title: L1 ALG-2-Tag control IP

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

description:
anti-GFP IP
SAMPLE 16

hyb_protocol: Hybridization was performed exactly as decribed in: Miska, E. A. et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5, R68 (2004)

scan_protocol: Scanning was performed exactly as in PMID: 15345052 (Genepix 4000B array scanner).

data_processing: The median of four individual microarray spots was used for analysis. 200 units were substracted as a global background based on an estimate of background exactly as described in PMID: 15345052. Images were processed using GenePix Pro 6 Acquisition and Analysis Microarray Software. Spot intensity data was then analysed using R version 2.13.1 and Bioconductor 2.8 packages including limma and gplots for visualisation. Normalized spot intensities were used for all data analysis. For inter-array normalisation all data were scaled based on total array intensities. Data were filtered using a cut-off of 5 fold above background.

source_name: whole animal lysate_anti-GFP_IP

label_protocol: Labelling was performed exactly as described in: Miska, E. A. et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5, R68 (2004)

growth_protocol: Animals were grown under standard conditions on solid media at 20 degrees Celsius.

extract_protocol: Extracts were prepared as in: Jannot G, Bajan S, Giguere NJ, Bouasker S, Banville IH, et al. (2011) The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans. EMBO Rep 12: 581-586

treatment_protocol: Animals were synchronized through bleaching of embryos.

tag: strain background

tag: developmental stage

tag: ip antibody

value: mouse monoclonal antibody anti-GFP 3E6

tag: ip antibody vendor

value: Invitrogen

tag: ip antibody cat. #


title: male breast cancer 33

status: Public on Feb 03 2012

type: RNA

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

description: replicate 33

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE2 Combat adjusted one the hybridization batches

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: male breast cancer

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: age

tag: size [mm]

tag: nottingham histological grade (nhg)

tag: er

value: positive

tag: pr

tag: year of diagnosis

tag: hybridization batch

tag: extraction date

tag: pathology department

tag: gender

value: male

tag: tissue

value: breast cancer tumor


title: TCDD_0.1_489

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

country: USA

institute: The Dow Chemical Company

hyb_protocol: On each microarray, 1.65 ug of labeled cRNA was hybridized for 17 hours and subsequently washed per the Agilent protocol.

scan_protocol: Microarrays were scanned using the Agilent dual laser DNA microarray scanner, model G2565AA, with 5 µm resolution. The extended dynamic range option was used.

data_processing: Scanned images were processed with Agilent Feature Extraction software. Within Genespring, the data for each microarray were normalized to the median signal intensity of the microarray. Data were then log2 transformed.

source_name: primary hepatocytes treated for 24h

label_protocol: For each sample, Alexa555-labeled cRNAs was generated from 500 ng of total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-cRNA Amplification Kit per the vendor’s protocol (Epicentre Biotechnologies, Madison, WI). The Aminoallyl-cRNA was then purified using Qiagen RNeasy Mini Elute Kit.

growth_protocol: Primary cultures of human hepatocytes were prepared from remnants of normal resected liver tissue from five women ages 44–77 years. The choice of only females was made based on the use of female rats in the two-year cancer bioassay (NTP 2006).  Each donor was fully consented under an institutional review board application approved by the individual institutions where liver resection surgery was conducted.  The resected liver tissue was determined to be disease free by a board-certified pathologist.  Four of the five human donors did not consume alcohol and all were free of hepatitis and HIV.  The research on the human samples was carried out in accordance with the principles of the current version of the Helsinki Declaration.  Each individual human was treated as a biological replicate.  Preplating cell viability, determined by trypan blue exclusion, ranged from 82 to 93% in human hepatocytes.  Following isolation, hepatocytes were resuspended in DMEM containing 5% fetal calf serum, insulin (4 ng/ml), and dexamethasone (1 nM).   The hepatocytes were then added to 24-well BioCoat (BD Biosciences) plates coated with collagen type 1 substratum and allowed to attach for 3–6 h at 37°C in a humidified chamber with 95% relative humidity and 5% CO2.  After attachment, the culture plates were swirled and the medium containing debris and unattached cells was aspirated.  Fresh, ice-cold, serum-free DMEM/Ham’s F12 medium containing 50 nM dexamethasone, 6.25 ng/ml insulin, 6.25 ng/ml transferrin, 6.25 ng/ml selenium (ITS+), and 0.25 mg/ml Matrigel was added to the culture plate and immediately returned to the humidified chamber. Serum-free medium was used since serum can significantly reduce the cellular uptake of TCDD. Medium was kept in the dark prior to use and was not changed during the incubation periods.

extract_protocol: Cells (24-well format) were washed with one volume of HBSS, lysed by addition of 0.35 ml of ABI Nucleic Acid Lysis Solution (Applied Biosystems, Foster City, CA), and frozen at -70 C.  Lysates were thawed and total RNA was isolated from each sample using an ABI 6100 Prepstation according to the manufacturer’s protocol.

treatment_protocol: Stock solutions of TCDD (100 µM) were diluted in DMSO and added to culture media (DMEM-Ham’s F12) to a final DMSO concentration of 0.1% .  The hepatocyte cultures were exposed for 24 h to the DMSO vehicle (0.1%) or one of the following TCDD concentrations: 0.00001, 0.0001, 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 10, 100 nM. Cell viability was examined at the 24 h time point in the vehicle control hepatocytes and hepatocytes treated with 100 nM TCDD.  Viability was assessed by morphological appearance, LDH leakage (CytoTox-ONE, Promega, Madison, WI), ATP levels (CellTiterGlo, Promega), and phase contrast microscopy (LeCluyse et al., 2000; Meunier et al., 2000).  Cell viability end points did not demonstrate treatment-related cytotoxicity.

value: primary hepatocytes

tag: sample

tag: treatment

value: TCDD

tag: tcdd dose


title: TCDD_0.3_489


title: Q100_rep3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing: Pre-processing of raw microarray data included probe-specific background correction, summation of probe set values, and normalization using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (https://carmaweb.genome.tugraz.at/carma) (Rainer et al., 2006). The quality of normalization was assessed by box plot and MA-graph analyses. Differences between treatments were visualized by Principal Component Analysis (PCA) plotting with MeV (MultiExperiment Viewer, http://www.tm4.org/mev) (Saeed et al., 2003). Data was initially filtered for missing values and then subjected to a CLEAR-test that combines differential expression and variability using the GEPAS web server at http://www.gepas.org (Joaquín et al., 2008). An unpaired t-test was followed by a Significance Analysis of Microarray (SAM) testing including a calculation that estimates the False Discovery Rate (FDR). The FDR was set to a non-stringent level of <12.5%. Differentially Expressed Genes (DEGs) showing a fold change of at least 1.25 were analyzed for their molecular functions, biological processes, and cellular components using the software packages GoMiner (Zeeberg et al., 2005) and DAVID (http://david.abcc.ncifcrf.gov/).

organism: Caenorhabditis elegans

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: N2 wild type C. elegans were maintained on nematode growth medium (NGM) plates using Escherichia coli OP50 as food. Untreated nematodes (the P0 generation) were chunked onto control and treatment plates (50, 100, and 200 µM Quercetin; 100, 200, and 300 µM Tannic Acid) and incubated at 20°C for 4 days. A synchronous culture was generated through egg preparation with sodium hypochlorite. Hatched L1s were rotated over night (20 rpm) and subsequently transferred to plates containing the respective doses of Quercetin or Tannic Acid. Worms were grown to the young (pre-reproductive) adult stage, harvested by rinsing off with M9 buffer, shock frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated following the standard procedures as defined by the Trizol protocol (Invitrogen) but modified to include a homogenization step with 0.5 mm glass beads to maximize cell breakage. The resultant RNA was further processed by means of a RNeasy purification followed by DNase digestion (Qiagen). All samples were stored at -80°C until further use.

value: larvae (L4)

value: whole animal

tag: strain

value: N2 (Bristol)

tag: genotype/variation

value: wild type

value: 100 µM Quercetin


title: Q200_rep1

treatment_protocol: N2 wild type C. elegans were maintained on nematode growth medium (NGM) plates using Escherichia coli OP50 as food. Untreated nematodes (the P0 generation) were chunked onto control and treatment plates (50, 100, and 200 µM Quercetin; 100, 200, and 300 µM Tannic Acid) and incubated at 20°C for 4 days. A synchronous culture was generated through egg preparation with sodium hypochlorite. Hatched L1s were rotated over night (20 rpm) and subsequently transferred to plates containing the respective doses of Quercetin or Tannic Acid. Worms were grown to the young (pre-reproductive) adult stage, harvested by rinsing off with M9 buffer, shock frozen in liquid nitrogen and stored at -80°C.

value: 200 µM Quercetin


title: male breast cancer 32

description: replicate 32


title: TCDD_0.03_489


title: Q50_rep3

value: 50 µM Quercetin


title: L1 ALG-1 control IP

description:
anti-ALG-1 IP
SAMPLE 15

source_name: whole animal lysate_anti-ALG-1_IP

tag: strain background

tag: developmental stage

tag: ip antibody

value: rabbit polyclonal antibody raised against ALG-1 (unpublished)


title: TCDD_0.001_489


title: TCDD_0.003_489


title: TCDD_0.01_489


title: Q50_rep2

tag: age


title: Q50_rep1


title: male breast cancer 31

description: replicate 31

tag: size [mm]

tag: nottingham histological grade (nhg)

tag: er

value: negative


title: L1 ALG-2-Tag IP

description:
anti-GFP IP
SAMPLE 14

value: alg-2; ALG-2::GFP

tag: ip antibody vendor

tag: ip antibody cat. #


title: male breast cancer 9

description: replicate 9

tag: pr

tag: year of diagnosis

tag: hybridization batch

tag: extraction date

tag: pathology department


title: Q control_rep3

source_name: Q control_rep3

tag: tissue

tag: treatment


title: male breast cancer 12

description: replicate 12

tag: gender


title: male breast cancer 39

description: replicate 39


title: TCDD_0.0001_489

tag: sample

tag: tcdd dose


title: L1 ALG-1 IP

description:
anti-ALG-1 IP
SAMPLE 13

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: ip antibody


title: male breast cancer 3

description: replicate 3

tag: age

tag: size [mm]

tag: nottingham histological grade (nhg)

tag: er


title: TCDD_0.00001_489


title: L2 ALG-2-Tag control IP

description:
anti-GFP IP
SAMPLE 12

value: mouse monoclonal antibody anti-GFP 3E6

tag: ip antibody vendor

tag: ip antibody cat. #


title: male breast cancer 1

description: replicate 1

tag: pr

tag: year of diagnosis

tag: hybridization batch

tag: extraction date


title: Q control_rep2

source_name: Q control_rep2

tag: tissue

tag: strain

tag: treatment


title: Q control_rep1

source_name: Q control_rep1


title: L2 ALG-1 control IP

description:
anti-ALG-1 IP
SAMPLE 11

tag: strain background


title: DMSO_0.0_489

tag: sample

value: DMSO

tag: tcdd dose


title: L2 ALG-2-Tag IP

description:
anti-GFP IP
SAMPLE 10

tag: genotype/variation

tag: developmental stage

tag: ip antibody

value: Invitrogen


title: L2 ALG-1 IP

description:
anti-ALG-1 IP
SAMPLE 9


title: TCDD_100.0_472


title: L3 ALG-1 control IP

description:
anti-ALG-1 IP
SAMPLE 7


title: male breast cancer 13 rep1

description: replicate 13

tag: age

tag: size [mm]

tag: nottingham histological grade (nhg)

value: positive

tag: pathology department

tag: gender

value: male


title: L3 ALG-2-Tag control IP

description:
anti-GFP IP
SAMPLE 8

tag: ip antibody vendor

tag: ip antibody cat. #


title: TCDD_10.0_472

value: primary hepatocytes


title: L3 ALG-2-Tag IP

description:
anti-GFP IP
SAMPLE 6


title: L3 ALG-1 IP

description:
anti-ALG-1 IP
SAMPLE 5


title: male breast cancer 48 rep1

description: replicate 48

tag: er

tag: pr

tag: year of diagnosis

tag: hybridization batch

tag: extraction date

value: breast cancer tumor


title: male breast cancer 40

description: replicate 40

tag: tissue


title: TCDD_1.0_472

tag: sample

tag: treatment

value: TCDD

tag: tcdd dose


title: TCDD_0.003_472


title: TCDD_0.1_472


title: male breast cancer 49

description: replicate 49


title: L4 ALG-2-Tag control IP

description:
anti-GFP IP
SAMPLE 4

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: ip antibody


title: TCDD_0.3_472


title: TCDD_0.01_472


title: male breast cancer 35

description: replicate 35

tag: age

tag: size [mm]

tag: nottingham histological grade (nhg)

tag: pathology department


title: male breast cancer 29

description: replicate 29

tag: er

tag: gender


title: male breast cancer 30

description: replicate 30

tag: pr

tag: year of diagnosis


title: L4 ALG-1 control IP

description:
anti-ALG-1 IP
SAMPLE 3


title: male breast cancer 34

description: replicate 34

tag: hybridization batch

tag: extraction date


title: TCDD_0.03_472

tag: tissue

tag: sample


title: male breast cancer 47

description: replicate 47


title: L4 ALG-1 IP

description:
anti-ALG-1 IP
SAMPLE 1


title: Macaque-PFC-182d

status: Public on Feb 02 2012

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

country: China

institute: Partner Institute for Computational Biology

description: Gene expression data from post-mortem superior frontal gyrus of a 182 day-old macauqe

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols.

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

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >1/3 of human or chimpanzee individuals. For further analysis, we mapped the transcript IDs to Ensemble Genes using the table provided at the Affymetrix support site (“http://www.affymetrix.com/analysis/downloads/na26/wtgene/HuGene-1_0-st-v1.na26.hg18.transcript.csv.zip”). For 127 expressed genes with multiple transcripts, we calculated the means across transcripts.

organism: Macaca mulatta

source_name: Dissected macaque post-mortem superior frontal gyrus

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All individuals used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used.

value: 182 days

value: superior frontal gyrus of the brain


title: Macaque-PFC-353d

description: Gene expression data from post-mortem superior frontal gyrus of a 353 day-old macauqe

value: 353 days


title: 14227241 - Col0 2 vs N575260 2

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Study of the impact of a deregulation in the NAD concentration in arabidopsis

hyb_protocol: N575260 2 Cy5 / Col0 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

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

growth_protocol: rosette - Media : Soil  hygrometry : 65%  Temperature : 20°C  Light : 8 hours-200 µmol quanta m-2 s-1

extract_protocol: N575260 2:8ug. (NucleoSpinRNAPlant.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: dev.stage (boyes et al. plant cell 2001)

source_name: Col0 2

extract_protocol: Col0 2:8ug. (NucleoSpinRNAPlant.pdf)


title: TCDD_0.00001_472

tag: treatment

tag: tcdd dose


title: Macaque-PFC-fetal-53d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 53 days before birth

value: 53 days before birth


title: Macaque-PFC-fetal-72d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 72 days before birth

value: 72 days before birth


title: L4 ALG-2-Tag IP

description:
anti-GFP IP
SAMPLE 2

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: ip antibody

tag: ip antibody vendor

tag: ip antibody cat. #


title: 14227562 - N575260 2 vs Col0 2

hyb_protocol: Col0 2 Cy5 / N575260 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age


title: Macaque-PFC-24d

description: Gene expression data from post-mortem superior frontal gyrus of a 24 day-old macauqe

tag: gender

value: 24 days


title: 14227238 - Col0 1 vs N575260 1

hyb_protocol: N575260 1 Cy5 / Col0 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N575260 1:8ug. (NucleoSpinRNAPlant.pdf)

source_name: Col0 1

extract_protocol: Col0 1:8ug. (Nucleospin_RNA_II.pdf)


title: Macaque-PFC-fetal-35d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 35 days before birth

value: 35 days before birth


title: Macaque-PFC-831d

description: Gene expression data from post-mortem superior frontal gyrus of a 831 day-old macauqe

value: 831 days


title: TCDD_0.001_472


title: Macaque-PFC-fetal-30d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 30 days before birth

value: 30 days before birth


title: TCDD_0.0001_472


title: Macaque-PFC-479d

description: Gene expression data from post-mortem superior frontal gyrus of a 479 day-old macauqe

value: 479 days


title: 14227239 - N575260 1 vs Col0 1

hyb_protocol: Col0 1 Cy5 / N575260 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: DMSO_0.0_472

value: DMSO


title: Macaque-PFC-1d

description: Gene expression data from post-mortem superior frontal gyrus of a 1 day-old macauqe

value: 1 day


title: Macaque-PFC-fetal-57d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 57 days before birth

value: male

value: 57 days before birth


title: T120 hr control

city: Auckland

first: Dorit

last: Naot

address: Private Bag 92019

department: Medicine

country: New Zealand

institute: University of Auckland

description: Gene expression data from bone marrow cells treated with vehicle for 120 hours

hyb_protocol: Single strand DNA at 5.5 microgram/reaction was fragmented, labeled with biotin, and hybridized to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The microarray results were analyzed using the Affymetrix software Expression Console and Partek® Genomics SuiteTM. The hybridization signals were normalized using Robust Multichip Average (RMA) methodology.

organism: Mus musculus

source_name: bone marrow cells, unterated, 120 hrs

label_protocol: Affymetrix WT cDNA Synthesis and Amplification kit was used for first strand cDNA synthesis from 100ng of total RNA and for second strand cDNA synthesis. cRNA was produced by an IVT reaction, followed by a second cycle of cDNA synthesis.

growth_protocol: Bone marrow was obtained from the long bones of 4- to 6-week old Swiss male mice, cells were seeded in 6-well plates in αMEM/ 10% FCS and 10−8 M 1,25(OH)2D3

extract_protocol: RNeasy kit (Qiagen) was used to extract RNA

treatment_protocol: Recombinant mouse adiponectin (Biovendor) was added to the treatment wells at a final concentration of 5 microgram/ml

value: bone marrow


title: T10 hr adiponectin

description: Gene expression data from bone marrow cells treated with adiponectin for 10 hours

source_name: bone marrow cells, adiponectin, 10 hrs


title: T24 hr adiponectin

description: Gene expression data from bone marrow cells treated with adiponectin for 24 hours

source_name: bone marrow cells, adiponectin, 24 hrs


title: T72 hr control

description: Gene expression data from bone marrow cells treated with vehicle for 72 hours

source_name: bone marrow cells, unterated, 72 hrs


title: T72 hr adiponectin

description: Gene expression data from bone marrow cells treated with adiponectin for 72 hours

source_name: bone marrow cells, adiponectin, 72 hrs


title: T120 hr adiponectin

description: Gene expression data from bone marrow cells treated with adiponectin for 120 hours

source_name: bone marrow cells, adiponectin, 120 hrs


title: T4 hr adiponectin

description: Gene expression data from bone marrow cells treated with adiponectin for 4 hours

source_name: bone marrow cells, adiponectin, 4 hrs


title: T24 hr control

description: Gene expression data from bone marrow cells treated with vehicle for 24 hours

source_name: bone marrow cells, unterated, 24 hrs


title: T4 hr control

description: Gene expression data from bone marrow cells treated with vehicle for 4 hours

source_name: bone marrow cells, unterated, 4 hrs


title: T10 hr control

description: Gene expression data from bone marrow cells treated with vehicle for 10 hours

source_name: bone marrow cells, unterated, 10 hrs


title: G2/M BaP-treated replicate 1

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

hyb_protocol: After quantification of labeled cRNA, The Cy3-labelled samples were mixed with an appropriate volume of Cy5-labelled reference for each assay, concentrated to less than 41.8µl and hybridised to the oligo microarrays using the Gene Expression Hybridization Kit (Agilent Technologies, UK). The hybridisation was carried out using Agilent SureHyb chambers for 17 hours in Rotisserie Hyb Oven set to 65ºC (Agilent Technologies, UK) and rotating at 10 rpm.

scan_protocol: After hybridisation, the arrays were washed by Agilent Gene Expression Wash Buffer following the instructions. The arrays were scanned with a Axon 4000B scanner at wavelength 635nm and 532nm.

data_processing: The images were analysed with BlueFuse software to extract expression values, then all data were loaded into GeneSpring V7.2 software. The data were LOWESS normalised and natural  log-ratios were used for t-test and other analyses. Normalised ratios were used for fold-change analysis.

source_name: G2/M BaP-treated replicate 1

label_protocol: Total RNA (4 µg) was reverse transcribed into cDNA by first incorporating a T7 oligo-dT-Promoter primer prior to generation of fluorescent cRNA (complimentary RNA) using the Agilent's Quick Amp Labeling kit (Agilent Technologies, UK). The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates Cy3- or Cy5-labelled CTP.   Following this, the labelled cRNA was purified using the Qiagen RNeasy Mini spin columns and quantified using the NanoDrop ND-1000 instrument (Thermo Scientific, USA).

growth_protocol: MCF-7 Cells were grown as adherent monolayers and maintained in Dulbecco’s modified Eagle’s medium with GlutamaxTM  I, 1000 mg/L D-glucose and sodium pyruvate (Invitrogen, Paisley, UK) and supplemented with 10% heat-inactivated foetal bovine serum (Invitrogen) and 100 U/mL penicillin and 100 g/mL streptomycin (Sigma-–Aldrich, Dorset, UK). Cells were incubated in a humidified 5% CO2 atmosphere at 37oC and sub-cultured every 72 h when the cells were 80% confluent. Culture conditions were manipulated in order to generate (1) asynchronous cells (N) by allowing normal growth for 72 h; (2) G0/G1-phase enriched cultures by serum deprivation for 48 h; (3) S-phase-enriched cultures by serum deprivation for 48 h followed by 18 h growth in complete media; and (4) G2/M-phase-enriched cultures by treatment for 24 h with 1 µg/mL aphidicolin followed by 0.25 μM colchicine for 12 h.

extract_protocol: Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK)

treatment_protocol: Cells were seeded at 2 × 10e5 cells/ml and BaP, dissolved in dimethylsulphoxide (DMSO), was added to give a final concentration of 2.5 µM for 12 hours. DMSO only was added to control cultures and its volume was kept at 0.3% of the total culture volume. Cells were harvested by trypsinisation followed by washing with PBS. Cell pellets were stored at -80ºC until further analysis.

tag: cell line

tag: phase

value: BaP for 12 hours

tag: biological replicate

source_name: universal human reference RNA

tag: reference

value: Stratagene universal human reference RNA (UHRR)


title: S BaP-treated 12h replicate 3

source_name: S BaP-treated 12h replicate 3

value: S


title: unsynchronised DMSO-treated replicate 3

source_name: unsynchronised DMSO-treated replicate 3

value: Unsynchronised (N)

value: DMSO for 12 hours


title: unsynchronised DMSO-treated replicate 2

source_name: unsynchronised DMSO-treated replicate 2


title: G2/M DMSO-treated replicate 1

source_name: G2/M DMSO-treated replicate 1


title: unsynchronised BaP-treated replicate 2

source_name: unsynchronised BaP-treated replicate 2


title: unsynchronised BaP-treated replicate 3

source_name: unsynchronised BaP-treated replicate 3


title: unsynchronised BaP-treated replicate 1

source_name: unsynchronised BaP-treated replicate 1


title: G2/M BaP-treated replicate 2

source_name: G2/M BaP-treated replicate 2


title: unsynchronised DMSO-treated replicate 1

source_name: unsynchronised DMSO-treated replicate 1


title: G2/M DMSO-treated replicate 3

source_name: G2/M DMSO-treated replicate 3


title: Macaque-PFC-fetal-42d

description: Gene expression data from post-mortem superior frontal gyrus of a macauqe with 42 days before birth

source_name: Dissected macaque post-mortem superior frontal gyrus

value: 42 days before birth

tag: tissue

value: superior frontal gyrus of the brain


title: G2/M BaP-treated replicate 3

source_name: G2/M BaP-treated replicate 3


title: G2/M DMSO-treated replicate 2

source_name: G2/M DMSO-treated replicate 2


title: S BaP-treated 12h replicate 2

source_name: S BaP-treated 12h replicate 2


title: S BaP-treated 12h replicate 1

source_name: S BaP-treated 12h replicate 1


title: S DMSO-treated 12h replicate 1

source_name: S DMSO-treated 12h replicate 1


title: S DMSO-treated 12h replicate 2

source_name: S DMSO-treated 12h replicate 2

source_name: universal human reference RNA


title: G1 BaP-treated 12 h replicate 1

source_name: G1 BaP-treated 12 h replicate 1


title: G1 DMSO-treated 12 h replicate 1

source_name: G1 DMSO-treated 12 h replicate 1


title: S DMSO-treated 12h replicate 3

source_name: S DMSO-treated 12h replicate 3


title: G1 BaP-treated 12 h replicate 3

source_name: G1 BaP-treated 12 h replicate 3


title: Tubulointerstitium from control living donor_LD_10 [HG-U133A]

city: Ann Arbor

first: Celine

middle: C

last: Berthier

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
Tub_LD10
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human by default CDF annotation were used for the normalization.

source_name: Kidney biopsy from human pre-transplant living donor

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

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

value: Tubulointerstitium from kidney biopsy


title: G1 BaP-treated 12 h replicate 2

source_name: G1 BaP-treated 12 h replicate 2


title: Tubulointerstitium from control living donor_LD_7 [HG-U133A]

description:
Tub_LD7
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: breast tumor part_IDC_rep1_8575

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description: breast tumor part_IDC

hyb_protocol: Aglient Gene Expression Hybridization Kit, hybridization protocol

scan_protocol: Scanned on an Agilent G2565BA scanner.

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

source_name: Infiltrating Ductal Carcinoma (IDC)

label_protocol: Agilent Quick Amp Labeling Kit, label protocol

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The surgical removed tumors of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.

value: female

value: primary tumor of breast

label: total RNA

source_name: Stratagene's Universal Human Reference RNA


title: G1 DMSO-treated 12 h replicate 2

source_name: G1 DMSO-treated 12 h replicate 2


title: Tubulointerstitium from control living donor_LD_6 [HG-U133A]

description:
Tub_LD6
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: breast tumor part_IDC_rep1_8573

description: breast tumor part_IDC

value: Stratagene's Universal Human Reference RNA


title: breast tumor part_rep1_8571

description: breast tumor part_atypical adenomyoepithelioma

source_name: atypical adenomyoepithelioma


title: breast tumor part_IDC_rep1_8577

description: breast tumor part_IDC


title: Tubulointerstitium from IgAN patient_IgA25 [HG-U133A]

description:
TubIgA25
Gene expression data from the tubulointerstitial compartment of human IgAN kidney

source_name: Kidney biopsy from human IgAN


title: Tubulointerstitium from control living donor_LD_8 [HG-U133A]

description:
Tub_LD8
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Tubulointerstitium from IgAN patient_IgA23 [HG-U133A]

description:
TubIgA23
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA18 [HG-U133A]

description:
Tub_IgA18
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA10 [HG-U133A]

description:
TubIgA10
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA24 [HG-U133A]

description:
TubIgA24
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA13 [HG-U133A]

description:
Tub_IgA13
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA21 [HG-U133A]

description:
Tub_IgA21
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from control living donor_LD_5 [HG-U133A]

description:
Tub_LD5
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: G1 DMSO-treated 12 h replicate 3

source_name: G1 DMSO-treated 12 h replicate 3


title: Tubulointerstitium from IgAN patient_IgA14 [HG-U133A]

description:
Tub_IgA14
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA22 [HG-U133A]

description:
Tub_IgA22
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA16 [HG-U133A]

description:
Tub_IgA16
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from control living donor_LD_9 [HG-U133A]

description:
Tub_LD9
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Tubulointerstitium from IgAN patient_IgA12 [HG-U133A]

description:
TubIgA12
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA19 [HG-U133A]

description:
Tub_IgA19
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA11 [HG-U133A]

description:
TubIgA11
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA20 [HG-U133A]

description:
Tub_IgA20
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA26 [HG-U133A]

description:
Tub_IgA26
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA27 [HG-U133A]

description:
Tub_IgA27
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA4 [HG-U133A]

description:
Tub_IgA4
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA5 [HG-U133A]

description:
Tub_IgA5
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA9 [HG-U133A]

description:
Tub_IgA9
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA8 [HG-U133A]

description:
Tub_IgA8
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA6 [HG-U133A]

description:
Tub_IgA6
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Early stage breast cancer patient_47

city: Erlangen

first: Michael

middle: Georg

last: Schrauder

address: Universitätsstrasse 21-23

department: Gynecology

country: Germany

institute: University Hospital Erlangen

description: Sample name: 104

hyb_protocol: According to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and VSN normalization. Following background (BG) correction, negative values were corrected to 1.

source_name: RNA from whole blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: After thawing 2.7 ml EDTA blood was transferred into PAXgene Blood RNA Tubes (PreAnalytix GmbH) and total RNA was extracted using the miRNeasy kit (Qiagen GmbH).

treatment_protocol: Blood sampling at breast cancer diagnosis (before treatment). Samples stored at -20 degree.

tag: year of birth

tag: tnm (t-stage)

tag: tnm (n-stage)

tag: tnm (tumor grading)

tag: tnm (her2-status)

value: positive


title: Early stage breast cancer patient_45

description: Sample name: 102

value: negative


title: Early stage breast cancer patient_48

description: Sample name: 105


title: Tubulointerstitium from IgAN patient_IgA7 [HG-U133A]

description:
Tub_IgA7
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Early stage breast cancer patient_46

description: Sample name: 103


title: Early stage breast cancer patient_44

description: Sample name: 101


title: B. subtilis wt:slrAx2 Replicate 3

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

description: Biological replicate 1 of 3.  Undomesticated B. sutilis wild-type vs two copies slrA harvested in Luria Bertani broth at and optical denisty (600nm) between 1.0-1.1

hyb_protocol: Hybridizations were incubated at 65˚C for 17 hours.  After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.

scan_protocol: Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology

data_processing: Standard lowess normalization using Bioconductor (and run in R) was performed on the processed signal given by the Agilent Feature Extraction Software (v 8.5.1.1) (used for background subtraction and lowess)  and the geometric mean of the probes was used to give the final value for each gene and nc-RNA.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: wild-type cells

label_protocol: 6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP .  Cy3 and Cy5 were purchased from GE Healthcare

growth_protocol: Cells were grown in Luria-Bertani broth to an Optical Density (600nm) of between 1.0-1.1

extract_protocol: RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit

treatment_protocol: After reaching the desired optical densitiy cells an equal volume of -20C methanol was added to the culture.  Cells were pelleted, supernatant was removed, and cell pellets were stored at -80C.

tag: genotype

value: wild-type

source_name: slrAx2 cells


title: B. subtilis wt:slrAx2 Replicate 1

description: Biological replicate 1 of 1.  Undomesticated B. sutilis wild-type vs two copies slrA harvested in Luria Bertani broth at and optical denisty (600nm) between 1.0-1.1


title: Early stage breast cancer patient_42

description: Sample name: 99


title: Early stage breast cancer patient_41

description: Sample name: 98


title: Early stage breast cancer patient_39

description: Sample name: 96


title: Early stage breast cancer patient_40

description: Sample name: 97


title: B. subtilis wt:slrAx2 Replicate 2

description: Biological replicate 1 of 2.  Undomesticated B. sutilis wild-type vs two copies slrA harvested in Luria Bertani broth at and optical denisty (600nm) between 1.0-1.1


title: Tubulointerstitium from IgAN patient_IgA3 [HG-U133A]

description:
Tub_IgA3
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Early stage breast cancer patient_35

description: Sample name: 92


title: Early stage breast cancer patient_37

description: Sample name: 94


title: Early stage breast cancer patient_38

description: Sample name: 95


title: Early stage breast cancer patient_36

description: Sample name: 93


title: Early stage breast cancer patient_43

description: Sample name: 100


title: Tubulointerstitium from IgAN patient_IgA1 [HG-U133A]

description:
Tub_IgA1
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA2 [HG-U133A]

description:
Tub_IgA2
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Early stage breast cancer patient_33

description: Sample name: 90


title: Early stage breast cancer patient_34

description: Sample name: 91


title: Early stage breast cancer patient_31

description: Sample name: 88


title: Tubulointerstitium from control living donor_LD_9 [HG-U133A_ENTREZG_10]

description:
Tub_LD9
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 were used for the normalization.


title: Early stage breast cancer patient_29

description: Sample name: 86


title: Early stage breast cancer patient_30

description: Sample name: 87


title: Early stage breast cancer patient_32

description: Sample name: 89


title: Tubulointerstitium from control living donor_LD_7 [HG-U133A_ENTREZG_10]

description:
Tub_LD7
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Early stage breast cancer patient_28

description: Sample name: 85


title: ADAR2_ko_ADAR1_ko expression array

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

description: US22502695_252800511444_S01_GE1_105_Jan09_1_4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: E11.5 femal mouse embryo

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Female mouse embryos were dissected on E11.5, homogenized and total RNA was extracted using peqGOLD TriFast reagent according to manufacturer´s instructions(PEQLAB Biotechnologie GmbH, Erlangen, Germany).

value: embryo

tag: developmental stage

tag: strain


title: Tubulointerstitium from control living donor_LD_8 [HG-U133A_ENTREZG_10]

description:
Tub_LD8
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: ADAR2_ko expression array

description: US22502695_252800511444_S01_GE1_105_Jan09_1_3


title: Early stage breast cancer patient_26

description: Sample name: 83


title: Early stage breast cancer patient_27

description: Sample name: 84


title: wildtype 2 expression array

description: US22502695_252800511444_S01_GE1_105_Jan09_1_2

value: wildtype


title: Tubulointerstitium from control living donor_LD_6 [HG-U133A_ENTREZG_10]

description:
Tub_LD6
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Early stage breast cancer patient_25

description: Sample name: 82


title: Tubulointerstitium from control living donor_LD_10 [HG-U133A_ENTREZG_10]

description:
Tub_LD10
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Tubulointerstitium from control living donor_LD_5 [HG-U133A_ENTREZG_10]

description:
Tub_LD5
Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney


title: Early stage breast cancer patient_24

description: Sample name: 81


title: Early stage breast cancer patient_23

description: Sample name: 80


title: Early stage breast cancer patient_22

description: Sample name: 79


title: Early stage breast cancer patient_19

description: Sample name: 76


title: wildtype 1 expression array

description: US22502695_252800511444_S01_GE1_105_Jan09_1_1


title: Early stage breast cancer patient_18

description: Sample name: 75


title: Early stage breast cancer patient_20

description: Sample name: 77


title: Early stage breast cancer patient_21

description: Sample name: 78


title: Early stage breast cancer patient_17

description: Sample name: 74


title: Early stage breast cancer patient_16

description: Sample name: 73


title: Early stage breast cancer patient_13

description: Sample name: 70


title: Early stage breast cancer patient_14

description: Sample name: 71


title: Early stage breast cancer patient_15

description: Sample name: 72


title: VIGS Prot comparison_8dai_rep2

city: Madrid

first: Francisco

last: Tenllado

state: Madrid

address: Ramiro de Maeztu, 9

department: Plant Biology

country: Spain

institute: Centro de Investigaciones Biológicas, CSIC

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050)

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the non-parametric algorithm Rank Products (Breitling et al. 2004) and available as RankProd package at Bioconductor (Hong et al. 2006). Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Nicotiana benthamiana

source_name: plants infected with TRV:00 at 8 dai

label_protocol: RNA was amplified with the MessageAmp II aRNA amplification kit (Ambion, Inc, Austin, USA) as described in the instruction manual. Aminoallyl UTP was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount of aRNA was quantified with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). aRNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies). 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Grown in soil in growth chamber using 16 h period of light (25±2°C) and 8 h of darkness (22±1°C), light intensity 70-90 mmol m-2 s-2 , 65±2 % humidity

extract_protocol: For each biological replicate, two symptomatic, non-inoculated upper leaves from each of ten plants per treatment were harvested and immediately frozen in liquid N2. Total RNA was extracted from plant leaves using Trizol reagent, followed by purification with RNeasy midiprep columns(Qiagen)

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old plants were inoculated with TRV by agroinfiltration with TRV:00

source_name: plants infected with TRV:PBE at 8dai

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old plants were inoculated with TRV:PBE by agroinfiltration with TRV:PBE.


title: VIGS Prot comparison_8dai_rep3

value: symptomatic, non-inoculated upper leaves

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old plants were inoculated with TRV:PBE by agroinfiltration with TRV:PBE


title: Early stage breast cancer patient_12

description: Sample name: 69


title: Early stage breast cancer patient_11

description: Sample name: 68


title: Early stage breast cancer patient_10

description: Sample name: 67


title: Early stage breast cancer patient_7

description: Sample name: 64


title: Early stage breast cancer patient_6

description: Sample name: 63


title: VIGS Prot comparison_4dai_rep3

source_name: plants infected with TRV:00 at 4 dai

source_name: plants infected with TRV:PBE at 4dai


title: Early stage breast cancer patient_8

description: Sample name: 65


title: Healthy control_55

description: Sample name: 55

value: healthy


title: Early stage breast cancer patient_9

description: Sample name: 66


title: Early stage breast cancer patient_4

description: Sample name: 61


title: Early stage breast cancer patient_5

description: Sample name: 62


title: Early stage breast cancer patient_1

description: Sample name: 58


title: Early stage breast cancer patient_2

description: Sample name: 59


title: VIGS Prot comparison_4dai_rep1


title: Early stage breast cancer patient_3

description: Sample name: 60


title: Healthy control_53

description: Sample name: 53


title: VIGS Prot comparison_4dai_rep2


title: SHR comparison_72hts_rep3

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_72hts_rep3

source_name: wild type plants infected with TMV-GFP at 72 hts

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old wild type plants were inoculated with TMV-GFP by rubbing sap from TMV-GFP-infected plants

source_name: N transgenic plants infected with TMV-GFP at 72 hts

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old N transgenic plants were inoculated with TMV-GFP by rubbing sap from TMV-GFP-infected plants.


title: Healthy control_54

description: Sample name: 54


title: Healthy control_56

description: Sample name: 56


title: Healthy control_52

description: Sample name: 52


title: Healthy control_57

description: Sample name: 57


title: VIGS Prot comparison_8dai_rep1


title: SN comparison_11dpi_rep3

source_name: plants infected with PVX/HCLH at 11dpi

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old plants were inoculated with PVX/HCLH by rubbing sap from PVX/HCLH infected plants

source_name: plants infected with PVX/HCWT at 11dpi

treatment_protocol: Samples (pooled systemic leaves) were collected at 7 or 11 days postinoculation (SN comparison), at 4 or 8 days after infiltration (VIGS Prot), and at 24 or 72 hours after temperature shift (SHR). 4 week old plants were inoculated with PVX/HCWT by rubbing sap from PVX/HCWT infected plants.


title: Healthy control_51

description: Sample name: 51


title: SHR comparison_72hts_rep1

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_72hts_rep1


title: SHR comparison_24hts_rep3

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_24hts_rep3

source_name: wild type plants infected with TMV-GFP at 24hts

source_name: N transgenic plants infected with TMV-GFP at 24 hts


title: SHR comparison_24hts_rep1

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_24hts_rep1


title: SHR comparison_24hts_rep2

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_24hts_rep2


title: SHR comparison_72hts_rep2

description: TMV-GFP-infected, N-transgenic_vs_TMV-GFP-infected, wild type_72hts_rep2


title: SN comparison_11dpi_rep2


title: Healthy control_40

description: Sample name: 40


title: Healthy control_44

description: Sample name: 44


title: Healthy control_46

description: Sample name: 46


title: Healthy control_39

description: Sample name: 39


title: Healthy control_43

description: Sample name: 43


title: Healthy control_50

description: Sample name: 50


title: Healthy control_49

description: Sample name: 49


title: Healthy control_45

description: Sample name: 45


title: Healthy control_47

description: Sample name: 47


title: Healthy control_48

description: Sample name: 48


title: Healthy control_35

description: Sample name: 35


title: Healthy control_34

description: Sample name: 34


title: Healthy control_41

description: Sample name: 41


title: Healthy control_30

description: Sample name: 30


title: Healthy control_36

description: Sample name: 36


title: Healthy control_37

description: Sample name: 37


title: Healthy control_42

description: Sample name: 42


title: Healthy control_38

description: Sample name: 38


title: Healthy control_24

description: Sample name: 24


title: Healthy control_28

description: Sample name: 28


title: Healthy control_29

description: Sample name: 29


title: Healthy control_31

description: Sample name: 31


title: Healthy control_32

description: Sample name: 32


title: Healthy control_33

description: Sample name: 33


title: SN comparison_7dpi_rep1

source_name: plants infected with PVX/HCLH at 7dpi

source_name: plants infected with PVX/HCWT at 7dpi


title: SN comparison_7dpi_rep2


title: 269_xenograft

city: Freiburg

first: Jaga

last: Virayah

address: Am Flughafen 12-14

institute: Oncotest GmbH

description: Gene expression data from xenograft

hyb_protocol: Standard Affymetix protocol for 3' IVT design

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

data_processing: The data were analysed using the Bioconductor software [gcrma package] in the R statistical computing environment

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

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

tag: cell source

value: Oncotest

value: male

tag: differentiation

value: poorly

tag: dukes stage

value: C

tag: origin

value: primary

tag: cell type

value: xenograft


title: cortical neuron KCl replicate3

description: Gene expression profile of embryonic mouse cortical neurons under KCl stimulus.

hyb_protocol: Hybridization mix was prepared according to standard Agilent hybridization procedures. Hybridization was performed at 65°C for 17h. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Arrays were scanned by a DNA microarray scanner (Agilent G2565BA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v10.5.1.1) using default parameters to get the probe intensities.The data were after log2 transformed and quantile normalized.

source_name: potassium chloride (KCl)_treated

label_protocol: 100ng Dephosphorylated RNA were labeled with Cyanine 3-pCp following standard Aglient protocols.

growth_protocol: Cortical neurons isolated from 15-day-old embryo mouse were cultured in vitro for 12 days.

treatment_protocol: Neurons were exposed to 25uM extracellular bicuculline (Bic) or 50mM potassium chloride (KCl) for 6 hours

value: cortical neurons from embryonic mouse

tag: developmetal stage


title: Healthy control_23

description: Sample name: 23

source_name: RNA from whole blood

tag: gender

value: female


title: 243_xenograft

description: Gene expression data from xenograft

tag: age


title: Healthy control_25

description: Sample name: 25


title: Healthy control_22

description: Sample name: 22


title: Healthy control_26

description: Sample name: 26


title: Healthy control_27

description: Sample name: 27


title: control-evo-4_anc-4

middle: Joseph

last: McDonald

address: 128 sec 2. Academia Rd

department: Molecular Biology

institute: Academia Sinica

hyb_protocol: Probe preparation and hybridization were performed as described Lieu, P.T., Jozsi, P., Gilles, P., and Peterson, T. (2005). Development of a DNA-labeling system for array-based comparative genomic hybridization. Journal of Biomolecular Techniques 16, 104-111.

scan_protocol: Standard scan protocol

data_processing: The intensities for each array were log2-transformed and normalized to LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: evolved non-mutator yeast

label_protocol: Probe preparation and hybridization were performed as described in Lieu, P.T., Jozsi, P., Gilles, P., and Peterson, T. (2005). Development of a DNA-labeling system for array-based comparative genomic hybridization. Journal of Biomolecular Techniques 16, 104-111.

growth_protocol: over night growth in YPD, the resuspension and growth for 3-4 hours until OD600 was approximatley 0.3.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Midi Kit

tag: evolved strain

value: evolved non-mutator yeast after 6700 generations

source_name: ancestral nonmutator strain

tag: strain type

value: ancestral nonmutator strain from which the 6700 nonmutator was derived


title: control-evo-2_anc-2


title: Healthy control_21

description: Sample name: 21

tag: year of birth

tag: tnm (t-stage)


title: MCF10A cells expressing control or obscurin shRNA, exposed to etoposide 48 hr, replicate 2

city: Baltimore

first: Aikaterini

last: Kontrogianni-Konstantopoulos

address: 108 N Greene St

institute: University of Maryland, Baltimore

description: Independent replicate 2 of 3; control and obscurin shRNA-expressing cells were treated with 150 uM etoposide for 48 hours prior to harvest.

hyb_protocol: Dried samples were resuspended in hybridization buffer (Agilent Gene Expression Hybridization Kit), supplemented with Poly-dA, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially (Agilent Gene Expression Wash Buffers 1 and 2), quickly spun dry, and scanned.

scan_protocol: Scanned on an Axon GenePix 4100A scanner. Images were quantified using GenePix Pro feature extraction software (Version 6.0.1.25).

data_processing: GenePix Pro feature extraction software was used for background subtraction and global normalization of the Ratio of Medians to 0.

source_name: MCF10A breast epithelial cells stably expressing obscurin shRNA

label_protocol: 10 ug of RNA was reverse transcribed using random hexamers and aminoallyl-dUTP. cDNA from control shRNA- and obscurin shRNA-expressing cells were coupled to NHS Cy3 and Cy5, respectively.

growth_protocol: MCF10A cells were stably transfected with control shRNA-1 or obscurin shRNA-2, and expression of the shRNA was retained by culture with 1.5 ug/mL puromycin.

extract_protocol: Cells were lysed in Trizol reagent and initial phase separation was performed. The RNA-containing aqueous phase was mixed with 70% ethanol and applied to a Qiagen RNeasy spin column, and then the manufacturer's instructions were followed to elute RNA.

treatment_protocol: At 70% confluency, cells were treated with 150 uM etoposide for 48 hours.

tag: cell line

value: non-tumorigenic breast epithelial cells

tag: shRNA

value: obscurin

tag: treatment

value: etoposide

source_name: MCF10A breast epithelial cells stably expressing scrambled control shRNA

value: control


title: 94_xenograft

description: Gene expression data from xenograft

value: middle


title: cortical neuron Bic replicate 3

description: Gene expression profile of embryonic mouse cortical neurons under Bic stimulus.

source_name: bicuculline (Bic)_treated


title: SN comparison_7dpi_rep3

tag: tissue

value: symptomatic, non-inoculated upper leaves


title: HCC-2998_xenograft

description: Gene expression data from xenograft

value: NCI

value: well


title: 280_xenograft

description: Gene expression data from xenograft

value: Oncotest

value: metastasis


title: cortical neuron KCl replicate 2

tag: strain


title: cortical neuron KCl replicate 1


title: COLO 205_xenograft

description: Gene expression data from xenograft

source_name: COLO 205_xenograft

tag: cell source

value: male

value: poorly

value: D


title: 1103_xenograft

description: Gene expression data from xenograft

tag: differentiation

value: primary

value: xenograft


title: MCF10A cells expressing control or obscurin shRNA, exposed to etoposide 48 hr, replicate 3

description: Independent replicate 3 of 3; control and obscurin shRNA-expressing cells were treated with 150 uM etoposide for 48 hours prior to harvest.


title: Healthy control_19

description: Sample name: 19

value: female

value: healthy

tag: tnm (n-stage)

tag: tnm (tumor grading)

tag: tnm (her2-status)


title: 269L_cell_line

description: Gene expression data from cell-line

tag: dukes stage

value: C

tag: origin

tag: cell type

value: cell-line


title: MCF10A cells expressing control or obscurin shRNA, exposed to etoposide 48 hr, replicate 1

description: Independent replicate 1 of 3; control and obscurin shRNA-expressing cells were treated with 150 uM etoposide for 48 hours prior to harvest.

value: non-tumorigenic breast epithelial cells

value: obscurin

value: etoposide


title: repeatM3_A3

source_name: evolved mutator yeast

tag: evolved strain

value: evolved mutator derived after 6700 generations

source_name: ancestral mutator strain

value: ancestral mutator strain from which the 6700 mutator was derived


title: repeatM2_A1

tag: strain type


title: control-evo-3_anc-3

value: evolved non-mutator yeast after 6700 generations

value: ancestral nonmutator strain from which the 6700 nonmutator was derived


title: SN comparison_11dpi_rep1

value: symptomatic, non-inoculated upper leaves


title: DLD-1_xenograft

description: Gene expression data from xenograft

value: NCI

tag: age

tag: gender

value: male

value: middle


title: cortical neuron control replicate 3

description: Gene expression profile of embryonic mouse cortical neurons.

source_name: control (no treatment)

value: cortical neurons from embryonic mouse

tag: developmetal stage


title: repeatM1_A1


title: Healthy control_20

description: Sample name: 20

tag: year of birth

tag: tnm (t-stage)


title: Healthy control_18

description: Sample name: 18


title: HCT-15_xenograft

description: Gene expression data from xenograft

value: ATCC

value: primary

value: xenograft


title: 94L_cell_line

description: Gene expression data from cell-line

value: Oncotest


title: M3_A3


title: Healthy control_17

description: Sample name: 17

value: female

value: healthy


title: cortical neuron Bic replicate 1


title: Healthy control_16

description: Sample name: 16


title: HT-29_cell_line

description: Gene expression data from cell-line

value: cell-line


title: M2_A2


title: M1_A1


title: cortical neuron Bic replicate 2


title: Healthy control_13

description: Sample name: 13


title: Healthy control_14

description: Sample name: 14


title: Healthy control_15

description: Sample name: 15


title: HCT-116LX_xenograft

description: Gene expression data from xenograft

value: poorly


title: SW-620_xenograft

description: Gene expression data from xenograft

value: C

value: metastasis


title: cortical neuron control replicate 2


title: cortical neuron control replicate 1


title: Healthy control_12

description: Sample name: 12


title: Healthy control_11

description: Sample name: 11


title: Healthy control_10

description: Sample name: 10


title: SNB19_IGFBP2_Clone5

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

hyb_protocol: 17 hours of hybridization at 65C.

scan_protocol: Arrays were scanned with Agilent's dual-laser-based scanner.

data_processing: Log10 ratios for individual probes were calculated using the GE2-v4_91 protocol for the Agilent Feature Extraction Software v9.5.3.1. Ratios were calculated as Cy5 / Cy3, where Cy3 was the reference channel with empty vector transfected cells.

source_name: SNB19 Clone #5, stably transfected with IGFBP2 wt

label_protocol: 500 ng of total RNA from each sample was labeled with Cy3- or Cy5-CTP.

growth_protocol: SNB19 cells were maintained in DMEM/F-12 medium, supplemented with 10% FBS and 1% antibiotic and antimycotic under 5% CO2 at 37C.

extract_protocol: Ambion mirVana™ miRNA Isolation Kit (catalog AM1560)

treatment_protocol: Cells were stably transfected with wild type IGFBP2, IGFBP2 D306E (RGE mutant), or empty vector (pcDNA3).

tag: transfection

value: IGFBP2 wt

tag: cell line

source_name: SNB19 with transfected empty vector

value: empty vector


title: SNB19_IGFBP2_Clone8

source_name: SNB19 Clone #8, stably transfected with IGFBP2 wt


title: Healthy control_8

description: Sample name: 8


title: SNB19_RGE_Clone24

source_name: SNB19 Clone #24, stably transfected with RGE-mutant IGFBP2

value: RGE-mutant IGFBP2


title: Biological Replicate 2(dye-swap)

city: Beijing

first: jing

last: wang

address: Tsinghu University

institute: Medical Systems Biology Research Center School of Medicine Tsinghua University

description: Dye-swap of Biological replicate 2,differentiation (treated ) vs normal(control)

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: U937 cells

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

growth_protocol: All cells were cultured in a sterile incubator at 37˚C

extract_protocol: Total RNA samples were extracted from normal U937 cells  and differentiated U937 cells  using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: Before microarray analysis,differentiation of U937 cells was induced by adding TPA (Sigma-Aldrich, St. Louis, USA) to a final concentration of 30 nM to the culture media and incubating the cells for 48 h.

tag: tissue

value: acute myeloid leukemia

source_name: U937 cells treated with TPA


title: Healthy control_6

description: Sample name: 6


title: Healthy control_7

description: Sample name: 7


title: Biological Replicate 1(dye-swap)

description: Dye-swap of Biological replicate 1,differentiation (treated ) vs normal(control)


title: Biological Replicate 2

description: Biological replicate 2,differentiation (treated ) vs normal(control)


title: Biological Replicate 1

description: Biological replicate 1,differentiation (treated ) vs normal(control)


title: Biological Replicate 3

description: Biological replicate 3,differentiation (treated ) vs normal(control)


title: Healthy control_5

description: Sample name: 5


title: Healthy control_9

description: Sample name: 9


title: SNB19_RGE_Clone2

source_name: SNB19 Clone #2, stably transfected with RGE-mutant IGFBP2


title: Chimp_meth_pt2

type: genomic

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

description: MeDIP-chip Technical Rep 1-3

hyb_protocol: The labeled DNA was hybridized against a GeneChip Chromosome 21/22 2.0R Array (Affymetrix) at 45˚C for 16 hours.   The array was washed and subsequently stained with Cy3-streptavidin in Fluidics Station 450 (Affymetrix) using GeneChip Hybridization, Wash, and Stain kit (Affymetrix).

scan_protocol: The fluorescent signal intensity at each probe spot was measured on GeneChip Scanner (Affymetrix).

data_processing:
A log2-transformed ratio of signals obtained from MeDIP and control DNA was calculated for each probe by Tilling Analysis Software.  The dataset was further processed by Baysian Tool for Methylation Analysis.  The raw BATMAN scores were normalized (median=0, SD=1) for comparison.
.sgr contains normalized methylation score in 100-bp windows, which is generated by BATMAN software and perl script.

molecule: genomic DNA

organism: Pan troglodytes

source_name: MeDIP DNA of peripheral blood cells from adult chimpanzee females

label_protocol: The immunoprecipitated DNA was amplified by WGA2 (Sigma Aldrich, Saint Louis, MO) to give a total of ~10 μg DNA, and then labeled with biotine-dUTP using GeneChip WT double stranded DNA terminal labeling kit (Affymetix, Santa Clara, CA).

extract_protocol: A mixture of genomic DNA of peripheral blood cells from four human or four chimpanzee female individuals (a total of 5 μg) was fragmented by sonication into a 0.3- to 1-kb size range, denatured at 95˚C for 10 min, and cooled on ice.  The denatured DNA was incubated with 5 μg of anti-5-methylcytosine antibody (Aviva Systems Biology, San Diego, CA) in 200 μl of IP buffer (10 mM sodium-phosphate, 140 mM NaCl, 0.05% Triton-X100 at pH7.0) for 3.5 hours at 4˚C.  The antibody-bound DNA fragments were magnetically collected after incubation with Dynabeads M-280 (Life Technologies, Grand Island, NY) coated with anti-mouse IgG antibody for 3 hours at 4˚C.  The beads were washed 5 times with 700 μl of IP buffer, resuspended in 250 μl of lysis buffer (50 mM TrisHCl at pH 8.0, 10 mM EDTA, 0.5% SDS) containing Proteinase K.  After incubation at 55˚C for 30 min, DNA was recovered by phenol-chloroform extraction and subsequent ethanol precipitation.

value: peripheral blood cells

tag: antibody

value: anti-5-methylcytosine antibody

tag: antibody vendor

value: Aviva System Biology

tag: antibody catalog#

source_name: Input DNA of peripheral blood cells from adult chimpanzee females

value: none, input


title: Healthy control_1

description: Sample name: 1

source_name: RNA from whole blood

tag: tnm (n-stage)

tag: tnm (tumor grading)

tag: tnm (her2-status)


title: Healthy control_3

description: Sample name: 3


title: Healthy control_4

description: Sample name: 4


title: Healthy control_2

description: Sample name: 2


title: U937_TPA_48h_rep1

description: differentiation (treated ) vs normal(control)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP,ambion) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction.  We took a cDNA labeling approach with Klenow enzyme after reverse transcription.


title: U937_TPA_48h_rep2


title: HCT-116_cell_line

description: Gene expression data from cell-line

tag: cell source

value: ATCC

value: male

tag: differentiation

tag: dukes stage

tag: origin

value: primary

tag: cell type


title: Human_meth_hg17

description: MeDIP-chip Technical Rep 1-3

source_name: MeDIP DNA of peripheral blood cells from adult human females

source_name: Input DNA of peripheral blood cells from adult human females


title: THP-1 cells +PMA 3d DMSO rep3

city: Olsztyn

first: Carsten

last: Carlberg

address: ul. Trylińskiego 18

department: Food Research

country: Poland

institute: Polish Academy of Sciences

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package

source_name: THP-1 cells +PMA 3d DMSO

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

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Total RNA was extracted using the Invisorb Spin Cell RNA Mini Kit (Invitek GmbH, Berlin, Germany) and checked for RNA integrity using a Biorad Experion automated electrophoresis system (Biorad, Nazareth, Belgium).

treatment_protocol: For differentiation into macrophages the cells were incubated for 3 days with 20 nM PMA. Prior to stimulation with 1 µM of the synthetic LXR ligand T09 (Sigma-Aldrich) or vehicle (DMSO), final concentration 0.1%) the medium was replaced by RPMI 1640 supplemented with 5% lipid-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and 20 nM PMA.

value: monocytic leucemia

tag: treatment

value: vehicle

value: 4 h


title: THP-1 cells +PMA 3d T09 rep3

description: replicate 3

source_name: THP-1 cells +PMA 3d T09


title: THP-1 cells +PMA 3d T09 rep2

description: replicate 2


title: THP-1 cells +PMA 3d T09 rep1

description: replicate 1


title: THP-1 cells +PMA 3d DMSO rep2

description: replicate 2


title: Pax_CMC_R3_arrayID468400

status: Public on Feb 01 2012

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

department: MEMEG

institute: Lund University

description: Paxillus involutus grown on carboxy methyl cellulose (CMC) medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 20. Hybridization on array 468400 and subarray A12.

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 20% PMT.

data_processing: The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).

organism: Paxillus involutus

source_name: P. involutus_mycelium_CMC

label_protocol: Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).

growth_protocol: Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in extracts of organic matter. The fungus was first grown for 9 days on a Minimum Melin Norkrans (MMN) medium and then starved for N during 24 h (Rineau et al. (201X) manuscript in preparation).

extract_protocol: Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MInElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).

treatment_protocol: Organic matter was extracted from forest litter (FH) and maize compost material using either cold (MC) or hot water (MH). Particles were removed by sequentially filtering (0.2 um) and low molecular weight compounds by ultrafiltration (cut-off 10 kDa). The organic matter extracts were added and the cultures were incubated for an additional 7 days. As a control growth was continued on MMN (MMN). In addition, the degradation of carboxy methyl cellulose (CMC) was analyzed (Rineau et al. (201X) manuscript in preparation).

tag: strain/accession

tag: genotype/variation

value: wild-type

value: mycelium

tag: medium

value: carboxy methyl cellulose (CMC)

tag: sample tracking control (stc)

tag: arrayid

tag: subarrayid


title: Pax_CMC_R2_arrayID468400

description: Paxillus involutus grown on carboxy methyl cellulose (CMC) medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 18. Hybridization on array 468400 and subarray A11.

tag: tissue


title: Pax_CMC_R1_arrayID468400

description: Paxillus involutus grown on carboxy methyl cellulose (CMC) medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 17. Hybridization on array 468400 and subarray A10.


title: Pax_MC_R3_arrayID468400

description: Paxillus involutus grown on hot-water maize compost (MH) medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 11. Hybridization on array 468400 and subarray A06.

source_name: P. involutus_mycelium_MC

value: maize compost material using cold water (MC)


title: Pax_MC_R1_arrayID468400

description: Paxillus involutus grown on cold-water maize compost (MC) medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 7. Hybridization on array 468400 and subarray A04.


title: Pax_MMN_R3_arrayID468400

description: Paxillus involutus grown on defined MMN medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 5. Hybridization on array 468400 and subarray A03.

source_name: P. involutus_mycelium_MMN (control)


title: Pax_MMN_R2_arrayID468400

description: Paxillus involutus grown on defined MMN medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 3. Hybridization on array 468400 and subarray A02.


title: Etv5 ChIP using anti-Etv5 antibody rep2

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

description:
Chip-chip mouse embryonic limb tissue Etv5
S2_Etv5

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The median signal intensity of the 4 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. The log enrichment for each group was calculated by subtracting the mean of log2 input intensities from the mean of log2 enriched intensities.

source_name: Input DNA from E11.5 limb tissue cells

label_protocol: 0.4 to 1.0 µg ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Dissected embryonic tissue was used

extract_protocol: Cells from dissected E11.5 forelimbs were immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously(Stock et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 350 µg chromatin was incubated with 5µg IgG (Santa Cruz, sc-2025) or 5 µg Gabpa, Ets1, Elf1, Etv4, Etv5 antibodies and washed and eluted as described in (Stock et al 2007). Reverse cross-linked DNA was purified as described above.

tag: developmental stage

value: distal limb

source_name: Etv5 ChIP DNA from E11.5 limb tissue cells

tag: chip antibody

value: anti-Etv5 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat#


title: Etv5 ChIP using anti-Etv5 antibody rep1

description:
Chip-chip mouse embryonic limb tissue Etv5
S1_Etv5


title: THP-1 cells +PMA 3d DMSO rep1

description: replicate 1


title: Pax_MMN_R1_arrayID468400

description: Paxillus involutus grown on defined MMN medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 1. Hybridization on array 468400 and subarray A01.


title: Etv4 ChIP using anti-Etv4 antibody rep3 dye-swap

description:
Chip-chip mouse embryonic limb tissue Etv4
S3_Etv4

source_name: Etv4 ChIP DNA from E11.5 limb tissue cells

value: anti-Etv4 antibody


title: Pax_MC_R2_arrayID468400

description: Paxillus involutus grown on cold-water maize compost (MC) medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 9. Hybridization on array 468400 and subarray A05.


title: Pax_FH_R3_arrayID468335

description: Paxillus involutus grown on hot-water extracted litter (FH) medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 11. Hybridization on array 468335 and subarray A06.

source_name: P. involutus_mycelium_FH

value: hot-water extracted forest litter (FH)


title: Pax_FH_R2_arrayID468335

description: Paxillus involutus grown on hot-water extracted litter (FH) medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 9. Hybridization on array 468335 and subarray A05.


title: Pax_MH_R3_arrayID468335

description: Paxillus involutus grown on hot-water maize compost (MH) medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 16. Hybridization on array 468335 and subarray A09.

source_name: P. involutus_mycelium_MH

value: maize compost material using hot water (MH)


title: Pax_MH_R1_arrayID468335

description: Paxillus involutus grown on hot-water maize compost (MH) medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 13. Hybridization on array 468335 and subarray A07.


title: Pax_FH_R1_arrayID468335

description: Paxillus involutus grown on hot-water extracted litter (FH) medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 7. Hybridization on array 468335 and subarray A04.


title: Elf1 ChIP using anti-Elf1 antibody rep1

description:
Chip-chip mouse embryonic limb tissue Elf1
S1_Elf1

source_name: Elf1 ChIP DNA from E11.5 limb tissue cells

value: anti-Elf1 antibody

value: Santa Cruz


title: Etv5 ChIP using anti-Etv5 antibody rep3 dye-swap

description:
Chip-chip mouse embryonic limb tissue Etv5
S3_Etv5


title: Pax_MH_R2_arrayID468335

description: Paxillus involutus grown on hot-water maize compost (MH) medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 15. Hybridization on array 468335 and subarray A08.


title: Elf1 ChIP using anti-Elf1 antibody rep2

description:
Chip-chip mouse embryonic limb tissue Elf1
S2_Elf1


title: Gabpa ChIP using anti-Gabpa antibody rep1

description:
Chip-chip mouse embryonic limb tissue Gabpa
S1_Gabpa

source_name: Gabpa ChIP DNA from E11.5 limb tissue cells

value: anti-Gabpa antibody


title: Pax_MMN_R3_arrayID468335

description: Paxillus involutus grown on defined MMN medium. Biological replicate 3 of 3 and spiked with Sample Tracking Control (STC) 5. Hybridization on array 468335 and subarray A03.

value: Minimum Melin Norkrans (MMN)


title: Pax_MMN_R2_arrayID468335

description: Paxillus involutus grown on defined MMN medium. Biological replicate 2 of 3 and spiked with Sample Tracking Control (STC) 3. Hybridization on array 468335 and subarray A02.


title: Pax_MMN_R1_arrayID468335

description: Paxillus involutus grown on defined MMN medium. Biological replicate 1 of 3 and spiked with Sample Tracking Control (STC) 1. Hybridization on array 468335 and subarray A01.


title: RTv6-CD20

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

description: dominance ranks : 1 = high, 5 = low

data_processing: The data were normalised using quantile normalization and variance stabilization using the lumi package in R. Probes were filtered from the full set of HT-12 probes based on the following criteria: 1) probes must have mapped (via blat) uniquely to the rhesus macaque genome (rheMac2) at 80% or greater identity; 2) probes must not have overlapped annotated segmental duplicates >1 kb in rhesus macaque; 3) probes must have exhibited evidence of detectable signal in at least one array sample (p < 0.001) compared to Illumina control probes.

source_name: B cells_rank 2

extract_protocol: RNA was extracted with the Qiagen RNEasy kit, including DNase I treatment, in accordance with the manufacturer's protocol. Quality control was performed with the Agilent Bioanalyzer.

tag: dominance rank

tag: age

value: adult

tag: gender

value: female

tag: tissue source

value: peripheral blood mononuclear cells

value: B cells


title: Etv4 ChIP using anti-Etv4 antibody rep2

description:
Chip-chip mouse embryonic limb tissue Etv4
S2_Etv4


title: RTv6-CD14

description: dominance ranks : 1 = high, 5 = low

source_name: monocytes_rank 2

tag: cell type

value: monocytes


title: Ets1 ChIP using anti-Ets1 antibody rep3

description:
Chip-chip mouse embryonic limb tissue Ets1
S3_Ets1

source_name: Ets1 ChIP DNA from E11.5 limb tissue cells

value: anti-Ets1 antibody

value: James Hagman


title: RUo4-CD14

description: dominance ranks : 1 = high, 5 = low

source_name: monocytes_rank 5


title: Etv4 ChIP using anti-Etv4 antibody rep1

description:
Chip-chip mouse embryonic limb tissue Etv4
S1_Etv4

value: distal limb


title: Gabpa ChIP using anti-Gabpa antibody rep2

description:
Chip-chip mouse embryonic limb tissue Gabpa
S2_Gabpa


title: RTv6-CD8

description: dominance ranks : 1 = high, 5 = low

source_name: cytotoxic T cells_rank 2

value: cytotoxic T cells


title: ROy4-CD8

description: dominance ranks : 1 = high, 5 = low

source_name: cytotoxic T cells_rank 1


title: Ets1 ChIP using anti-Ets1 antibody rep1

description:
Chip-chip mouse embryonic limb tissue Ets1
S1_Ets1


title: Ets1 ChIP using anti-Ets1 antibody rep2 dye-swap

description:
Chip-chip mouse embryonic limb tissue Ets1
S2_Ets1


title: RUo4-CD8

description: dominance ranks : 1 = high, 5 = low

source_name: cytotoxic T cells_rank 5


title: ROy4-CD14

description: dominance ranks : 1 = high, 5 = low

source_name: monocytes_rank 1


title: RTv6-CD4

description: dominance ranks : 1 = high, 5 = low

source_name: helper T cells_rank 2

value: helper T cells


title: ROy4-CD20

description: dominance ranks : 1 = high, 5 = low

source_name: B cells_rank 1


title: RUo4-CD20

description: dominance ranks : 1 = high, 5 = low

source_name: B cells_rank 5


title: ROy4-CD4

description: dominance ranks : 1 = high, 5 = low

source_name: helper T cells_rank 1


title: RDv6-CD20

description: dominance ranks : 1 = high, 5 = low

source_name: B cells_rank 4


title: RQq4-CD4

description: dominance ranks : 1 = high, 5 = low

source_name: helper T cells_rank 3


title: RQq4-CD8

description: dominance ranks : 1 = high, 5 = low

source_name: cytotoxic T cells_rank 3


title: RUo4-CD4

description: dominance ranks : 1 = high, 5 = low

source_name: helper T cells_rank 5


title: RDv6-CD14

description: dominance ranks : 1 = high, 5 = low

source_name: monocytes_rank 4


title: RQq4-CD14

description: dominance ranks : 1 = high, 5 = low

source_name: monocytes_rank 3


title: RQq4-CD20

description: dominance ranks : 1 = high, 5 = low

source_name: B cells_rank 3