title: Rh3 - CD34- GCSF plus AMD3100 - mAdbID:98308

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 98308

hyb_protocol: Sample Hybridization Protocol Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.76 Temperature: 30.23

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 300, and spot size less than 25um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy3) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

extract_protocol:
RNA extraction with TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: blood

value: PBMC

organism: Macaca mulatta

source_name: CD34- GCSF plus AMD3100 Mobilized

label_protocol:
Cy5 Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy5) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

treatment_protocol:
Treatment type: compound
Agent: GCSF plus AMD3100
Treatment dose: 10 ug / kg (GCSF); 1mg / kg (AMD3100)
Treatment time: 5 days (GCSF); 2 hours (AMD3100)
In-vivo treatment: Rhesus macaques recieved GCSF for 5 days. On the 5th day donors recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.


title: Wenzel_1-1_DMSO-control-2wk-shoots_Rep1_ATH1

status: Public on Dec 05 2009

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: 4C for at least 2 days 3 hr chlorine gas Growth Room Agar 70% 20oC Own medium: see Lincoln et al. 1990. Plant Cell 2: 1071-1080. Shoot tissue from ca 2wk old plants with ca 6 rosette leaves.

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col-0, control

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 were sterilized with chlorine gas and plated onto sterile ATS media (Lincoln et al., 1990) supplemented with either N-(1-Naphthyl) phthalamic acid (NPA; Sigma, St. Louis, MO) dissolved in DMSO to a final concentration of 10 mM, or an equivalent volume of DMSO for control material. Seeds were stratified for at least 2 days at 4C and then grown at ca 20C with 16h illumination for 2 weeks (shoot material). Shoot tissues were immediately immersed in liquid nitrogen after excision, stored at -80C, and total RNA purified according to Chang et al. (1993). Lincoln et al. 1990. Plant Cell 2: 1071-1080 Chang et al. 1993. Biology Reporter 11: 113-116

extract_protocol: see Chang et al. 1993. Biology Reporter 11: 113-116

tag: ecotype

tag: developmental stage

tag: tissue

value: shoot

tag: stock code

tag: treatment

value: DMSO control


title: Rh3 - CD34+ GCSF plus AMD3100 - mAdbID:98307

description: mAdb experiment ID: 98307

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.51 Temperature: 30.02

organism: Homo sapiens

tag: cell type

source_name: CD34+ GCSF plus AMD3100 Mobilized


title: RTSV infected TW16 6DAI replication3

status: Public on Dec 07 2009

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 3 of 3, RTSV infected TW16 at 6DAI

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Indica Group

source_name: RTSV TW16 6DAI rep 3

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media :Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth environment: greenhouse
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 6 DAI

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen RNeasy maxi kit
manual: Qiagen

treatment_protocol:
treatment method: tube method (Cabauatan et al.1995)
growth stage:  9-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: rice tungro spherical virus (RTSV)
virus inoculation: three viruliferous green leafhoppers (Nephotettix virescence) per 1 seedling
Virus inoculation: 24hours
Light condition: Natural conditions
Tempareture: 28±3℃

tag: infection

value: RTSV TW16 6DAI

tag: replicate

tag: strain

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

value: whole plant 5 cm above ground

source_name: Mock TW16 6DAI rep 3

treatment_protocol:
treatment method: tube method (Cabauatan et al.1995)
growth stage:  9-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: mock inoculation
virus inoculation: three virus-free green leafhoppers (Nephotettix virescence) per 1 seedling
virus inoculation: 24hours
Light condition: Natural conditions
Tempareture: 28±3℃

value: Mock TW16 6DAI


title: Rh2 - CD34- GCSF plus AMD3100 - mAdbID:98306

description: mAdb experiment ID: 98306

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 4.43 Temperature: 29.71


title: R160vH114_DAMD

type: genomic

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Medulloblastoma R160 DAMD, Technical Rep 1-2, Promoter Array

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Affymetrix Human Tiling 2.0R Arrays and 1.0R Promoter Arrays were analyzed using Tiling Array Software (v 1.1.02, Affymetrix). Raw data were scaled to a target intensity of 100 and normalized by quantile normalization. For probe analysis, a bandwidth of 250 bp was used and perfect match (PM) probes were used in a Wilcoxon Rank Sum two-sided test.

molecule: genomic DNA

source_name: Medulloblastoma R160 DAMD Assay

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

extract_protocol: Genomic DNA was extract from cell lines, primary medulloblastoma and adult cerebellum using a QIAGEN Blood & Cell Culture DNA kit per manufacturer's instructions. The DAMD assay and variations of denaturation conditions were performed as described (Diede et al., 2009). A total of 2 µg of genomic DNA was used as starting material for the DAMD assay. The sample was split into two tubes such that 1 µg was digested with KpnI (10 Units, NEB) and 1 µg was digested with SbfI (10 Units, NEB) for at least 8 hours in a total volume of 20 µl for each digestion. The restriction enzymes were then heat inactivated at 65˚C for 20 minutes. The KpnI and SbfI digests were combined, and then split evenly into two tubes. To the 20 µl of the DNA mixture, 27.36 µl of water and 1.64 µl of 3M NaCl was added such that the final concentration of NaCl was 100 mM and the total volume was 49 µl. For the formamide variation of the protocol to more specifically enrich for DNA palindromes, formamide was added to a final concentration of 50% before DNA denaturing. Denaturation was performed by boiling samples in a water bath for 7 minutes followed by rapid renaturation by immersing samples in an ice-water bath for at least 3 minutes. S1 (Invitrogen) digestion was performed by adding 6 µl 10x S1 nuclease buffer, 4 µl 3M NaCl, and 1 µl of S1 (diluted to 100 Units/µl using S1 Dilution buffer). Samples were then incubated for 60 minutes at 37˚C. S1 was inactivated by extraction with phenol followed by a phenol:chloroform extraction. DNA was ethanol precipitated in the presence of 20 µg of glycogen, and the DNA pellet was resuspended in 80 µl of 1/10 TE. The sample was then divided evenly into two tubes, with one tube subjected to digestion with MseI (40 Units, NEB) and the other tube with MspI (40 Units, NEB) for at least 6 hours at 37˚C (final volume of each digestion was 50 µl). Restriction enzymes were subsequently heat inactivated at 65˚C for 20 minutes. For ligation-mediated PCR, linkers were first created by combining 100 µl of a 100 pmol/µl solution of each oligo with 6.9 µl of 3M NaCl (final concentration 100 mM) and boiling in a water bath for 7 minutes. The water bath was then allowed to slowly cool to 25˚C to allow for annealing. Linkers were recovered by ethanol precipitation and the DNA pellet was resuspended in 500 µl of water. For the MseI linker, JW-102g was annealed to JW103pcTA. For the MspI linker, JW-102g was annealed to JW103pc-2. Linkers were then ligated onto the MseI or MspI digested DNA by adding 5 µl of the appropriate linker to the 50 µl digest, then 7 µl 10x T4 DNA ligase buffer, 1 µl T4 DNA ligase (400 Units, NEB) and 7 µl water for a final volume of 70 µl. Ligation was performed at 16˚C for at least 8 hours and then heat inactivated at 65˚C for 10 minutes. Linkers were then removed using a YM-50 Microcon (Amicon) filter by adding the 70 µl ligation mixture to the column followed by the addition of 160 µl of 1/10 TE. Columns were spun at 12000xg in a microcentrifuge for 5 minutes to almost dryness. 20 µl of 1/10 TE was then added to the membrane, incubated at room temperature for 5 minutes, and then the DNA was recovered by spinning at 1000xg for 3 minutes per the manufacturer’s protocol. 4 µl of this DNA was used as template for a PCR using the appropriate MseI (JW-102gMse) or MspI (JW-102gMsp) primer (4 µl DNA, 10 µl 10x PCR buffer, 10 µl 2mM dNTPs, 20 µl 5x GC-rich solution, 12 µl primer (10 pmol/µl), 1 µl Taq, 43 µl water (reagents from Roche FastStart Taq kit). PCR conditions were as follows: 96˚C 6 minutes, 30 cycles of 96˚C 30 seconds, 55˚C 30 seconds, 72˚C 30 seconds, with final extension of 72˚C for 7 minutes. MseI and MspI PCR products were combined and purified using a YM-30 Microcon (Amicon) filter. The 200 µl of PCR reaction was placed on the column and 300 µl of 1/10 TE was added. The column was spun at 14000xg until sample was concentrated to ~25 µl, and DNA was recovered into a new tube (1000xg for 3 minutes). This DNA was used as the input for biotin labeling.

value: Primary medulloblastoma sample

source_name: H114 DAMD Assay

value: Adult normal cerebellum


title: Sfh 3xFLAG SL1344 pSfR27 BR2

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: biological replicate 2

hyb_protocol: Cy3 labeled ChIP DNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using a GenePix 4100A scanner (Axon Instruments). Cy3 and Cy5 images were acquired at 10 um resolution using a laser power of 100%. Scanned images were analyzed using GenePix Pro 6.1 software

data_processing: median normalization of mean of ratios (532/635) values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Sfh ChIP DNA from SL1344 (pSfR27) cells

label_protocol: Fluorescent labeling of DNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[20 ul of ChIP DNA and 300 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344 (pSfR27) cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS.  DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. Experimental ChIP conditions – 1350 ul chromatin + 5μl of monoclonal H113 anti-H-NS antibodies (Lucchini et al., 2006) or 10 ug of FLAG monoclonal antibodies (Sigma-Aldrich, Cat. No. F3165). The samples were incubated at 4°C overnight on a rotating wheel. 50 ul homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

tag: chip antibody

source_name: Input DNA from SL1344

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2


title: H-NS SL1344 pSfR27 biological replicate 2

description: biological replicate 2

source_name: H-NS ChIP DNA from SL1344 (pSfR27) cells

value: H-NS


title: Wenzel_1-2_NPA-treated-2wk-shoots_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: 4C for at least 2 days 3 hr chlorine gas Growth Room Agar 70% 20oC Own medium: see Lincoln et al. 1990. Plant Cell 2: 1071-1080. Modification: add N-(1-Naphthyl) phthalamic acid (NPA; Sigma, St. Louis, MO) dissolved in DMSO to a final concentration of 10 uM. Shoot tissue from ca 2wk old plants with ca 6 rosette leaves.

source_name: Col-0, NPA

value: NPA


title: Rh2 - CD34+ GCSF plus AMD3100 - mAdbID:98305

description: mAdb experiment ID: 98305

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 4.39 Temperature: 29.35


title: SL1344 pSfR27 sfh minus biological rep 2

type: mixed

description: biological replicate 2

hyb_protocol: Cy3 labeled cDNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using a GenePix 4100A scanner (Axon instruments). Cy3 and Cy5 images were acquired at 10um resolution using a laser power of 100%. Scanned images were analyzed GenePix Pro 6.1 software. This software was used to quantify the fluorescent intensities of each spot representing an array element

source_name: SL1344 (pSfR27) sfh- cells

label_protocol: cDNA synthesis was performed with the Superscript double-stranded cDNA synthesis kit (Invitrogen), following the random-priming method outlined by the manufacturer. Fluorescent labeling of DNA samples for transcriptomic experiments were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ml of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ml). *[1000 ng of cDNA and 1000 ng of sonicated genomic DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ul of stop buffer added to terminate the reaction.

growth_protocol: Cultures of S. Typhimurium SL1344 (pSfR27) and SL1344 (pSfR27) delta sfh were inoculated 1:100 into 25 mls fresh Lennox broth and grown at 37oC until OD600 0.2 was reached

extract_protocol: Total RNA was extracted from the cells using the SV total RNA isolation kit from promega as described (www.ifr.ac.uk/safety/molmicro).

value: SL1344 (pSfR27) delta sfh

source_name: SL1344 control DNA

extract_protocol: Sonicated genomic DNA was used as a reference in these experiments and was purified by standard phenol-chloroform extraction followed by sodium acetate/ethanol precipitation.


title: SL1344 pSfR27 biological rep 1

description: biological replicate 1

source_name: SL1344 (pSfR27) cells


title: SL1344 pSfR27 sfh minus biological rep 1

description: biological replicate 1


title: Weise_1-2_Col-WT_Rep2_ATH1

description: Growth chamber Levington F2 (Fine peat/with intercept an insecticide) with extra grit 4mm at 40%. 75% 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2.

growth_protocol: Plants were sewn in flats of modified commercial soil and grown in a growth chamber with a 12 hour photoperiod, quantum flux of 100 micromol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20 degrees Celsius

extract_protocol: Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA)according to kit directions. Samples were then treated with DNaseI (Invitrogen, CA, USA) according to manufactures directions

tag: genotype

value: wild type

value: leaves


title: R162vH114_DAMDform

description: Medulloblastoma R162 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R162 DAMD Assay + 0.5% formamide

source_name: H114 DAMD Assay + 0.5% formamide


title: R160vH114_DAMDform

description: Medulloblastoma R160 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R160 DAMD Assay + 0.5% formamide


title: R162vH114_DAMD

description: Medulloblastoma R162 DAMD, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R162 DAMD Assay


title: R147vH114_DAMDform

description: Medulloblastoma R147 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R147 DAMD Assay + 0.5% formamide


title: R147vH114_DAMD

description: Medulloblastoma R147 DAMD, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R147 DAMD Assay


title: Sfh 3xFLAG SL1344 pSfR27 BR1

description: biological replicate 1


title: Rh1 - CD34+ GCSF plus AMD3100 - mAdbID:98303

description: mAdb experiment ID: 98303

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.34 Temperature: 28.62

source_name: Pooled Normal Donor PBMC

source_name: CD34+ GCSF plus AMD3100 Mobilized


title: HCT116vDKO_DAMDform

description: HCT116 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: HCT116 DAMD Assay + 0.5% formamide

value: HCT116 colon cancer cell line

source_name: DKO DAMD Assay + 0.5% formamide


title: Rh1 - CD34- GCSF plus AMD3100 - mAdbID:98304

description: mAdb experiment ID: 98304

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.35 Temperature: 28.98

source_name: CD34- GCSF plus AMD3100 Mobilized


title: R123vH114_DAMD

description: Medulloblastoma R123 DAMD, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R123 DAMD Assay

source_name: H114 DAMD Assay


title: Rh3 - CD34- GCSF - mAdbID:95716

description: mAdb experiment ID: 95716

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.04 Temperature: 34.08

source_name: CD34- GCSF Mobilized

treatment_protocol:
Treatment type: compound
Agent: GCSF
Treatment dose: 10 ug / kg
Treatment time: 5 days
In-vivo treatment: Rhesus macaques recieved GCSF for 5 days. Then the PBSC were collected by aphoresis.


title: Rh2 - CD34- GCSF - miRNA - mAdbID:99572

description: mAdb experiment ID: 99572

hyb_protocol: miRNA Sample Hybridization Protocol Other: The miRNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to HyDye fluors (Amersham Biosciences, Piscataway, NJ, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.6 Temperature: 29.01

source_name: EBV-infected B-cell Line Reference

label_protocol:
Hy3 Labeling Protocol
Other: Total RNA was labeled with Hy3 by using Exiqon miRNA labeling kit following the manufacturer's instructions.

value: EBV-infected B-cell line

source_name: CD34- GCSF Mobilized - Hy5 label

label_protocol:
Hy5 Labeling Protocol
Other: Total RNA was labeled with Hy5 by using Exiqon miRNA labeling kit following the manufacturer's instructions.


title: Rh1 - CD34- AMD3100 - miRNA - mAdbID:99570

description: mAdb experiment ID: 99570

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.61 Temperature: 28.8

source_name: CD34- AMD3100 Mobilized - Hy5 label

treatment_protocol:
Treatment type: compound
Agent: AMD3100
Treatment dose: 1 mg / kg (AMD3100)
Treatment time: 2 hours
In-vivo treatment: Rhesus macaques recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.

value: blood


title: Rh3 - CD34- GCSF - miRNA - mAdbID:99568

description: mAdb experiment ID: 99568

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.64 Temperature: 28.49


title: Rh2 - CD34+ GCSF - miRNA - mAdbID:99571

description: mAdb experiment ID: 99571

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.57 Temperature: 28.89

source_name: CD34+ GCSF Mobilized - Hy5 label


title: Rh1 - CD34+ -AMD3100 - miRNA - mAdbID:99569

description: mAdb experiment ID: 99569

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.59 Temperature: 28.65

source_name: CD34+ AMD3100 Mobilized - Hy5 label


title: HCT116vDKO_DAMD

description: HCT116 DAMD, Technical Rep 1-2, Promoter Array

source_name: HCT116 DAMD Assay

source_name: DKO DAMD Assay


title: Rh3 - CD34+ GCSF - mAdbID:95728

description: mAdb experiment ID: 95728

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.16;; 4.36 Temperature: 27.76

value: PBMC

source_name: CD34+ GCSF Mobilized


title: Rh3 - CD34+ GCSF - miRNA - mAdbID:99567

description: mAdb experiment ID: 99567

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.62 Temperature: 28.31


title: Rh2 - CD34+ GCSF - mAdbID:95715

description: mAdb experiment ID: 95715

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.04 Temperature: 34.05


title: R123vH114_DAMDform

description: Medulloblastoma R123 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: Medulloblastoma R123 DAMD Assay + 0.5% formamide

source_name: H114 DAMD Assay + 0.5% formamide


title: Rh2 - CD34- GCSF - mAdbID:95749

description: mAdb experiment ID: 95749

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.16;; 4.31 Temperature: 28.01

source_name: Pooled Normal Donor PBMC


title: Rh1 - CD34+ GCSF - miRNA - mAdbID:99565

description: mAdb experiment ID: 99565

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.64 Temperature: 27.97


title: Rh2 - CD34- AMD3100 - miRNA - mAdbID:99564

description: mAdb experiment ID: 99564

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.68 Temperature: 27.79


title: Rh1 - CD34+ GCSF - mAdbID:95705

description: mAdb experiment ID: 95705

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.07 Temperature: 33.9


title: Rh3 - CD34- AMD3100 - miRNA - mAdbID:99562

description: mAdb experiment ID: 99562

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.69 Temperature: 27.33


title: Rh1 - CD34- GCSF - mAdbID:95708

description: mAdb experiment ID: 95708

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.05 Temperature: 34.02


title: Rh2 - CD34- AMD3100 - mAdbID:95679

description: mAdb experiment ID: 95679

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.1 Temperature: 33.56

source_name: CD34- AMD3100 Mobilized


title: Rh1 - CD34- GCSF - miRNA - mAdbID:99566

description: mAdb experiment ID: 99566

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.63 Temperature: 28.19


title: Mueller-Moule_1-9_vtc2_Rep3_ATH1

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

growth_protocol: After seed sterilisation, seeds were kept in water for 3 days in the dark at 4 degrees. Seeds were sterilised by surface treatment with 25% bleach (Danklorix, Germany) and 0.02% Triton X-100 for 6 minutes followed by three washes with de-ionized water. Growth chamber Agar minimal plant nutrient agar plates (Haughn and Somerville, 1986.Mol Gen Genet 204:430-434). Plants were grown for 14 days to stage 1.04 (4 rosette leaves > 1mm).

extract_protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.

value: vtc2-1 mutation

value: whole plant

tag: genetic background

tag: genetic variation

value: induced_mutation - EMS


title: Rh2 - CD34+ -AMD3100 - mAdbID:95678

description: mAdb experiment ID: 95678

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.53 Temperature: 27.12

source_name: CD34+ AMD3100 Mobilized


title: Mueller-Moule_1-8_vtc2_Rep2_ATH1


title: Mueller-Moule_1-7_vtc2_Rep1_ATH1


title: Mueller-Moule_1-5_vtc1_Rep2_ATH1

value: vtc1-1 mutation


title: Mueller-Moule_1-6_vtc1_Rep3_ATH1


title: Mueller-Moule_1-4_vtc1_Rep1_ATH1


title: Rh3 - CD34+ -AMD3100 - miRNA - mAdbID:99561

description: mAdb experiment ID: 99561

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.71 Temperature: 27.12


title: Rh3 - CD34- GCSF plus AMD3100 - miRNA - mAdbID:99554

description: mAdb experiment ID: 99554

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.16;; 4.44 Temperature: 29.9

source_name: CD34- GCSF plus AMD3100 Mobilized - Hy5


title: Rh2 - CD34+ GCSF plus AMD3100 - miRNA - mAdbID:99551

description: mAdb experiment ID: 99551

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.53 Temperature: 29.47

source_name: CD34+ GCSF plus AMD3100 Mobilized - Hy5


title: Rh1 - CD34- GCSF plus AMD3100 - miRNA - mAdbID:99550

description: mAdb experiment ID: 99550

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.57 Temperature: 29.32


title: Rh1 - CD34+ GCSF plus AMD3100 - miRNA - mAdbID:99549

description: mAdb experiment ID: 99549

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.55 Temperature: 29.2


title: 477

status: Public on Dec 04 2009

city: Redwood City

first: David

middle: Scott

last: Johnson

state: CA

address: 2686 Middlefield Road, Suite C

institute: Gene Security Network

hyb_protocol: as per Illumina's instructions except reduced time to 6 hours

scan_protocol: as per Illumina's instructions

data_processing: Genotypes are inherently inaccurate in single cell microarray data due to biases introduced during multiple displacement amplification. Therefore genotypes were not produced, and instead raw intensity data was used to build probabilistic models under the framework of the Parental Support algorithm.

label: C-Bio and A-DNP

source_name: sperm cells from Gene Security family 231

label_protocol: as per Illumina's instructions except reduced amplification time to 6 hours

extract_protocol: Single cells were isolated from buccal swabs, semen samples, adult blood, immortalized cell lines, and Day 3 cryopreserved embryos. Single tissue culture (lymphocytes) and buccal cells were isolated using a sterile stripper tip (Midatlantic Diagnostic, Mt. Laurel, NJ, USA) affixed to a pipette (Drummond Scientific, Broomall, PA, USA) and a stereoscope (Leica, Wetzlar, Germany). Embryos were thawed, and then individual blastomeres were separated using a micromanipulator (Transferman NK2-Eppendorf, Westbury, NY, USA) after zona pellucida drilling using acidified Tyrode’s solution. Sperm cells were manually isolated using a micromanipulator (Transferman NK2-Eppendorf). Aside from sperm, single cells were washed sequentially four times with wash buffer (5.6mg/ml KCl, 6mg/ml bovine serum albumin). Two different lysis/amplification protocols were used in the analysis: (i) Rubicon Whole Genome Amplification (Ann Arbor, MI, USA), and (ii) multiple displacement amplification (MDA) with Proteinase K Buffer (PKB). Protocol (i) was performed according to the manufacturer’s instructions. For protocol (ii), cells were placed in 5µl PKB (Arcturus PicoPure Lysis Buffer, 50mM DTT), incubated at 56°C for one hour, and then heat inactivated at 95°C for ten minutes. MDA reactions were incubated at 30°C for 2.5 hours and then 65°C for five minutes. Genomic DNA from bulk tissue (Epicentre MasterAmp Buccal Swabs, Madison, WI, USA) was isolated using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). No template controls (buffer blanks) were performed for each amplification method. All buffer blanks produced intensities equivalent to the noise floor (an intensity of 1000 in the 95th percentile on the green detection channel).

tag: cell amplication

value: single sperm cell amplified by MDA


title: Rh2 - CD34- GCSF plus AMD3100 - miRNA - mAdbID:99552

description: mAdb experiment ID: 99552

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.42 Temperature: 29.56


title: 478

value: sperm cells from Gene Security family 231


title: Rh3 - CD34+ GCSF plus AMD3100 - miRNA - mAdbID:99553

description: mAdb experiment ID: 99553

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.57 Temperature: 29.71


title: Rh2 - CD34+ -AMD3100 - miRNA - mAdbID:99563

description: mAdb experiment ID: 99563

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.68 Temperature: 27.55


title: Rh3 - CD34+ -AMD3100 - mAdbID:103243

description: mAdb experiment ID: 103243

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.66 Temperature: 30.81


title: Rh1 - CD34- AMD3100 - mAdbID:103242

description: mAdb experiment ID: 103242

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.58 Temperature: 30.57


title: 474


title: 475


title: Mueller-Moule_1-3_Col-0_Rep3_ATH1


title: Mueller-Moule_1-2_Col-0_Rep2_ATH1


title: Rh1 - CD34+ -AMD3100 - mAdbID:103241

description: mAdb experiment ID: 103241

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.54 Temperature: 30.39


title: 473


title: 457

source_name: blood cell from Gene Security family 231

value: single cell amplified by Rubicon WGA


title: 456

value: blood cell from Gene Security family 231


title: 459


title: 454


title: Mueller-Moule_1-1_Col-0_Rep1_ATH1


title: 455


title: 452


title: 458


title: 451


title: 446


title: 447


title: 449


title: 450


title: 448


title: 445


title: 453


title: 443


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title: 432


title: 431


title: 442


title: 430


title: 428


title: 422


title: 420


title: 423


title: 419


title: 421


title: 424


title: 433


title: 427


title: 416

source_name: lymphoblast from Coriell family 1463

value: lymphoblast from Coriell family 1463


title: 415


title: 410


title: 414


title: 411


title: 417


title: 409


title: 413


title: 429


title: 412


title: 405


title: 476


title: 418


title: 407


title: 425


title: 406


title: 404


title: 403


title: 426


title: 401


title: 408


title: 397


title: 400


title: 402


title: 398


title: 399


title: 396


title: 395

source_name: lymphoblast from Coriell family 1423

value: lymphoblast from Coriell family 1423


title: 390


title: 394


title: 392


title: 391


title: 383


title: 393


title: 386


title: 385


title: 389


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title: 377


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title: 375


title: 374


title: 387


title: 373


title: 372


title: 371


title: Rh3 - CD34- AMD3100 - mAdbID:103244

description: mAdb experiment ID: 103244

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.7 Temperature: 31.03


title: 370


title: 358

value: single cell amplified by MDA


title: 369


title: 364


title: 362


title: 361


title: 363


title: 360


title: 354


title: 356


title: 352


title: 359


title: 355


title: 353


title: 345


title: 349


title: 343


title: 336


title: 332


title: 334


title: 333


title: 330

source_name: lymphoblast from Coriell family 1990

value: lymphoblast from Coriell family 1990


title: 357


title: 331


title: 327


title: 325


title: 326


title: 328


title: 321


title: 324


title: 329


title: 351


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title: 60


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title: 59


title: 75


title: Nadeau_1-4_Col1g11-inflorescence-tips-pool2_Rep1_ATH1

description: Growth chamber Commercial soil: Promix BX manufactured by Premier Horticulture. Sphagnum, perlite, vermiculite, micro and macronutrients, wetting agent

source_name: Col-3 gl1

growth_protocol: Seeds were planted with toothpicks on the surface of sterilized Promix BX in 4 inch pots placed in covered 1020 flats. Pots were placed in the growth chamber and the covers were removed after one week. Plants were grown at 22C, 70% humidity and 16 hours light, 125 Âµmol/m2 sec light intensity. Plants were subirrigated with deionized water once per week, and fertilized with Peter's Fertilizer (1.27g/L) once per week

extract_protocol: Qiagen RNAeasy kit protocol

value: inflorescence tip


title: Garton_1-7_wildtype-warm_Rep2_ATH1

description: Seeds were sown directly onto trays of compost and placed at 4 degrees centigrade for 48 hours prior to transfer to a growth room Growth Room 6 parts Levington's M3 6 parts John Innes no. 3 1 part perlite 70% 20oC Control plants were harvested following 38 days growth in short days at 20oC. The entire rosette was removed from the plant and flash frozen.

source_name: Col-0, warm

growth_protocol: Seeds were sown in trays containing compost comprised of 6 parts Levington's M3, 6 parts John Innes no. 3 and 1 part perlite. The trays were placed at 4 degrees centigrade for 48 hours prior to transfer to the growth room. Growth conditions were short day (8hrs light, 16 hrs dark), 20 degrees centigrade at 70% humidity. Light intensity was 100 micro Einsteins.

value: aerial tissues

value: wild type


title: Garton_1-6_wildtype-cold_Rep1_ATH1

source_name: Col-0, cold


title: Garton_1-2_sfr3-cold_Rep1_ATH1

description: Seeds were sown directly onto trays of compost and placed at 4 degrees centigrade for 48 hours prior to transfer to a growth room Growth Room 6 parts Levington's M3 6 parts John Innes no. 3 1 part perlite 70% 20oC Plants were harvested following 38 days growth in short days at 20oC. The aerial parts of the plants were harvested and flash frozen in liquid nitrogen.

source_name: sfr3, cold

value: EMS

value: sfr3 mutant


title: Nadeau_1-2_Col1g11-inflorescence-tips-pool1_Rep1_ATH1


title: Garton_1-4_sfr3-cold_Rep2_ATH1


title: Garton_1-8_wildtype-cold_Rep2_ATH1


title: Garton_1-5_wildtype-warm_Rep1_ATH1


title: West_2-5_atm_Rep2_ATH1

growth_protocol: Overnight 4C in dark 10 minutes soaking in sterilisation solution (10 % (v/v) house hold bleach, 1 % (v/v) Triton X-100) followed by 5 repeat rinses of sd H2O. Seedlings grown on 0.5 x MS media containing 1 % phytoagar and 1 % sucrose in a growth room with the following conditions: 9/15 hrs light/dark, 22°C, 65 Ã‚ÂµEm-2s-1 Growth Room Phytagar Standard media autoclave Murashige and Skoog basal salt mixture.

extract_protocol: As per manufacturer's instructions

value: AtATM3 mutant


title: West_2-3_Col0_Rep3_ATH1

value: whole plant


title: West_2-2_Col0_Rep2_ATH1


title: West_2-6_atm_Rep3_ATH1


title: Garton_1-3_sfr3-warm_Rep2_ATH1

source_name: sfr3, warm


title: West_2-1_Col0_Rep1_ATH1


title: Garton_1-1_sfr3-warm_Rep1_ATH1


title: Nadeau_1-3_tmm1-inflorescence-tips-pool2_Rep1_ATH1


title: Nadeau_1-1_tmm1-inflorescence-tips-pool1_Rep1_ATH1


title: West_2-4_atm_Rep1_ATH1


title: dpy-9(e12) at iso, rep3

city: Philadelphia

first: Todd

last: Lamitina

state: PA

address: 3700 Hamilton Walk, A702

department: Physiology

institute: University of Pennsylvania

description: Gene expression data for osr mutant under isotonic

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained according to manufacturer supplied protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 scanner.  The average of two sequential scans was calculated for each feature.

data_processing: The data were analyzed with Partek Genomics Suite using using GC-RMA as the normalization method.

organism: Caenorhabditis elegans

source_name: dpy-9(e12) on 51 mM NaCl NGM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Hypochlorite synchronized animals were grown to young adults at 20degrees C on standard NGM plates (51 mM NaCl).

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

treatment_protocol: Animals were washed from plates with M9 solution and placed onto 51 mM NaCl or 200 mM NaCl NGM plates for the indicated time interval.  Osr mutants were grown on 51 mM NaCl for the entire experiment.  At the indicated time, animals were washed from the plates with either isotonic or hypertonically adjusted M9, as required, and 500-1000 young adult animals were selected and sorted into collection tubes with a COPAS Biosort.

value: Whole worm

tag: stage

value: Syncronized and COPAS selected young adults


title: osm-11(n1604) at iso, rep3

source_name: osm-11(n1604) on 51 mM NaCl NGM


title: dpy-9(e12) at iso, rep1


title: dpy-9(e12) at iso, rep2


title: dpy-10(e128) at iso, rep1

source_name: dpy-10(e128) on 51 mM NaCl NGM


title: dpy-10(e128) at iso, rep2


title: Yun_1-6_atgsnor1-3-untreated-control_Rep2_ATH1

description: Growth Room 20'C

source_name: atgsnor1-3, untreated

growth_protocol: The seeds were germinated on commercial compost. The plants were grown in a growth room with a temperature of 20C and a relative humidity of 65%. The photoperiod was 18 h of light and 6 h of dark

value: 4 weeks old

value: leaf tissue

value: untreated


title: osm-11(n1604) at iso, rep2


title: dpy-10(e128)  at iso, rep3


title: osm-8(n1518) at iso, rep3

source_name: osm-8(n1518) on 51 mM NaCl NGM


title: 34-2-BL-I

source_name: Day 3 cleavage stage embryo 1061 from family 34

value: single blastomere amplified by MDA


title: 62


title: osm-8(n1518) at iso, rep1


title: N2 at 200 for 1 generation, rep2

description: Gene expression data for secondary responses to hypertonicity

source_name: Synchronized and sorted N2 on 200 mM NaCl NGM for 1 generation


title: N2 at 200 for 6 hours, rep2

source_name: Synchronized and sorted N2 on 200 mM NaCl NGM for 6 hours


title: N2 at 200 for 15min, rep2

description: Gene expression data for immediate response to hypertonicity

source_name: Synchronized and sorted N2 on 200 mM NaCl NGM for 15 min


title: N2 at 200 for 15min, rep1


title: N2 at 200 for 1 hour, rep1

source_name: Synchronized and sorted N2 on 200 mM NaCl NGM for 1 hour


title: N2 at 200 for 1 generation, rep1


title: 34-1-BL-C

source_name: Day 3 cleavage stage embryo 1060 from family 34


title: osm-8(n1518) at iso, rep2


title: N2 at 200 for 1 hour, rep2


title: 34-2-BL-J

value: Day 3 cleavage stage embryo 1061 from family 34


title: osm-7(n1515) at iso, rep1

source_name: osm-7(n1515) on 51 mM NaCl NGM


title: osm-7(n1515) at iso, rep3


title: osm-7(n1515) at iso, rep2


title: N2 at 200 for 1 hour, rep3


title: 34-2-BL-K


title: N2 at 200 for 6 hours, rep3


title: osm-11(n1604) at iso, rep1


title: N2 at 200 for 6 hours, rep1


title: 34-1-BL-A

value: Day 3 cleavage stage embryo 1060 from family 34


title: 29-3-BL-X

source_name: Day 3 cleavage stage embryo 1047 from family 29


title: 29-3-BL-W

value: Day 3 cleavage stage embryo 1047 from family 29


title: 34-1-BL-B


title: 29-3-BL-U


title: 29-3-BL-V


title: N2 at iso, rep2

description: Gene expression data from control animals

source_name: Synchronized and sorted N2 on 51 mM NaCl NGM


title: N2 at 200 for 1 generation, rep3


title: 29-3-BL-S


title: N2 at 200 for 15min, rep3


title: N2 at iso, rep1


title: 29-3-BL-R


title: 29-2-BL-M

source_name: Day 3 cleavage stage embryo 1046 from family 29


title: N2 at iso, rep3


title: 29-2-BL-L

value: Day 3 cleavage stage embryo 1046 from family 29


title: 29-2-BL-N


title: 29-2-BL-P


title: 29-1-BL-H

source_name: Day 3 cleavage stage embryo 1045 from family 29


title: 29-2-BL-K


title: 29-2-BL-J


title: 29-2-BL-I


title: 29-1-BL-F

value: Day 3 cleavage stage embryo 1045 from family 29


title: 29-3-BL-T


title: 29-1-BL-G


title: 29-1-BL-E


title: 29-1-BL-B


title: 29-1-BL-D


title: 28-4-BL-Y

source_name: Day 3 cleavage stage embryo 1054 from family 28


title: 28-4-BL-Z

value: Day 3 cleavage stage embryo 1054 from family 28


title: 28-3-BL-W

source_name: Day 3 cleavage stage embryo 1053 from family 28


title: 29-1-BL-A


title: 28-3-BL-U

value: Day 3 cleavage stage embryo 1053 from family 28


title: 28-3-BL-T


title: 28-3-BL-S


title: 28-2-BL-L

source_name: Day 3 cleavage stage embryo 1052 from family 28


title: 28-1-BL-F

source_name: Day 3 cleavage stage embryo 1051 from family 28


title: 28-3-BL-V


title: 28-2-BL-K

value: Day 3 cleavage stage embryo 1052 from family 28


title: 28-1-BL-G

value: Day 3 cleavage stage embryo 1051 from family 28


title: 28-1-BL-E


title: 28-3-BL-Q


title: 28-1-BL-A


title: 28-3-BL-R


title: 28-2-BL-J


title: 28-2-BL-I


title: 27-4-BL-Y

source_name: Day 3 cleavage stage embryo 1059 from family 27


title: 28-1-BL-C


title: 28-1-BL-B


title: 27-4-BL-Z

value: Day 3 cleavage stage embryo 1059 from family 27


title: 29-3-BL-Q


title: 27-4-BL-AC


title: 27-3-BL-W

source_name: Day 3 cleavage stage embryo 1058 from family 27


title: 27-4-BL-AE


title: 27-3-BL-U

value: Day 3 cleavage stage embryo 1058 from family 27


title: 28-4-BL-AA


title: 27-3-BL-R


title: 27-3-BL-T


title: 27-2-BL-L

source_name: Day 3 cleavage stage embryo 1057 from family 27


title: 27-2-BL-O

value: Day 3 cleavage stage embryo 1057 from family 27


title: 27-3-BL-X


title: 27-2-BL-J


title: 27-4-BL-AF


title: 15-3-BL-S

source_name: Day 3 cleavage stage embryo 1070 from family 15


title: 27-3-BL-Q


title: 15-2-BL-M

source_name: Day 3 cleavage stage embryo 1069 from family 15


title: 27-1-BL-A

source_name: Day 3 cleavage stage embryo 1056 from family 27


title: 27-2-BL-I


title: 27-1-BL-E

value: Day 3 cleavage stage embryo 1056 from family 27


title: 27-1-BL-D


title: 15-2-BL-L

value: Day 3 cleavage stage embryo 1069 from family 15


title: 27-1-BL-G


title: 15-2-BL-K


title: 15-5-BL-AJ

source_name: Day 3 cleavage stage embryo 1072 from family 15


title: 15-5-BL-AI

value: Day 3 cleavage stage embryo 1072 from family 15


title: 15-3-BL-Q

value: Day 3 cleavage stage embryo 1070 from family 15


title: 27-4-BL-AB

value: single blastomere amplified by MDA


title: 15-3-BL-R


title: 15-1-BL-F

source_name: Day 3 cleavage stage embryo 1068 from family 15


title: 15-1-BL-C

value: Day 3 cleavage stage embryo 1068 from family 15


title: 15-2-BL-J


title: 15-1-BL-E


title: 15-1-BL-B


title: 15-2-BL-I


title: 15-1-BL-A


title: 13-8-BL-W

source_name: Day 3 cleavage stage embryo 1079 from family 13


title: 13-8-BL-Y

value: Day 3 cleavage stage embryo 1079 from family 13


title: 15-5-BL-AH


title: 15-1-BL-G


title: 15-1-BL-D


title: 13-8-BL-S


title: 13-7-BL-P

source_name: Day 3 cleavage stage embryo 1078 from family 13


title: 13-8-BL-Z


title: 13-8-BL-U


title: 13-8-BL-V


title: 13-7-BL-R

value: Day 3 cleavage stage embryo 1078 from family 13


title: 13-6-BL-H

source_name: Day 3 cleavage stage embryo 1075 from family 13


title: 13-7-BL-K


title: 13-6-BL-G

value: Day 3 cleavage stage embryo 1075 from family 13


title: 13-7-BL-O


title: 13-7-BL-Q


title: 13-6-BL-B


title: 13-5-BL-AR

source_name: Day 3 cleavage stage embryo 1077 from family 13


title: 13-6-BL-A


title: 13-7-BL-M


title: 13-6-BL-E


title: 13-7-BL-N


title: 13-6-BL-D


title: 13-5-BL-AO

value: Day 3 cleavage stage embryo 1077 from family 13


title: 13-8-BL-T


title: 13-6-BL-C


title: 13-5-BL-AM


title: 13-5-BL-AK


title: 13-2-BL-D

source_name: Day 3 cleavage stage embryo 1474 from family 13


title: 13-3-BL-G

source_name: Day 3 cleavage stage embryo 1475 from family 13


title: 13-5-BL-AQ


title: 13-5-BL-AL


title: 13-12-BL-K

source_name: Day 3 cleavage stage embryo 1076 from family 13


title: 13-11-BL-D

source_name: Day 3 cleavage stage embryo 1074 from family 13


title: 13-5-BL-AS


title: 13-11-BL-C

value: Day 3 cleavage stage embryo 1074 from family 13


title: 13-7-BL-J


title: 13-3-BL-D

value: Day 3 cleavage stage embryo 1475 from family 13


title: 13-1-BL-I

source_name: Day 3 cleavage stage embryo 1473 from family 13


title: 13-1-BL-E

value: Day 3 cleavage stage embryo 1473 from family 13


title: 13-6-BL-F


title: 13-1-BL-G


title: 13-3-BL-A

value: single blastomere amplified by Rubicon WGA


title: 13-12-BL-I

value: Day 3 cleavage stage embryo 1076 from family 13


title: 13-2-BL-A

value: Day 3 cleavage stage embryo 1474 from family 13


title: 13-12-BL-J


title: 13-1-BL-D


title: 486

source_name: sperm cells from Gene Security family 28

value: single sperm cell amplified by MDA


title: 487

source_name: sperm cells from Gene Security family 15


title: 13-1-BL-H


title: 13-1-BL-A


title: 13-5-BL-AN


title: 483

value: sperm cells from Gene Security family 28


title: 482

value: sperm cells from Gene Security family 15


title: 488


title: 13-1-BL-B


title: 472


title: 485


title: 469


title: 468


title: 481


title: 470


title: 479


title: 466


title: 480


title: 471


title: 463


title: 462


title: 467


title: 465


title: 461


title: 365

source_name: buccal cell from Gene Security family 15

value: single cell amplified by MDA


title: 367

source_name: buccal cell from Gene Security family 28


title: 464


title: 484


title: 350

source_name: lymphoblast from Coriell family 1463

value: lymphoblast from Coriell family 1463


title: 344

source_name: blood cell from Gene Security family 231


title: 368

value: buccal cell from Gene Security family 28


title: 342

value: blood cell from Gene Security family 231


title: 338


title: 346


title: 340


title: 347


title: 460


title: 337


title: 276

source_name: lymphoblast from Coriell family 1990

value: lymphoblast from Coriell family 1990


title: 271


title: 339


title: 252


title: 341


title: 256


title: 348


title: 366

value: buccal cell from Gene Security family 15


title: 255


title: 254


title: 250


title: 249


title: 248


title: 247


title: 277


title: 246


title: 245


title: 251


title: 244


title: 240


title: 243


title: 239


title: 242


title: 216


title: 57


title: 94


title: 241


title: 93


title: 253


title: 58


title: 55


title: 92


title: 54


title: 53


title: 56


title: 52


title: 50


title: 51


title: 46


title: 47


title: 44


title: 42


title: 43


title: 45


title: 41


title: 40


title: 36


title: 39


title: 37


title: 34


title: 49


title: 31


title: 35


title: 48


title: 33


title: 32


title: 28


title: 27


title: 38


title: 24


title: 29


title: 25


title: 22


title: 17


title: 23


title: 20


title: 21


title: 19


title: 18


title: 16


title: 26


title: 15


title: 30


title: 14


title: 12


title: 11


title: 13


title: 8


title: 10


title: 9


title: pol II unstimulated

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

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

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
GFF files include scaled, log2 (ChIP/Input) ratio in the 6th column. Positional information is based on human genome build 35.

source_name: pol II ChIP DNA from unstimulated T cell

label_protocol: ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 1x10^7 cells were fixed with 1% formaldehyde in culture medium for 5 min at room temperature followed by quenching with 0.125 M glycine for 15 min. The cells were washed twice with ice-cold PBS and the ChIP pellets are harvested and stored at -80 C  before performing the ChIP assay. The detailed ChIP assays are published in Byun et al PNAS 2009.

treatment_protocol: Jurkat cells were unstimulated

tag: antibody

value: pol II

tag: cell line

value: Jurkat T cells

value: unstimulated

source_name: input DNA


title: pol II stimulated (2) with P/I

source_name: pol II ChIP DNA from P/I stimulated T cell

treatment_protocol: Jurkat cells were cultured in the presence of P/I to stimulate for each time point.

value: stimulated


title: pol II unstimulated (2)


title: 5


title: 6


title: pol II stimulated with P/I


title: 4


title: 3


title: p300 unstimulated (2)

source_name: p300 ChIP DNA from unstimulated T cell


title: p300 stimulated (2) with P/I

source_name: p300 ChIP DNA from P/I stimulated T cell


title: p300 unstimulated


title: 2


title: 7


title: p300 stimulated with P/I


title: 1


title: MC3T3 Rb Knockout, biological rep2

city: Tampa

first: Douglas

last: Cress

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: Moffitt Cancer Institute

description: Expression data from mouse osteoblast cell with retinoblastoma tumor suppressor(Rb) knock-out.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.

data_processing: The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: Primary cultured Rb-knockout Mus musculus osteoblast cells immortalized

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.

extract_protocol: Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.

treatment_protocol: Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.

value: osteoblast cells

value: Rb Knockout


title: MC3T3 Rb Knockout, biological rep3


title: MC3T3 Wild type, biological rep1

description: Expression data from wild-type mouse osteoblast cell .

source_name: Primary cultured wild-type Mus musculus osteoblast cells immortalized

value: Wild type


title: MC3T3 Wild type, biological rep2


title: MC3T3 Rb Knockout, biological rep1


title: MC3T3 Wild type, biological rep3


title: Gr1lo 3

city: New York

first: Gwendalyn

middle: J

last: Randolph

state: NY

address: 1425 Madison Ave

department: Gene and Cell Medicine

institute: Mount Sinai School of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: All arrays were analysed with ArrayAssist (Stratagene). We used GC-RMA, and then in conjunction with MAS5 analysis to determine present or absent genes we compared the two subsets within each species (eg: we compared mouse Ly-6chi monocytes to mouse Ly-6C lo monocytes) using an unpaired T test with asymptotic P value computation and Benjamini-Hochburg correction.

source_name: mouse Gr1lo (Ly-6clo) monocytes

label_protocol: For mouse samples, RNA amplification, direct labeling, hybridization, and slide scanning were carried out as described in Grabner R, 2009, with slight modifications. We enhanced the in vitro transcription-time from 4 h to 64 h and added fresh nucleotides and T7 polymerase alternating every 8 h and 16 h.

extract_protocol: For mouse samples, sorted samples were pelleted and immediately resuspended in TRIzol (Invitrogen, Carlsbad, CA) and stored at -80˚C until RNA isolation. RNA was isolated with RNeasy Micro-RNA isolation kit (Qiagen, Valencia, CA), with the exception that Qiagen kit spin filters were replaced with Zymo-Spin IC columns (Zymo Research, Orange, CA). For human samples, cells were treated with TRI-reagent and stored at -80°C. 10 µg linear acrylamide   was added to lysates and RNA was isolated by phenol/chloroform extraction  and precipitation

tag: monocyte subsets

value: Gr1lo (Ly-6clo) monocytes

tag: age

value: 12-week old


title: Gr1lo 4


title: Gr1lo 1


title: Gr1lo 2


title: Gr1hi 4

source_name: mouse Gr1hi (Ly-6chi) monocytes

value: Gr1hi (Ly-6chi) monocytes


title: Gr1hi 3


title: Gr1hi 1


title: Hapmap_DS_2 (Agilent 251469334262)

status: Public on Dec 03 2009

city: Cambridge

first: Christina

last: Curtis

address: Robinson Way

department: Computational Biology/Oncology

institute: University of Cambridge

description: Genomic DNA extracted from two HapMap individuals interrogated on the Agilent Human Genome CGH Microarray Kit 244A.

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Data were processed from raw text files using R and limma (using limma's “agilent” source option). Probes apparently not 60 bases in length were removed and arrays were normalized using the normexp deconvolution background correction method and loess regression of log-ratios to remove dye-bias.

source_name: Hapmap

label_protocol: standard Agilent protocol

extract_protocol: standard Agilent protocol

tag: sample


title: Hapmap_1 (Agilent 251469348770)


title: Hapmap_DS_1 (Agilent 251469334263)


title: Sum159_3 (Agilent 251469348774)

description: Genomic DNA extracted from cell line was was interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.

source_name: Cell Line

source_name: Pooled Normal

value: Pool


title: Gr1hi 2


title: 7201_Match_2 (Agilent 251469334236)

description: Genomic DNA extracted from breast tumors was was interrogated for copy number against matched normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.

source_name: Breast carcinoma

source_name: Matched Normal


title: Pool_1 (Agilent 251469334140)

description: Pooled normal genomic DNA was interrogated for copy number against pooled normal genomic DNA (as a control) on the Agilent Human Genome CGH Microarray Kit 244A.


title: Sum159_1 (Agilent 251469348771)


title: Pool_2 (Agilent 251469348773)


title: MT3_DS_2 (Agilent 251469348866)

description: Genomic DNA extracted from cell line was was interrogated for copy number against pooled normal genomic DNA in DyeSwap on the Agilent Human Genome CGH Microarray Kit 244A.


title: MT3_DS_1 (Agilent 251469348867)


title: Sum159_2 (Agilent 251469348772)


title: Sum159_Dil_1 (Agilent 251469338277)

description: 30% Genomic DNA extracted from cell line was mixed with 70% pooled normal genomic DNA and then interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.


title: 7206_Match_DS_1 (Agilent 251469348554)

description: Genomic DNA extracted from breast tumors was was interrogated for copy number against matched normal genomic DNA in DyeSwap on the Agilent Human Genome CGH Microarray Kit 244A.


title: MT3_1 (Agilent 251469334232)


title: MT3_Dil_3 (Agilent 251469334114)


title: MT3_Dil_1 (Agilent 251469334155)


title: Match_Pool_1 (Agilent 251469338232)

description: Normal genomic DNA from one individual was interrogated for copy number against pooled normal genomic DNA (as a control) on the Agilent Human Genome CGH Microarray Kit 244A.


title: MT3_Dil_2 (Agilent 251469348560)


title: 7207_Dil_3 (Agilent 251469348527)

description: 50% Genomic DNA extracted from breast tumors was mixed with 50% matched DNA from normal tissue and then interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.


title: 7206_Dil_2 (Agilent 251469334231)

description: 70% Genomic DNA extracted from breast tumors was mixed with 30% matched DNA from normal tissue and then interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.


title: 7207_Dil_2 (Agilent 251469348526)


title: 7204_Match_1 (Agilent 251469334141)


title: 7204_Pool_2 (Agilent 251469348643)

description: Genomic DNA extracted from breast tumors was was interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.


title: 7207_Dil_1 (Agilent 251469334259)


title: 7204_Pool_1 (Agilent 251469334162)


title: 7201_Pool_1 (Agilent 251469346101)


title: 7195_Pool_2 (Agilent 251469346099)


title: 7201_Match_1 (Agilent 251469334156)


title: 7195_Pool_1 (Agilent 251469346098)


title: 7214_Pool_1 (Agilent 251469348558)


title: 7214_Match_1 (Agilent 251469334230)


title: 7207_Pool_2 (Agilent 251469348557)


title: 7206_Pool_1 (Agilent 251469348644)


title: 7207_Pool_1 (Agilent 251469348556)


title: 7206_Pool_2 (Agilent 251469348645)


title: MT3_Dil_2 (Nimblegen 9411702)

description:
30% Genomic DNA extracted from cell line was mixed with 70% pooled normal genomic DNA and then interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0.
NimbleScan version=2.4.31

hyb_protocol: standard Nimblegen protocol

scan_protocol: Manufacturer's NimbleScan Protocol. See samples section for sample specific versions.

data_processing: standard Nimblegen protocol

label_protocol: standard Nimblegen protocol

growth_protocol: standard Nimblegen protocol

extract_protocol: standard Nimblegen protocol

treatment_protocol: standard Nimblegen protocol


title: Sum159_Dil_3 (Nimblegen 9423102)


title: Sum159_Dil_2 (Nimblegen 9412002)


title: Sum159_Dil_1 (Nimblegen 5411002)

description:
30% Genomic DNA extracted from cell line was mixed with 70% pooled normal genomic DNA and then interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0.
NimbleScan version=2.4.27


title: 7206_Dil_2 (Nimblegen 5519602)

description:
70% Genomic DNA extracted from breast tumors was mixed with 30% matched DNA from normal tissue and then interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.27


title: MT3_Dil_1 (Nimblegen 9400702)


title: MT3_2 (Nimblegen 9398502)

description:
Genomic DNA extracted from cell line was was interrogated for copy number against pooled normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.
NimbleScan version=2.4.31

hyb_protocol: Manufacturer's NimbleScan Protocol.

data_processing: Manufacturer's NimbleScan Protocol.


title: 7206_Dil_3 (Nimblegen 6327202)


title: Sum159_1 (Nimblegen 9390502)

description:
n/a
NimbleScan version=2.4.31


title: 7207_Dil_2 (Nimblegen 5408902)

description:
50% Genomic DNA extracted from breast tumors was mixed with 50% matched DNA from normal tissue and then interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.27


title: Sum159_2 (Nimblegen 9390602)

description:
n/a
NimbleScan version=2.4.31


title: Hapmap_DS_2 (Nimblegen 9398902)

description:
Genomic DNA extracted from two HapMap individuals interrogated in Dyeswap on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.31


title: 7207_Dil_1 (Nimblegen 5408602)


title: 7206_Match_1 (Agilent 251469334261)


title: MT3_1 (Nimblegen 9398402)

description:
Genomic DNA extracted from cell line was was interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.31


title: MT3_DS_1 (Nimblegen 9403202)

description:
n/a
NimbleScan version=2.4.31


title: MT3_Dil_3 (Nimblegen 9423702)


title: Hapmap_1 (Nimblegen 9398602)

description:
Genomic DNA extracted from two HapMap individuals interrogated on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.31


title: Hapmap_2 (Nimblegen 9399202)


title: MT3_DS_2 (Nimblegen 9412102)

description:
n/a
NimbleScan version=2.4.31


title: 7206_Dil_1 (Nimblegen 5411602)


title: 7206_Pool_DS_1 (Nimblegen 9412502)

description:
Genomic DNA extracted from breast tumors was was interrogated for copy number against pooled normal genomic DNA in Dyeswap on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.31


title: Pool_1 (Nimblegen 9424202)

description:
Pooled normal genomic DNA was interrogated for copy number against pooled normal genomic DNA (as a control) on the Agilent Human Genome CGH Microarray Kit 244A.
NimbleScan version=2.4.31


title: 7206_Dil_1 (Agilent 251469348646)


title: Hapmap_DS_1 (Nimblegen 9398802)


title: 7207_Dil_3 (Nimblegen 6323702)


title: 7204_Match_1 (Nimblegen 5400102)

description:
Genomic DNA extracted from breast tumors was was interrogated for copy number against matched normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.27


title: 7204_Pool_1 (Nimblegen 5399702)

description:
Genomic DNA extracted from breast tumors was was interrogated for copy number against pooled normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.27


title: 7201_Pool_2 (Nimblegen 6319202)


title: 7201_Pool_1 (Nimblegen 5396302)


title: 7204_Pool_2 (Nimblegen 5399902)


title: 7206_Match_DS_1 (Nimblegen 9454202)

description:
Genomic DNA extracted from breast tumors was was interrogated for copy number against matched normal genomic DNA in Dyeswap on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.
NimbleScan version=2.4.31


title: 7206_Match_DS_2 (Nimblegen 9611302)


title: 7214_Pool_2 (Nimblegen 5402602)


title: 7201_Match_1 (Nimblegen 5398402)


title: 7195_Pool_2 (Nimblegen 5399502)


title: 7195_Pool_1 (Nimblegen 5399602)


title: 7195_Match_1 (Nimblegen 6320802)


title: 7214_Pool_1 (Nimblegen 6321502)


title: 7206_Match_1 (Nimblegen 6322102)


title: 7207_Pool_1 (Nimblegen 6320702)


title: 7206_Pool_2 (Nimblegen 5405102)


title: 7207_Pool_2 (Nimblegen 6319702)


title: 7207_Match_1 (Nimblegen 6319802)


title: 7206_Pool_1 (Nimblegen 5405202)


title: 7214_Match_1 (Nimblegen 5402102)


title: 7214T_2 (Illumina)

description: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).

hyb_protocol: Manufacturers instructions: 1. denature 750ng DNA, 2. whole genome ampliofication, 3. frangemtation of the DNA, 4. hybridization to 50mers on array

scan_protocol: Manufacturers default

data_processing: Data were processed using BeadStudio Genotyping Module 3.2.32

label: Biotin

label_protocol: post-hybridization labelling: single base extension using labled dNTPs

extract_protocol: Genomic DNA from breast tumors and matched normals was extracted with Qiagen's Dneasy kit. The extractions were not done manually but using Qiagen's Quiacube. Input = 20x10um sections per sample.


title: 7214T_3 (Illumina)


title: MT3_3 (Illumina)

description: Genomic DNA extracted from a cell line was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: 7201T_3 (Illumina)


title: 7206Tdil_1 (Illumina)

description: 50% breast tumor DNA mixed with 50% matched normal  DNA


title: MT3dil_3 (Illumina)

description: 30% cell line DNA mixed with 70% normal breast DNA


title: 7206N_1 (Illumina)

description: Genomic DNA extracted from a matched normal was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: 7206Tdil_2 (Illumina)


title: 7214N_1 (Illumina)


title: 7207T_3 (Illumina)


title: SUM159_3 (Illumina)


title: NA15510_3 (Illumina)

description: Genomic DNA extracted from a hapmap sample was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: Pool_2 (Illumina)

description: Genomic DNA extracted from a pool of normal samples was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: 7195T_3 (Illumina)


title: MT3_2 (Illumina)


title: 7204N_1 (Illumina)


title: 7195T_2 (Illumina)


title: SUM159dil_2 (Illumina)


title: NA10851_3 (Illumina)


title: 7206T_1 (Illumina)


title: 7206T_3 (Illumina)


title: SUM159dil_3 (Illumina)


title: 7207T_2 (Illumina)


title: 7206T_2 (Illumina)


title: 7207Tdil_2 (Illumina)


title: SMS-LHN

first: Jayanti

last: Jagannathan

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

hyb_protocol: Illumina Human 6 expression Bead chip standard protocol

extract_protocol: Trizol RNA extraction reagent protocol

tag: tissue type

value: neuroblastoma

value: cell line SMS-LHN

tag: mycn status

tag: gender

tag: inss

tag: risk

tag: ploidy

tag: shimada


title: 7214T_1 (Illumina)


title: SMS-KAN

scan_protocol: Illumina Human 6 expression Bead chip standard protocol

value: cell line SMS-KAN


title: NA10851_2 (Illumina)


title: SY5Y

data_processing: Illumina Human 6 expression Bead chip standard protocol

value: cell line SY5Y


title: SKNFI_dup

label_protocol: Illumina Human 6 expression Bead chip standard protocol

value: cell line SKNFI_dup


title: SKNFI

growth_protocol: Illumina Human 6 expression Bead chip standard protocol

value: cell line SKNFI


title: SKNDZ

treatment_protocol: Illumina Human 6 expression Bead chip standard protocol

value: cell line SKNDZ


title: SKNBE2

value: cell line SKNBE2


title: SKNAS_dup

value: cell line SKNAS_dup


title: SKNDZ_dup

value: cell line SKNDZ_dup


title: SAN

value: cell line SAN


title: SKNSH

value: cell line SKNSH


title: NGP_dup

value: cell line NGP_dup


title: NGP

value: cell line NGP


title: 7204T_3 (Illumina)


title: NLF

value: cell line NLF


title: SUM159dil_1 (Illumina)


title: NBLS_dup

value: cell line NBLS_dup


title: SKNAS

value: cell line SKNAS


title: NBEBc1

value: neuroblastoma

value: cell line NBEBc1


title: MT3dil_1 (Illumina)


title: 7195N_1 (Illumina)


title: 7204T_2 (Illumina)


title: NA15510_2 (Illumina)


title: SUM159_1 (Illumina)

description: Genomic DNA extracted from cell lines was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: 7204T_1 (Illumina)


title: 7201N_1 (Illumina)


title: SUM159_2 (Illumina)


title: Pool_1 (Illumina)

value: Pool


title: 7207Tdil_1 (Illumina)


title: NBLS

value: cell line NBLS


title: 7195T_1 (Illumina)


title: FK506 treatment time-point 4,IC50

status: Public on Dec 16 2009

city: Singapore

first: Guangan

last: Hu

address: 60 Nanyang Drive

department: School of biological sciences

country: Singapore

institute: Nanyang Technological Unversity

description: no additional information

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: Dd2, start 33hpi, 6hr after treatment

label_protocol: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Laboratory strain 3D7 and Dd2, sorbitol synchronized. Parasites grow in a 2% suspension of purified human RBCs and RPMI 1640 media supplemented with 0.25% Albumax, 2 g/l sodium bicarbonate, 0.1 mM hypoxanthine, 25 mM HEPES (pH 7.4), and 50 μg/l gentamycin, at 37°C, 5% O2, and 6% CO2. The 3D7 parasites for microarray reference pool were mixed with 6 time-series samples (every 8hrs through a 48hr life cycle), harvested from a 6 liter biofermenter synchronized culture.

treatment_protocol: Synchronzied parasite cultures are splitted into proper number flasks (75ml culture/flask). Total number is double number of time points for one experiment. Half flasks are treated with one compound with the final concentration of IC50 or IC90, and half flasks are negative controls. After the treatment of different time points, parasites in each flask were harvested for total RNA isolation and microarray hybridizations.

tag: strain

tag: treatment group

tag: time point

value: 6 hr

source_name: reference pool


title: NB1691

value: cell line NB1691


title: 7207T_1 (Illumina)


title: NB1771

value: cell line NB1771


title: KCN

value: cell line KCN


title: KELLY

value: cell line KELLY


title: NA15510_1 (Illumina)

description: Genomic DNA extracted from Hapmap cell lines was genotyped using Infinium HumanCNV370 Genotyping BeadChips (Illumina).


title: IMR5

value: cell line IMR5


title: IMR32_dup

value: cell line IMR32_dup


title: 7207N_1 (Illumina)


title: LAN6

value: cell line LAN6


title: IMR32

value: cell line IMR32


title: NB1771_dup

value: cell line NB1771_dup


title: MT3_1 (Illumina)


title: CHP901

value: cell line CHP901


title: NB16

value: cell line NB16


title: CHP134_dup

value: cell line CHP134_dup


title: NB1643

value: neuroblastoma

value: cell line NB1643


title: NA10851_1 (Illumina)


title: MT3dil_2 (Illumina)


title: 7201T_2 (Illumina)


title: CHOP2079

source_name: tumor RNA

value: primary tumor


title: CHLA79

value: cell line CHLA79


title: CHOP2059


title: LAN5

value: cell line LAN5


title: SO045308

value: cell line SO045308


title: SO044479

value: cell line SO044479


title: CHOP2074


title: CHOP1992


title: CHOP2058


title: BE2c

value: cell line BE2c


title: CHOP2001


title: CHOP1940


title: CHOP1956


title: CHOP2006


title: CHOP1964


title: CHOP2050


title: CHOP1977


title: KELLY_dup

value: cell line KELLY_dup


title: CHOP2028


title: CHP134

value: cell line CHP134


title: CHOP1953


title: CHOP1972


title: CHOP1938


title: CHOP1931


title: CHOP1913


title: CHOP1930


title: CHOP1904


title: CHOP2023


title: CHOP1891


title: CHOP1878


title: CHOP1867


title: CHOP1853


title: CHOP1881


title: MT3_r3 (Affymetrix A354-50)

description:
Genomic DNA extracted from cell lines was profiled for copy number alterations using the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.

hyb_protocol: Samples were hybridized according to the manurfacturer's protocol

scan_protocol: Samples were scanned according to the manurfacturer's protocol

data_processing: Data were processed using SNP-RMA implemented in the aroma.affymetrix package

source_name: Cell line

label_protocol: Samples were labeled according to the manurfacturer's protocol


title: CHOP1851


title: CHOP1823


title: MT3_r1 (Affymetrix A354-48)


title: CHOP1736


title: MT3_r2 (Affymetrix A354-49)


title: CHOP1719


title: NA10851_r3 (Affymetrix A354-47)

description:
Genomic DNA extracted from HapMap cell lines was profiled for copy number alterations using the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: CHOP1848


title: CHOP1691


title: NA10851_r2 (Affymetrix A354-46)


title: 7201T_1 (Illumina)


title: NA10851_r1 (Affymetrix A354-45)


title: CHOP1749


title: NA15510_r3 (Affymetrix A354-44)


title: CHOP1743


title: CHOP1701


title: CHOP1798


title: CHOP1669


title: NA15510_r1 (Affymetrix A354-42)


title: NA15510_r2 (Affymetrix A354-43)


title: CHOP1613


title: CHOP1638


title: CHOP1683


title: SUM159_r3 (Affymetrix A354-41)


title: CHOP1591


title: SUM159_r1 (Affymetrix A354-39)


title: CHOP1603


title: CHOP1636


title: CHOP1595


title: CHOP1587


title: 7201N (Affymetrix A354-35)

description:
Genomic DNA was extracted from matched normal tissue was mixed and profiled for copy number alterations on the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: CHOP1585


title: CHOP1562


title: CHOP1386


title: 7204N (Affymetrix A354-36)


title: CHOP1492


title: 7195N (Affymetrix A354-34)


title: POOL_r1 (Affymetrix A354-37)

description:
Genomic DNA extracted a pool of reference normals was profiled for copy number alterations using the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.

value: Pool


title: POOL_r2 (Affymetrix A354-38)


title: SUM159_r2 (Affymetrix A354-40)


title: CHOP1501


title: 7214N (Affymetrix A354-33)


title: CHOP1395


title: CHOP1456


title: CHOP1577


title: CHOP1379


title: CHOP1468


title: CHOP1417


title: CHOP1204


title: CHOP1199


title: 7206N (Affymetrix A354-31)


title: CHOP1181


title: CHOP1167


title: CHOP1213


title: CHOP1382


title: CHOP1437


title: MT3_30_r3 (Affymetrix A354-30)

description:
30% Genomic DNA extracted from cell-lines was mixed with 70% matched DNA from normal tissue and profiled for copy number alterations on the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: MT3_30_r2 (Affymetrix A354-29)


title: CHOP1013


title: SUM159_30_r3 (Affymetrix A354-27)

description:
70% Genomic DNA extracted from cell-lines was mixed with 30% matched DNA from normal tissue and profiled for copy number alterations on the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: CHOP1062


title: CHOP1002


title: CHOP0558


title: CHOP1009


title: 7207N (Affymetrix A354-32)


title: 7207T_50_r2 (Affymetrix A354-23)

description:
50% Genomic DNA extracted from breast tumors was mixed with 50% matched DNA from normal tissue and profiled for copy number alterations on the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: 7207T_50_r1 (Affymetrix A354-22)


title: Aorta_non-transgenic C57BL/6J control_1

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description:
Gene expression data from aortas isolated from non-transgenic C57BL/6J control mice.
Cont-1

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybridization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

source_name: Aortas isolated from non-transgenic C57BL/6J control mice

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: The study was initiated with 4-6 week-old APOE-deficient mice on a C57BL/6J background, and non-transgenic C57BL/6J controls. Mice had free access to food and water, and were fed a standard rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). For atherosclerosis treatment, one subgroup of APOE-deficient mice received captopril in drinking water (20 mg/kg) for 7 months. At an age of 32-34 weeks, aortas were isolated from three study groups (APOE-deficient, captopril-treated APOE-deficient, and nontransgenic control mice), dissected free of fat, and immediately frozen in liquid nitrogen.

extract_protocol: Total aortic RNA was isolated with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study was performed with aortas isolated from three groups of mice (32-34 weeks of age), i.e. untreated APOE-deficient mice (APOE), APOE-deficient mice treated with captopril (20 mg/kg in drinking water) for 7 months (Capto), and nontransgenic control mice (Cont).

tag: genotype

value: non-transgenic

tag: tissue

value: aorta

value: 32-34 weeks


title: Aorta_non-transgenic C57BL/6J control_2

description:
Gene expression data from aortas isolated from non-transgenic C57BL/6J control mice.
Cont-2


title: CHOP1060


title: MT3_30_r1 (Affymetrix A354-28)


title: CHOP0968


title: SUM159_30_r2 (Affymetrix A354-26)


title: CHOP1003


title: 7207T_50_r3 (Affymetrix A354-24)


title: Aorta_APOE-deficient and captopril treated_2

description:
Gene expression data from aortas isolated from captopril-treated APOE-deficient mice.
Capto-2

source_name: Aortas isolated from captopril-treated APOE-deficient mice

value: APOE-deficient

tag: treatment

value: captopril

tag: treatment time

value: 7 months


title: CHOP0505

value: neuroblastoma


title: SUM159_30_r1 (Affymetrix A354-25)


title: CHOP0986


title: CHOP0982


title: CHOP1092


title: 7206T_30_r3 (Affymetrix A354-21)

description:
70% Genomic DNA extracted from breast tumors was mixed with 30% matched DNA from normal tissue and profiled for copy number alterations on the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.


title: CHOP1007


title: CHOP0495


title: CHOP0355


title: Aorta_APOE-deficient with atherosclerosis_2

description:
Gene expression data from atherosclerotic aortas isolated from APOE-deficient mice.
APOE-2

source_name: Aortas isolated from atherosclerotic APOE-deficient mice

tag: disease

value: atherosclerosis


title: Aorta_APOE-deficient and captopril treated_1

description:
Gene expression data from aortas isolated from captopril-treated APOE-deficient mice.
Capto-1

tag: age


title: CHOP0440

value: primary tumor


title: colonic MSC - biological replicate 2

city: St. Louis

first: Thaddeus

middle: S.

last: Stappenbeck

state: MO

address: 660 S. Euclid Avenue, Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: Data analyses performed using dChip (May 8, 2008 release)

source_name: colonic MSC from C57BL/6

label_protocol: Amplified RNA was labeled with Turbo Labeling Biotin (MDS).

extract_protocol:
Total RNA from lysed cells using Qiagen RNEasy Miniprep kit (#74106)
Amplification using RiboAmp Plus from MDS Analytical Technologies according to provided protocol.

tag: cell type

value: mesenchymal stem cells

tag: tissue source

value: Isolated from flushed colon


title: 7204T_r3 (Affymetrix A354-18)

description:
Genomic DNA extracted breast tumours was profiled for copy number alterations using the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.

tag: sample


title: 7206T_30_r2 (Affymetrix A354-20)


title: CHOP0401

tag: tissue type

tag: mycn status

tag: gender


title: Aorta_APOE-deficient with atherosclerosis_1

description:
Gene expression data from atherosclerotic aortas isolated from APOE-deficient mice.
APOE-1


title: CHOP1159

tag: inss

tag: risk

tag: ploidy


title: bone marrow MSC - biological replicate 2

source_name: bone marrow MSC from C57BL/6

tag: strain

value: Isolated from bone marrow


title: 7206T_30_r1 (Affymetrix A354-19)


title: colonic MSC - biological replicate 1


title: CHOP0493

tag: shimada


title: CHOP0481


title: 7204T_r1 (Affymetrix A354-16)


title: bone marrow MSC - biological replicate 1

source_name: Cultured bone marrow MSC from C57BL/6


title: 7201T_r1 (Affymetrix A354-13)


title: CHOP0483


title: CHOP0333


title: 7204T_r2 (Affymetrix A354-17)


title: 7201T_r2 (Affymetrix A354-14)


title: 7201T_r3 (Affymetrix A354-15)


title: CHOP0309


title: CHOP0298


title: CHOP0283


title: CHOP0273


title: 7195T_r3 (Affymetrix A354-12)


title: 7195T_r2 (Affymetrix A354-11)


title: CHOP0265


title: CHOP0238


title: JCW25 Vs JCW26 120min (replicate 3)

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

description: JCW25 Vs JCW26 120min (P3)

hyb_protocol: Microarray prehybridization was performed in 5x SSC (SSC: 150 mM NaCl, 15mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. (Fluka, Sigma-Aldrich, Buchs SG, Switzerland). Labeled cDNA was dried in a vacuum trap and used as probe after resuspension in 110 μl of hybridization solution (50% Formamide, 5xSSC, 0.1% SDS, 100 μg/ml salmon sperm from Invitrogen, Carlsbad, CA, USA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).

scan_protocol: GenePix 4000B fluorescence scanner and analyzed by Genepix® Pro 6.0 software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada).

data_processing: Data was filtered according to spot quality. Only those spots with intensities at least twice the background signal and with at least 75% of pixels with intensities above background plus two standard deviations were selected for further calculations. Following these  criteria, over 70% of spots in each array were usually found suitable for further analysis. Ratio of medians was used to calculate the VALUEs.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae JCW25 strain, 120min

label_protocol: 20 µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following indirect labeling protocol (CyScribe postlabeling kit, GE-Healthcare). Labeling efficiency was evaluated by measuring Cy3 or Cy5 absorbance in Nanodrop Spectrophotometer.

growth_protocol: Yeast cells were grown in minimal media until logarithmic phase.

extract_protocol: Total RNA extracted by RiboPure RNA extraction kit (Ambion) following manufacturer's instructions.

treatment_protocol: Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0 and 120 min top2 inactivation (35C).

value: After growth to log phase, 120min at 35C

source_name: Saccharomyces cerevisiae JCW26 strain, 120min

tag: genotype

value: FY251 carrying allele top2-4


title: JCW25 Vs JCW26 120min (replicate 2)

description: JCW25 Vs JCW26 120min (P2)