen tumor samples were used for HPV analysis and for all tumor samples microdissection was performed to enrich for tumor tissue. DNA and RNA was extracted as described by Tabor et al. (Tabor M. Clin. Cancer Res., 7, 1523-1532)

tag: Head and Neck Squamous cell carcinoma

source_name: Pooled reference DNA

tag: Pooled DNA from blood of 10 normal individuals


title: VUMC_HNSCC_51


title: MRCC07

city: Houston


title: VUMC_HNSCC_47


title: VUMC_HNSCC_48


title: Endometrium day18 IVP rep5


title: VUMC_HNSCC_49


title: VUMC_HNSCC_42


title: VUMC_HNSCC_46


title: VUMC_HNSCC_44


title: VUMC_HNSCC_40


title: VUMC_HNSCC_38


title: VUMC_HNSCC_33


title: VUMC_HNSCC_26


title: VUMC_HNSCC_45


title: VUMC_HNSCC_35


title: VUMC_HNSCC_39


title: VUMC_HNSCC_25


title: VUMC_HNSCC_32


title: VUMC_HNSCC_22


title: VUMC_HNSCC_36


title: VUMC_HNSCC_21


title: VUMC_HNSCC_23


title: VUMC_HNSCC_31


title: VUMC_HNSCC_41


title: VUMC_HNSCC_34


title: VUMC_HNSCC_24


title: VUMC_HNSCC_37


title: VUMC_HNSCC_20


title: VUMC_HNSCC_30


title: Small RNA from serous ovarian cancer tissue

city: Seattle

first: Muneesh

last: Tewari

state: WA

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: 18-25nt size-fractionated RNA

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Custom bioinformatic data analysis pipeline.  Processing and annotation of sequences based on identity to known transcribed RNAs or as novel miRNAs was performed using a custom bioinformatics pipeline. The data analysis pipeline identifies sequences that match previously annotated features in the genome and sets those sequences aside for further analysis.  We first compared our sequences using BLAST [6] against a database constructed of known miRNA mature sequences (Figure S1-a) and a database constructed of the precursor sequences (miRBase release 12.0) [7,8] and then profiled the previously annotated miRNAs (Figures 2, 3). Once we removed all the matches to known miRNAs, we then compared the sequences to other non-coding RNAs (Figure S1-b) including tRNAs, rRNAs, and piRNAs. Matches to the Repbase database were also removed (Dec. 2006 version) [9]. Exact matches to known genes in the RefSeq mRNA database (downloaded from the UCSC Table Browser) [10] (Figure S1-c) were also filtered out.   Once the annotated RNAs were removed, we BLASTed the remaining sequences against the human genome (UCSC Genome Browser, version hg18, March 2006 assembly, NCBI Build 36.1) (Figure S1-d). If a sequence mapped to more than 20 loci in the genome, it was removed from further analysis. When BLASTed against the human genome, we found that many sequences were not exact matches, with mismatches typically occurring at the 3’ end due to non-templated addition of 1-3 nucleotides. We chose to trim non-matching sequences if they had an exact match to the human genome starting at the 5’ end of the sequence and has a contiguous match of 17 or more nucleotides. The 3’ end of the sequence was trimmed back until the sequence was an exact match to the genome. The trimmed sequences were then re-screened for matches to annotated features in the genome as previously described.

label: not applicable

source_name: ovarian cancer tissue

label_protocol: not applicable

growth_protocol: Cell culture and clinical materials. Normal primary human ovarian surface epithelial (HOSE) cells were obtained from the normal ovaries of postmenopausal women using a modification of the technique described previously in [25]. In all cases, specimens were taken from normal-appearing ovarian surface epithelium, which was confirmed following histopathological review.  Primary HOSE cells were cultured using media described in [26] at 37˚C in 5% CO2. Ovarian cancer snap-frozen specimens corresponding to Stage III/IV epithelial ovarian cancer (19 serous, four clear cell and 10 endometrioid) contained >70% malignant epithelial cellularity as assessed by pathologist review of an adjacent stained tissue section. Ovarian cancer specimens were obtained from the Pacific Ovarian Cancer Research Consortium Repository. Specimens were collected under Institutional Review Board approved protocols.

extract_protocol: RNA extraction and miRNA library preparation. Normal primary HOSE cultures (passage 4-7) were lysed in 600 µl mirVana Lysis/Binding buffer (Ambion, Inc., Austin, TX). Tumor specimens (~100 mg each) were homogenized in a Qiagen Tissuelyser with 600 μl mirVana Lysis/Binding buffer. Total RNA was extracted from both sample types using the mirVanaTM miRNA isolation kit (Ambion) per the manufacturer’s protocol. RNA from snap-frozen tumors (19 serous, four clear cell and 10 endometrioid tumors, respectively) was pooled according to histologic subtype. MicroRNA cloning was performed as previously described [27], (http://web.wi.mit.edu/bartel/pub/protocols/miRNACloningUpdate0705.pdf) with modifications at the amplification steps to prepare the samples for massively parallel sequencing by 454 Life Sciences.

value: serous ovarian cancer


title: VUMC_HNSCC_18


title: VUMC_HNSCC_14


title: VUMC_HNSCC_16


title: VUMC_HNSCC_17


title: VUMC_HNSCC_27


title: VUMC_HNSCC_19


title: VUMC_HNSCC_29


title: VUMC_HNSCC_6


title: VUMC_HNSCC_10


title: VUMC_HNSCC_12


title: VUMC_HNSCC_9


title: VUMC_HNSCC_28


title: VUMC_HNSCC_8


title: VUMC_HNSCC_11


title: Small RNA from clear cell ovarian cancer tissue

description: 18-25nt size-fractionated RNA

value: clear cell ovarian cancer


title: VUMC_HNSCC_13


title: anti-IgE + DEX + FK506

city: Chicago

first: Atsushi

last: Kato

state: IL

address: 240 E. Huron St.

department: Allergy-Immunology Division

institute: Northwestern University Feinberg School of Medicine

description: Human peripheral blood-derived mast cells were sensitized with 1 ug/ml human myeloma IgE (Calbiochem) for 48 hours. After washing, the mast cells were preincubated with 1 uM DEX (dexamethasone), 0.1 uM FK506 or 0.01% DMSO for 1 hour and then stimulated with 1.5 ug/ml anti-IgE antibody (DakoCytomation, Denmark) for 6 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (Affymetrix) using Affymetrix default analysis settings. To normalize the variations in staining intensity among chips, the 'Average Difference' values for all genes on a given chip were divided by the median value for expression of all genes on the chip.

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

extract_protocol: Total RNA was extracted with RNeasy (Qiagen) and digested with DNase I (Qiagen) according to the manufacturer's instructions.

tag: cell type

value: peripheral blood-derived mast cells

tag: agent

value: preincubated with dexamethasone (DEX) and FK506, and then stimulated with anti-IgE antibody


title: anti-IgE + FK506

source_name: Human peripheral blood-derived mast cells

value: preincubated with FK506 and then stimulated with anti-IgE antibody


title: anti-IgE + DEX

value: preincubated with dexamethasone (DEX) and then stimulated with anti-IgE antibody


title: VUMC_HNSCC_3


title: VUMC_HNSCC_15


title: VUMC_HNSCC_5


title: Small RNA from primary cultures of normal human ovarian surface epithelium (HOSE)

description: 18-25nt size-fractionated RNA

source_name: normal ovarian surface epithelium


title: Small RNA from endometrioid ovarian cancer tissue

description: 18-25nt size-fractionated RNA

value: endometrioid ovarian cancer


title: VUMC_HNSCC_2


title: Low Early-Life SES Subject # 793

status: Public on Mar 11 2009

city: Vancouver

first: Gregory

middle: E

last: Miller

state: BC

address: 2136 W Mall

department: Psychology

country: Canada

institute: UBC

hyb_protocol: RNA was hybridized to Illumina HumanRef-8 v3.0 Expression Beadchips following manufacturer's instructions

scan_protocol: Chips were scanned on an Illumina Beadstation 500 at the McGill University and Génome Québec Innovation Centre.

data_processing: None - these are raw hybridization intensities, averaged across the 30 bead replicates, provided by Illumina Beadstudio

source_name: PBMC

label_protocol: Used the Illumina TotalPrep RNA  Amplification Kit following manufacturer's instructions

extract_protocol: PBMC were then homogenized in QiaShredder Spin Columns (Qiagen) and the lysates were frozen at -80° C until RNA was extracted using AllPrep DNA/RNA kits (Qiagen; Mississauga, ON).

treatment_protocol: Leukocytes were collected by antecubtial  venipuncture and PBMC were then isolated by density-gradient centrifugation

tag: socio-economic status

value: Low Early-Life SES

value: PBMC


title: VUMC_HNSCC_4


title: VUMC_HNSCC_7


title: High Early-Life SES Subject # 796

value: High Early-Life SES


title: Low Early-Life SES Subject # 792


title: VUMC_HNSCC_1


title: Low Early-Life SES Subject # 802


title: High Early-Life SES Subject # 790


title: High Early-Life SES Subject # 799


title: High Early-Life SES Subject # 804


title: High Early-Life SES Subject # 788


title: anti-IgE + DMSO

value: preincubated with vehicle control DMSO and then stimulated with 15 ug/ml anti-IgE antibody


title: High Early-Life SES Subject # 803


title: Low Early-Life SES Subject # 789


title: VUMC_HNSCC_43


title: Low Early-Life SES Subject # 801


title: Low Early-Life SES Subject # 785