title: NA12239 rep1 genotyping at HMS (Human660W-Quad) rev2

value: Female

value: lymphoblastoid cell lines


title: Muscle VP16-3

status: Public on Jun 30 2011

type: RNA

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

country: USA

institute: Merck Research Laboratories

description: Mice overexpressing reverse tetracycline-transactivator (rtTA) exhibited all four sequelae of metabolic syndrome (visceral obesity, insulin resistance, dyslipidemia, and hypertension), a pro-inflammatory state and marked hepatic steatosis. Gene expression profiling of the adipose tissue, muscle and liver revealed changes in gene expression of key factors involved in lipid metabolism, insulin resistance, and inflammation.

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

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

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

molecule: total RNA

organism: Mus musculus

source_name: Muscle

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: tissue

value: Muscle

tag: genotype

value: WT

tag: genetic background

value: FVB

value: rtTA transgenic


title: NA15510 rep1 genotyping at HMS (Human660W-Quad) rev2

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 1M platform we used QuantiSNP, iPattern, PennCNV, cnvPartition and Partek
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

tag: gender

tag: cell type

tag: cell line

tag: genotyping center

value: HMS


title: NA18517 rep 3 genotyping at TCAG (Human660W-Quad) rev2

scan_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

value: TCAG


title: Muscle VP16-2


title: NA10851 rep 3 genotyping at TCAG (Human660W-Quad) rev2

label_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

value: Male


title: NA18980 rep 3 genotyping at TCAG (Human660W-Quad) rev2


title: Vac__day 7_rep16

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalised using cubic spline algorithm in Illumina BeadStudio V2.0

label: biotin

source_name: Vaccine_day 7_rep16

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit kit for Illumina arrays

extract_protocol: RNA was extracted using PAXgene RNA

treatment_protocol: Whole blood samples collected using PAXgene RNA tubes and stored at -20 degrees Celcius until processing

value: Paxgene Whole Blood RNA Samples


title: Liver WT-3

source_name: Liver

value: Liver


title: Muscle VP16-1


title: NA18576 rep 3 genotyping at TCAG (Human660W-Quad) rev2


title: MIP_HF rep 2

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

description: Gene expression in beta cells of high fat fed MIP replicate 2

hyb_protocol: Hybridised for overnight at 45C on Mouse MOE 430_2 GeneChips. GeneChips were processed with standard Affymetric Protocols.

scan_protocol: GeneChips scanned with HP GeneArray Scanner

data_processing: CEL files imported into Affy in Bioconductor. Normalisation with RMA (with background subtraction). Normalised gene expression values (RMA with background subtraction) were converted to linear scale from log2 scale. R v2.8.0, Biobase_2.2.2, and affy_1.20.2 were used.

source_name: MIP High fat fed replicate 2

label_protocol: Affymetrix IVT Express

growth_protocol: Mice (all male) were housed in standard conditions on a 12 h light/dark cycle and fed standard rodent chow (Special Diet Services, Edinburgh, UK).

extract_protocol: Pancreata perfused with collagenase and islets isolated by hand picking. Isolated islets (around 500) coming from at least 3 mice (around 200/mice) have been directly lysed in Trizol to extract total RNA.

treatment_protocol: KsJ wild type and MIP-HSD1 heterozygous mice were high fat fed for 12 weeks. Mice were given 58% of saturated fat as energy with sucrose (D12331, Research Diets, New Brunswick, NJ) for 12 weeks from 4 weeks of age.

value: Pancreatic beta cells

tag: strain

tag: genotype/variation


title: Liver WT-2


title: Vac__day 7_rep15

source_name: Vaccine_day 7_rep15


title: MIP_HF rep 3

description: Gene expression in beta cells of high fat fed MIP replicate 3

source_name: MIP High fat fed replicate 3


title: Liver WT-1


title: Vac__baseline_rep15


title: MIP_HF rep 4

description: Gene expression in beta cells of high fat fed MIP replicate 4

source_name: MIP High fat fed replicate 4


title: Vac__baseline_rep17


title: NA18517 rep 2 genotyping at TCAG (Human660W-Quad) rev2


title: NA15510 rep 3 genotyping at TCAG (Human660W-Quad) rev2


title: Vac__day 7_rep14

source_name: Vaccine_day 7_rep14


title: Vac__baseline_rep16


title: MIP_HF rep 1

description: Gene expression in beta cells of high fat fed MIP replicate 1

source_name: MIP High fat fed replicate 1


title: NA18980 rep 2 genotyping at TCAG (Human660W-Quad) rev2


title: NA18576 rep 2 genotyping at TCAG (Human660W-Quad) rev2


title: Vac__day 7_rep13

source_name: Vaccine_day 7_rep13


title: Liver VP16-3


title: INS-GAS male mice with H. pylori infection treated with placebo 3

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

description: Gene expression data from  INS-GAS mouse stomachs chronically infected with H. pylori and treated with placebo

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent 4X44K Mouse genome array (Part #G4122F. Design #014868)

scan_protocol: GeneChips were scanned using Agilent Microarray Scanner for one color setting for the 44K array

data_processing: Data were quantile normalized and read with Feature Extraction software 9.1

source_name: INS-GAS mouse stomach, Helicobacter pylori, placebo

label_protocol: Biotinylated cRNA were prepared according to the standard One-Color Microarray-Based gene expression Analysis, low input quick amp labeling protocol (AGILENT) protocol

growth_protocol: Mice maintained under normal husbandry conditions

extract_protocol: Trizol and purified with RNeasy/DNase kit

treatment_protocol: Infected with H pylori for 28 weeks.  Treated with subcutaneous pellet of 0.25mg 17beta-estradiol, 15mg Tamoxfien or 5mg placebo for 12 weeks

value: stomach

value: male

tag: infectious agent

value: Helicobacter pylori

tag: duration of infection

value: 28 weeks

tag: hormone treatment

value: placebo

tag: treatment duration

value: 12 weeks

tag: transgene

value: INS-GAS

value: FVB/N


title: KsJ_HF rep 3

description: Gene expression in beta cells of high fat fed KsJ replicate 3

source_name: KsJ High fat fed replicate 3

value: KsJ


title: KsJ_HF rep 2

description: Gene expression in beta cells of high fat fed KsJ replicate 2

source_name: KsJ High fat fed replicate 2


title: KsJ_HF rep 4

description: Gene expression in beta cells of high fat fed KsJ replicate 4

source_name: KsJ High fat fed replicate 4


title: Liver VP16-2

value: WT

value: FVB


title: NA10851 rep 2 genotyping at TCAG (Human660W-Quad) rev2

value: lymphoblastoid cell lines


title: Vac__baseline_rep14


title: INS-GAS male mice with H. pylori infection treated with Tamoxifen 2

description: Gene expression data from  INS-GAS mouse stomachs chronically infected with H. pylori and treated with Tamoxifen

source_name: INS-GAS mouse stomach, Helicobacter pylori, Tamoxifen

value: Tamoxifen


title: NA12239 rep 2 genotyping at TCAG (Human660W-Quad) rev2

value: Female

value: TCAG


title: Vac__baseline_rep13

value: Paxgene Whole Blood RNA Samples


title: INS-GAS male mice with H. pylori infection treated with Tamoxifen 1


title: Liver VP16-1

value: Liver

value: rtTA transgenic


title: NA12239 rep1 genotyping at TCAG (Human660W-Quad) rev2


title: Kidney medulla WT-3

source_name: Kidney medulla

value: Kidney medulla


title: Vac__day 7_rep12

source_name: Vaccine_day 7_rep12


title: Kidney medulla WT-2


title: NA15510 rep1 genotyping at TCAG (Human660W-Quad) rev2


title: NA18517 rep1 genotyping at TCAG (Human660W-Quad) rev2


title: NA18980 rep1 genotyping at TCAG (Human660W-Quad) rev2


title: Mouse in vivo iTreg cells, replicate pool 3

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 45101 transcripts

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.

source_name: EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 3

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

growth_protocol: Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.

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

treatment_protocol: Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.

tag: source

value: FoxP3-deficient BALB/c Foxp3K276X mice

tag: age

value: 50 days old

value: iTreg


title: KsJ_HF rep 1

description: Gene expression in beta cells of high fat fed KsJ replicate 1

source_name: KsJ High fat fed replicate 1

value: Pancreatic beta cells


title: Vac__baseline_rep11


title: INS-GAS male mice with H. pylori infection treated with estradiol 2

description: Gene expression data from  INS-GAS mouse stomachs chronically infected with H. pylori and treated with estradiol

source_name: INS-GAS mouse stomach, Helicobacter pylori, estradiol

value: stomach

value: male

value: Helicobacter pylori

value: 28 weeks

value: estradiol

value: 12 weeks

value: INS-GAS


title: Mouse in vivo iTreg cells, replicate pool 2

source_name: EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 2


title: 6234 balb/c -> balb rag2-/- IL13-/- (new)

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

description: Universal Mouse Reference RNA (Stratagene).

hyb_protocol: Agilent Protocols and Hybridization Kits.

scan_protocol: GenePix 400B scanner (Axon Instruments).

data_processing: Feature extraction with GenePix 5.1 software.

source_name: balb/c -> balb rag2-/- IL13-/-

label_protocol: Agilent Linear Amplification Low RNA Input Kit.

growth_protocol: cGVHD mice generated by splenocyte transfer of B10.D2 into balb/c; syngeneic controls balb/c into balb/c.

extract_protocol: Total RNA isolated using Trizol methods; cleaned up with Qiagen RNeasy mini-columns.

treatment_protocol: Skin harvested from cGVHD mice at 2 weeks post splenocyte transfer.

value: skin

source_name: Universal Mouse Reference

value: multiple


title: Mouse in vivo iTreg cells, replicate pool 1

source_name: EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 1


title: Mouse in vivo nTreg cells, replicate pool 3

source_name: EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 3

value: nTreg


title: NA18576 rep1 genotyping at TCAG (Human660W-Quad) rev2

value: Female

value: lymphoblastoid cell lines

value: TCAG


title: Vac__baseline_rep12

value: Paxgene Whole Blood RNA Samples


title: Vac__day 7_rep10

source_name: Vaccine_day 7_rep10


title: INS-GAS male mice with H. pylori infection treated with estradiol 3

value: FVB/N


title: Kidney medulla VP16-2

value: Kidney medulla

value: WT

value: FVB

value: rtTA transgenic


title: Kidney medulla WT-1


title: 6232 B10.D2 -> balbc rag2-/- IL13-/- (new), replicate 1


title: Kidney medulla VP16-1


title: Mouse in vivo nTreg cells, replicate pool 2

source_name: EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 2

value: FoxP3-deficient BALB/c Foxp3K276X mice

value: 50 days old


title: Vac__baseline_rep10


title: Vac__day 7_rep11

source_name: Vaccine_day 7_rep11


title: Kidney cortex WT-3

source_name: Kidney cortex

value: Kidney cortex


title: INS-GAS male mice with H. pylori infection treated with estradiol 1

value: stomach

value: male

value: Helicobacter pylori

value: 28 weeks

value: estradiol

value: 12 weeks


title: 6232 B10.D2 -> balb rag2-/- IL13/- (new)

value: skin

value: multiple


title: Kidney medulla VP16-3


title: NA12239 rep 3 genotyping at TCAG (Human660W-Quad) rev2

value: Female

value: lymphoblastoid cell lines

value: TCAG


title: INS-GAS male mice with H. pylori infection treated with placebo 1

source_name: INS-GAS mouse stomach, Helicobacter pylori, placebo

value: placebo

value: INS-GAS

value: FVB/N


title: 6230 balb/c -> balb rag2-/- IL13/- (new)

source_name: balb/c -> balb rag2-/- IL13/-


title: Mouse in vivo nTreg cells, replicate pool 1

source_name: EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 1

value: FoxP3-deficient BALB/c Foxp3K276X mice

value: nTreg


title: Kidney cortex WT-2

value: Kidney cortex

value: WT

value: FVB


title: Vac__day 7_rep09

source_name: Vaccine_day 7_rep09

value: Paxgene Whole Blood RNA Samples


title: Vac__baseline_rep09


title: Kidney cortex WT-1


title: Kidney cortex VP16-3

value: rtTA transgenic


title: 6226 B10.D2->balb rag2-/- IL13-/-(new)


title: CPG-stimulated B-CLL repl 9

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description: Biological replicate 9 of 9

hyb_protocol: The Hybridization was performed acording to Ambion protocol.

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA.

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile

source_name: CPG stimulated purified cell of  CLL

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol).

extract_protocol: Total RNA was extracted according to TRIZOL reagent protocol

treatment_protocol: CLL cells were purified by negative selection using anti-CD3, anti-CD14 and anti-CD16 mouse monoclonal antibodies and Dynabeads coated with a pan anti-mouse IgG antibody. The purity of the CLL cells after negative selection was monitored by flow-cytometry and the percentage of CD5+/CD19+ cells exceeded 98% for each sample. CLL cells were resuspended in RPMI complete medium at a density of 2 × 105 and stimulated with 7.5 μg/ml complete phosphorothioate CpG ODN oligonucleotide 2006 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) or left unstimulated for 18 h.

value: B-CLL

source_name: reference

tag: sample origin

value: pooled normal PB B cells of healthy donors


title: Vac__day 7_rep08

source_name: Vaccine_day 7_rep08

tag: tissue


title: Kidney cortex VP16-2

tag: genotype


title: 6229 balb/c -> balb rag2-/- IL13-/- (new)

value: skin


title: CPG-stimulated B-CLL repl 8

description: Biological replicate 8 of 9


title: CPG-stimulated B-CLL repl 7

description: Biological replicate 7 of 9


title: Vac__baseline_rep08


title: 6224 B10D2 -> balb rag2-/- IL13-/- (new)

value: multiple


title: CPG-stimulated B-CLL repl 6

description: Biological replicate 6 of 9


title: NA15510 rep 2 genotyping at TCAG (Human660W-Quad) rev2

value: Female


title: Vac__baseline_rep07


title: eWAT WT-3

source_name: eWAT

value: eWAT

tag: genetic background


title: Kidney cortex VP16-1


title: 6223 B10.D2 -> balb rag2-/- IL13-/-  (new)


title: 6154 B10D2 -> balb rag2-/- (new)

source_name: B10D2 -> balb rag2-/-


title: Vac__day 7_rep06

source_name: Vaccine_day 7_rep06


title: Vac__day 7_rep07

source_name: Vaccine_day 7_rep07


title: CPG-stimulated B-CLL repl 3

description: Biological replicate 3 of 9


title: 6225 balb/c ->balb rag2-/- IL13-/-(new)

source_name: balb/c ->balb rag2-/- IL13-/-

source_name: Universal Mouse Reference


title: CPG-stimulated B-CLL repl 5

description: Biological replicate 5 of 9


title: eWAT WT-1


title: eWAT WT-2


title: 6153 balb/c -> balb rag2-/- (new)

source_name: balb/c -> balb rag2-/-


title: Vac__baseline_rep06


title: CPG-stimulated B-CLL repl 4

description: Biological replicate 4 of 9


title: NA10851 rep1 genotyping at TCAG (Human660W-Quad) rev2

tag: gender

value: Male

value: lymphoblastoid cell lines

value: TCAG


title: Vac__day 7_rep05

source_name: Vaccine_day 7_rep05


title: Vac__day 7_rep04

source_name: Vaccine_day 7_rep04


title: 6151  B10.D2->balb rag2-/- (new)


title: INS-GAS male mice with H. pylori infection treated with placebo 2

value: stomach

value: male

value: Helicobacter pylori

value: 28 weeks

value: placebo

value: 12 weeks

value: INS-GAS

value: FVB/N


title: Vac__baseline_rep05

value: Paxgene Whole Blood RNA Samples


title: CPG-stimulated B-CLL repl 2

description: Biological replicate 2 of 9

value: B-CLL

value: pooled normal PB B cells of healthy donors


title: 5719 balb/c -> balb rag2-/- IL4Ra-/- (new)

source_name: balb/c -> balb rag2-/- IL4Ra-/-

value: skin

value: multiple


title: 6152 B10.D2 -> balb rag2-/- (new)


title: SCG_BMP_24h_rep2

city: Davis

first: Pamela

middle: J

last: Lein

state: CA

address: 2161 Haring Hall

institute: UC Davis

description:
06A-11H1A_BMP242_164PL
Microarray processing batch 2

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45⁰C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE.  The staining and washing were performed using GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script, EukGE_WSv5 450.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix GeneChip Scanner 3000 with AutoLoader.  The array image scan was processed using Affymetrix GeneChip Operating Software (GCOS) v. 1.2, which employs the Microarray Suite, version 5.0 (MAS 5.0) algorithm.  Image processing resulted in the generation of raw, probe level data in the CEL file format.

data_processing: The data were processed by Partek Genomic Suite (Partek, Inc, St. Louis, MO) software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.  The batch correction statistical algorithm was applied to minimize the technical variation observed between the two microarray processing batches, which differed by scan date and cRNA amount hybridized to the microarray.

organism: Rattus norvegicus

source_name: SCG cultured neurons,+ BMP7, 24h

label_protocol: Each total RNA sample was labeled and amplified following the recommended protocol in the Affymetrix GeneChip Expression Analysis Technical Manual, rev.3 (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).  Using x µg of total RNA as input for all samples, messenger RNA was amplified and labeled in two steps.  In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen), followed by an ethanol precipitation of the labeled target.  The target was fragmented to produce a uniform distribution of short cRNAs.  10µg (microarray processing batch1) or 5ug (microarray processing batch2) of each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

growth_protocol: All procedures involving animals were performed according to protocols approved by the Institutional Animal Care and Use Committee at Johns Hopkins University.  Superior cervical ganglia (SCG) were dissected from E21 Holtzmann rat pups.  SCG were dissociated (Higgins, D, et al 1991) were plated on Collagen I-coated dishes in C2 culture media (serum-free medium) plus beta-nerve growth factor (100ng/ml, Harlan Bioproducts, Indianapolis, IN) as previously described.  One day after plating, cells were treated with Ara-C (Sigma) for 48 hours to deplete cultures of non-neuronal cells including glial cells that would otherwise generate and excrete BMP.  On day four, media was changed to C2 without Ara-C.  The neuronal growth protocol was repeated three times to give three independent, biological replicates.

extract_protocol: Following incubation with or without BMP7 for the prescibed length of time (6 or 24h), superior cervical ganglia (SCG) neurons were dislodged from the cultured plate and pooled to yield a sufficient number of cells per treatment condition.  Total RNA was isolated from each pooled sample according to the RNeasy Total RNA kit (Qiagen, Valencia, CA) manufacturer’s protocol.  RNA concentration was determined by spectrophotometric absorbance at 260nm, and the 260nm to 280nm absorbance ratio was calculated to define RNA purity.

treatment_protocol: On day five in culture, neuronal cultures were incubated in C2 culture media only (control) for 24h or with 50 ng/ml bone morphogenic protein-7 (BMP7, Curis, Cambridge, MA) in C2 for 6 or 24 hours.  The experimental design described herein resulted in three total conditions: (1) C2 media only for 24h (Control), (2) C2 +BMP 6h, and (3) C2 +BMP 24h.  This treatment protocol was repeated three times for each of the three biological replicates included in the study.

value: Holtzman

tag: treatment


title: 5720 B10.D2->balb rag2-/- IL4Ra-/-(new)

tag: cell line


title: Unstimulated B-CLL repl 9

description: Biological replicate 9 of 9

source_name: unstimulated purified cell of  CLL


title: Vac__day 7_rep03

source_name: Vaccine_day 7_rep03


title: Unstimulated B-CLL repl 7

description: Biological replicate 7 of 9


title: Unstimulated B-CLL repl 8

description: Biological replicate 8 of 9


title: CPG-stimulated B-CLL repl 1

description: Biological replicate 1 of 9


title: 5717 balb/c -> balb rag2-/- IL4Ra-/- (new)


title: 5718 B10D2 -> balb rag2-/- IL14Ra-/- (new)


title: Unstimulated B-CLL repl 6

description: Biological replicate 6 of 9


title: Vac__baseline_rep04


title: SCG_BMP_6h_rep3

description:
08A-11H1A_BMP6h3_164PL
Microarray processing batch 2

source_name: SCG cultured neurons,+ BMP7, 6h

value: +BMP7, 6h


title: SCG_BMP_24h_rep1

description:
03A-11H1A_BMP241_164PL
Microarray processing batch 1


title: SCG_BMP_24h_rep3

description:
09A-11H1A_BMP243_164PL
Microarray processing batch 2


title: eWAT VP16-1

description: Mice overexpressing reverse tetracycline-transactivator (rtTA) exhibited all four sequelae of metabolic syndrome (visceral obesity, insulin resistance, dyslipidemia, and hypertension), a pro-inflammatory state and marked hepatic steatosis. Gene expression profiling of the adipose tissue, muscle and liver revealed changes in gene expression of key factors involved in lipid metabolism, insulin resistance, and inflammation.

value: eWAT

value: WT

value: FVB

value: rtTA transgenic


title: eWAT VP16-3


title: eWAT VP16-2


title: Vac__baseline_rep03


title: SCG_control_24h_rep3

description:
07A-11H1A_CONT3_164PL
Microarray processing batch 2

source_name: SCG cultured neurons, control, 24h

value: Control (culture media only)l, 24h


title: SCG_BMP_6h_rep1

description:
02A-11H1A_BMP6h1_164PL
Microarray processing batch 1


title: SCG_BMP_6h_rep2

description:
05A-11H1A_BMP6h2_164PL
Microarray processing batch 2


title: 5704 B10D2 -> balb rag2-/-  (new)


title: 5703  balb/c->balb rag2-/- (new)

source_name: balb/c->balb rag2-/-


title: 5702 balb/c ->balb rag2-/- (new)

source_name: balb/c ->balb rag2-/-


title: SCG_control_24h_rep2

description:
04A-11H1A_CONT2_164PL
Microarray processing batch 2

value: Control (culture media only), 24h


title: Unstimulated B-CLL repl 1

description: Biological replicate 1 of 9

source_name: reference


title: Vac__day 7_rep01

source_name: Vaccine_day 7_rep01


title: Vac__baseline_rep02


title: Unstimulated B-CLL repl 5

description: Biological replicate 5 of 9


title: Vac__baseline_rep01


title: Unstimulated B-CLL repl 2

description: Biological replicate 2 of 9


title: prostate cancer: 77

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

description: technical replicate of 77_NORM

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 18K human unique genes and transcripts (Human 1A Glass Oligo Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the pattern file. Data processing and normalization were performed using the Agilent Human 22k platform-specific error model. Replicated expression profiles were combined to form log10 expression ratios to measure the modulation in the sample compared to the reference.

source_name: prostate cancer

label_protocol: RNA isolated from each tissue and from a commercial pool of RNA from organ donor healthy prostates (Becton Dickinson) was amplified by means of the Amino Allyl MessageAmp I aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) and total RNA was isolated by using TriReagent (Sigma Aldrich). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

tag: disease

value: prostate cancer

tag: tag type

tag: stage

tag: gleason grade

tag: reference


title: SCG_control_24h_rep1

description:
01A-11H1A_CONT1_164PL
Microarray processing batch 1

tag: strain


title: Severe Influenza_day 5_patient D

source_name: Severe Influenza_day 5_patient D


title: Severe Influenza_day 3_patient D

source_name: Severe Influenza_day 3_patient D


title: 5703 balb/c -> balb rag2-/-  (new), replicate 1

source_name: Universal Mouse Reference


title: bovine_stroma_rep6

city: East Lansing

first: Heather

last: Dover

state: MI

address: B290 Anthony Hall

department: Animal Science

institute: Michigan State University

hyb_protocol: Gene chips were hybridized in an Affymetrix 640 Hybridization oven at 45°C for 16 hours with 60rpm rotation.  After hybridization, gene chips were washed according to Affymetrix protocol on a Fluidics station using non-stringent (6xSSPE, 0.01% Tween 20, 0.005% antifoam) and stringent  (100mM MES, 0.1M NaCl, 0.01% Tween20) wash buffers.  Arrays were stained using SAPE stain and antibody solutions.  SAPE contains 2ug/ul BSA, 10ug/ml streptavidin Phycoerythrin (SAPE) in 100mM MES, 1M NaCl, 0.05% Tween 20 and 0.005% antifoam.  The antibody solution contains:  2mg/ml BSA, 0.1mg/ml goat IgG , 3ug/ml biotinylated anti-streptavidin antibodies in 100mB MES, 1M NaCl, 0.05% Tween 20 and 0.005% antifoam.

scan_protocol: Genechips were then scanned using an Affymetrix Genearray scanner GSC3000, with 7G upgrade.  The efficiency of amplification and hybridization were assessed by incorporating Affymetrix Poly-A RNA and Hybridization controls with every sample.

data_processing: Gene expression analysis was performed using BioConductor version 2.0 software.  Data preprocessing was performed using the RMA method as implemented in the BioConductor package and using updated probe set mappings such that a single probe set describes each gene.  Differential expression analysis was tested using moderated t-tests from gene-specific linear mixed model analysis as implemented in the MAANOVA package.

organism: Bos taurus

source_name: mammary gland, intralobular stroma

label_protocol: Target preparation was accomplished using NuGen WT Ovation Pico Technology following manufacturer protocol to generate products for the Bovine Affymetrix GeneChip.

extract_protocol: Laser capture microdissection (LCM) and isolation of total RNA.Serial tissue sections (7 mm) were prepared from OCT preserved tissue with a cryostat microtome using RNase-free techniques and stored at -80°C until use (less than 8 weeks).  On day of LCM, tissue sections were fixed and stained in In Situ Hybridization Pap Jars (Evergreen Scientific, Los Angeles, CA) using the Histogene Kit (Molecular Devices, Sunnyvale, CA) following manufacturer’s directions and left in xylene until LCM to ensure tissue was dehydrated. Populations of epithelial cells and intralobular stromal tissue were isolated by LCM using an Arcturus PixCell IIe LCM system (Arcturus Engineering now Molecular Devices) with CapSure LCM Transfer Film (Molecular Devices) according to manufacturer’s protocol.   Tissue captured onto transfer film was immediately immersed in 50 ml of isolation buffer from Acturus’ Picopure kit (Molecular Devices), and total RNA was isolated and purified by pooling lysates from several slides of the same samples following manufacturer’s protocol for laser captured frozen tissue.  Recovered RNA was subsequently analyzed using a Bioanalyzer 2100 (Agilent Inc; Palo Alto, CA) to determine quality and quantity by use of the Picochip and multiple standards.

treatment_protocol: Biopsied tissue was immediately placed in cold media (Waymouth’s Media 752/1; Sigma, St Louis, MO; with 50 µg gentamicin per ml, Invitrogen, Carlsbad, CA; and 100 U penicillin  – 100 µg streptomycin per ml, Sigma) and transported to the lab.  Biopsied tissue was washed three times in phosphate-buffered-saline (PBS) containing; 100 U penicillin – 100 µg streptomycin per ml (Sigma, St Louis, MO), and 1.5 µg Amphotericin-B per ml (Invitrogen) and cut into 0.5 cm3 explants. Explants were placed on siliconized lens paper, and cultured in a humidified chamber (5% CO2, 50% O2) at 37C for 2 h in Waymouth’s media supplemented with 5 mg/ml Insulin (Sigma), 0.1 mg/ml Hydrocortisone (Sigma) and 50 μM 5-bromo 2-deoxyuridine (BrdU; COMPANY).  The tissue was embedded in Tissue Tek OCT cryostat embedding compound (Ames Co, Division of Miles Laboratory, Elkhart, ID), snap frozen in liquid nitrogen and stored at -80°C for laser capture microdissection.

tag: pregnancy stage

value: 3 weeks prepartum

tag: milking status

value: dry

tag: latation number


title: 5702 balb/c -> balb rag2-/-  (new), replicate1

source_name: balb/c -> balb rag2-/-


title: Unstimulated B-CLL repl 3

description: Biological replicate 3 of 9


title: Vac__day 7_rep02

source_name: Vaccine_day 7_rep02


title: 5702 balb/c -> balb rag2-/-  (new), replicate 2


title: 5701 B10.D2->balb rag2-/- (new)


title: bovine_epithelia_rep6

source_name: mammary gland, intralobular epithelial cells


title: Severe Influenza_day 4_patient D

source_name: Severe Influenza_day 4_patient D


title: bovine_stroma_rep5


title: prostate cancer: 76

description: technical replicate of 76_NORM

tag: age

value: commercial pool of RNA from organ donor healthy prostates (Becton Dickinson)


title: prostate cancer: 75

description: technical replicate of 75_NORM

source_name: commercial pool of RNA from organ donor healthy prostates


title: 5700 balb/c -> balb rag2-/-  (new)


title: Severe Influenza_day 2_patient D

source_name: Severe Influenza_day 2_patient D

value: Paxgene Whole Blood RNA Samples


title: prostate cancer: 73

description: technical replicate of 73_NORM


title: Severe Influenza_day 1_patient D

source_name: Severe Influenza_day 1_patient D


title: prostate cancer: 74

description: technical replicate of 74_NORM


title: 4534 B10.D2 -> balb rag2-/- IL4Ra-/- (new)


title: Severe Influenza_day 5_patient C

source_name: Severe Influenza_day 5_patient C


title: bovine_stroma_rep4


title: bovine_epithelia_rep5


title: prostate cancer: 71

description: technical replicate of 71_NORM


title: Unstimulated B-CLL repl 4

description: Biological replicate 4 of 9

source_name: unstimulated purified cell of  CLL

value: B-CLL

tag: sample origin


title: prostate cancer: 72

description: technical replicate of 72_NORM


title: Severe Influenza_day 4_patient C

source_name: Severe Influenza_day 4_patient C

tag: tissue


title: 4533 B10.D2 -> balb rag2-/- IL4Ra/- (new)

source_name: B10.D2 -> balb rag2-/- IL4Ra/-


title: 4535 balb/c ->balb rag2-/- IL4Ra-/-(new)

source_name: balb/c ->balb rag2-/- IL4Ra-/-


title: bovine_epithelia_rep3


title: bovine_epithelia_rep4


title: MT transgenic ventral prostrate 3

city: Boston

first: Sang Hyun

last: Lee

state: MA

address: 44 Binney Street, SM970

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Gene expression data

hyb_protocol: Conducted at DFCI Microarray core facility. Affymetrix standard protocol

scan_protocol: Conducted at DFCI Microarray core facility. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: The gene expression cell files (.CEL) were normalized with the RMA method implemented in the BRB Array Tools (developed by Dr. Richard Simon and the BRB-ArrayTools Development Team).

source_name: Transgenic (polyoma virus middle T antigen)

extract_protocol: Trizol extraction and cleaned with RNeasy miniprep kit (Qiagen)

value: male

value: 8 weeks

value: ventral prostate


title: Severe Influenza_day 3_patient C

source_name: Severe Influenza_day 3_patient C


title: MT transgenic ventral prostrate 2

description: Gene expression data

label_protocol: Conducted at DFCI Microarray core facility. Affymetrix standard protocol


title: bovine_stroma_rep3


title: MT transgenic ventral prostrate 4

description: Gene expression data


title: bovine_stroma_rep2


title: Severe Influenza_day 2_patient C

source_name: Severe Influenza_day 2_patient C


title: liver_30mpk_rep5

city: Groton

first: William

last: Esler

state: CT

address: Eastern Point Road

institute: Pfizer

description: animals were gavaged daily with treatment

hyb_protocol: The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual Rat Expression Array 230 2.0 chip (a.k.a rat2302) GeneChip®.  The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations.  This was performed by the vendor Gene Logic Incorporated.

scan_protocol: The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.

data_processing: All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).

source_name: liver of high fat fed rats treated 6 weeks with PF-04923503 30mpk

label_protocol: cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix.  cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix.  cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively.  The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel.  This was performed by the vendor Gene Logic Incorporated.

growth_protocol: 7 week old Sprague dawley rats were fed a high fat content diet (59% kCal diet from fat; Dyets Inc. 112245) during the coures of the experiment

extract_protocol: Total RNA was isolated from frozen rat liver using standard Qiagen RNeasy kit by the vendor Gene Logic Incorporated.

treatment_protocol: Rats were gavaged daily for six weeks with vehicle (0.5% methylcellulose), 10mg/kg, or 30mg/kg. Animals were euthanized with CO2 at the end of the study. Liver was collected, frozen in liquid nitrogen, and stored at -80C.

value: Sprague dawley rat-Charles River

tag: age at start

value: 7 weeks

value: liver

tag: diet

value: high fat (Dyets 112245)

tag: animal weight at start

value: 6 weeks daily vehicle PF-04923503 30mpk


title: bovine_stroma_rep1

source_name: mammary gland, intralobular stroma


title: liver_30mpk_rep4

tag: gender

tag: treatment


title: bovine_epithelia_rep2


title: Severe Influenza_day 5_patient B

source_name: Severe Influenza_day 5_patient B


title: Severe Influenza_day 4_patient B

source_name: Severe Influenza_day 4_patient B


title: Severe Influenza_day 3_patient B

source_name: Severe Influenza_day 3_patient B


title: liver_30mpk_rep3


title: Severe Influenza_day 2_patient B

source_name: Severe Influenza_day 2_patient B


title: bovine_epithelia_rep1

source_name: mammary gland, intralobular epithelial cells


title: Wild type ventral prostrate 4

description: Gene expression data

source_name: Wild type

value: FVB


title: liver_10mpk_rep5

source_name: liver of high fat fed rats treated 6 weeks with PF-04923503 10mpk

value: 6 weeks daily vehicle PF-04923503 10mpk


title: Wild type ventral prostrate 3

description: Gene expression data


title: Wild type ventral prostrate 2

description: Gene expression data


title: Severe Influenza_day 1_patient C

source_name: Severe Influenza_day 1_patient C


title: liver_30mpk_rep2


title: MT transgenic ventral prostrate 1

description: Gene expression data


title: Severe Influenza_day 4_patient A

source_name: Severe Influenza_day 4_patient A


title: liver_10mpk_rep4


title: liver_10mpk_rep3


title: Severe Influenza_day 2_patient A

source_name: Severe Influenza_day 2_patient A


title: Wild type ventral prostrate 1

description: Gene expression data


title: Severe Influenza_day 3_patient A

source_name: Severe Influenza_day 3_patient A


title: Severe Influenza_day 1_patient B

source_name: Severe Influenza_day 1_patient B


title: liver_vehicle_rep5

source_name: liver of high fat fed rats treated 6 weeks with vehicle 0.5% methylcellulose

value: 6 weeks daily vehicle 0.5% methylcellulose


title: liver_10mpk_rep1


title: liver_30mpk_rep1


title: liver_10mpk_rep2


title: bacterial pneumonia_day 2_patient F

source_name: bacterial pneumonia_day 2_patient F


title: liver_vehicle_rep4


title: bacterial pneumonia_day 3_patient F

source_name: bacterial pneumonia_day 3_patient F


title: Severe Influenza_day 1_patient A

source_name: Severe Influenza_day 1_patient A


title: liver_vehicle_rep3


title: liver_vehicle_rep1


title: NA18576 rep 3 genotyping at TCAG (Mapping250K_Nsp)

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and CHP files (generated by Affymetrix Genotyping Console using the Birdseed algorithm) were used to call copy number variation by Partek GS, Genotyping Console v.3.0.2, BirdSuite v.1.5.2 and iPattern
Genotype Call (SNP call): AA, AB, BB, and NoCall

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: Female

tag: cell type

value: lymphoblastoid cell lines

tag: cell line

tag: genotyping center

value: TCAG


title: bacterial pneumonia_day 1_patient F

source_name: bacterial pneumonia_day 1_patient F


title: liver_vehicle_rep2


title: NA15510 rep 3 genotyping at TCAG (Mapping250K_Nsp)


title: NA15510 rep 2 genotyping at TCAG (Mapping250K_Nsp)


title: NA10851 rep 3 genotyping at TCAG (Mapping250K_Nsp)

value: Male


title: NA18980 rep 2 genotyping at TCAG (Mapping250K_Nsp)


title: bacterial pneumonia_day 3_patient E

source_name: bacterial pneumonia_day 3_patient E

value: Paxgene Whole Blood RNA Samples


title: NA12239 rep 3 genotyping at TCAG (Mapping250K_Nsp)


title: P. falciparum-thiostrepton-treated-2

city: London

first: Sarah

last: Tarr

address: Gower Street

department: ISMB

institute: UCL

description: Gene expression data from LD70 thiostrepton-treated Plasmodium falciparum

hyb_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).

data_processing: Raw CEL files were imported into Bioconductor (Gentleman et al., 2004) for data analysis.  Microarrays were analysed for RNA degradation prior to normalisation.  Non-Plasmodium probesets were removed using the altcdfenvs package (Gautier et al., 2004) and microarray data were normalised using GCRMA (Wu et al., 2004).  Differential gene expression was analysed using Linear Models for Microarray Analysis (LIMMA) (Smyth, 2004).

label: Biotin

organism: Plasmodium falciparum

source_name: P. falciparum, treated

growth_protocol: Blood stage P. falciparum 3D7 was maintained in continuous culture in vitro at 37 ºC using the candle-jar method.  Cultures were maintained in citrated human blood at 2 % hematocrit with complete culture media (RPMI 1640 + L-Glutamine (Gibco) with 5 % w/v AlbuMAX I (Invitrogen), 50 μg.ml-1 hypoxanthine, 25 mM HEPES (Gibco) and 25 μg.ml-1 gentamycin (Sigma), pH of 7.6).  Parasitaemia was assessed by thin blood smears stained with Giemsa (Sigma).  Percentage infection of red blood cells was determined by cell counts under an oil immersion light microscope.  Synchronous parasites were obtained by the Stockholm sorbitol method on two consecutive life cycles

extract_protocol: RNA was harvested using Trizol (Invitrogen) as described (Kyes, 2004).  RNA concentration and purity were determined using a NanoDrop (Thermo) and RNA integrity was tested using an Agilent Bioanalyzer (Cambridge Genomic Services, Department of Pathology)

treatment_protocol: Triplicate 15 ml cultures containing synchronous, ring stage parasites at 5 % parasitaemia were treated with 2 uM thiostrepton in DMSO (or 1/2000 vol. DMSO for controls) for 24 hours.

value: Thiostrepton


title: P. falciparum-thiostrepton-treated-1

scan_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).


title: NA18576 rep 2 genotyping at TCAG (Mapping250K_Nsp)


title: bacterial pneumonia_day 2_patient E

source_name: bacterial pneumonia_day 2_patient E


title: P. falciparum-thiostrepton-treated-3

label_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).


title: bacterial pneumonia_day 1_patient E

source_name: bacterial pneumonia_day 1_patient E


title: P. falciparum-dmso-control-3

description: Gene expression data from untreated Plasmodium falciprum

source_name: P. falciparum, control

value: DMSO


title: bacterial pneumonia_day 4_patient E

source_name: bacterial pneumonia_day 4_patient E


title: Saccharomyces uvarum CBS 7001 rep2

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

hyb_protocol: Winzeler et al,  Genetics 2003

scan_protocol: Standard Affymetrix protocol

data_processing: Background of the different CEL files has been calculated and subtracted with MAS5. Then the pm signals of each probe were extracted. Then the signal ratios were normalized across all arrays, and log2 ratio calculated between the sample array (IFO1948) or the signal of two sample array (CBS380) with the average of the signal of the two ref arrays (CBS7001). GSE28225_intensities.txt and GSE28225_logratios.txt files are linked to the Series record. The coordinates of each probe on S288C genome are included.

organism: Saccharomyces uvarum

source_name: Saccharomyces uvarum CBS 7001

label_protocol: Winzeler et al,  Genetics 2003

growth_protocol: Overnight YPD shaken culture 28°

extract_protocol: DNA extraction according to Legras et al. 2003 FEMS microbiol letters.


title: bacterial pneumonia_day 5_patient E

source_name: bacterial pneumonia_day 5_patient E


title: P. falciparum-dmso-control-2


title: bacterial pneumonia_day 5_patient D

source_name: bacterial pneumonia_day 5_patient D


title: NA12239 rep 2 genotyping at TCAG (Mapping250K_Nsp)


title: NA18980 rep1 genotyping at TCAG (Mapping250K_Nsp)


title: bacterial pneumonia_day 4_patient D

source_name: bacterial pneumonia_day 4_patient D


title: NA15510 rep1 genotyping at TCAG (Mapping250K_Nsp)


title: Saccharomyces bayanus IFO1948

organism: Saccharomyces bayanus

source_name: Saccharomyces bayanus IFO1948


title: NA18576 rep1 genotyping at TCAG (Mapping250K_Nsp)


title: bacterial pneumonia_day 3_patient D

source_name: bacterial pneumonia_day 3_patient D


title: NA10851 rep 2 genotyping at TCAG (Mapping250K_Nsp)


title: Saccharomyces bayanus CBS380 rep1

source_name: Saccharomyces bayanus CBS380


title: bacterial pneumonia_day 2_patient D

source_name: bacterial pneumonia_day 2_patient D


title: NA12239 rep1 genotyping at TCAG (Mapping250K_Nsp)


title: P. falciparum-dmso-control-1


title: NA18576 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: NA18980 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: NA10851 rep1 genotyping at TCAG (Mapping250K_Nsp)


title: Saccharomyces bayanus CBS380 rep2


title: Yeast_skp1-25_35°C

city: Los Angeles

first: Mariam

last: Aghajan

address: 650 Charles E. Young Drive South, CHS 23-231

institute: UCLA

description: growth in YPDA media

hyb_protocol: Hybridization of labeled cRNA probes to Affymetrix GeneChip Yeast Genome 2.0 arrays (www.affymetrix.com) was done according to manufacturer’s specifications.

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 and raw data generated using the GeneChip Operating System GCOSv1.4.

data_processing: Gene expression data were normalized in dChip (www.dchip.org). Model-based expression indices (MBEIs) were calculated and log2 transformed. We have only shown the data pertaining to the Saccharomyces cerevisiae probes and had deleted the data pertaining to Saccharomyces pombe since that data is irrelevant to our study, which only uses S. cerevisiae. We do show ALL Saccharomyces cerevisiae probe data.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae, skp1-25, 35°C

label_protocol: Biotin-labeled cRNA probes were generated from total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Yeast cells were grown to mid-log phase (0.5–2 x 107 cells/ml) at 25°C (RT), 300 rpm, in YPDA medium before selected samples were subjected to heat-inactivation for 1 hour at 35°C.

extract_protocol: Total RNA was isolated using the RiboPure™-Yeast kit (Ambion) and RNA quality was checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Following 1 hour incubation at either permissive (RT) or non-permissive (35°C) temperature, cells were harvested and flash frozen in liquid nitrogen.


title: bacterial pneumonia_day 4_patient C

source_name: bacterial pneumonia_day 4_patient C


title: bacterial pneumonia_day 5_patient C

source_name: bacterial pneumonia_day 5_patient C


title: NA18517 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_skp1-25_RT

description: growth in YPDA media

source_name: S. cerevisiae, skp1-25, RT


title: NA18980 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: bacterial pneumonia_day 3_patient C

source_name: bacterial pneumonia_day 3_patient C


title: Saccharomyces uvarum CBS 7001 rep1


title: bacterial pneumonia_day 1_patient D

source_name: bacterial pneumonia_day 1_patient D


title: NA15510 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: NA12239 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: NA10851 rep3 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_skp1-11_RT

description: growth in YPDA media

source_name: S. cerevisiae, skp1-11, RT


title: NA18517 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: NA18576 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_skp1-11_35°C

description: growth in YPDA media

source_name: S. cerevisiae, skp1-11, 35°C


title: Yeast_cdc4-3_35°C

description: growth in YPDA media

source_name: S. cerevisiae, cdc4-3, 35°C


title: Yeast_cdc4-3_RT

description: growth in YPDA media

source_name: S. cerevisiae, cdc4-3, RT


title: bacterial pneumonia_day 3_patient B

source_name: bacterial pneumonia_day 3_patient B


title: bacterial pneumonia_day 2_patient C

source_name: bacterial pneumonia_day 2_patient C


title: AOM/DSS-induced colon tumor

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: MeDIP-CGI microarray analysis of AOM/DSS-induced colon tumors

hyb_protocol: Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.

scan_protocol: Arrays were washed and scanned immediately with Agilent microarray scanner G2565BA. Images were quantified using Agilent Feature Extraction 9.1 Software.

data_processing: Arrays were processed using Agilent Feature Extraction 9.1 software and normalized (background subtraction and interarray median normalization) using Agilent Chip Analytics 1.3 software.

source_name: MeDIP of AOM/DSS-induced colon tumor

label_protocol: Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

growth_protocol: A pool of two AOM/DSS-induced colon tumors in BALB/c mice and a pool of two normal colonic epithelial cell samples obtained from untreated BALB/c mice by the crypt isolation technique were used.  Samples were stored at -80 ˚C.

extract_protocol: High molecular weight DNA was extracted by the phenol/chloroform method.

tag: dna treatment

value: Sonicated and immunoprecipitated with anti-5-methyl cytidine antibody (Diagenode, Liége, Belgium)

value: BALB/c

source_name: AOM/DSS-induced colon tumors

value: Sonicated


title: bacterial pneumonia_day 1_patient C

source_name: bacterial pneumonia_day 1_patient C


title: normal colonic epithelial cell sample

description: MeDIP-CGI microarray analysis of normal colonic epithelial cell samples obtained from untreated BALB/c mice

source_name: MeDIP of normal colonic epithelial cell sample

value: A pool of two normal colonic epithelial cell samples obtained by the crypt isolation technique

source_name: normal colonic epithelial cell samples


title: Yeast_cdc34-3_RT

description: growth in YPDA media

source_name: S. cerevisiae, cdc34-3, RT


title: bacterial pneumonia_day 2_patient B

source_name: bacterial pneumonia_day 2_patient B


title: Yeast_cdc34-3_35°C

description: growth in YPDA media

source_name: S. cerevisiae, cdc34-3, 35°C


title: bacterial pneumonia_day 1_patient B

source_name: bacterial pneumonia_day 1_patient B


title: NA18980 rep1 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_cdc53-1_35°C

description: growth in YPDA media

source_name: S. cerevisiae, cdc53-1, 35°C


title: NA12239 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: bacterial pneumonia_day 5_patient A

source_name: bacterial pneumonia_day 5_patient A


title: NA15510 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: NA12239 rep1 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_met30-6_35°C_rep2

description: growth in YPDA media

source_name: S. cerevisiae, met30-6, 35°C


title: bacterial pneumonia_day 4_patient A

source_name: bacterial pneumonia_day 4_patient A


title: bacterial pneumonia_day 3_patient A

source_name: bacterial pneumonia_day 3_patient A


title: NA10851 rep2 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_met30-6_35°C_rep1

description: growth in YPDA media


title: Yeast_cdc53-1_RT

description: growth in YPDA media

source_name: S. cerevisiae, cdc53-1, RT


title: bacterial pneumonia_day 2_patient A

source_name: bacterial pneumonia_day 2_patient A


title: Yeast_met30-6_RT_rep2

description: growth in YPDA media

source_name: S. cerevisiae, met30-6, RT


title: NA18517 rep1 genotyping at TCAG (GenomeWideSNP_6)


title: Bj110_DMSO vs. P6_Rep 3_Dyeswap

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 1.5-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Treatment (P6)_Rep 3

label_protocol: 30 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Five micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

value: USDA 110, Medium:Arabinose-Gluconate, Growth condition:aerobic, Treatment:Pterocarpan 6 (P6) (20 uM)_24 h_without shaking

source_name: Control (DMSO)_Rep 3

value: USDA 110, Medium:Arabinose-Gluconate, Growth condition:aerobic, Treatment:solvent (DMSO)_24 h_without shaking


title: NA10851 rep1 genotyping at TCAG (GenomeWideSNP_6)

city: Toronto

first: Stephen

last: Scherer

address: 686 Bay Street

institute: The Hospital for Sick Children


title: NA18517 rep3 genotyping at WTSI (GenomeWideSNP_6)

value: WTSI


title: bacterial pneumonia_day 1_patient A

city: Kingswood

first: Grant

last: Parnell

address: Nepean Hospital

institute: University of Sydney

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalised using cubic spline algorithm in Illumina BeadStudio V2.0

source_name: bacterial pneumonia_day 1_patient A

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit kit for Illumina arrays

extract_protocol: RNA was extracted using PAXgene RNA


title: NA15510 rep1 genotyping at TCAG (GenomeWideSNP_6)


title: NA18576 rep1 genotyping at TCAG (GenomeWideSNP_6)


title: Yeast_met30-6_RT_rep1

description: growth in YPDA media


title: Bj110_DMSO vs. P6_Rep 3


title: NA12239 rep3 genotyping at WTSI (GenomeWideSNP_6)


title: Bj110_DMSO vs. P6_Rep 2_Dyeswap

source_name: Treatment (P6)_Rep 2

source_name: Control (DMSO)_Rep 2


title: Yeast_PY1_35°C_rep2

description: growth in YPDA media

source_name: S. cerevisiae, PY1, 35°C


title: Yeast_PY1_35°C_rep1

description: growth in YPDA media


title: 13969701 - 8RV196 vs. 8RV319

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description: To provide quantitative geneticists studying natural variation in our RIL populations with information and resources necessary to speed up QTL cloning and candidate genes identification. This articulates around the creation of two major resources and their integration into databases to make the information accessible to users: A. Whole transcriptome survey, B. Production of complementary material.

hyb_protocol: 8RV319 Cy5 / 8RV196 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

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

growth_protocol: aerial - Plants grown in Greenhouse, where temperatures were 20°C/day and 15°C/night. Also in long day conditions (16hr days)with a complement of artificial light 105µE/m²/sec when necessary.

extract_protocol: 8RV319:5ug. (Qiagen RNeasy)

treatment_protocol: no treatment

tag: developmental stage

value: Boyes 1.06 (Boyes et al. Plant Cell 2001)

tag: population

value: ril cvi x col-0

extract_protocol: 8RV196:5ug. (Qiagen RNeasy)


title: NA15510 rep3 genotyping at WTSI (GenomeWideSNP_6)


title: NA18576 rep3 genotyping at WTSI (GenomeWideSNP_6)


title: Yeast_PY1_RT_rep2

description: growth in YPDA media

source_name: S. cerevisiae, PY1, RT

tag: strain


title: Bj110_DMSO vs. P6_Rep 2


title: NA18517 rep2 genotyping at WTSI (GenomeWideSNP_6)


title: NA18517 rep 3 genotyping at TCAG (HumanOmni2.5-Quad) rev 2

hyb_protocol: Standard Illumina protocol for HumanOmni2.5-Quad Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 1M platform we used QuantiSNP, iPattern, PennCNV, cnvPartition and Partek
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.


title: NA10851 rep3 genotyping at WTSI (GenomeWideSNP_6)


title: Bj110_DMSO vs. P6_Rep 1_Dyeswap

source_name: Treatment (P6)_Rep 1

source_name: Control (DMSO)_Rep 1


title: NA18517 rep 2 genotyping at TCAG (HumanOmni2.5-Quad) rev 2

scan_protocol: Standard Illumina protocol for HumanOmni2.5-Quad Beadchip


title: NA18980 rep2 genotyping at WTSI (GenomeWideSNP_6)


title: Yeast_PY1_RT_rep1

description: growth in YPDA media


title: NA18980 rep3 genotyping at WTSI (GenomeWideSNP_6)


title: NA12239 rep 2 genotyping at TCAG (HumanOmni2.5-Quad) rev 2

label_protocol: Standard Illumina protocol for HumanOmni2.5-Quad Beadchip


title: W303 1A, biological rep. 3

status: Public on Jun 29 2011

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing:
Microarray data analysis was performed using DNA-Chip Analyzer. PM probes, invariant set normalization, and model-based expression were used in this step. Outliers were treated as missing data. Genes showing at least 1.5-fold expression change compared to its isogenic wild-type strain were considered as altered (parameters: absolute difference between signal in mutant vs wild-type strain > 100; difference p-value > 0.05).
Expression values obtenained using DNA-Chip Analyzer (www.dchip.org; Li & Wong 2001).

source_name: Wild type W303 1A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium

extract_protocol: Total RNA were isolated with the RNeasy Midi kit (QIAGEN)

value: wild type strain W303-1A

tag: genotype/variation


title: W303 1A, biological rep. 2


title: W303 1A, biological rep. 1


title: NA18576 rep 3 genotyping at TCAG (HumanOmni2.5-Quad) rev 2

value: Female


title: NA18576 rep2 genotyping at WTSI (GenomeWideSNP_6)

value: lymphoblastoid cell lines


title: NA15510 rep 3 genotyping at TCAG (HumanOmni2.5-Quad) rev 2

value: TCAG


title: Bj110_DMSO vs. P6_Rep 1


title: tho2∆, biological rep. 2

source_name: Mutant tho2∆

value: deletion strain RK2-6C


title: tho2∆, biological rep. 1


title: sub2∆, biological rep. 2

source_name: Mutant sub2∆

value: deletion strain DLY23 sub2∆


title: hpr1∆, biological rep. 3

source_name: Mutant hpr1∆

value: deletion strain SChY58a


title: sub2∆, biological rep. 1


title: NA12239 rep2 genotyping at WTSI (GenomeWideSNP_6)


title: hpr1∆, biological rep. 2


title: Brassica rapa_Leaf_R500_Low P_Rep_2

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

institute: University of Western Australia

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Brassica 95k Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 018073_D_F_20071106) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. gProcessedSignal values within arrays were normalized to the 50th percentile. Normalized signal values for individual probes were standardized to the median signal value for the probe across all arrays.

organism: Brassica rapa

source_name: Leaf tissue from parent R500, Low P

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown from seed in individual pots (9cm x 9cm x 8cm; Desch Plantpak B.V., Waalwijk, NL) containing a moistened peat-based compost, under controlled-environment conditions. The potting mix consisted of 25% sand and 75% (v/v) compost (Shamrock medium grade sphagnum peat, Scotts UK, Bromford, UK). Unfertilised, the potting mix had an Olsen extractable P (Olsen et al., 1954) of 8 mg L-1.  The compost contained the following nutrients in sufficient amounts to prevent deficiencies as follows: NH4NO3 (0.4 g L-1), KNO3 (0.75 g L-1), ground limestone 2.25 g L-1, magnesium limestone 2.25 g L-1, and a fritted trace elements mixture containing B, Cu, Fe, Mn, Mo and Zn (WM255, Fargro Ltd, Littlehampton, UK) at 0.4 g L-1. Potting mixes were made in bulk using a paddle mixer (Model 156, St Moritz, Spalding, UK). The CE was a walk-in high specification growth room (Weiss-Gallenkamp, Loughborough, UK), set to a 16 h photoperiod using metal halide lamps, giving a photon flux density between 400 and 700 nm (PAR) of 250 µmol photons m-2 s-1 at plant height. The day/night settings for temperature and relative humidity were 18/15ºC and 76/71%.

extract_protocol: All plants were harvested 21 days after sowing. For each line at each treatment, fully-expanded leaves from 3 plants (6-leaf stage, not flowering) were sampled, snap-frozen in liquid nitrogen, freeze-dried, ground, and stored at -80°C. RNA was extracted from leaf samples using a modified TRIzol extraction method (Hammond et al., 2006). Extracted total RNA was purified using the ‘RNA Cleanup’ protocol for RNeasy columns with on-column DNase digestion to remove residual genomic DNA (Qiagen, Crawley, UK). Samples of total RNA were checked for integrity and quality using an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P were produced by incorporating 0.075 g and 0.45 g of sieved (mesh 500 µm) single superphosphate (SSP, 7% P) per litre of compost, and used to induce a growth response based on previous studies with Brassica (Broadley et al., 2008, 2010; Hammond et al., 2009; White et al., 2010).

value: leaf

tag: parent

value: Low P


title: Brassica rapa_Leaf_BraIRRI211_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI211, Low P

tag: ril


title: hpr1∆, biological rep. 1


title: NA15510 rep2 genotyping at WTSI (GenomeWideSNP_6)


title: NA18980 rep 3 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI341_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI341, Optimal P

value: Optimal P


title: NA10851 rep2 genotyping at WTSI (GenomeWideSNP_6)

value: Male


title: NA15510 rep 2 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI018_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI018, Optimal P


title: Brassica rapa_Leaf_BraIRRI171_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI171, Low P


title: Brassica rapa_Leaf_BraIRRI041_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI041, Optimal P


title: Brassica rapa_Leaf_BraIRRI198_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI198, Optimal P


title: NA18517 rep1 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI190_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI190, Optimal P


title: Brassica rapa_Leaf_BraIRRI222_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI222, Low P


title: NA18576 rep 2 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI223_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI223, Low P


title: Brassica rapa_Leaf_BraIRRI183_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI183, Optimal P


title: Brassica rapa_Leaf_BraIRRI124_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI124, Low P


title: Brassica rapa_Leaf_BraIRRI373_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI373, Optimal P


title: Brassica rapa_Leaf_BraIRRI002_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI002, Low P


title: Brassica rapa_Leaf_BraIRRI016_Optimal P_Rep_2-2

source_name: Leaf tissue from RIL BraIRRI016, Optimal P


title: Brassica rapa_Leaf_BraIRRI021_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI021, Optimal P


title: Brassica rapa_Leaf_BraIRRI325_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI325, Low P


title: Brassica rapa_Leaf_BraIRRI030_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI030, Low P


title: Brassica rapa_Leaf_BraIRRI332_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI332, Low P


title: Brassica rapa_Leaf_BraIRRI250_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI250, Optimal P


title: Brassica rapa_Leaf_BraIRRI009_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI009, Low P


title: Brassica rapa_Leaf_R500_Optimal P_Rep_2

source_name: Leaf tissue from parent R500, Optimal P


title: NA18980 rep 2 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: NA18517 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: NA18980 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: Brassica rapa_Leaf_BraIRRI337_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI337, Low P


title: Brassica rapa_Leaf_BraIRRI042_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI042, Optimal P


title: Brassica rapa_Leaf_BraIRRI204_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI204, Optimal P


title: Brassica rapa_Leaf_BraIRRI282_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI282, Optimal P


title: Brassica rapa_Leaf_BraIRRI346_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI346, Low P


title: Brassica rapa_Leaf_BraIRRI154_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI154, Optimal P


title: Brassica rapa_Leaf_BraIRRI143_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI143, Low P


title: NA18576 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: Brassica rapa_Leaf_BraIRRI146_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI146, Low P


title: Brassica rapa_Leaf_BraIRRI288_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI288, Low P


title: Brassica rapa_Leaf_BraIRRI007_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI007, Low P


title: Brassica rapa_Leaf_BraIRRI229_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI229, Low P


title: Brassica rapa_Leaf_BraIRRI104_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI104, Optimal P


title: Brassica rapa_Leaf_BraIRRI380_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI380, Optimal P


title: Brassica rapa_Leaf_BraIRRI093_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI093, Low P


title: Brassica rapa_Leaf_BraIRRI232_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI232, Optimal P


title: NA12239 rep1 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI228_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI228, Optimal P


title: Brassica rapa_Leaf_BraIRRI103_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI103, Optimal P


title: Brassica rapa_Leaf_BraIRRI363_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI363, Optimal P


title: Brassica rapa_Leaf_BraIRRI069_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI069, Optimal P


title: Brassica rapa_Leaf_BraIRRI080_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI080, Optimal P


title: Brassica rapa_Leaf_BraIRRI147_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI147, Optimal P


title: Brassica rapa_Leaf_BraIRRI154_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI154, Low P


title: Brassica rapa_Leaf_BraIRRI213_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI213, Optimal P


title: Brassica rapa_Leaf_BraIRRI176_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI176, Optimal P


title: Brassica rapa_Leaf_BraIRRI360_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI360, Optimal P


title: Brassica rapa_Leaf_BraIRRI277_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI277, Low P


title: Brassica rapa_Leaf_BraIRRI036_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI036, Low P


title: Brassica rapa_Leaf_BraIRRI204_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI204, Low P


title: Brassica rapa_Leaf_BraIRRI284_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI284, Optimal P


title: NA15510 rep1 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: NA15510 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: NA12239 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: Brassica rapa_Leaf_BraIRRI016_Low P_Rep_2-2

source_name: Leaf tissue from RIL BraIRRI016, Low P


title: NA18980 rep1 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI318_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI318, Low P


title: Brassica rapa_Leaf_BraIRRI199_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI199, Low P


title: Brassica rapa_Leaf_BraIRRI289_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI289, Optimal P


title: NA10851 rep1 genotyping at WTSI (GenomeWideSNP_6)


title: Brassica rapa_Leaf_BraIRRI025_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI025, Low P


title: Brassica rapa_Leaf_BraIRRI229_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI229, Optimal P


title: Brassica rapa_Leaf_BraIRRI288_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI288, Optimal P


title: Brassica rapa_Leaf_IMB211_Low P_Rep_2

source_name: Leaf tissue from parent IMB211, Low P


title: NA18576 rep1 genotyping at TCAG (HumanOmni2.5-Quad) rev 2


title: Brassica rapa_Leaf_BraIRRI115_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI115, Optimal P


title: Brassica rapa_Leaf_BraIRRI201_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI201, Low P


title: Brassica rapa_Leaf_BraIRRI248_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI248, Low P


title: Brassica rapa_Leaf_BraIRRI041_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI041, Low P


title: Brassica rapa_Leaf_BraIRRI171_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI171, Optimal P


title: Brassica rapa_Leaf_BraIRRI213_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI213, Low P


title: Brassica rapa_Leaf_BraIRRI242_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI242, Optimal P


title: Brassica rapa_Leaf_BraIRRI187_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI187, Optimal P


title: Brassica rapa_Leaf_IMB211_Optimal P_Rep_2

source_name: Leaf tissue from parent IMB211, Optimal P


title: Brassica rapa_Leaf_BraIRRI301_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI301, Optimal P


title: Brassica rapa_Leaf_BraIRRI016_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI016, Optimal P


title: Brassica rapa_Leaf_BraIRRI235_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI235, Optimal P


title: Brassica rapa_Leaf_BraIRRI143_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI143, Optimal P


title: Brassica rapa_Leaf_BraIRRI325_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI325, Optimal P


title: Brassica rapa_Leaf_BraIRRI089_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI089, Low P


title: Brassica rapa_Leaf_BraIRRI093_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI093, Optimal P


title: Brassica rapa_Leaf_BraIRRI234_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI234, Low P


title: Brassica rapa_Leaf_BraIRRI251_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI251, Low P


title: Brassica rapa_Leaf_BraIRRI235_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI235, Low P


title: Brassica rapa_Leaf_BraIRRI215_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI215, Optimal P


title: Brassica rapa_Leaf_BraIRRI234_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI234, Optimal P


title: Brassica rapa_Leaf_BraIRRI215_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI215, Low P


title: Brassica rapa_Leaf_BraIRRI332_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI332, Optimal P


title: Brassica rapa_Leaf_BraIRRI250_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI250, Low P


title: Brassica rapa_Leaf_BraIRRI341_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI341, Low P


title: Brassica rapa_Leaf_BraIRRI376_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI376, Low P


title: Brassica rapa_Leaf_BraIRRI182_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI182, Optimal P


title: Brassica rapa_Leaf_BraIRRI080_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI080, Low P


title: Brassica rapa_Leaf_BraIRRI329_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI329, Low P


title: Brassica rapa_Leaf_BraIRRI300_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI300, Optimal P


title: Brassica rapa_Leaf_BraIRRI060_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI060, Optimal P


title: Brassica rapa_Leaf_IMB211_Low P_Rep_1

source_name: Leaf tissue from parent IMB211, Low P


title: Brassica rapa_Leaf_BraIRRI232_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI232, Low P


title: Brassica rapa_Leaf_BraIRRI198_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI198, Low P


title: Brassica rapa_Leaf_BraIRRI187_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI187, Low P


title: Brassica rapa_Leaf_BraIRRI337_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI337, Optimal P


title: Brassica rapa_Leaf_BraIRRI284_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI284, Low P


title: Brassica rapa_Leaf_BraIRRI289_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI289, Low P


title: Brassica rapa_Leaf_BraIRRI255_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI255, Optimal P


title: Brassica rapa_Leaf_BraIRRI264_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI264, Low P


title: Brassica rapa_Leaf_BraIRRI150_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI150, Optimal P


title: Brassica rapa_Leaf_BraIRRI089_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI089, Optimal P


title: Brassica rapa_Leaf_BraIRRI376_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI376, Optimal P


title: Brassica rapa_Leaf_BraIRRI363_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI363, Low P


title: Brassica rapa_Leaf_BraIRRI146_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI146, Optimal P


title: Brassica rapa_Leaf_BraIRRI025_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI025, Optimal P


title: Brassica rapa_Leaf_BraIRRI147_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI147, Low P


title: Brassica rapa_Leaf_BraIRRI329_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI329, Optimal P


title: Brassica rapa_Leaf_BraIRRI069_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI069, Low P


title: Brassica rapa_Leaf_BraIRRI282_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI282, Low P


title: Brassica rapa_Leaf_BraIRRI300_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI300, Low P


title: Brassica rapa_Leaf_IMB211_Optimal P_Rep_1

source_name: Leaf tissue from parent IMB211, Optimal P


title: Brassica rapa_Leaf_BraIRRI242_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI242, Low P


title: Brassica rapa_Leaf_BraIRRI253_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI253, Optimal P


title: Brassica rapa_Leaf_BraIRRI016_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI016, Low P


title: Brassica rapa_Leaf_BraIRRI199_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI199, Optimal P


title: Brassica rapa_Leaf_BraIRRI065_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI065, Low P


title: Brassica rapa_Leaf_BraIRRI030_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI030, Optimal P


title: Brassica rapa_Leaf_BraIRRI264_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI264, Optimal P


title: Brassica rapa_Leaf_BraIRRI042_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI042, Low P


title: Brassica rapa_Leaf_BraIRRI201_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI201, Optimal P


title: Brassica rapa_Leaf_BraIRRI166_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI166, Low P


title: Brassica rapa_Leaf_BraIRRI060_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI060, Low P


title: Brassica rapa_Leaf_BraIRRI205_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI205, Low P


title: Brassica rapa_Leaf_BraIRRI018_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI018, Low P


title: Brassica rapa_Leaf_BraIRRI124_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI124, Optimal P


title: Brassica rapa_Leaf_BraIRRI251_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI251, Optimal P


title: Brassica rapa_Leaf_BraIRRI255_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI255, Low P


title: Brassica rapa_Leaf_BraIRRI248_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI248, Optimal P


title: Brassica rapa_Leaf_BraIRRI182_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI182, Low P


title: Brassica rapa_Leaf_BraIRRI211_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI211, Optimal P


title: Brassica rapa_Leaf_BraIRRI001_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI001, Optimal P


title: Brassica rapa_Leaf_BraIRRI166_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI166, Optimal P


title: Brassica rapa_Leaf_BraIRRI176_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI176, Low P


title: Brassica rapa_Leaf_BraIRRI373_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI373, Low P


title: Brassica rapa_Leaf_BraIRRI007_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI007, Optimal P


title: Brassica rapa_Leaf_BraIRRI104_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI104, Low P


title: Brassica rapa_Leaf_BraIRRI301_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI301, Low P


title: Brassica rapa_Leaf_BraIRRI001_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI001, Low P


title: Brassica rapa_Leaf_BraIRRI190_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI190, Low P


title: Brassica rapa_Leaf_BraIRRI360_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI360, Low P


title: Brassica rapa_Leaf_BraIRRI065_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI065, Optimal P


title: Brassica rapa_Leaf_BraIRRI002_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI002, Optimal P


title: Brassica rapa_Leaf_R500_Optimal P_Rep_3

source_name: Leaf tissue from parent R500, Optimal P


title: Brassica rapa_Leaf_BraIRRI346_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI346, Optimal P


title: Brassica rapa_Leaf_IMB211_Optimal P_Rep_3

source_name: Leaf tissue from parent IMB211, Optimal P


title: Brassica rapa_Leaf_BraIRRI222_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI222, Optimal P


title: Brassica rapa_Leaf_BraIRRI036_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI036, Optimal P


title: Brassica rapa_Leaf_BraIRRI174_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI174, Low P


title: Brassica rapa_Leaf_IMB211_Low P_Rep_3

source_name: Leaf tissue from parent IMB211, Low P


title: Brassica rapa_Leaf_R500_Low P_Rep_3

source_name: Leaf tissue from parent R500, Low P


title: Brassica rapa_Leaf_BraIRRI277_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI277, Optimal P


title: Brassica rapa_Leaf_BraIRRI380_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI380, Low P


title: Brassica rapa_Leaf_BraIRRI253_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI253, Low P


title: Brassica rapa_Leaf_BraIRRI228_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI228, Low P


title: Brassica rapa_Leaf_BraIRRI150_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI150, Low P


title: Brassica rapa_Leaf_BraIRRI115_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI115, Low P


title: Brassica rapa_Leaf_R500_Low P_Rep_1


title: Brassica rapa_Leaf_BraIRRI174_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI174, Optimal P


title: Brassica rapa_Leaf_BraIRRI021_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI021, Low P


title: Brassica rapa_Leaf_BraIRRI205_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI205, Optimal P


title: Brassica rapa_Leaf_BraIRRI223_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI223, Optimal P


title: Brassica rapa_Leaf_R500_Optimal P_Rep_1

source_name: Leaf tissue from parent R500, Optimal P


title: pho80Δcbf1Δ vs pho80Δpho4Δcbf1Δ in high Pi conditions replicate 1

first: Xu

last: Zhou

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
Biological replicate
Part II

hyb_protocol: 300 ng Cy3-labeled and 300 ng Cy5-labeled cDNA was competitively hybridized to Agilent 8×15K S. cerevisiae two-color expression microarrays (G2509F) in Agilent hybridization buffer for 17 hours at 60 °C.

scan_protocol: Microarrays were washed and scanned immediately using an Axon 4000B scanner

data_processing: The average intensity of the Cy3 and Cy5 fluorescence at each spot was then extracted using GenePix 5.1 software.  Lowess and quantile normalization were performed using the MATLAB bioinformatics toolbox before further analysis.

label_protocol: Purified cDNA samples were then labeled with NHS-ester Cy3 or Cy5 (GE Biosciences).

growth_protocol: Monobasic potassium phosphate was added to phosphate-free medium to make high phosphate (Pi) medium containing a final concentration of 10 mM inorganic phosphate. All media were adjusted to pH 4.0 with HCl2.  Yeast strains were grown at 30 °C with shaking and cell samples were collected at early/mid-logarithmic phase (OD600 0.3 ~ 0.4).

extract_protocol: Cell cultures were added directly into cold methanol (~ -50 °C) with volume ratio of 2:3, and incubated in an ethanol-dry ice bath for at least 20 minutes.  Cells were collected by centrifugation and quickly washed with ice-cold water to remove alcohol, and resuspended in RNAlater solution (Ambion).  For each sample, 5×107 cells were used to isolate total RNA with the RNase Mini kit (Qiangen), and RNA integrity was analyzed on an agarose gel or with an Agilent bioanalyzer.  cDNA was synthesized from 10 μg total RNA with 1:1 ratio of random 10-mers and oligo-dT primers (Operon), and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma), using the Superscript III reverse transcription system (Invitrogen).  cDNA was purified with a PCR purification kit (Qiagen) after hydrolyzing RNA.

treatment_protocol: To induce the Pi starvation response, yeast cells were first grown in 10 mM Pi medium to early/mid-logarithmic phase.  Cells were then harvested by filtering and washed 2 – 3 times with no Pi medium pre-warmed to 30 °C.  Finally, cells were resuspended in pre-warmed no Pi medium and grown at 30 °C for 60 minutes.

tag: protocol

value: High Pi (10 mM Pi)

tag: agent

value: inorganic phosphate


title: pho80Δ vs pho80Δpho4Δ in high Pi conditions replicate 2

description:
Biological replicate
Part II


title: pho80Δcbf1Δ vs pho80Δpho4Δcbf1Δ in high Pi conditions replicate 2

description:
Biological replicate
Part II


title: pho80Δ vs pho80Δpho4Δ in high Pi conditions replicate 1

description:
Biological replicate
Part II


title: cbf1Δpho4Δ vs wild type in high Pi conditions replicate 1

description:
Biological replicate
Part II

source_name: Wild type

value: Wild type


title: cbf1Δpho4Δ vs wild type in high Pi conditions replicate 3

description:
Biological replicate
Part II


title: cbf1Δ vs wild type in high Pi conditions replicate 4

description:
Biological replicate
Part II


title: cbf1Δpho4Δ vs wild type in high Pi conditions replicate 4

description:
Biological replicate
Part II


title: rtg3Δtye7Δ vs wild type in high Pi conditions replicate 2

description:
Biological replicate
Part II


title: cbf1Δpho4Δ vs wild type in high Pi conditions replicate 2

description:
Biological replicate
Part II


title: cbf1Δ vs wild type in high Pi conditions replicate 3

description:
Biological replicate
Part II


title: rtg3Δtye7Δ vs wild type in high Pi conditions replicate 1

description:
Biological replicate
Part II


title: Brassica rapa_Leaf_BraIRRI009_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI009, Optimal P

tag: tissue


title: Brassica rapa_Leaf_BraIRRI318_Optimal P_Rep_2

source_name: Leaf tissue from RIL BraIRRI318, Optimal P


title: cbf1Δ vs wild type in high Pi conditions replicate 2

description:
Biological replicate
Part II


title: cbf1Δ vs wild type in high Pi conditions replicate 1

description:
Biological replicate
Part II


title: Brassica rapa_Leaf_BraIRRI076_Low P_Rep_2

source_name: Leaf tissue from RIL BraIRRI076, Low P


title: Wild type no vs high Pi conditions Replicate 4

description:
Biological replicate
Part II

value: No Pi (0 mM Pi)

value: control