title: Aspergillus oryzae grown on the substrate I10_Shake Flask 1

description:
Processed data file: ctrl_vs_I10.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 6


title: AML-056-Tumor

status: Public on Jul 15 2013

type: genomic

city: Tokyo

first: Ayana

last: Kon

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

department: Cancer Genomics Project

country: Japan

institute: The University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR software.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: AML primary sample

label_protocol: Affymetrix standard protocol.

extract_protocol: Genomic DNA was obtained from bone marrow or peripheral blood samples.

tag: disease status

value: acute myeloid leukemia

tag: tissue

value: tumor


title: Synovial fluid of Rheumatoid arthritis (RA)  sample 1

type: RNA

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Gene expression profiling of synovial fluid derived mononuclear cells from RA patient using whole human genome microarray

hyb_protocol: The Cyanine-3 labeled cRNA molecules were fragmented and hybridized onto human genome DNA microarrays (1X44, 4x44K, Agilent Technologies) for 17 hrs at 65°C with 10 rpm. Later, Arrays were washed using gene expression wash buffers according to the manufacturer’s hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies).

scan_protocol: Agilent microarray scanner (G2505B) was used to scan the microarray slides. One color scan settings were used for 4x44 K  and 1x44 K array slides (scan resolution 5 um, dye channel was set to green, green PMT was set to 100%).

data_processing: Agilent feature extraction software was used to processes the images.

molecule: total RNA

source_name: Knee aspirated synovial fluid RA sample1

label_protocol: Total RNA (~500ng) was reverse transcribed from each sample and linear amplification carried out using the low RNA input linear amplification kit (Agilent Technologies , Palo Alto, CA) to synthesize the first and second strands of cDNA and this cDNA was used as a template for generating cRNAs. Simultaneous amplification and Cyanine-3 (Perkin Elmer) dye incorporstion was done for labeling of cRNA as per the manufacturer’s protocol (Agilent Quick Amp Labeling Kit (Catalog #.51900442, Agilent technologies). The labeled cRNA molecules were purified using RNeasy spin columns (Qiagen, Valencia, CA).

extract_protocol: Total RNA extraction carried out from approximately 5 X 100000 synovial fluid derived mononuclear cells from  both the disease types. Purification was done using RNeasy Lipid Tissue Mini kit (Catalog # 74804, QIAGEN, CA 91355, USA) as per manufacturer’s protocol. The range of RNA concentration isolated form samples was 1-5 µg/ 5X105 cells and 2-5 µg/5X100000 cells in SpA and RA respectively. Integrity of the isolated RNA was checked by 2100 Bioanalyzer (Agilent Technologies) that measures the ratio of 28S and 18S ribosomal RNAs to compute the integrity of total mRNA.

treatment_protocol: Some RA patients were under going drug treatment with either methotrexate or Hydroxychloroquinone and the rest on none or on some generic pain killers

tag: date of collection

tag: fluid

value: Turbid, highly viscous and non bloody

tag: gender

value: Female

tag: age (y)

tag: case history

value: Came with pain and swollen knees

tag: treatment

value: Pain killers

tag: cell type

value: mononuclear cells from synovial fluid

tag: disease state

value: Rheumatoid arthritis


title: AML-043-Tumor

description: Hybridized to 250K_Nsp


title: AML-048-Tumor

description: Hybridized to 250K_Nsp


title: Leaf_07506-01versus12120-03_rep1

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description: both clones are diploids

hyb_protocol: Hybridization and slide processing were performed using the 1 × 44 k POCI array (Kloosterman et al. 2008) using the Arrayit microarray hybridization cassette (Arrayit Corp, Sunnyvale, CA, USA) according to manufacturer specifications.

scan_protocol: Slides were scanned on the GenePix 4000B Microarray Scanner (MDS Analytical Technologies, Ottawa, ON, Canada), and data were extracted using the manufacturer’s software.

data_processing:
Microarray data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions, Gaithersburg, MD, USA). Double channel analysis of 07506-01 and 12120-03 data was done using print-tip loess normalization with a smoothing factor of 0.1.
Normalized log2 transformation of 07506-01/12120-03 (Cy5/Cy3) fluorescence ratio for each gene with negative ratio values retained.

organism: Solanum tuberosum

label_protocol: Total RNA was purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) and DNAse I treated before first- and second-strand synthesis following the Ambion MessageAmp™ II aRNA amplification kit protocol (Life Technologies, Burlington, ON, Canada) using the following minor modifications. For first-strand synthesis, 2 μg of total RNA was used in the reaction followed by second-strand synthesis with half of the recommended enzyme concentrations. Purified cDNA was used for in vitro transcription using an indirect amino-allyl-labeling method with a 1:3 incorporation ratio of uridine triphosphate (UTP)/5-(3-aminoallyl)-UTP. In vitro transcription was performed at 37°C with a lid temperature of 40°C for a period of 15 h, after which samples were purified according to the manufacturer’s protocol. Unincorporated nucleotides were removed using filter cartridges provided with the kit.  Purified aminoallyl RNA (aRNA) samples were dried using a speedvac at 45 oC and stored at -80 °C.  For sample labeling, 5-7 μg of aRNA was resuspended in 5 μl freshly made carbonate buffer (0.1 M Na2CO3) adjusted to pH 9. Equal amounts of either Cy5 or Cy3 dye (GE Healthcare, Mississauga, ON, Canada) were added to aRNA from 07506-01 or 12120-03, respectively, and incubated for 2 h at room temperature. Each of the three replicate Cy5-labelled sRNA samples (1 μg each) from 07506-01 was paired with a Cy3-labelled aRNA sample from 12120-03 and co-hybridized on a single slide. A fourth slide consisted of swapping dye labels between 07506-01 and 12120-03 for replicate 1.  Samples were purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) prior to application on slides.  Dye incorporation was measured using a ND-100 Spectrophotometer v3.3 (Nanodrop Technologies, Wilmington, DE, USA).

growth_protocol: Two diploid potato clones, 07506-01 and 12120-03, were developed at the Agriculture and Agri-Food Canada Potato Research Centre (AAFC-PRC) in Fredericton, New Brunswick, Canada. The diploid clones were primarily based on hybrids between Solanum phureja or S. stenotomum and Solanum. tuberosum L. Phureja Group and Stenotomum Group (De Jong 1987).  The experiment was performed at the Potato Research Centre, Agriculture and Agri-Food Canada (AAFC), Fredericton, NB, Canada (45° 52' N, 66° 31' W) during 2008.  Seed tubers were obtained from the Benton Ridge Substation of AAFC in Benton, New Brunswick, Canada, which is a certified virus-free breeding farm.   07506-01 and 12120-03 seed tubers were sown in a plot carrying V. dahliae on May 15, 2008.  Fertilizer was banded about 7.5 cm to each side and 5 cm below the potato seed pieces at planting according to normal production practices at 200 kg N ha-1 as ammonium nitrate, 150 kg P2O5 ha-1 and 150 kg K2O ha-1. The plants were hilled on July 10, 2008. Standard commercial practices were used for control of diseases, insects and weeds. No irrigation was applied.

extract_protocol: Clones 07506-01 and 12120-03 were planted in three replicates in the field in a randomized block design with five plants per replicate plot.  The plants from the field were used for gene expression analysis.  One leaflet 1 to 1.5 cm in width was collected from the expanding top leaf from each plant at ten weeks after planting in the field.  The leaflets from the five plants for each replicate plot were combined and immediately frozen in liquid nitrogen and stored at -80°C until processed. Frozen leaflets from field plants was ground using bead matrix 4, speed 6, for 40 s in a FastPrep instrument (MP Biomedicals, Montreal, PQ, Canada).  Total RNA and DNA were co-extracted using a scaled-down hot borate extraction method (Tai et al. 2007, Wan and Wilkins 1994) and quality was checked using a BioAnalyzer (Agilent, Mississauga, ON, Canada).  The nucleic acid extract was split: for RNA extraction the samples were treated with DNase I and for DNA extraction the samples were treated with RNAse A.

treatment_protocol: Experiment was a comparison between two potato genotypes.

value: leaf

tag: age

value: 10 weeks after planting

label_protocol: Total RNA was purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) and DNAse I treated before first- and second-strand synthesis following the Ambion MessageAmp™ II aRNA amplification kit protocol (Life Technologies, Burlington, ON, Canada) using the following minor modifications. For first-strand synthesis, 2 μg of total RNA was used in the reaction followed by second-strand synthesis with half of the recommended enzyme concentrations. Purified cDNA was used for in vitro transcription using an indirect amino-allyl-labeling method with a 1:3 incorporation ratio of uridine triphosphate (UTP)/5-(3-aminoallyl)-UTP. In vitro transcription was performed at 37°C with a lid temperature of 40°C for a period of 15 h, after which samples were purified according to the manufacturer’s protocol. Unincorporated nucleotides were removed using filter cartridges provided with the kit.  Purified aminoallyl RNA (aRNA) samples were dried using a speedvac at 45 oC and stored at -80 oC.  For sample labeling, 5-7 μg of aRNA was resuspended in 5 μl freshly made carbonate buffer (0.1 M Na2CO3) adjusted to pH 9. Equal amounts of either Cy5 or Cy3 dye (GE Healthcare, Mississauga, ON, Canada) were added to aRNA from 07506-01 or 12120-03, respectively, and incubated for 2 h at room temperature. Each of the three replicate Cy5-labelled sRNA samples (1 μg each) from 07506-01 was paired with a Cy3-labelled aRNA sample from 12120-03 and co-hybridized on a single slide. A fourth slide consisted of swapping dye labels between 07506-01 and 12120-03 for replicate 1.  Samples were purified using RNeasy MinElute Spin Columns (Qiagen, Toronto, ON, Canada) prior to application on slides.  Dye incorporation was measured using a ND-100 Spectrophotometer v3.3 (Nanodrop Technologies, Wilmington, DE, USA).

extract_protocol: Clones 07506-01 and 12120-03 were planted in three replicates in the field in a randomized block design with five plants per replicate plot.  The plants from the field were used for gene expression analysis.  One leaflet 1 to 1.5 cm in width was collected from the expanding top leaf from each plant at ten weeks after planting in the field.  The leaflets from the five plants for each replicate plot were combined and immediately frozen in liquid nitrogen and stored at -80oC until processed. Frozen leaflets from field plants was ground using bead matrix 4, speed 6, for 40 s in a FastPrep instrument (MP Biomedicals, Montreal, PQ, Canada).  Total RNA and DNA were co-extracted using a scaled-down hot borate extraction method (Tai et al. 2007, Wan and Wilkins 1994) and .  quality was checked using a BioAnalyzer (Agilent, Mississauga, ON, Canada).  The nucleic acid extract was split: for RNA extraction the samples were treated with DNase I and for DNA extraction the samples were treated with RNAse A.


title: AML-049-Tumor

description: Hybridized to 250K_Nsp


title: AML-045-Tumor

description: Hybridized to 250K_Nsp


title: Aspergillus oryzae grown on the substrate I1_Shake Flask 1

city: Gothenburg

first: D.B.R.K. Gupta

last: Udatha

state: Sweden

address: Medicinaregatan 9C

department: Department of Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

description:
Processed data file: ctrl_vs_I1.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 3

hyb_protocol: cRNA was quantified in a spectrophotometer. cRNA quality was assessed using a BioAnalyzer. A GeneChip Fluidics Station FS-400 (fluidics protocol FS450_001) and a GeneChip Scanner 3000 were used for hybridization and scanning.

scan_protocol: Arrays were washed and stained using a GeneChip Fluidics Station FS-400, and scanned on an Agilent GeneArray Scanner 3000.

data_processing: The scanned probe array images were converted into data files using the Agilent software.

organism: Aspergillus oryzae RIB40

label_protocol: Standard Agilent protocol

growth_protocol:
The composition of the batch cultivation medium was the following (in g L-1): 20 g glucose monohydrate, 2.0 g MgSO4.7H2O, 2 g K2SO4, 2.0 g KH2PO4, 5.0 g (NH4)2SO4, 0.5 ml L-1 pluronic acid (PE-6100) (BASF SE, Ludwigshafen, Germany) and 0.6 ml L-1 of trace elements solution. Trace elements solution composition (in g L-1): 14.3 g ZnSO4.7H2O, 8.5 g MnSO4.H2O, 13.8 g FeSO4.7H2O, 2.5 g CuSO4.5H2O, 3 g citric acid monohydrate (as a chelating agent) and 0.5 g NiCl2.6H2O. A. oryzae spore propagation medium (Cove-N-Gly) (in g L-1): 218 g sorbitol, 10 g glycerol 99.5%, 2.02 g KNO3, 25 g agar and 50 ml L-1 of salt solution. Cove-N-Gly salt solution (in g L-1): 26 g KCl, 26 g MgSO4.7H2O, 76 g KH2PO4 and 50 ml L-1 of trace elements solution. Cove-N-Gly trace elements solution (in mg L-1): 40 mg Na2B4O7.10H2O, 400 mg CuSO4.5H2O, 1,200 mg FeSO4.7H2O, 700 mg MnSO4.H2O, 800 mg Na2MoO4.2H2O and 10 g ZnSO4.7H2O.
A. oryzae RIB40 batch fermentations were inoculated with spores propagated on Cove-N-Gly spore propagation medium plates incubated for 5 days at 30 C. To obtain enough mycelia with well dispersed filamentous growth grown under the same conditions to start enzyme induction with ten different protein inducing oligosaccharides in 250 mL shake flask cultivations, two consecutive batch cultivations were carried out. A. oryzae batch fermentations were performed in 3.6 L Infors bioreactors with a working volume of 2.8 L. Reactors were equipped with two Rushton four-blade disc turbines, no baffles, pH and temperature control. The temperature was maintained at 30 C and the pH was controlled by automatic addition of by addition of 10% H3PO4 or 10% NH3 solution. The pH was set to 3.5 to prevent spore aggregation and kept constant throughout the cultivation. The stirring speed was initially set at 200 rpm and the aeration rate to 0.1 vvm (volume of gas per volume of liquid per minute). After germination, these parameters were increased to 1000 rpm and 1 vvm and kept steady throughout all the rest of the fermentation. The batch cultivation was used to harvest biomass for consecutive induction by any of the different oligosaccharides at the final concentration listed in brackets: 1,3:1,4-β-glucohexaose (66.67 mg L-1), Glc-Maltotriosyl-maltotriose (333.33 mg L-1), 1,4-β-D-xylopentaose (66.67 mg L-1), 1,5-alpha-L-Arabinoheptaose (100 mg L-1), Galactosyl-mannotriose (133.33 mg L-1), sophorose (66.67 mg L-1), D-turanose (333.33 mg L-1), D-melibiose (333.33 mg L-1), 1,4-β-D-mannohexaose (133.33 mg L-1), cellohexaose (200 mg L-1), xyloglucan reduced (X3GLC4) (333.33 mg L-1) and glucose (as control, 20 g L-1). Unless otherwise stated, the oligosaccharides used were obtained from Megazyme (Megazyme, International Ireland Ltd, Wicklow, Ireland); solely sophorose, D-melibiose and D-turanose were obtained from Sigma (Sigma-Aldrich Inc., St. Louis, MO, United States). Oligosaccharides were very well dissolved in water, filtered sterilized and added to each of the three shake flask replicates. Mycelium was harvested after ~32 h cultivation in mid-exponential phase. Mycelium was washed with sterile mineral media without carbon source, squeezed and weighed under sterile conditions. 800 mg of wet weighed mycelia were used for inoculation of each shake flask cultivation.

extract_protocol: For gene expression analysis, mycelium was harvested after 2 h cultivation with the respective inducer from each of the three biological replicates. The cultures were filtered through sterile Miracloth (Calbiochem, San Diego, CA, USA) and washed with a suitable amount of 0.9 % NaCl solution. The mycelium was quickly dried by squeezing and subsequently frozen in liquid nitrogen. Samples were stored at -80°C until RNA extraction. A. oryzae total RNA was extracted using the Qiagen RNeasy Mini Kit (QIAGEN Nordic, Ballerup, Denmark), according to the protocol for isolation of total RNA from plant and fungi. For the purpose, approximately 500 mg of frozen mycelium was ground to powder using a ceramic mortar and pestle. Mycelium was kept in liquid nitrogen throughout the grinding processing. All samples were inspected for good quality of total RNA extracted with a BioAnalyzer (2100 BioAnalyzer, Agilent Technologies Inc., Santa Clara, CA, USA). RNA quantification was performed in a spectrophotometer (Biophotometer 6131, Eppendorf AG, Hamburg, Germany) and total RNA was stored at -80 oC until further processing.

tag: genotype/variation

value: Wild-type

tag: phenotype

value: normal

tag: accession

value: Aspergillus oryzae sequenced strain RIB40

tag: grown on substrate

tag: substrate description

value: mycelium


title: AML-083-Tumor

description: Hybridized to 250K_Nsp


title: Spleen B

city: New York

first: Daniel

middle: J

last: Nolan

state: NY

address: 1300 York Ave

department: Genetic Medicine

country: USA

institute: Weill Cornell Medical College

description: Spleen Endothelial Cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
All Data was processed using GeneSpring 11 software with RMA normalization
MoGene-1_0-st-v1, HuGene-1_0-st-v1
MoGene-1_0-st-v1-r3, HuGene-1_0-st-v1-r3

organism: Mus musculus

source_name: WT C57BL/6 adult Male

label_protocol: Nugen Ovation Amplification, Ovation Exon Module, Encore Biotin Module for preparation, fragmentation, and labeling.

extract_protocol: PicoPure RNA isolation kit

tag: marker

value: Ve-Cad+ Isolectin+ IgG-

tag: strain

value: Spleen Endothelial Cells

value: male


title: Leaf_07506-01versus12120-03_rep2

description: both clones are diploids

hyb_protocol: Hybridization and slide processing were performed using the 1 × 44 k POCI array (Kloosterman et al. 2008) using the Arrayit microarray hybridization cassette (Arrayit Corp, Sunnyvale, CA, USA) according to manufacturer specifications. Slides were scanned on the GenePix 4000B Microarray Scanner (MDS Analytical Technologies, Ottawa, ON, Canada), and data were extracted using the manufacturer’s software.

tag: tissue


title: AML-046-Tumor

description: Hybridized to 250K_Nsp

tag: disease status

value: acute myeloid leukemia


title: Aspergillus oryzae grown on the substrate I1_Shake Flask 3

description:
Processed data file: ctrl_vs_I1.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 5


title: Muscle A

description: Muslce Endothelial Cells

value: CD34+ Isolectin+ IgG-

value: Muslce Endothelial Cells


title: Muscle B

description: Muslce Endothelial Cells


title: Aspergillus oryzae grown on the substrate I11_Shake Flask 3

description:
Processed data file: ctrl_vs_I11.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 11

value: Xyloglucan


title: AML-039-Tumor

description: Hybridized to 250K_Nsp

value: tumor


title: Tesits C

description: Testicle Endothelial Cells

value: CD34+ Ve-Cad+ IgG-

value: Testicle Endothelial Cells


title: Aspergillus oryzae grown on the substrate I1_Shake Flask 2

description:
Processed data file: ctrl_vs_I1.csv
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 4


title: Aspergillus oryzae grown on the substrate glucose_Shake Flask 2

description:
Processed data file: This sample is used as control
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 2

value: glucose


title: Spleen C

description: Spleen Endothelial Cells


title: Testis A

description: Testicle Endothelial Cells


title: Aspergillus oryzae grown on the substrate glucose_Shake Flask 1

description:
Processed data file: This sample is used as control
This sample is of wild-type Aspergillus oryzae. Biological replicates were used in this experiment, each from separate cultures.
Sample 1


title: AML-040-Tumor

description: Hybridized to 250K_Nsp


title: hESC-EC CXCR4 B

description: CXCR4+ hESC-ECs

source_name: Human Embryonic Stem Cells

value: CD31+ VPR+

value: Human Embryonic Stem Cells


title: hESC-EC CXCR4 C

description: CXCR4+ hESC-ECs


title: hESC-EC CXCR4 A

description: CXCR4+ hESC-ECs


title: AML-042-Tumor

description: Hybridized to 250K_Nsp


title: hESC-EC Prominin C

description: Prominin1+ hESC-ECs


title: AML-036-Tumor

description: Hybridized to 250K_Nsp


title: AML-037-Tumor

description: Hybridized to 250K_Nsp


title: Testis B

description: Testicle Endothelial Cells


title: Spleen A

description: Spleen Endothelial Cells


title: AML-051-Tumor

description: Hybridized to 250K_Nsp


title: AML-035-Tumor

description: Hybridized to 250K_Nsp


title: hESC-EC Prominin B

description: Prominin1+ hESC-ECs


title: AML-034-Tumor

description: Hybridized to 250K_Nsp


title: ATP1A1 mutant aldosterone-producing adenoma 1

status: Public on Jul 14 2013

city: Cambridge

first: Elena

middle: Aisha Binti

last: Azizan

state: Cambridgeshire

address: Box 110, Addenbrooke's Hospital

department: University of Cambridge

country: United Kingdom

institute: Clinical Pharmacology Unit

description: CACN/ATP mutant APA

hyb_protocol: Following fragmentation, 25 ng/uL of fragmented sscDNA were hybridized for 16 hr at 45oC on GeneChip Human Gene ST1.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_0007 fluidics script.

data_processing:
Quality control, data processing and analysis was performed using GeneChip Command Console Software (Affymetrix, Santa Clara, CA, USA) and Partek Genomic Suite™ v. 6.5 (Partek Inc., St. Louis, MO). All samples were normalized by the GC-RMA method (Gene Chips Robust Multichip Analysis) with Quantile normalisation and Median Polish for Probe set summarization. False discovery rate control (Benjamini and Hochberg method) was used to correct for multiple testing. Differentially expressed genes were defined by a fold change difference >2 and p<0.05.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label: biotin

source_name: ATP1A1 mutant APA

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion and Affymetrix protocol from 200ng total RNA (Ambion WT Expressoin Kit p/n4425209, GeneChip WT Terminal Labelling and Hybridisation User Mannual, Affymetrix p/n702808).

growth_protocol: not applicable

extract_protocol: Samples were kept in RNA later (Ambion) till extracted for RNA. Total DNA-free RNA was isolated using the TRIzol® Plus RNA Purification System (#12183-555, Life Technologies) along with the PureLink® DNase Set (#12185010, Life Technologies). KCNJ5, CACNA1D, and ATP1A1 mutant aldosterone producing adenomas were identified by Sanger Sequencing.

treatment_protocol: not applicable

value: primary hyperaldosteronism

value: aldosterone-producing adenoma

value: ATP1A1 mutant


title: ATP1A1 mutant aldosterone-producing adenoma 2

description: CACN/ATP mutant APA


title: hESC-EC Prominin A

description: Prominin1+ hESC-ECs


title: CACNA1D mutant aldosterone-producing adenoma 1

description: CACN/ATP mutant APA

source_name: CACNA1D mutant APA

value: CACNA1D mutant


title: KCNJ5 mutant aldosterone-producing adenoma 8

description: KCNJ5 mutant APA

source_name: KCNJ5 mutant APA

value: KCNJ5 mutant


title: CACNA1D mutant aldosterone-producing adenoma 2

description: CACN/ATP mutant APA


title: KCNJ5 mutant aldosterone-producing adenoma 7

description: KCNJ5 mutant APA


title: CACNA1D mutant aldosterone-producing adenoma 3

description: CACN/ATP mutant APA


title: KCNJ5 mutant aldosterone-producing adenoma 5

description: KCNJ5 mutant APA


title: KCNJ5 mutant aldosterone-producing adenoma 4

description: KCNJ5 mutant APA


title: AML-031-Tumor

description: Hybridized to 250K_Nsp


title: KCNJ5 mutant aldosterone-producing adenoma 6

description: KCNJ5 mutant APA


title: KCNJ5 mutant aldosterone-producing adenoma 3

description: KCNJ5 mutant APA


title: KCNJ5 mutant aldosterone-producing adenoma 2

description: KCNJ5 mutant APA


title: AML-027-Tumor

description: Hybridized to 250K_Nsp


title: AML-032-Tumor

description: Hybridized to 250K_Nsp


title: KCNJ5 mutant aldosterone-producing adenoma 1

description: KCNJ5 mutant APA


title: AML-024-Tumor

description: Hybridized to 250K_Nsp


title: AML-026-Tumor

description: Hybridized to 250K_Nsp


title: AML-030-Tumor

description: Hybridized to 250K_Nsp


title: Bile duct cancer 22

status: Public on Jul 13 2013

city: Seoul

first: Mee Joo

last: Kang

address: 101 Daehak-ro, Chongno-gu

country: South Korea

institute: Seoul National University College of Medicine

description: Sample 22

hyb_protocol: Labeled DNA samples were hybridized to the NimbleGen aCGH array for 42-72 h at 42°C, according to the manufacturer's instructions (NimbleGen, Madison, USA).

scan_protocol: The arrays were scanned with a NimbleGen MS 200 Microarray scanner set at 532 nm and 635 nm, with a resolution of 2 µm, to produce images in TIFF format according to the manufacturer's instructions.

data_processing: The array data were exported, processed and analyzed using NimbleScan v2.5. Arrays were processed using manufacturer's standard settings with NimbleScan v2.5 segMNT, including spatial correction (LOESS) and qspline fit normalization, in order to compensate for differences in signal between the two dyes. CNV segments that have more than 10 probes and logR ratio ≥ ± 0.3 were defined as CNV call. SignalMap v.1.9 was used for visual presentation of the resulting data (Roche).

source_name: Genomic DNA reference sample

label_protocol: One µg of each genomic DNA test sample was labeled with Cy3 using a Cy3-random nonamer, whereas 0.5 µg of each genomic DNA reference sample was labeled with Cy5 using a Cy5-random nonamer.

extract_protocol: Immediately after tumor resection, 5 x 5 mm pieces of tumor tissue were fresh frozen and stored in -70C liquid nitrogen. Routinely processed 4-um thick paraffin-embedded sections from the same lesion were stained with hematoxylin and eosin and examined histologically.  DNA was extracted from tumor tissue using QIAamp® Mini kits (QIAGEN Sciences, Germantown, PA, USA), according to the manufacturer’s instructions. DNA concentrations were determined spectrophotometrically, and DNA purity and integrity were evaluated by calculating the 260/280 ratio and by electrophoresis on 1% agarose gels.

tag: reference source info

value: blood drawn from peripheral vein of a Caucasian male, and the cell line was made by EBV transformation of B-lymphocyte

source_name: DNA of Bile duct cancer 22 tumor tissue

tag: location

value: proximal

tag: gross

value: papillary

tag: histologic grade

value: moderately differentiated

tag: tumor t stage

tag: tumor n stage

tag: perineural invasion

value: yes

tag: recurrence

tag: disease_free (mo)

tag: follow_up (mo)


title: Bile duct cancer 21

description: Sample 21

tag: gender

value: male

source_name: DNA of Bile duct cancer 21 tumor tissue

tag: age

value: female

value: flat

value: no


title: AML-008-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia

value: tumor


title: Bile duct cancer 18

description: Sample 18

source_name: DNA of Bile duct cancer 18 tumor tissue


title: Bile duct cancer 16

description: Sample 16

source_name: DNA of Bile duct cancer 16 tumor tissue

value: distal


title: Bile duct cancer 17

description: Sample 17

source_name: DNA of Bile duct cancer 17 tumor tissue


title: Bile duct cancer 20

description: Sample 20

source_name: DNA of Bile duct cancer 20 tumor tissue

value: nodular

value: poorly differentiated


title: Bile duct cancer 24

description: Sample 24

source_name: DNA of Bile duct cancer 24 tumor tissue

value: well differentiated


title: AML-010-Tumor

description: Hybridized to 250K_Nsp


title: AML-009-Tumor

description: Hybridized to 250K_Nsp


title: AML-025-Tumor

description: Hybridized to 250K_Nsp


title: Bile duct cancer 23

description: Sample 23

source_name: DNA of Bile duct cancer 23 tumor tissue


title: Bile duct cancer 12

description: Sample 12

source_name: DNA of Bile duct cancer 12 tumor tissue


title: ASC LMNA-KD MeDIP Repl2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted

source_name: ASC LMNA-KD MeDIP Chip DNA

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: DMEM/F12, 10% FCS

extract_protocol:
histone ChIPs: ChIP of modified histones was done as described (Sørensen et al  2010 Mol Biol  Cell) using antibodies to H3K9me3 (Diagenode, pAb-056-050), H3K27me3 (Millipore, 07-449) and H3K4me3 (Abcam, Ab8580). In short, cells were cross-linked for 8 min with 1% formaldehyde and sonicated to ~400 bp fragments using a Bioruptor (Diagenode). Chromatin (100 µl at 0.5 A260 U/µl) was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed, RNAse-treated, purified by phenol-chloroform isoamylalcohol extraction, amplified using the WGA4 kit (Sigma-Aldrich), cleaned up and eluted in MilliQ water.
Lamin A/C ChIPs: For ChIP of LMNA, cells were cross-linked as above and chromatin prepared by lysis (5 min on ice) and sonication (total of 45 min in a Bioruptor) in the following lysis buffer: 10 mM Tris-HCl, pH 7.5, 10 mM KCl, 2 mM EDTA, 1% Triton X-100, protease inhibitors. Chromatin (100 µl at 2 A260 U/µl) was incubated overnight at 4oC with 2.4 μg anti-lamin A/C antibody (Santa Cruz, sc-7292) coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed in lysis buffer and processed as for histone ChIPs.
MeDIP: MeDIP was performed as described (Sørensen and Collas, 2009. Meth Mol Biol 567, 249-262). In short, genomic DNA was purified and fragmented by probe sonication to 300-500 base pair fragments. Methylated fragments were immunoprecipitated using anti-5 mC antibodies (Diagenode). Immunoprecipitated (MeDIP) and input DNA was amplified by 14 PCR cycles using the WGA2 kit (Sigma-Aldrich) and cleaned up using the MinElute PCR purification kit (Qiagen). Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on the same promoter arrays as those used for ChIP-chip.

tag: cell type

value: Adipose Stem Cells

tag: cell treatment

value: LMNA knock-down (cultured)

tag: chip antibody

value: anti 5-mC (Diagenode MAb-5MCYT)

source_name: ASC LMNA-KD MeDIP Input DNA


title: Bile duct cancer 15

description: Sample 15

value: blood drawn from peripheral vein of a Caucasian male, and the cell line was made by EBV transformation of B-lymphocyte

source_name: DNA of Bile duct cancer 15 tumor tissue

value: proximal


title: Bile duct cancer 11

description: Sample 11

source_name: DNA of Bile duct cancer 11 tumor tissue

value: moderately differentiated


title: AML-033-Tumor

description: Hybridized to 250K_Nsp

source_name: AML primary sample

tag: tissue


title: AML-002-Tumor

description: Hybridized to 250K_Nsp

tag: disease status


title: AML-011-Tumor

description: Hybridized to 250K_Nsp


title: Bile duct cancer 9

description: Sample 9

tag: reference source info

source_name: DNA of Bile duct cancer 9 tumor tissue

value: yes


title: AML-007-Tumor

description: Hybridized to 250K_Nsp


title: Bile duct cancer 6

description: Sample 6

value: male

source_name: DNA of Bile duct cancer 6 tumor tissue

tag: location


title: Bile duct cancer 13

description: Sample 13

source_name: Genomic DNA reference sample

source_name: DNA of Bile duct cancer 13 tumor tissue

tag: gross


title: Bile duct cancer 8

description: Sample 8

source_name: DNA of Bile duct cancer 8 tumor tissue

tag: histologic grade


title: Bile duct cancer 10

description: Sample 10

source_name: DNA of Bile duct cancer 10 tumor tissue

value: papillary

tag: tumor t stage


title: Bile duct cancer 14

description: Sample 14

source_name: DNA of Bile duct cancer 14 tumor tissue

value: female

value: flat

tag: tumor n stage


title: Bile duct cancer 5

description: Sample 5

source_name: DNA of Bile duct cancer 5 tumor tissue

tag: perineural invasion


title: ASC LMNA-KD MeDIP Repl1


title: Ifnar2-/-_IFNb_1

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent gene expression hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray scanner (G2505B) using one color scan settings for 4x44k array slides (scan area 61x21.6mm, scan resolution 5um, dye channel is set to Green and Extended Dynamic range selected at 100% and 10% Green PMT)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_95 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ifnar2-/- peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were kept under regular 12hr light/dark cycles, and fed ad libitum.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini columns according to the manufacturers instructions.  The protocol includes an on-column DNAse digestion step.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Mice were humanely culled 3hr post injection and the PEC's extracted by flushing the peritoneal cavity with cold, sterile PBS and lysed immediately for RNA extraction.

tag: strain

tag: genotype

value: Ifnar2 -/-

value: Female

value: 8 weeks

value: Peritoneal Exudate Cells

tag: treatment

value: IFN beta


title: Ifnar2-/-_PBS_2

source_name: Ifnar2-/- peritoneal exudate cells,  PBS treated 3hr, replicate 2

tag: gender

value: PBS


title: AML-005-Tumor

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia

value: tumor


title: AdultTestes_red[1]/e[1](WT)_rep3

city: Ithaca

first: Jongmin

last: Kim

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000-7G

data_processing: Data were background adjusted and normalized using R program (v2.13.2) with the BioConductor package GCRMA.

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~250ng total RNA (GeneChip 3' IVT expression kit)

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 25 °C

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

treatment_protocol: Magn, WT(red, e), aly, and sa testes without seminal vesicle and accessory glands were dissected in icecold PBS containing 0.1% DEPC in 30 min intervals and immediately frozen in liquid nitrogen before transferred to -80°C. Total RNA was extracted using TRIzol (Invitrogen). Five micrograms of total RNA was processed for each replicate.

tag: genotype/variation

tag: age

value: 0~1 day post eclosion

value: adult testes without seminal vesicles and accessory glands


title: Adipose Stem Cells LMNA Knockdown rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: Adipose stem cells

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

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

tag: cell treatment

value: LMNA-KD by shRNA

tag: culture

value: DMEM/F12, 10% FCS

value: Adipose tissue


title: AML-001-Tumor

description: Hybridized to 250K_Nsp

tag: tissue


title: Bile duct cancer 19

description: Sample 19

value: male

value: blood drawn from peripheral vein of a Caucasian male, and the cell line was made by EBV transformation of B-lymphocyte

source_name: DNA of Bile duct cancer 19 tumor tissue

value: proximal

value: moderately differentiated

value: yes

tag: recurrence

tag: disease_free (mo)

tag: follow_up (mo)


title: AdultTestes_red[1]/e[1](WT)_rep1


title: Ifnar2-/-_IFNb_2

source_name: Ifnar2-/- peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 2

value: Ifnar2 -/-

value: Female

tag: cell type


title: Adipose Stem Cells LMNA Knockdown rep1


title: Adipose Stem Cells LMNA Knockdown rep3


title: Bile duct cancer 4

description: Sample 4

tag: reference source info

source_name: DNA of Bile duct cancer 4 tumor tissue

tag: location

tag: gross

value: nodular

tag: histologic grade

value: well differentiated


title: Adipose Stem Cells rep3


title: Ifnar2-/-_IFNb_3

source_name: Ifnar2-/- peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 3

tag: strain

value: 8 weeks

value: Peritoneal Exudate Cells

value: IFN beta


title: WT_IFNb_2

source_name: Wildtype peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 2

tag: genotype

value: Wild Type


title: Ifnar2-/-_PBS_1

source_name: Ifnar2-/- peritoneal exudate cells,  PBS treated 3hr, replicate 1

tag: treatment

value: PBS


title: AdultTestes_magn[12c]/magn[12c];pSC2_rep2

value: magn[12c]/magn[12c];pSC2 mutation

value: 0~1 day post eclosion

value: adult testes without seminal vesicles and accessory glands


title: Adipose Stem Cells rep2

value: DMEM/F12, 10% FCS

value: Adipose tissue


title: WT_IFNb_3

source_name: Wildtype peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 3

tag: gender


title: WT_IFNb_1

source_name: Wildtype peritoneal exudate cells, treated 3hr 10,000IU/ml Interferon beta, replicate 1


title: WT_PBS_3

source_name: Wildtype peritoneal exudate cells, PBS treated 3hr, replicate 3


title: SDR (male) vs HHR (male)

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

hyb_protocol: Labeled DNAs were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were extensively washed.

scan_protocol: Microarrays were scanned on an Agilent scanner, then images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software  was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: SDR

label_protocol: Genomic DNAs were labelled with Cy5 and Cy3 using Aligent genomic DNA Enzymatic labeling kit.

growth_protocol: Animals were housed in the Institute for Animal Experiments of Hirosaki University Graduate School of Medicine.

extract_protocol: Genomic DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: Animals had free access to water and food.

value: male

value: Sprague-Dawley

value: liver

source_name: HHR

value: Hirosaki hairless

value: Liver


title: Adipose Stem Cells rep1


title: AdultTestes_magn[12c]/magn[23b]_rep1

tag: genotype/variation

value: magn[12c]/magn[23b] mutation


title: AdultTestes_magn[12c]/magn[12c];pSC2_rep1

tag: age


title: AdultTestes_magn[12c]/magn[23b]_rep2


title: AdultTestes_red[1]/e[1](WT)_rep2


title: AdultTestes_sa[1]/sa[2]_rep3

value: sa[1]/sa[2] mutation


title: Bile duct cancer 7

description: Sample 7

source_name: Genomic DNA reference sample

value: blood drawn from peripheral vein of a Caucasian male, and the cell line was made by EBV transformation of B-lymphocyte

source_name: DNA of Bile duct cancer 7 tumor tissue

value: proximal

value: flat

value: moderately differentiated

tag: tumor t stage

tag: tumor n stage

tag: perineural invasion

value: yes


title: liver of Mecp2-null mice, biological rep4

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

institute: New York Institute of Technology

description: Liver from Mecp2 -/y mice

hyb_protocol: cRNA yields and 5ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix Mouse Exon 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing:
The Affymetrix Power Tools (APT) command line program was used to process raw data using the robust multichip average method and generate gene-level expression values based on the core probesets using median polish.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Mecp2 -/y, liver

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Mouse striatum and liver dissected from 8-week-old male mice

extract_protocol: Total RNA was extracted from the striatum and liver of 8-week-old male mice using TRIzol reagent (Invitrogen Corporation, Carlsbad, CA, USA), DNase I treated, and purified using the miRNAeasy mini kit according to the manufacturer’s protocol (Qiagen, Valencia, CA, USA).

tag: tissue

value: 8 week

value: Mecp2 -/y


title: SDR (female) vs HHR (female)

value: female


title: liver of Mecp2-null mice, biological rep5

description: Liver from Mecp2 -/y mice


title: WT_PBS_2

source_name: Wildtype peritoneal exudate cells, PBS treated 3hr, replicate 2

value: Wild Type

value: Female

value: 8 weeks

value: Peritoneal Exudate Cells

value: PBS


title: liver of Mecp2-null mice, biological rep2

description: Liver from Mecp2 -/y mice

value: liver

value: male


title: AdultTestes_sa[1]/sa[2]_rep2

value: 0~1 day post eclosion

value: adult testes without seminal vesicles and accessory glands


title: liver of Mecp2-null mice, biological rep1

description: Liver from Mecp2 -/y mice


title: AdultTestes_sa[1]/sa[2]_rep1

value: sa[1]/sa[2] mutation


title: Control replicate 3 and IUGR replicate 4

city: Philadelphia

first: Lane

middle: Johanna

last: Jaeckle Santos

state: PA

address: 421 Curie Blvd, BRB II/III 1341

department: CRRWH

institute: University of Pennsylvania School of Medicine

description: biological replicate 3

hyb_protocol: samples were hybridized overnight to the 4x44k Rat gene expresion microarray

scan_protocol: microarray was scanned with a G2565B DNA microarray scanner

data_processing: Data was normalized using the normalizeWithinArrays function of the limma package.  The statistical significance of differential gene expression was assessed using the SAMR package.

source_name: control replicate 3

label_protocol: amplifed cDNA (BioPrime) was labeled with Cy3/Cy5 labelled nucleotides.

growth_protocol: Timed pregnant Sprague Dawley rats purchased commercially from Charles River

extract_protocol: total RNA was extracted from pancreatic islets using TRIzol according to manufacturer's instructions.

treatment_protocol: at e18, surgical bilateral uterine artery ligation was performed on pregant dams, or sham surgery. After pups were allowed to be spontaneously delivered, offspring were sacrificed at postnatal day 14.

tag: condition

value: control

value: post-natal day 14

value: isolated pancreatic islets

source_name: IUGR replicate 4

value: IUGR


title: AdultTestes_aly[2]/aly[5p]_rep3

value: aly[2]/aly[5p] mutation


title: liver of wild-type mice, biological rep5

description: Liver from wild-type mice

source_name: wild-type, liver

value: 8 week

value: wild-type


title: WT_PBS_1

source_name: Wildtype peritoneal exudate cells, PBS treated 3hr, replicate 1

value: Wild Type


title: liver of wild-type mice, biological rep4

description: Liver from wild-type mice


title: liver of wild-type mice, biological rep3

description: Liver from wild-type mice


title: Control replicate 4 and IUGR replicate 3

description: biological replicate 4

source_name: control replicate 4

source_name: IUGR replicate 3


title: IUGR replicate 1 and Control replicate 2

description: biological replicate 2

source_name: IUGR replicate 1

source_name: control replicate 2


title: Ifnar2-/-_PBS_3

source_name: Ifnar2-/- peritoneal exudate cells,  PBS treated 3hr, replicate 3

value: Ifnar2 -/-

value: Female


title: AdultTestes_aly[2]/aly[5p]_rep2


title: IUGR replicate 2 and Control replicate 1

description: biological replicate 1

source_name: IUGR replicate 2

source_name: control replicate 1


title: AdultTestes_aly[2]/aly[5p]_rep1


title: liver of Mecp2-null mice, biological rep3

description: Liver from Mecp2 -/y mice

value: Mecp2 -/y


title: liver of wild-type mice, biological rep2

description: Liver from wild-type mice


title: Bile duct cancer 3

description: Sample 3

value: blood drawn from peripheral vein of a Caucasian male, and the cell line was made by EBV transformation of B-lymphocyte

source_name: DNA of Bile duct cancer 3 tumor tissue

value: proximal

value: nodular

value: moderately differentiated

value: yes

tag: recurrence

tag: disease_free (mo)

tag: follow_up (mo)


title: 3800c

city: Beijing

first: Gao

last: Ying

address: Qinghua East Street

country: China

institute: Tsinghua University

description:
GeoChip data for soil sample collected at the 3800 m elevation, replicate 3
Soil microbes

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured bacterium

source_name: Soil microbes in Tibetan grasslands

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: different elevations


title: Bile duct cancer 2

description: Sample 2

source_name: Genomic DNA reference sample

value: male

tag: reference source info

source_name: DNA of Bile duct cancer 2 tumor tissue

tag: location

tag: gross

value: well differentiated

value: no


title: striatum of Mecp2-null mice, biological rep5

description: Striatum from Mecp2 -/y mice

source_name: Mecp2 -/y, striatum

tag: strain

value: striatum


title: liver of wild-type mice, biological rep1

description: Liver from wild-type mice

value: liver


title: striatum of Mecp2-null mice, biological rep4

description: Striatum from Mecp2 -/y mice


title: Bile duct cancer 1

description: Sample 1

source_name: DNA of Bile duct cancer 1 tumor tissue

value: distal

value: flat

tag: histologic grade


title: 3800a

description:
GeoChip data for soil sample collected at the 3800 m elevation, replicate 1
Soil microbes


title: 3800b

description:
GeoChip data for soil sample collected at the 3800 m elevation, replicate 2
Soil microbes


title: PML4-K562

first: xiang

last: Lv

address: No.5 Dongdansantiao

institute: PUMC&CAMS

description: Gene expression data from PML4-overexpressing K562 cells

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

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

data_processing: The data were analyzed with 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: K562 cells overexpressing PML4

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

treatment_protocol: Transfected with retrovirus overexpressing PML4 or control vector pMSCV and selected with G418 for 3 weeks

tag: cell line

tag: transfection

value: PML4 overexpression


title: striatum of Mecp2-null mice, biological rep3

description: Striatum from Mecp2 -/y mice

tag: age

value: 8 week

tag: gender

tag: genotype/variation


title: striatum of Mecp2-null mice, biological rep2

description: Striatum from Mecp2 -/y mice


title: 08-hESCs-H9-p29

city: Los Angeles

first: James

middle: A

last: Byrne

state: CA

address: 610 Charles E. Young Drive East

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description: Gene expression data from cell lines

hyb_protocol: Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.

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

data_processing: Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.

source_name: Human embryonic stem cells (H9)

label_protocol: 100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA

growth_protocol: All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.

extract_protocol: Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.  This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

treatment_protocol: Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.

tag: cell type

value: Human embryonic stem cells (H9)


title: PMSCV-K562

description: Gene expression data from control K562 cells

source_name: K562 cells transfected with control vector

value: control


title: ASC-ad Lamin A Repl2

source_name: ASC-ad Lamin A/C ChIP DNA

extract_protocol:
ChIP of modified histones was done as described (Sørensen et al  2010 Mol Biol  Cell) using antibodies to H3K9me3 (Diagenode, pAb-056-050), H3K27me3 (Millipore, 07-449) and H3K4me3 (Abcam, Ab8580). In short, cells were cross-linked for 8 min with 1% formaldehyde and sonicated to ~400 bp fragments using a Bioruptor (Diagenode). Chromatin (100 µl at 0.5 A260 U/µl) was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed, RNAse-treated, purified by phenol-chloroform isoamylalcohol extraction, amplified using the WGA4 kit (Sigma-Aldrich), cleaned up and eluted in MilliQ water.
For ChIP of LMNA, cells were cross-linked as above and chromatin prepared by lysis (5 min on ice) and sonication (total of 45 min in a Bioruptor) in the following lysis buffer: 10 mM Tris-HCl, pH 7.5, 10 mM KCl, 2 mM EDTA, 1% Triton X-100, protease inhibitors. Chromatin (100 µl at 2 A260 U/µl) was incubated overnight at 4oC with 2.4 μg anti-lamin A/C antibody (Santa Cruz, sc-7292) coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed in lysis buffer and processed as for histone ChIPs.
MeDIP was performed as described (Sørensen and Collas, 2009. Meth Mol Biol 567, 249-262). In short, genomic DNA was purified and fragmented by probe sonication to 300-500 base pair fragments. Methylated fragments were immunoprecipitated using anti-5 mC antibodies (Diagenode). Immunoprecipitated (MeDIP) and input DNA was amplified by 14 PCR cycles using the WGA2 kit (Sigma-Aldrich) and cleaned up using the MinElute PCR purification kit (Qiagen). Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on the same promoter arrays as those used for ChIP-chip.

value: Adipocytes

tag: cell treatment

value: Differentiated from ASCs for 21 days

tag: chip antibody

value: Lamin A/C, sc-7292

source_name: ASC-ad Lamin A/C Input DNA


title: 3600c

description:
GeoChip data for soil sample collected at the 3600 m elevation, replicate 3
Soil microbes


title: ASC-ad Lamin A Repl1


title: 3400c

description:
GeoChip data for soil sample collected at the 3400 m elevation, replicate 3
Soil microbes


title: 3600b

description:
GeoChip data for soil sample collected at the 3600 m elevation, replicate 2
Soil microbes


title: 06-hIPSC-postEx-p28

description: Gene expression data from cell lines

source_name: Human induced pluripotent stem cells - post-Excision


title: striatum of wild-type mice, biological rep5

description: Striatum from wild-type mice

source_name: wild-type, striatum

tag: tissue

value: wild-type


title: 07-hESCs-H9-p29

description: Gene expression data from cell lines


title: striatum of wild-type mice, biological rep4

description: Striatum from wild-type mice


title: ASC LMNA-KD H3K27me3 Repl2

source_name: ASC LMNA-KD H3K27me3 ChIP DNA

value: Adipose Stem Cells

value: LMNA knock-down (cultured)

value: H3K27me3, Millipore 07-449

source_name: ASC LMNA-KD H3K27me3 Input DNA


title: 05-hIPSC-postEx-p28

description: Gene expression data from cell lines

value: Human induced pluripotent stem cells - post-Excision


title: striatum of wild-type mice, biological rep3

description: Striatum from wild-type mice

value: male


title: 04-hIPSC-preEx-p32

description: Gene expression data from cell lines

source_name: Human induced pluripotent stem cells - pre-Excision


title: ASC LMNA-KD H3K9me3 Repl2

source_name: ASC LMNA-KD H3K9me3 ChIP DNA

value: H3K9me3, Diagenode, pAb-056-050

source_name: ASC LMNA-KD H3K9me3 Input DNA


title: 3400b

description:
GeoChip data for soil sample collected at the 3400 m elevation, replicate 2
Soil microbes

source_name: Soil microbes in Tibetan grasslands


title: 3400a

description:
GeoChip data for soil sample collected at the 3400 m elevation, replicate 1
Soil microbes


title: 3200c

description:
GeoChip data for soil sample collected at the 3200 m elevation, replicate 3
Soil microbes


title: 3200b

description:
GeoChip data for soil sample collected at the 3200 m elevation, replicate 2
Soil microbes


title: striatum of wild-type mice, biological rep1

description: Striatum from wild-type mice

value: striatum


title: 01-HDFs-p5

description: Gene expression data from cell lines

source_name: Primary adult human skin cells

value: Primary adult human skin cells


title: 3200a

description:
GeoChip data for soil sample collected at the 3200 m elevation, replicate 1
Soil microbes


title: ASC LMNA-KD H3K4me3 Repl1

source_name: ASC LMNA-KD H3K4me3 ChIP DNA

value: H3K4me3, Abcam, Ab8580

source_name: ASC LMNA-KD H3K4me3 Input DNA


title: 02-HDFs-p5

description: Gene expression data from cell lines


title: 03-hIPSC-preEx-p32

description: Gene expression data from cell lines

value: Human induced pluripotent stem cells - pre-Excision


title: ASC LMNA-KD H3K9me3 Repl1


title: ASC LMNA-KD Lamin A Repl1

source_name: ASC LMNA-KD Lamin A/C ChIP DNA

source_name: ASC LMNA-KD Lamin A/C Input DNA


title: striatum of Mecp2-null mice, biological rep1

description: Striatum from Mecp2 -/y mice

source_name: Mecp2 -/y, striatum

value: 8 week

value: Mecp2 -/y


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 12hrs) V2_R

status: Public on Jul 12 2013

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Agilent protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: Agilent protocol

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: Described in Hu et al. 2005, BioTechniques, 38:121-124 (PMID 15679094).

growth_protocol: growth in DMEM:F12 complete media with supplements

treatment_protocol: plus anti-HGF treatment every two hours after 36 in coculutre with fibroblasts

tag: sample type

value: direct coculture

tag: treatment


title: 3600a

description:
GeoChip data for soil sample collected at the 3600 m elevation, replicate 1
Soil microbes

tag: different elevations


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 4hrs) V2_R

value: plus anti-HGF treatment every two hours after 36 in coculutre with fibroblasts


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 8hrs) V2


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 8hrs) V2_R


title: ASC H3K9me3 Repl1

source_name: ASC H3K9me3 ChIP DNA

value: Untreated (cultured)

source_name: ASC H3K9me3 Input DNA


title: ASC H3K9me3 Repl2


title: M_MCF10DCIS serum free 2 HGF PC5_129_8

description: M_MCF10DCIS serum free 2 HGF PC5_129_8

source_name: M_MCF10DCIS serum free 2 HGF PC5_129_8

growth_protocol: growth in DMEM:F12 serum free

treatment_protocol: plus rHGF treatment every 2 hours for 6 hours

value: monoculture


title: ASC LMNA-KD Lamin A Repl2

value: Adipose Stem Cells

value: Lamin A/C, sc-7292


title: ASC H3K27me3 Repl2

source_name: ASC H3K27me3 ChIP DNA

value: H3K27me3, Millipore 07-449

source_name: ASC H3K27me3 Input DNA


title: ASC H3K27me3 Repl1


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 12hrs) V2


title: M_MCF10DCIS serum free PC5_129_5

description: M_MCF10DCIS serum free PC5_129_5

source_name: M_MCF10DCIS serum free PC5_129_5

treatment_protocol: coculture with reduction mammary fibroblasts


title: M_MCF10DCIS serum free 2 HGF PC5_129_7

description: M_MCF10DCIS serum free 2 HGF PC5_129_7

source_name: M_MCF10DCIS serum free 2 HGF PC5_129_7

value: plus rHGF treatment every 2 hours for 6 hours


title: ASC Lamin A Repl2

source_name: ASC Lamin A/C ChIP DNA

source_name: ASC Lamin A/C Input DNA


title: ASC LMNA-KD H3K27me3 Repl1

source_name: ASC LMNA-KD H3K27me3 ChIP DNA

value: LMNA knock-down (cultured)

source_name: ASC LMNA-KD H3K27me3 Input DNA


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF NT) V2

value: coculture with reduction mammary fibroblasts


title: M_MCF10DCIS DMEM/complete 2 PC5_129_2

description: M_MCF10DCIS DMEM/complete 2 PC5_129_2

source_name: M_MCF10DCIS DMEM/complete 2 PC5_129_2


title: striatum of wild-type mice, biological rep2

description: Striatum from wild-type mice

source_name: wild-type, striatum

value: striatum

value: male

value: wild-type


title: ASC H3K4me3 Repl1

source_name: ASC H3K4me3 ChIP DNA

value: H3K4me3, Abcam, Ab8580

source_name: ASC H3K4me3 Input DNA


title: CB1190_succinate_rep2

first: Christopher

middle: Michael

last: Sales

address: 3141 Chestnut St, Curtis 251

department: Civil, Architectural & Environmental Engineering

institute: Drexel University

hyb_protocol: Hybridization followed the procedure of the Affymetrix protocol for Modified FlexMidi_euk2v3 for P. aeruginosa Array.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Primary data was generated with R/Bioconductor version 2.9. The rma function from the affy package was used to summarize the probe intensities for each probe set by background-adjusment, quantile normalization and the median polish linear fitting procedure.

organism: Pseudonocardia dioxanivorans CB1190

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, succinate-grown

label_protocol: cDNA was obtained from 5 ug of RNA following the Affymetrix protocol for RT. RNA template was degraded with NaOH treatment. cDNA was fragmented with DNaseI, and fragmented cDNA were terminally labeled with biotin.

growth_protocol: Cells were grown in AMS medium amended with either 5 mM of THF or succinate.

extract_protocol: Nucleic acids were obtained following cell lysis with heating and bead-beating in the presence of SDS and phenol. Phenol/chloroform extraction, followed by column-based purification, was performed. Nucleics were treated with DNaseI and RNA was finally purified by RNeasy purification.

treatment_protocol: Cells were harvested by filtration and scraped from filters into vials that were frozen at -80C.

value: succinate


title: CB1190_succinate_rep3


title: CB1190_succinate_rep1


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF NT) V2_R

source_name: Human Reference B


title: M_MCF10DCIS DMEM/complete PC5_129_1

description: M_MCF10DCIS DMEM/complete PC5_129_1

source_name: M_MCF10DCIS DMEM/complete PC5_129_1


title: I_MCF10DCIS:RMF 2 (6h) DMEM PC5_129_4

description: I_MCF10DCIS:RMF 2 (6h) DMEM PC5_129_4

source_name: I_MCF10DCIS:RMF 2 (6h) DMEM PC5_129_4

value: indirect coculture


title: ASC Lamin A Repl1


title: C_MCF10DCIS:RMFs (1:1, 48hrs, antiHGF 4hrs) V2

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: ASC H3K4me3 Repl2


title: CB1190_THF_rep2

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, THF-grown

value: THF


title: CB1190_THF_rep1


title: CB1190_THF_rep3


title: lung tissues_Ad-RFP_LPS_rep3

city: Nanjing

first: wujian

last: xu

state: Jiangshu

address: 305 Esat Zhongshan Road

department: The department of respiratory disease

institute: Jinling Hospital

hyb_protocol: The pre-hybridization of MOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.

source_name: lung tissue, negtive adenovirus treated, with LPS, 12h

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: lung


title: M_MCF10DCIS serum free 2 PC5_129_6

description: M_MCF10DCIS serum free 2 PC5_129_6

source_name: M_MCF10DCIS serum free 2 PC5_129_6


title: lung tissues_Ad-Nogo-B_LPS_rep2

source_name: lung tissue, Nogo-B adenovirus treated, with LPS, 12h


title: lung tissues_Ad-RFP_rep3

source_name: lung tissue, negtive adenovirus treated, without LPS, 12h


title: lung tissues_Ad-Nogo-B_rep1

source_name: lung tissue, Nogo-B adenovirus treated, without LPS, 12h


title: lung tissues_Ad-Nogo-B_LPS_rep3


title: lung tissues_Ad-Nogo-B_LPS_rep1


title: lung tissues_Ad-RFP_LPS_rep1


title: lung tissues_Ad-RFP_LPS_rep2


title: lung tissues_Ad-RFP_rep2


title: lung tissues_Ad-Nogo-B_rep2


title: I_MCF10DCIS:RMF (6h) DMEM PC5_129_3

description: I_MCF10DCIS:RMF (6h) DMEM PC5_129_3

source_name: I_MCF10DCIS:RMF (6h) DMEM PC5_129_3


title: lung tissues_Ad-RFP_rep1


title: MDA-MB-436_day3_methyl

city: Baltimore

first: Francescopaolo

last: Di Cello

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkin University School of Medicine

description:
MDA-MB-436_day3
MDA-MB-436 d3

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following the manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014 N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample were loaded onto a 12-sample chip and the chips were assembled into an hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, the chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

scan_protocol: Polymer-coated chips were image-processed using an Illumina’s iScan scanner.

data_processing:
Data were extracted using teh Methylation Module of GenomeStudio v1.0 Software. Methylation status of each CpG site was presented as beta-value based on following definition: beta  value = (signal intensity of methylation_detection probe)/(signal intensity of methylation_detection probe + signal intensity of non_methylation_detection probe + 100).
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: MDA-MB-436 breast cancer cell line, day 3

label_protocol: DNA bisulfite conversion was carried out using the EZ DNA Methylation Kit (Zymo Research) following the manufacturer’s manual with modifications for Illumina Infinium Methylation Assay. Briefly, 0.5 – 1.0 ug of genomic DNA was first mixed with 5 ul of M-Dilution Buffer and incubate at 37C for 15 minutes and then mixed with 100 ul of CT Conversion Reagent prepared as indicated in the manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95C for 30 seconds and 50C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification. Concentration of eluted DNA was measured using a Nanodrop-1000 spectrometer.

growth_protocol: Cells were grown for three days changing media every day

extract_protocol: Genomic DNA was purified by phenol-chloroform extraction. Quality was assessed by low concentration agarose gel (0.6%) electrophoresis and spectrometry of OD260/280 and OD 260/230 ratio.

value: Female

tag: disease

value: Breast cancer

tag: er


title: lung tissues_Ad-Nogo-B_rep3

tag: strain


title: MDA-MB-453_day3_methyl

description:
MDA-MB-453_day3
MDA-MB-453 d3

source_name: MDA-MB-453 breast cancer cell line, day 3


title: ZR-75-30_day3_methyl

description:
ZR-75-30_day3
ZR-75-30 d3

source_name: ZR-75-30 breast cancer cell line, day 3


title: SUM159PT_day3_methyl

description:
SUM159PT_day3
SUM159PT d3

source_name: SUM159PT breast cancer cell line, day 3


title: MDA-MB-175-VII_day3_methyl

description:
MDA-MB-175-VII_day3
MDA-MB-175-VII d3

source_name: MDA-MB-175-VII breast cancer cell line, day 3


title: MDA-MB-468_day3_methyl

description:
MDA-MB-468_day3
MDA-MB-468 d3

source_name: MDA-MB-468 breast cancer cell line, day 3


title: HCC38_day3_methyl

description:
HCC38_day3
HCC38 d3

source_name: HCC38 breast cancer cell line, day 3


title: SUM149PT_day3_methyl

description:
SUM149PT_day3
SUM149PT d3

source_name: SUM149PT breast cancer cell line, day 3


title: SK-BR-3_day3_methyl

description:
SK-BR-3_day3
SK-BR-3 d3

source_name: SK-BR-3 breast cancer cell line, day 3


title: MDA-MB-231_day3_methyl

description:
MDA-MB-231_day3
MDA-MB-231 d3

source_name: MDA-MB-231 breast cancer cell line, day 3


title: T47D_day3_methyl

description:
T47D_day3
T47D d3

source_name: T47D breast cancer cell line, day 3


title: MDA-MB-415_day3_methyl

description:
MDA-MB-415_day3
MDA-MB-415 d3

source_name: MDA-MB-415 breast cancer cell line, day 3


title: HCC1954_day3_methyl

description:
HCC1954_day3
HCC1954 d3

source_name: HCC1954 breast cancer cell line, day 3


title: HCC1937_day3_methyl

description:
HCC1937_day3
HCC1937 d3

source_name: HCC1937 breast cancer cell line, day 3


title: ZR-75-1_day3_methyl

description:
ZR-75-1_day3
ZR-75-1 d3

source_name: ZR-75-1 breast cancer cell line, day 3


title: MDA-MB-361_day3_methyl

description:
MDA-MB-361_day3
MDA-MB-361 d3

source_name: MDA-MB-361 breast cancer cell line, day 3


title: HCC1187_day3_methyl

description:
HCC1187_day3
HCC1187 d3

source_name: HCC1187 breast cancer cell line, day 3


title: HCC1569_day3_methyl

description:
HCC1569_day3
HCC1569 d3

source_name: HCC1569 breast cancer cell line, day 3


title: BT-474_day3_methyl

description:
BT-474_day3
BT-474 d3

source_name: BT-474 breast cancer cell line, day 3


title: CXCR4 knockout 8

city: Tao-Yuan

first: Guo-Jen

last: Huang

address: 259 Wen-Hwa 1st Road

country: Taiwan

institute: Chang Gung University

description: This BeadChip targets approximately 25,600 well-annotated RefSeq transcripts, over 19,100 unique genes, and enables the interrogation of eight samples in parallel.

hyb_protocol: After 17-h hybridization at 55°C, beadchips were washed according to recommended protocols from Illumina. FluoroLink Cy3-labeled Streptavidin (Amersham Biosciences) was used to detect expression signals.

scan_protocol: The BeadStation 500 G system was then used to scan the beadchips.

data_processing: Raw expression values were log2 transformed and median normalized.

source_name: cerebellum

label_protocol: Messenger RNA molecules were amplified using the MessageAmp II Kit (Ambion) according to the manufacturer's instructions. First strand cDNA was synthesized using  1ug of total RNA and oligo(dT) primers. In vitro transcription was carried out at 37°C for 14 h during which biotinylated UTPs (75 mM Biotin-16-UTP, Ambion) were used for RNA labeling.

extract_protocol: The cerebellum was dissected for RNA extraction by using TissueLyser and RNeasy Lipid Tissue Kit (Qiagen).

value: cerebellum

value: Cxcr4 null


title: CAMA1_day3_methyl

description:
CAMA1_day3
CAMA1 d3

source_name: CAMA1 breast cancer cell line, day 3


title: CXCR4 knockout 7


title: CXCR4 knockout 6


title: CXCR4 knockout 3


title: wildtype 8

value: wildtype


title: EFM192A_day3_methyl

description:
EFM192A_day3
EFM192A d3

source_name: EFM192A breast cancer cell line, day 3


title: CXCR4 knockout 5


title: EFM19_day3_methyl

description:
EFM19_day3
EFM19 d3

source_name: EFM19 breast cancer cell line, day 3


title: MCF7_day3_methyl

description:
MCF7_day3
MCF7 d3

source_name: MCF7 breast cancer cell line, day 3


title: CXCR4 knockout 2


title: HCC1500_day3_methyl

description:
HCC1500_day3
HCC1500 d3

source_name: HCC1500 breast cancer cell line, day 3


title: BT-20_day3_methyl

description:
BT-20_day3
BT-20 d3

source_name: BT-20 breast cancer cell line, day 3


title: wildtype 7


title: wildtype 6


title: wildtype 5


title: CXCR4 knockout 4


title: HCC1419_day3_methyl

description:
HCC1419_day3
HCC1419 d3

source_name: HCC1419 breast cancer cell line, day 3


title: Striatum XX male 4

first: Tuck

middle: Cheong

last: Ngun

address: 695 Charles E Young Dr S Gonda 5524

department: Human Genetics

institute: UCLA

description:
Biological Replicate 4, Batch 1
XXSry_4a

data_processing: Microarray data were processed using the statistical software program R (http://www.r-project.org/). Data were first background corrected using the nec function in the limma package (W. Shi, Oshlack, & Smyth, 2010). Probes with low-quality data (detection p-value of >0.05 in more than a third of the samples) were then removed from the dataset. Next, batch effects were corrected using the ComBat R script and the data underwent quantile normalization and log2 transformation using the limma package (Johnson, Li, & Rabinovic, 2007).

source_name: Striatum XX male

label_protocol: Biotinylated cRNA were prepared by the UCLA Neuroscience Genomics Core.

extract_protocol: Total RNA was isolated from the striatum using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).

value: 152 days

value: Striatum


title: Striatum XX male 5

description:
Biological Replicate 5, Batch 1
XXSry_5a


title: Striatum XX male 8

description:
Biological Replicate 8, Batch 2
XXSry_8a


title: Striatum XX male 7

description:
Biological Replicate 7, Batch 2
XXSry_7a


title: Striatum XX male 3

description:
Biological Replicate 3, Batch 1
XXSry_3a


title: wildtype 4


title: Striatum XX male 6

description:
Biological Replicate 6, Batch 2
XXSry_6a


title: Striatum XX male 2

description:
Biological Replicate 2, Batch 1
XXSry_2a


title: Striatum XX male 1

description:
Biological Replicate 1, Batch 1
XXSry_1a


title: wildtype 2


title: Striatum XY male 11

description:
Biological Replicate 11, Batch 2
XYSry_5b

source_name: Striatum XY male


title: C_RMF:MCF10DCIS(2:1,48h)_rep1

source_name: Human Reference B

value: direct coculture

value: coculture with reduction mammary fibroblasts


title: C_RMF:MCF10DCIS(1:4,48h)_rep1


title: C_RMF:MCF10DCIS(2:1,48h)


title: Striatum XY male 10

description:
Biological Replicate 10, Batch 2
XYSry_2b


title: Striatum XY male 9

description:
Biological Replicate 9, Batch 2
XYSry_1b


title: Striatum XY male 8

description:
Biological Replicate 8, Batch 2
XYSry_8a_6b


title: C_RMF:MCF10DCIS(1:4,48h)


title: Striatum XY male 3

description:
Biological Replicate 3, Batch 1
XYSry_3a_4b


title: C_RMF:MCF10DCIS(1:2,48h)


title: C_RMF:MCF10DCIS(1:2,48h)_rep1


title: Striatum XY male 4

description:
Biological Replicate 4, Batch 1
XYSry_4a_3b


title: Striatum XY male 2

description:
Biological Replicate 2, Batch 1
XYSry_2a


title: Striatum XY male 5

description:
Biological Replicate 5, Batch 1
XYSry_5a


title: Striatum XY male 1

description:
Biological Replicate 1, Batch 1
XYSry_1a


title: Striatum XY male 6

description:
Biological Replicate 6, Batch 1
XYSry_6a


title: Cu Tn7 3938 whole gDNA son ref

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description:
Saccharomyces bayanus var uvarum
extracted primer 1,2,3,4 gdna Cu w/ sonicated mix of acy323, acy 899, acy525 gdna

hyb_protocol: Description : Mix 500 ng of Cy5 DNA, 500 ng Cy3 DNA, and water to 200 ul. Prepare 10X control targets (Agilent) per kit directions. Add 50 ul 10X control targets to each tube. Mix. Incubate 95C 5 min. Cool RT 5 min. Add 250 ul 2X hybridization buffer. Set up hybe according to Agilent protocol. Hybe 60C for 17 hours in Agilent hybe oven.

scan_protocol: Scan Power : 100 PMT Volts : 724 Pixel Size : 5 Laser on time : 29670 Laser Power : 10.00 Scan Date : 2008-05-13 Scan Temperature : 26.54 Scan Time : 11:34:25 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 0, 2960

organism: Saccharomyces bayanus

source_name: extracted primer 1,2,3,4 gdna Cu cy5

label_protocol: Description : DNA labeling is done per Bio-Prime array CGH kit instructions using 21 uL extracted DNA. Purify labeled DNA with Zymo DNA Clean and Concentrator 5 columns. Elute in 21 uL water.

extract_protocol:
Prep DNA from 100 ml culture using the Qiagen Genomic DNA kit. Measure starting DNA concentration with a fluorometer. Digest 2-3 ug DNA using appropriate enzyme and buffers. Ethanol precipitate. Mix equal amounts of DNA from each digest if multiple digests required.
Mix 500/2000 ng of pooled restriction digested DNA, 15 uL HSE buffer (Qiagen), 1.5 uL probe mix (Qiagen), and water to bring to 30 uL total. Heat for 15 minutes at 95C, then transfer to a Qiagen EZ-1-6 robot and allow to re-nature and extend for 20 minutes at 65C. Use Qiagen Haploprep Cartridge (Catalog #4340001/H100.C-48) to wash and capture. Elute by heating to 80C 20 minutes. Collect supernatant.

tag: species

value: S. bayanus

tag: strain name

value: copper resistant strain

tag: genotype

value: contains Tn7 insertion

source_name: sonicated mix of acy323, acy 899, acy525 gdna cy3

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/MDyeastDNAprep.pdf

value: mixed

tag: sex/mating type


title: Striatum XY male 7

description:
Biological Replicate 7, Batch 2
XYSry_7a_7b

tag: age


title: Striatum XXY male 8

description:
Biological Replicate 8, Batch 2
XXYSry_8a_6b

source_name: Striatum XXY male


title: C_RMF:MCF10DCIS(1:1,48h)_rep1

tag: cell line


title: C_RMF:MCF10DCIS(1:0,48h)

value: monoculutre


title: wildtype 3

description: This BeadChip targets approximately 25,600 well-annotated RefSeq transcripts, over 19,100 unique genes, and enables the interrogation of eight samples in parallel.

tag: genotype/variation


title: C_RMF:MCF10DCIS(0:1,48h)_rep1

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: hyb16602

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

description: Gene expression data from Escherichia coli (2-WTB2)

hyb_protocol: Affymetrix Procaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: Scan procedure was carried out at VIB Nucleomics Core (LEUVEN, Belgium) according to Affymetrix recommendation.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

organism: Escherichia coli

source_name: Escherichia coli

label_protocol: Labelling was performed according to the Affymetrix protocol (Affymetrix, Santa Clara, CA, US).

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturer’s protocol.

value: Wild Type


title: PND5 foreskin-DBP500-biological rep7

city: Wilmington

first: Jack

last: Pike

address: 1600 Rockland Road

department: Urology Research

institute: AI duPont Hospital for Children

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

source_name: DBP500_postnatal day 5

label_protocol: Ambion TotalPrep RNA Amplification Kit

extract_protocol: Qiagen Rneasy RNA Extraction Kit

treatment_protocol: Pregnant Sprague Dawley rats were dosed daily with corn oil, 100 or 500 mg/kg/day dibutyl phthalate by oral gavage from gestational day 16-20.  Pups were euthanized on either gestational day 20 or postnatal day 5 for tissue collection

value: Sprague Dawley

tag: exposed to

value: 500 mg/kg/day Dibutyl phthalate  (DBP)

tag: time point (pup age)

value: postnatal day 5

value: foreskin


title: C_RMF:MCF10DCIS(1:1,48h)


title: Striatum XXY male 7

description:
Biological Replicate 7, Batch 2
XXYSry_7a_3b

tag: tissue


title: C_RMF:MCF10A(1:0,48h)

tag: reference


title: PND5 foreskin-DBP500-biological rep6


title: C_RMF:MCF10DCIS(0:1,48h)

tag: sample type


title: wildtype 1

value: cerebellum


title: Striatum XXY male 6

description:
Biological Replicate 6, Batch 2
XXYSry_6a_5b


title: hyb16603

description: Gene expression data from Escherichia coli  (3-WTC4)


title: hyb16604

description: Gene expression data from Escherichia coli  (4-23A2)

value: ydcR (b1439) MUTANT


title: Striatum XXY male 2

description:
Biological Replicate 2, Batch 1
XXYSry_2a_7b

value: 152 days


title: Striatum XXY male 1

description:
Biological Replicate 1, Batch 1
XXYSry_1a

value: Striatum


title: Striatum XXY male 3

description:
Biological Replicate 3, Batch 1
XXYSry_3a_2b


title: Striatum XXY male 4

description:
Biological Replicate 4, Batch 1
XXYSry_4a


title: PND5 foreskin-DBP500-biological rep1


title: Striatum XX female 9

description:
Biological Replicate 9, Batch 2
XX_9b

source_name: Striatum XX female


title: Striatum XX female 8

description:
Biological Replicate 8, Batch 2
XX_8b


title: PND5 foreskin-DBP500-biological rep3


title: PND5 foreskin-DBP500-biological rep2


title: Striatum XX female 7

description:
Biological Replicate 7, Batch 2
XX_7b


title: Striatum XXY male 5

description:
Biological Replicate 5, Batch 1
XXYSry_5a_4b


title: PND5 foreskin-DBP100-biological rep6

source_name: DBP100_postnatal day 5

value: 100 mg/kg/day Dibutyl phthalate  (DBP)


title: Striatum XX female 5

description:
Biological Replicate 5, Batch 1
XX_5b


title: Striatum XY male 12

description:
Biological Replicate 12, Batch 2
XYSry_8b


title: Striatum XX female 4

description:
Biological Replicate 4, Batch 1
XX_4b


title: PND5 foreskin-DBP500-biological rep4


title: Striatum XX female 6

description:
Biological Replicate 6, Batch 2
XX_6b


title: PND5 foreskin-DBP500-biological rep5


title: PND5 foreskin-DBP100-biological rep7


title: hyb16605

description: Gene expression data from Escherichia coli  (5-23B2)


title: PND5 foreskin-DBP100-biological rep3


title: Striatum XX female 2

description:
Biological Replicate 2, Batch 1
XX_2b


title: Striatum XX female 3

description:
Biological Replicate 3, Batch 1
XX_3b


title: PND5 foreskin-DBP100-biological rep4


title: Striatum XX female 1

description:
Biological Replicate 1, Batch 1
XX_1b


title: PND5 foreskin-DBP100-biological rep2


title: BNST/POA XY male 8

description:
Biological Replicate 8, Batch 2
B_XY.Sry_8

source_name: BNST/POA XY male

extract_protocol: Total RNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).

value: BNST/POA


title: PND5 foreskin-DBP100-biological rep1


title: BNST/POA XY male 6

description:
Biological Replicate 6, Batch 2
B_XY.Sry_6


title: PND5 foreskin-corn oil-biological rep7

source_name: Corn oil control_postnatal day 5

value: Corn oil control


title: BNST/POA XY male 5

description:
Biological Replicate 5, Batch 1
B_XY.Sry_5


title: BNST/POA XY male 7

description:
Biological Replicate 7, Batch 2
B_XY.Sry_7


title: PND5 foreskin-corn oil-biological rep5


title: BNST/POA XY male 4

description:
Biological Replicate 4, Batch 1
B_XY.Sry_4


title: PND5 foreskin-corn oil-biological rep1


title: GD20 foreskin-DBP500Study-DBP-biological rep4

source_name: DBP500_gestational day 20

value: gestational day 20


title: PND5 foreskin-corn oil-biological rep6


title: PND5 foreskin-corn oil-biological rep2


title: PND5 foreskin-corn oil-biological rep4


title: PND5 foreskin-corn oil-biological rep3


title: BNST/POA XY male 2

description:
Biological Replicate 2, Batch 1
B_XY.Sry_2


title: GD20 foreskin-DBP500Study-DBP-biological rep2


title: BNST/POA XY male 1

description:
Biological Replicate 1, Batch 1
B_XY.Sry_1


title: GD20 foreskin-DBP500Study-DBP-biological rep5


title: GD20 foreskin-DBP500Study-DBP-biological rep3


title: BNST/POA XY male 3

description:
Biological Replicate 3, Batch 1
B_XY.Sry_3


title: BNST/POA XXY male 8

description:
Biological Replicate 8, Batch 2
B_XXY.Sry_8

source_name: BNST/POA XXY male


title: GD20 foreskin-DBP500Study-corn oil-biological rep6

source_name: Corn oil control_gestational day 20


title: GD20 foreskin-DBP500Study-DBP-biological rep1


title: PND5 foreskin-DBP100-biological rep5


title: GD20 foreskin-DBP500Study-corn oil-biological rep5


title: BNST/POA XXY male 3

description:
Biological Replicate 3, Batch 1
B_XXY.Sry_3


title: BNST/POA XXY male 2

description:
Biological Replicate 2, Batch 1
B_XXY.Sry_2


title: GD20 foreskin-DBP500Study-corn oil-biological rep4


title: BNST/POA XXY male 6

description:
Biological Replicate 6, Batch 2
B_XXY.Sry_6


title: BNST/POA XXY male 4

description:
Biological Replicate 4, Batch 1
B_XXY.Sry_4


title: BNST/POA XXY male 5

description:
Biological Replicate 5, Batch 1
B_XXY.Sry_5


title: BNST/POA XXY male 7

description:
Biological Replicate 7, Batch 2
B_XXY.Sry_7


title: GD20 foreskin-DBP100Study-DBP-biological rep5

source_name: DBP100_gestational day 20


title: GD20 foreskin-DBP500Study-corn oil-biological rep2


title: BNST/POA XX male 6

description:
Biological Replicate 5, Batch 1
B_XXSry_6

source_name: BNST/POA XX male


title: BNST/POA XX male 7

description:
Biological Replicate 6, Batch 2
B_XXSry_7


title: BNST/POA XXY male 1

description:
Biological Replicate 1, Batch 1
B_XXY.Sry_1


title: GD20 foreskin-DBP500Study-corn oil-biological rep3


title: GD20 foreskin-DBP100Study-DBP-biological rep1


title: GD20 foreskin-DBP100Study-DBP-biological rep4


title: GD20 foreskin-DBP500Study-corn oil-biological rep1


title: BNST/POA XX male 5

description:
Biological Replicate 4, Batch 1
B_XXSry_5


title: GD20 foreskin-DBP100Study-DBP-biological rep3


title: BNST/POA XX male 8

description:
Biological Replicate 7, Batch 2
B_XXSry_8


title: GD20 foreskin-DBP100Study-DBP-biological rep2


title: BNST/POA XX male 3

description:
Biological Replicate 3, Batch 1
B_XXSry_3


title: WT CSES7

city: Jerusalem

first: Tal

last: Bruck

address: Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

description: Gene expression data from CSES7

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen)

extract_protocol: total RNA from the parthenogenetic fibroblast and undifferentiated samples was isolated using RNA Extraction kit (RBC),  RNA from both normal iPS and HESCs was isolated using Qiagen Rneasy mini kit

treatment_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.

tag: treatment

value: control

tag: gender

value: Female

tag: cell type

value: undifferentiated induced pluripotent stem cell


title: BNST/POA XX female 7

description:
Biological Replicate 7, Batch 2
B_XX_7

source_name: BNST/POA XX female


title: BNST/POA XX male 1

description:
Biological Replicate 1, Batch 1
B_XXSry_1


title: ELK-1 overexpressing cell C17

description: Gene expression data from ELK-1 overexpressing cell clone 7

source_name: ELK-1 overexpressing cell clone 17

value: ELK-1 overexpressing


title: ELK-1 overexpressing cell C7

source_name: ELK-1 overexpressing cell clone 7


title: GD20 foreskin-DBP100Study-corn oil-biological rep5


title: BNST/POA XX female 6

description:
Biological Replicate 6, Batch 2
B_XX_6


title: GD20 foreskin-DBP100Study-corn oil-biological rep3


title: BNST/POA XX male 2

description:
Biological Replicate 2, Batch 1
B_XXSry_2


title: BNST/POA XX female 8

description:
Biological Replicate 8, Batch 2
B_XX_8


title: GD20 foreskin-DBP100Study-corn oil-biological rep6


title: GD20 foreskin-DBP100Study-corn oil-biological rep2


title: BNST/POA XX female 3

description:
Biological Replicate 3, Batch 1
B_XX_3


title: BNST/POA XX female 2

description:
Biological Replicate 2, Batch 1
B_XX_2


title: GD20 foreskin-DBP100Study-corn oil-biological rep4


title: RAG2+ B cells from BM pool 3

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

hyb_protocol: Hybridisation to Affymetrix Mouse GeneChip ST 1.0 chips was done using normal Affymetrix protocols, using an Affymetrix 645 oven and washed using standard Affymetric protocols using the Affymetrix Fluidics station 450

scan_protocol: The chips were scanned on an Affymetrix Scanner 3000 7G running Affymetrix Gene Command console ver 3.2

data_processing: The data were analyzed with Affymetrix Expression console ver 1.3.0.187 using Analysis algorithm RMA

source_name: RAG2+ B lineage cells from bone marrow

label_protocol: 4.5 - 47 ng total RNA was amplified using the Nugen Ovation PicoWTA kit followed by the processing of 3 ug cDNA through the Nugen WT-Ovation Exon Module then labelling of 2.5 ug cDNA using the Nugen Ovation Biotin Module.

growth_protocol: Cells were sorted from tissue preparations

extract_protocol: RAG2-GFP mouse bone marrow and small intestines were removed and cell preparations were made. RAG2-GFP+ cells were sorted and RNA extracted using Trizol.

treatment_protocol: Mice were housed in a regular SPF facility

value: Post-natal day 17-25

value: Bone Marrow


title: GD20 foreskin-DBP100Study-corn oil-biological rep1

value: Sprague Dawley


title: Striatum XXY male 9

description:
Biological Replicate 9, Batch 2
XXYSry_1b


title: BNST/POA XX female 5

description:
Biological Replicate 5, Batch 1
B_XX_5


title: BNST/POA XX female 4

description:
Biological Replicate 4, Batch 1
B_XX_4


title: BNST/POA XX female 1

description:
Biological Replicate 1, Batch 1
B_XX_1


title: RAG2+ B cells from BM pool 2


title: RAG2+ B cells from BM pool 1


title: RAG2+ B cells from LP pool 1

source_name: RAG2+ B lineage cells from small intestine lamina propria

value: Lamina Propria


title: RAG2+ B cells from LP pool 2


title: RAG2+ B cells from LP pool 3