title: E_coli_RL08_pTrc99aBTEH204A-EZ_glucose_midlog-rep3

description: This sample is of non-fatty acid overproducing Escherichia coli K-12 delta-fadD delta-araBAD expressing non-functional Umbellularia california acyl-acyl carrier protein thioesterase (BTE-H204A) on plasmid pTrc99A. It was grown in shake flasks in EZ rich defined medium + 0.2% glucose + 0.01 mM biotin and induced at OD600 0.2 with 50 uM IPTG and sampled in mid-log phase (OD600 0.8). It is the third of three negative control biological replicates used in this experiment, each from separate cultures.


title: 1618-6501T

status: Public on May 24 2011

type: genomic

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

description: Original Sample title: 6501T

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: average beta value = Max(Cy5,0)/[Max(Cy3,0) + Max(Cy5,0) + 100]

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: lung tumor tissue

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: gender

tag: age

tag: ethnicity

value: European

tag: disease state

value: lung cancer

tag: biomaterial

value: lung tumor tissue


title: E_coli_RL08_pTrc99aBTEH204A-EZ_glucose_midlog-rep1

type: RNA

city: Madison

first: Rebecca

last: Lennen

state: WI

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

country: USA

institute: University of Wisconsin-Madison

description: This sample is of non-fatty acid overproducing Escherichia coli K-12 delta-fadD delta-araBAD expressing non-functional Umbellularia california acyl-acyl carrier protein thioesterase (BTE-H204A) on plasmid pTrc99A. It was grown in shake flasks in EZ rich defined medium + 0.2% glucose + 0.01 mM biotin and induced at OD600 0.2 with 0.2% L-arabinose and sampled in mid-log phase (OD600 0.8). It is the first of three negative control biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Cy3-labeled cDNA samples were hybridized to Roche NimbleGen (Madison, WI) Escherichia coli K-12 (accession number NC_000913) microarray slides containing 4 arrays per slide and 72000 probes per array, according to the NimbleGen Arrays User's Guide. See www.nimblegen.com.

scan_protocol: The arrays were scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) with a photomultiplier tube gain to achieve 1 x 10-5 normalized counts at saturated intensity level. The images were processed and .pair files were generated based on non-normalized intensities. See www.nimblegen.com.

data_processing: Scanned probe intensities were imported into ArrayStar software (DNASTAR, Madison, WI), and processed with Robust Microarray Analysis (RMA) background correction, quantile normalization to adjust the probe intensity distributions to be the same across all cross-compared arrays, and RMA median polish summarization to generate gene level signal values from the normalized probe intensities (Bolstad et al. Bioinformatics 19(2):185). Mean intensities were determined across all array and sample technical replicates, and then across biological replicates to yield the final expression values. P-values were calculated across biological replicates by a Moderated t-Test (Smyth, Stat. Appl. Genet. Mol. Biol. 3:3) in ArrayStar software.

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli RL08/pTrc99A-BTE-H204A, EZ glucose, mid-log phase

label_protocol: 10 µg of RNA was used to synthesize cDNA, and 1 µg was labeled with Cy3 according to the NimbleGen Arrays User's Guide. See www.nimblegen.com.

growth_protocol: Escherichia coli K-12 MG1655 ΔfadD ΔaraBAD harboring different plasmids was grown at 37ºC in EZ rich defined medium (Teknova, Hollister, CA) supplemented with 0.2% glucose or 0.4% glycerol, and 0.01 mM biotin, and either 100 ug/mL ampicillin (pTrc99A-BTE(-H204A)) or 25 ug/mL kanamycin and 34 ug/mL chloramphenicol (pBAD35-BTE(-H204A) and pBAD33(-ACC)) and induced at OD600 0.2 with either 50 uM IPTG (pTrc99A-BTE(-H204A)) or 0.2% L-arabinose (pBAD35-BTE(-H204A) and pBAD33(-ACC)). Baffled shake flasks with 5X headspace were used for EZ glucose cultures (pTrc99A-BTE(-H204A)), with 250 rpm shaking. A baffled fermentor (12 L working volume, 4 L culture volume) with controlled pH (7.0 ± 0.2), agitation (700 rpm), and aeration (4 L/min air) was used for EZ glycerol cultures (pBAD35-BTE(-H204A) and pBAD33(-ACC)). Samples were taken at various times as defined.

extract_protocol: Total RNA was purified from frozen cell pellets using the RNAprotect Bacteria reagent kit (Qiagen, Valencia, CA) with lysozyme treatment and proteinase K digestion of cell lysates. Purification of total RNA was performed using the RNeasy Mini Kit (Qiagen).

treatment_protocol: 10 OD600-mL of culture was added to chilled 1/8th volume of 5% saturated phenol in ethanol, with deionized water added to maintain ratio of aqueous solution to phenol/ethanol, and centrifuged (5000 x g, 4ºC, 12 min). The supernatants were removed and the cell pellets were flash frozen in a dry ice/ethanol bath, and stored at -80ºC until further processing.

tag: genotype

value: K-12 MG1655 delta-fadD delta-araBAD

tag: plasmids

tag: phenotype

value: normal


title: HOSE2225

city: Boston

first: Michael

last: Birrer

state: MA

address: 70 Blossom Street

department: Medicine

institute: MGH

description: Gene expression data from ovarian surface epithelial cells

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.

label: Biotin

source_name: Normal

label_protocol: Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)

extract_protocol: Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained  by 1% methyl green, rinsed in deionized water, and air-dried.  Microdissection was performed using a MD LMD laser microdissecting microscope (Leica).  Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)

treatment_protocol: Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA).  A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications.  All specimens were collected under protocols approved by the institutional review boards of the institution.

tag: tissue

value: ovary

tag: cell type

value: Normal ovarian surface epithelium


title: 1617-6499T

description: Original Sample title: 6499T


title: HOSE2237


title: HOSE2064


title: HOSE2230


title: HOSE2061


title: HOSE2085


title: HOSE2228


title: 1616-6338T

description: Original Sample title: 6338T


title: HOSE2234


title: 1615-6220T

description: Original Sample title: 6220T


title: HOSE2008


title: HOSE2226


title: 1612-4653T

description: Original Sample title: 4653T


title: 1614-6008T

description: Original Sample title: 6008T


title: 1613-4654T

description: Original Sample title: 4654T


title: 1610-4648T

description: Original Sample title: 4648T


title: 160-AUT33-01

description: Original Sample title: AUT33-01

source_name: leukocytes

value: autism

value: leukocytes


title: 1609-4645T

description: Original Sample title: 4645T


title: 1608-4644T

description: Original Sample title: 4644T


title: 1611-4652T

description: Original Sample title: 4652T


title: CCOC-805G

description: Gene expression data from Ovarian Clear Cell Cancer

source_name: Ovarian Clear Cell Cancer

value: Primary tumors from clear cell ovarian cancer


title: CCOC-810G


title: hsa-pre-miR-146b A549 stable transfectants, culture 1

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description:
A4-1
Biological replicate 1

hyb_protocol: Hybridization reagents were mixed with 750 ng of labeled RNA, and the mixture was hybridized overnight at 58 ºC to HumanRef-8 v3.0 Expression BeadChips™ array (Illumina®).

scan_protocol: Following washing and staining with Cy3 dye-labeled streptavidin, BeadChips™ (Illumina®) were imaged using the BeadArray Reader (Illumina®)

data_processing: Data was acquired with GenomeStudio™ software (version 2010.1, Illumina®), and then processed for background-correction, variance-stabilizing transformation, and then robust splines-normalization between arrays using the lumi Bioconductor package (version 1.14) for R language (version 2.11.1) with default settings.

source_name: A549/146b cells

label_protocol: Illumina® TotalPrep RNA Amplification kit (Ambion®) was used to convert 500 ng of RNA to cDNA which was then transcribed in vitro to generate biotin-labeled RNA.

growth_protocol: Cells were cultured to 80%-95% confluence in 10 cm tissue culture plates in +DMEM medium containing 10% fetal bovine serum and 2 µg/ml puromycin, at 37 ºC with 5% carbon dioxide and 90% humidity.

extract_protocol: Total RNA was isolated using Purelink™ RNA isolation kit (Invitrogen®) as per the manufacturer's recommended protocol. RNA quantity and quality was assessed on a Bioanalyzer™ 2100 instrument (Agilent®). The RNA preparations had 260 nm/280 nm absorbance ratios in the 1.9-2.0 range, 260 nm/230 nm absorbance ratios >1.8, and RNA integrity numbers >7.

treatment_protocol: Adherent cells on a 10 cm culture dish were rinsed with phosphate-buffered saline, and treated at 37 ºC for 5 minutes with 0.75 ml of 0.05% trypsin with 0.25 mM ethylene-diamine-tetraacetic acid. Phosphate-buffered saline (10 ml) was used to collect the detached cells which were then spun down at 500 g for 10 minutes at room temperature. The cell pellet was used to isolate RNA.

tag: cell line

value: A549 lung cancer cells

tag: disease

value: Lung adenocarcinoma

tag: transfection

value: pLemiR plasmid with hsa-pre-miR-146b


title: CCOC-451G


title: Empty vector A549 stable transfectants, culture 2

description:
A0-3
Biological replicate 2

source_name: A549/vec cells

value: Empty pLemiR plasmid


title: hsa-pre-miR-146b A549 stable transfectants, culture 2

description:
A4-3
Biological replicate 2


title: CCOC-2501


title: CCOC-671G


title: yku80-del-1-b

status: Public on May 23 2011

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only  dye-bias corrections for yeast.
limma, A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.    The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain

source_name: refpool

value: wild type


title: yku70-del-1-b


title: CCOC-2348G


title: yng1-del-matA-1-b


title: yng1-del-matA-1-a


title: CCOC-2316


title: CCOC-1411G


title: CCOC-1638


title: Array CGH analysis of A549 Clone 0

city: Berlin

first: Artur

last: Muradyan

address: Ihnestr. 73

country: Germany

description: Array CGH analysis of A549 Clone 0

hyb_protocol: Hybridization was done overnight at 42 C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned at 10 um resolution using an Agilent scanner. PMT settings: 100/100%

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.2 and -0.2, respectively.

source_name: DNA isolated from A549 cell line, Clone 0.

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

growth_protocol: The aneuploid A549 male non-small cell lung cancer (NSCLC) adenocarcinoma cell line was grown as monolayer in DMEM medium containing L-glutamine, 10% FCS (Invitrogen; Carlsbad, CA)

extract_protocol: DNA was isolated from cultured cell lines at the same passage using standard phenol/chloroform DNA preparation technique.

treatment_protocol: Sham (0Gy) irradiated A549 cell line.

value: male

value: derived from an adenocarcinoma of the lung

tag: treatment group

value: Sham (0Gy) irradiated

source_name: DNA isolated from EBV-transformed cell line (reference)

extract_protocol: DNA was extracted from cultured cell line using standard phenol-chloroform extraction procedures

value: EBV-transformed lymphoblastoid cell line


title: yku70-del-1-a


title: yaf9-del-1-b

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: Empty vector A549 stable transfectants, culture 1

description:
A0-1
Biological replicate 1


title: CCOC-1609


title: Array CGH analysis of A549 Clone 2

institute: Max Planck Institute for Molecular Genetics

description: Array CGH analysis of A549 Clone 2

source_name: DNA isolated from A549 cell line, Clone 2.

treatment_protocol: 6Gy irradiated A549 cell line.

value: 6Gy irradiated


title: yaf9-del-1-a


title: Array CGH analysis of A549 Clone 1

description: Array CGH analysis of A549 Clone 1

source_name: DNA isolated from A549 cell line, Clone 1.


title: A549 Clone 4 vs. Clone 0

description: Array CGH analysis of A549 Clone 4 vs. Clone 0

source_name: DNA isolated from A549 cell line, Clone 4.

extract_protocol: DNA was isolated from cultured cell lines at the same passage using standard phenol/chloroform DNA preparation technique. Whole genome amplified by GenomePlex (Sigma).


title: yku80-del-1-a


title: A549 Clone 3 vs. Clone 0

description: Array CGH analysis of A549 Clone 3 vs. Clone 0

source_name: DNA isolated from A549 cell line, Clone 3.


title: Array CGH analysis of A549 Clone 3

description: Array CGH analysis of A549 Clone 3


title: vps72-del-1-a


title: vps75-del-1-a


title: A549 Clone 1 vs. Clone 0

description: Array CGH analysis of A549 Clone 1 vs. Clone 0


title: vps75-del-1-b


title: vps72-del-1-b


title: vps71-del-1-b


title: A549 Clone 2 vs. Clone 0

description: Array CGH analysis of A549 Clone 2 vs. Clone 0


title: vps71-del-1-a


title: ume1-del-1-c


title: swi3-del-2-a


title: tos4-del-2-b


title: ume1-del-1-b


title: swd3-del-matA-1-b


title: swr1-del-1-a


title: swp82-del-1-a


title: swi3-del-2-b


title: swc7-del-1-d


title: swc5-del-2-b


title: tos4-del-1-a


title: swr1-del-1-b


title: swd1-del-matA-1-a


title: swc3-del-2-b


title: swc3-del-2-a


title: swc7-del-1-b


title: swd1-del-matA-1-b


title: swd3-del-matA-1-a


title: swc5-del-2-a


title: spp1-del-matA-1-b


title: snf6-del-1-b


title: snf6-del-1-a


title: spp1-del-matA-1-a


title: snf5-del-1-a


title: snf2-del-1-d


title: snf11-del-1-b


title: snf2-del-1-a


title: snf5-del-1-b


title: snf12-del-1-b


title: snf12-del-1-a


title: sir3-del-1-a


title: sir4-del-1-a


title: sir4-del-1-b


title: sir1-del-2-b


title: stb2-del-1-a


title: sir2-del-1-a


title: set1-del-matA-1-a


title: sir1-del-2-a


title: snf11-del-1-a


title: sif2-del-1-b


title: sir2-del-1-b


title: set2-del-1-b


title: sif2-del-1-a


title: sds3-del-2-a


title: sin3-del-2-b


title: sin3-del-1-a


title: set3-del-1-a


title: set1-del-matA-1-b


title: set3-del-1-b


title: sir3-del-1-b


title: sas2-del-1-a


title: sas3-del-1-b


title: sap30-del-1-a


title: sdc1-del-matA-1-b

extract_protocol: yeast mRNA extraction v1.3


title: rxt3-del-1-b


title: rxt3-del-1-a


title: rtf1-del-1-a


title: rsc30-del-2-a


title: rsc30-del-3-b


title: set2-del-1-a


title: rtt102-del-1-b


title: rtt106-del-1-c


title: rtt109-del-1-a


title: rsc2-del-1-a


title: sap30-del-1-b


title: rtg2-del-3-b


title: rtg2-del-3-a


title: rtt109-del-1-b


title: sas3-del-1-a


title: sas4-del-1-a


title: rtf1-del-1-b


title: sas5-del-1-c


title: sds3-del-2-b


title: sas5-del-1-b


title: sas2-del-1-b


title: shg1-del-1-a


title: rsc2-del-2-b


title: rfm1-del-1-a


title: rtt106-del-1-b


title: rxt2-del-1-b


title: rfm1-del-2-b


title: rsc1-del-2-a


title: sdc1-del-matA-1-a


title: rxt2-del-1-a


title: sas4-del-1-b


title: rpd3-del-1-a


title: rco1-del-1-a


title: rpd3-del-1-b


title: pho23-del-1-a


title: rco1-del-1-b


title: pho23-del-1-b


title: paf1-del-2-a


title: npl6-del-3-b


title: nto1-del-1-b


title: rad6-del-2-a


title: not4-del-2-a


title: nto1-del-1-a


title: npl6-del-3-a


title: rad6-del-2-b


title: not4-del-2-b


title: not3-del-2-b


title: not3-del-2-a


title: nhp10-del-1-a


title: med3-del-1-a


title: med5-del-1-b


title: med31-del-1-a


title: paf1-del-2-b


title: med9-del-3-a


title: msi1-del-1-b


title: med9-del-3-b


title: med31-del-1-b


title: med2-del-1-b


title: nap1-del-1-b


title: med18-del-2-b


title: med20-del-2-b


title: med20-del-2-a


title: med18-del-2-a


title: nhp10-del-1-b


title: med5-del-1-a


title: med3-del-1-b


title: med2-del-1-a


title: leo1-del-2-a


title: med16-del-1-a


title: med15-del-1-b


title: lge1-del-1-a


title: med1-del-1-a


title: leo1-del-2-b


title: med16-del-1-b


title: lge1-del-1-b


title: jhd2-del-2-a


title: jhd2-del-2-b


title: ldb7-del-1-c


title: med15-del-1-a


title: msi1-del-1-a


title: jhd1-del-2-b


title: jhd1-del-2-a


title: ldb7-del-1-b


title: isw1-del-1-b


title: med1-del-1-b


title: ioc3-del-1-b


title: ies6-del-1-c


title: ioc2-del-1-b


title: rsc1-del-1-b


title: ioc4-del-1-b


title: ies3-del-1-a


title: isw1-del-1-a


title: ies6-del-1-b


title: ies5-del-1-a


title: itc1-del-1-a


title: ioc2-del-1-a


title: ies2-del-1-a


title: ies3-del-1-b


title: ioc4-del-1-a


title: ies1-del-1-b


title: ies4-del-2-a


title: ies5-del-1-b


title: ies4-del-2-b


title: ioc3-del-1-a


title: ies1-del-1-a


title: htl1-del-2-b


title: ies2-del-1-b


title: htz1-del-1-b


title: hpc2-del-1-b


title: htl1-del-2-a


title: htz1-del-1-a


title: hst1-del-1-b


title: hst1-del-1-a


title: hos2-del-1-a


title: hpc2-del-1-a


title: hmt1-del-2-a


title: hos4-del-1-a


title: hir3-del-2-a


title: hos2-del-1-b


title: hos1-del-1-a


title: hmt1-del-2-b


title: hos4-del-1-b


title: hif1-del-1-a


title: Overexpression FT2, Rep 3

city: Monticello

first: Joshua

last: Adams

state: AR

address: PO Box 3468

department: Forest Resources

institute: University of Arkansas-Monticello

description:
35S-FT2-3
Gene expression of leaf tissue.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Pre-processing was done using the GCRMA algorithm in the R and Bioconductor packages.

label: biotin

organism: Populus tremula x Populus alba

source_name: leaves, overexpressed FT2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For 35S samples, leaf tissues were collected at approximately 9 AM. For HSP promotion treatments, leaf samples were harvested at day 21 before the end of heat shock treament. All plants were of the approximate same developmental stage and were about 1 to 2 years old.

extract_protocol: RNA was extracted with a hot-borate method (Wan and Wilkins; 1994), followed by a Dnase I digestion and clean-up using the Rneasy Mini Kit (Quigen, Valencia, CA).

treatment_protocol: Treatments represent the FT1 and FT2 under both constitutive overexpression and heat shock promotion, as well as the respective controls.

value: leaf

value: 1-2 years

tag: affected gene

tag: treatment

value: overexpression


title: hhf2-del-1-a


title: hir2-del-2-b


title: Overexpression empty vector control for FT2 leaves, Rep 3

description:
35S-WT2-3
Gene expression of leaf tissue.

source_name: leaves, pBI101 control

value: control


title: hir2-del-2-a


title: hir1-del-1-b


title: Overexpression FT2, Rep 1

description:
35S-FT2-1
Gene expression of leaf tissue.


title: Overexpression empty vector control for FT2 leaves, Rep 2

description:
35S-WT2-2
Gene expression of leaf tissue.


title: hhf2-del-1-b


title: hir3-del-1-b


title: hif1-del-1-b


title: Overexpression empty vector control for FT2 leaves, Rep 1

description:
35S-WT2-1
Gene expression of leaf tissue.


title: hda3-del-1-b


title: hir1-del-1-a


title: Overexpression empty vector control for FT1 leaves, Rep 3

description:
35S-WT1-3
Gene expression of leaf tissue.


title: hda2-del-2-b


title: hda3-del-1-a


title: hda1-del-1-b


title: Overexpression empty vector control for FT1 leaves, Rep 4

description:
35S-WT1-4
Gene expression of leaf tissue.


title: Overexpression empty vector control for FT1 leaves, Rep 2

description:
35S-WT1-2
Gene expression of leaf tissue.


title: Overexpression FT1, Rep 4

description:
35S-FT1-4
Gene expression of leaf tissue.

source_name: leaves, overexpressed FT1


title: Overexpression FT1, Rep 2

description:
35S-FT1-2
Gene expression of leaf tissue.


title: Overexpression FT1, Rep 3

description:
35S-FT1-3
Gene expression of leaf tissue.


title: hda2-del-1-a


title: Overexpression FT2, Rep 2

description:
35S-FT2-2
Gene expression of leaf tissue.


title: hda1-del-1-a


title: hat1-del-1-a


title: Overexpression empty vector control for FT1 leaves, Rep 1

description:
35S-WT1-1
Gene expression of leaf tissue.


title: hat2-del-1-a


title: hat1-del-1-b


title: Wild-type control for heat-inducible FT1 and FT2 leaves, Rep 2

description:
HSP-WT-2
Gene expression of leaf tissue.

organism: Populus tremula x Populus tremuloides

source_name: leaves, wild-type control


title: Wild-type control for heat-inducible FT1 and FT2 leaves, Rep 1

description:
HSP-WT-1
Gene expression of leaf tissue.


title: Wild-type control for heat-inducible FT1 and FT2 leaves, Rep 3

description:
HSP-WT-3
Gene expression of leaf tissue.


title: itc1-del-1-b


title: esc8-del-1-a


title: Heat-inducible FT2, Rep 4

description:
HSP-FT2-4
Gene expression of leaf tissue.

source_name: leaves, heat-induced FT2

value: heat induction


title: Overexpression FT1, Rep 1

description:
35S-FT1-1
Gene expression of leaf tissue.


title: Heat-inducible FT2, Rep 1

description:
HSP-FT2-1
Gene expression of leaf tissue.


title: Wild-type control for heat-inducible FT1 and FT2 leaves, Rep 4

description:
HSP-WT-4
Gene expression of leaf tissue.


title: esc8-del-1-b


title: Heat-inducible FT2, Rep 3

description:
HSP-FT2-3
Gene expression of leaf tissue.


title: hat2-del-1-b


title: ecm5-del-2-b


title: Heat-inducible FT1, Rep 3

description:
HSP-FT1-4
Gene expression of leaf tissue.

source_name: leaves, heat-induced FT1


title: eaf7-del-1-b


title: ecm5-del-2-a


title: Heat-inducible FT2, Rep 2

description:
HSP-FT2-2
Gene expression of leaf tissue.


title: eaf6-del-1-a


title: eaf5-del-1-a


title: eaf5-del-1-d


title: Heat-inducible FT1, Rep 1

description:
HSP-FT1-1
Gene expression of leaf tissue.


title: eaf7-del-1-a


title: eaf6-del-1-b


title: Heat-inducible FT1, Rep 2

description:
HSP-FT1-2
Gene expression of leaf tissue.


title: leaf sample from June 2006, rep3

description: Gene expression of leaf tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 (Affymetrix).

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages. Additionally, the block effect as estimated by the limma model was removed from the GCRMA values.

organism: Populus deltoides

source_name: leaves of Populus deltoides sampled in June 2006

growth_protocol: Samples were collected from a 30-year old Populus deltoides tree growing next to a stream. Samples were taken for all months except for March at the end of the second week of the month. March samples were collected prior to the terminal bud opening, approximately in the third week of the month.

extract_protocol: RNA was extracted with a hot-borate method (Wan and Wilkins; 1994) followed by a Dnase I digestion and clean-up using Rneasy Mini Kit (Quigen, Valencia, CA).

treatment_protocol: NA, sampels represent wild-type tissues

value: leaf tissue

tag: developmental stage

value: sexually mature tree

tag: collection date

value: June of 2006

tag: block


title: leaf sample from June 2006, rep1

description: Gene expression of leaf tissue


title: leaf sample from June 2006, rep2

description: Gene expression of leaf tissue


title: leaf sample from May 2006, rep3

description: Gene expression of leaf tissue

source_name: leaves of Populus deltoides sampled in May 2006

value: May of 2006


title: dpb4-del-2-a


title: leaf sample from May 2006, rep2

description: Gene expression of leaf tissue


title: leaf sample from May 2006, rep1

description: Gene expression of leaf tissue


title: eaf3-del-3-a


title: leaf sample from April 2006, rep2

description: Gene expression of leaf tissue

source_name: leaves of Populus deltoides sampled in April 2006

value: April of 2006


title: leaf sample from April 2006, rep3

description: Gene expression of leaf tissue


title: leaf sample from April 2006, rep1

description: Gene expression of leaf tissue


title: eaf3-del-3-b


title: eaf1-del-tag-HA-1-b


title: eaf1-del-tag-HA-1-a


title: preformed leaf sample from March 2006, rep2

description: Gene expression of preformed leaf tissue

source_name: preformed leaves of Populus deltoides sampled in March 2006

value: preformed leaf tissue

value: March of 2006


title: preformed leaf sample from March 2006, rep3


title: dpb4-del-2-b

source_name: refpool

value: wild type


title: preformed leaf sample from March 2005, rep3

source_name: preformed leaves of Populus deltoides sampled in March 2005

value: March of 2005


title: dls1-del-1-c


title: preformed leaf sample from March 2005, rep2


title: preformed leaf sample from March 2005, rep1


title: preformed leaf sample from March 2006, rep1


title: cti6-del-3-a


title: preformed leaf sample from February 2005, rep3

source_name: preformed leaves of Populus deltoides sampled in February2005

value: February of 2005


title: dep1-del-1-a


title: preformed leaf sample from February 2005, rep2

source_name: preformed leaves of Populus deltoides sampled in February 2005


title: ctr9-del-1-b


title: dot1-del-1-b


title: dep1-del-1-b


title: preformed leaf sample from December 2005, rep1

source_name: preformed leaves of Populus deltoides sampled in December 2005

value: December of 2005


title: cti6-del-1-b


title: preformed leaf sample from December 2005, rep2


title: preformed leaf sample from February 2005, rep1


title: cpr1-del-1-a


title: preformed leaf sample from December 2005, rep3


title: cpr1-del-1-b


title: dls1-del-1-b


title: ctr9-del-1-a


title: chz1-del-1-a


title: preformed leaf sample from September 2005, rep2

source_name: preformed leaves of Populus deltoides sampled in September 2005

value: September of 2005


title: cdc73-del-1-a


title: cdc73-del-1-b


title: chd1-del-1-b


title: Ssa_H5Rip_63d_replicate 6

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Microarray hybridizations were performed using Agilent’s 4 x 44K Atlantic salmon microarray slides containing 4 grids with the same ~ 44 000 features (Design ID 020938), using a one-color approach. All hybridizations, including washes and drying steps were carried out on a HS4800 automated hybridization station using quad chambers (Tecan, Männedorf, Switzerland). Briefly, slides were initially washed with Agilent’s aOligo aCGH Prehybridization buffer for 1 min at 65°C and injected with a 60 µl of hybridization mix containing 30 µl of fragmentation mix and 30 µl of Agilent’s 2x GEx hybridization Buffer Hi-RPM per chamber. The injected material was hybridized for 17 hour at 65°C. Following hybridization slides were washed twice with Agilent’s gene expression wash buffer 1 at 23°C for 1 min, twice with Agilent’s gene expression wash buffer 2 with 0.01 wash buffer additive at 37°C for 1 min and then dried under nitrogen

scan_protocol: Microarray slides were scanned at a resolution of 5 µm using a ScanArray Gx microarray scanner (Perkin Elmer, MA, USA) with the laser power set at 90%. For each slide, PMT settings were set to 60.

data_processing: TIFF images were quantified using the SpotReader feature extraction software (Niles Scientific, CA, USA). Numerical intensities from each spot were extracted and descriptive statistics were calculated and exported in a GenePix Results (GPR) file. Features that did not meet certain default criteria in SpotReader were flagged as bad. These default criteria included flagging spots which had more than 50 % of the pixels saturated, spots with less than 8 pixels in diameter and spots with high background The bad flag values computed were then used to filter out genes that had missing values (-50,-75,-100 GPR flag values) on more than half of the slides used in each group (e.g. H5Rc fish) for a particular statistical analysis performed. Median intensity value minus background for each spot remaining after filtering were log2 transformed and normalized using a median centering approach.

organism: Salmo salar

label_protocol: RNA amplification and labeling for microarray was performed using the one-color Low Input Quick Amp Labeling kit (Agilent, CA, USA) and following the manufacturer’s recommendations. Briefly, 200 ng of each RNA sample was reverse transcribed, amplified and labeled using Cy3 dyes resulting in Cy3 labeled amplified RNA (aRNA). Purification of the labeled aRNA was performed using NucleoSpin RNA clean up columns (Macherey-Nagel, CA, USA) following the manufacturer’s recommendations. Following purification, labeled aRNA samples were then quantified using the NanoDrop 8000 to verify the yield of aRNA and the labeling efficiency. 1.65 µg of each purified aRNA was prepared for hybridization using the fragmentation step described in Agilent’s Low Input Quick Amp labeling kit protocol. Briefly each aRNA was fragmented by mixing 1.65 µg of aRNA in a volume of 22.8 µl, with 6 µl of 10X blocking agent and 1.2 µl of 25X fragmentation buffer and heating the mix at 60°C for 30 min.

extract_protocol: Total RNA from RNAlater preserved salmon head-kidney samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the NucleoSpin RNA II (Macherey-Nagel, PA, USA) and following the manufacturer’s protocol. An on column DNase digestion step was performed on each sample. RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA). Only RNA samples with RNA Quality Indicator (RQI) values above 8 were used for analysis. RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

value: Head-kidney

tag: time


title: preformed leaf sample from September 2005, rep1


title: preformed leaf sample from September 2005, rep3


title: caf40-del-2-b


title: Ssa_H5Rip_63d_replicate 5


title: Ssa_H5Rip_63d_replicate 1


title: Ssa_H5Rip_63d_replicate 2


title: Ssa_H5Rip_63d_replicate 3


title: chd1-del-1-a


title: Ssa_H5Rip_63d_replicate 4


title: caf40-del-2-a


title: caf4-del-1-b


title: caf16-del-1-a


title: Ssa_H5Rip_20d_replicate 5


title: Ssa_H5Rip_20d_replicate 6


title: Ssa_H5Rip_20d_replicate 4


title: caf16-del-1-b


title: caf130-del-1-a


title: cac1-del-1-b


title: Ssa_H5Rip_20d_replicate 1


title: Ssa_H5Rip_20d_replicate 2


title: caf4-del-1-a


title: Ssa_H5Rip_10d_replicate 6


title: cac2-del-1-b


title: Ssa_H5Rip_10d_replicate 5


title: Ssa_H5Rip_10d_replicate 4


title: caf130-del-1-b


title: cac2-del-1-a


title: Ssa_H5Rip_20d_replicate 3


title: bur2-del-2-b


title: bre2-del-matA-1-a


title: Ssa_H5Rip_10d_replicate 3


title: cac1-del-1-a


title: btt1-del-1-b


title: bre1-del-2-a

hyb_protocol: Hybridization protocol v2.2

label_protocol: aminoallyl labeling v2.1.1


title: Ssa_H5Rip_10d_replicate 1


title: Ssa_H5Rip_3d_replicate 5


title: ash1-del-2-b


title: Ssa_H5Rip_24h_replicate 6


title: Ssa_H5Rip_3d_replicate 6


title: Ssa_H5Rip_10d_replicate 2


title: ash1-del-2-a


title: Ssa_H5Rip_3d_replicate 4


title: bre2-del-matA-1-b


title: asf1-del-2-a


title: bur2-del-1-a


title: Ssa_H5Rip_24h_replicate 5


title: bre1-del-2-b


title: Ssa_H5Rip_3d_replicate 1


title: Ssa_H5Rip_3d_replicate 3


title: Ssa_H5Rip_3d_replicate 2


title: arp8-del-1-a


title: Ssa_H5Rip_24h_replicate 4


title: Ssa_H5Rip_24h_replicate 2


title: arp8-del-2-b


title: Ssa_H5Rip_24h_replicate 3


title: arp5-del-1-a


title: asf1-del-1-d


title: arp5-del-1-c


title: Ssa_H5Rip_6h_replicate 5


title: ahc1-del-1-a


title: Ssa_H5Rip_6h_replicate 6


title: arp6-del-2-a


title: Ssa_H5Rip_6h_replicate 1


title: Ssa_H5Rip_6h_replicate 2


title: Ssa_H5Rip_24h_replicate 1


title: Ssa_Nc_63d_replicate 1


title: Ssa_Nc_41d_replicate 4


title: arp6-del-2-b


title: Ssa_Nc_63d_replicate 2


title: Ssa_Nc_63d_replicate 3


title: Ssa_Nc_41d_replicate 1


title: Ssa_Nc_41d_replicate 2


title: Ssa_Nc_29d_replicate 6


title: STZ + insulin 6

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description: Replicate 6

data_processing: The data were normalized using average normalization in GenomeStudio v1.0.6

organism: Rattus norvegicus

source_name: Retina

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.  Cy3-Streptavidin was incorporated during Wash and Block protocol as a fluor for scanning.

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

value: Sprague-Dawley

value: STZ + insulin

value: retina


title: Ssa_H5Rip_6h_replicate 3


title: STZ + insulin 5

description: Replicate 5


title: Ssa_H5Rip_6h_replicate 4


title: Ssa_Nc_29d_replicate 4


title: Ssa_Nc_41d_replicate 3


title: Normal brain (2NB1F)

city: New York

first: Liang

last: Lei

address: 1130 St. Nicholas Ave Rm 1001

institute: Columbia University

description:
2NB1F.CEL
Gene expression data from normal brain

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Raw data was normalized and summarized by robust multichip average (RMA). The data were analyzed with affy package in R/Bioconductor.

organism: Mus musculus

source_name: Normal brain

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

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

value: Normal brain

tag: age

value: 6-8 weeks


title: Ssa_Nc_29d_replicate 5


title: STZ + insulin 4

description: Replicate 4


title: STZ + insulin 7

description: Replicate 7


title: Normal brain (2NB2F)

description:
2NB2F.CEL
Gene expression data from normal brain

tag: genotype


title: Tumor in Ptenf/f; p53f/f mice (2ptenp53 F1S)

description:
2ptenp53 F1S.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.

source_name: Tumor in Ptenf/f; p53f/f mice

value: Tumor

value: Ptenf/f; p53f/f


title: Tumor in Ptenf/f; p53f/f mice (2ptenp53 M1)

description:
2ptenp53 M1.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Tumor in Ptenf/f; p53f/f mice (2ptenp53 R3F)

description:
2ptenp53 R3f.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Normal brain (2NB3F)

description:
2NB3F.CEL
Gene expression data from normal brain


title: Ssa_Nc_29d_replicate 3


title: STZ + insulin 3

description: Replicate 3


title: Ssa_Nc_23d_replicate 5


title: Ssa_Nc_29d_replicate 1


title: STZ + insulin 1

description: Replicate 1


title: Tumor in Ptenf/f mice (2pten M11)

description:
2pten M11.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.

source_name: Tumor in Ptenf/f mice

value: Ptenf/f


title: STZ + insulin 2

description: Replicate 2


title: Ssa_Nc_29d_replicate 2


title: Ssa_Nc_23d_replicate 4


title: Ssa_Nc_23d_replicate 3


title: STZ 5

description: Replicate 5

value: STZ


title: STZ 3

description: Replicate 3


title: Ssa_Nc_20d_replicate 6


title: Ssa_Nc_20d_replicate 4


title: Tumor in Ptenf/f mice (2pten JM3)

description:
2pten JM3.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Tumor in Ptenf/f mice (2pten 5F)

description:
2pten 5F.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_Nc_20d_replicate 5


title: Ssa_Nc_23d_replicate 2


title: Ssa_Nc_23d_replicate 1


title: STZ 4

description: Replicate 4


title: Ssa_Nc_20d_replicate 1


title: STZ 2

description: Replicate 2


title: Ssa_Nc_20d_replicate 3


title: Tumor in Ptenf/f mice (2pten F7)

description:
2pten F7.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: STZ 1

description: Replicate 1


title: Tumor in Ptenf/f mice (2pten YFP1)

description:
2pten YFP1.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Tumor in Ptenf/f mice (2pten F9)

description:
2pten F9.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_H5Rc_63d_replicate 6


title: Ssa_Nc_20d_replicate 2


title: Control 7

description: Replicate 7

value: Control


title: Tumor in Ptenf/f; p53f/f mice (1ptenp53 10)

description:
1ptenp53 10.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_H5Rc_63d_replicate 5


title: Ssa_H5Rc_63d_replicate 4


title: Ssa_H5Rc_63d_replicate 2


title: Ssa_H5Rc_41d_replicate 6


title: Tumor in Ptenf/f; p53f/f mice (1ptenp53 9)

description:
1ptenp53 9.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Control 6

description: Replicate 6


title: Tumor in Ptenf/f; p53f/f mice (1ptenp53 11)

description:
1ptenp53 11.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Control 5

description: Replicate 5


title: Ssa_H5Rc_63d_replicate 3


title: Tumor in Ptenf/f; p53f/f mice (1ptenp53 7)

description:
1ptenp53 7.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_H5Rc_63d_replicate 1


title: Control 4

description: Replicate 4


title: Tumor in Ptenf/f mice (1pten 6)

description:
1pten 6.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Tumor in Ptenf/f mice (1pten 4)

description:
1pten 4.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Piperaquine-resistant_clone1_revertant

city: La Jolla

first: Neekesh

middle: V

last: Dharia

state: CA

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

description: Genomic DNA hybridization of piperaquine-resistant clone 1 that reverted to piperaquine-sensitive off drug pressure

hyb_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).

data_processing: Briefly for polymorphism detection, using a sliding window of three overlapping probes we scanned for sets probes that had significantly lower hybridization when compared to the reference indicative of a polymorphism as determined by z-test using a p-value cutoff of 1´10-5 and a reference 3D7 hybridization. Gene copy number variation scanning was performed by calculating the log2 ratio of the mean intensity for probes to a gene divided by the mean intensity of the probes for a reference 3D7 hybridization as previously described (Dharia et al. 2009).

organism: Plasmodium falciparum

source_name: Genomic DNA from piperaquine-resistant clone 1 derived in vitro from Dd2 that "reverted" to piperaquine-sensitive in absence of drug pressure

label_protocol: Fifteen micrograms of genomic DNA from each isolate and 2.5 ng each of Bio B, Bio C, Bio D, and Cre Affymetrix control plasmids (Affymetrix Inc., Santa Clara, CA, USA) were fragmented with DNaseI and end-labeled with biotin (Winzeler et al. 1998).

growth_protocol: Experiments described in this study were performed with an isogenic line of P. falciparum Dd2 parasites, newly recloned using limiting dilution (19), referred to as Dd2 1pa, utilized previously (11, 45). Parasites were cultured in an asynchronous manner in vitro using standard conditions and media (16, 58), supplemented with 5% Albumax (Invitrogen, Carlsbad, CA, USA). Parasites were isolated from infected erythrocytes by treatment with 0.1% (w/v) saponin, prior to nucleic acid purification.

extract_protocol: Genomic DNA was isolated by standard phenol-chloroform extraction.

treatment_protocol: Selection of piperaquine-resistant parasites. Selection of resistant parasites was conducted as described previously (42). Briefly, Dd2 1pa parasites were propagated in vitro in red blood cells (RBC) and triplicate 60 ml cultures with an initial inoculum of 3.3 x 109 infected RBC were challenged with either 47 nM or 140 nM PQP (AvaChem Scientific, San Antonio, TX, USA) added to the culture medium. These concentrations were based on the peak plasma concentrations obtained in human plasma, when compound was administered alone or with a high fat meal, respectively (2, 52, 55, 57). In addition, triplicate flasks were inoculated with 10 infected RBC as a growth control, to gauge when parasites would be first detected by microscopy. The medium was changed every other day, maintaining the initial drug concentration, and fresh RBC were added once per week. Cultures were maintained under continuous drug pressure for 80 days. Giemsa-stained blood smears of cultures were examined to detect parasite outgrowth, and a parasitemia of 2% infected RBC was set as the standard for defining a positive culture. Clonal isolates of resistant parasites from drug-challenged cultures were obtained by limiting dilution.

tag: parasite clone


title: Control 2

description: Replicate 2


title: Control 1

description: Replicate 1


title: Ssa_H5Rc_29d_replicate 6


title: Ssa_H5Rc_41d_replicate 1


title: Ssa_H5Rc_41d_replicate 3


title: Ssa_H5Rc_41d_replicate 4


title: PGF_0003_gene-level

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

country: France

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7

description: gene-level analysis carried out with custom CDF (HuEx10stv2_Hs_VEGAG.cdf (v10))

hyb_protocol: Samples were hybridized to the Affymetrix Human Exon 1.0 ST array for 16 hours at 45°C following manufacturer’s instructions. Hybridized arrays were then washed and stained on a GeneChip Fluidics 450 workstation (Affymetrix) using the FS450_0001 protocol.

scan_protocol: The arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
CEL files were processed in Affymetrix Power Tools (APT) to generate probe, exon and gene level intensities. Probe-level data were extracted using apt-cel-extract with a GC-based background correction and then normalised using VSN in R/BioConductor, allowing direct comparison with the data for the same samples hybridised to our custom MHC array. Exon and gene level intensities were generated using the RMA algorithm and VEGA probeset definitions (alternative CDFs from the Microarray Lab (v10), University of Michigan)
gene analysis CDF: HuEx10stv2_Hs_VEGAG.cdf (v10)

source_name: PGF

label_protocol: We used the GeneChip Whole Transcript (WT) Sense Target Labeling kit (Affymetrix, Santa Clara, USA), following manufacturer's instruction, starting with 1.5 ug of total RNA and including the ribosomal RNA depletion step (Ribominus kit, Invitrogen). Then, cDNA was synthesized using random hexamers tailed with a T7 promoter to avoid 3’ bias, and the complementary strand of RNA was generated by an in vitro transcription reaction. Subsequently a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the messenger RNA and denoted “ccDNA”. This was fragmented [range 40-70 bases] and end-labeled with biotin.

growth_protocol: Lymphoblastoid cell lines COX, PGF and QBL were grown in triplicate at a minimum density of 6x105 cells/mL in RPMI 1640 (Sigma, lot 16K2379) supplemented with 10% Fetal Calf Serum Gold (PAA, lot A64095-0537) and 2mM L-glutamine (PAA, lot M00406-0102) at 37oC in a 5% CO2 wet environment. Cells were harvested at 8x105-1x106 cells/mL in log growth phase.

extract_protocol: Total RNA was isolated using RNeasy midiprep kits (Qiagen) according to manufacturer's recommendations including the additional on column DNase I digestion. Quantifications were done by Nanodrop (ThermoScientific) and integrity was verified using a 2100 bioanalyzer (Agilent). All samples had a RIN (RNA integrity number) greater than 9. Genomic DNA contamination was checked by real-time PCR and was less than 0.1%.

tag: biological source

value: Lymphoblastoid cell line

tag: haplotype

value: Unstimulated


title: Tumor in Ptenf/f mice (1pten 5)

description:
1pten 5.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.

tag: tissue


title: QBL_0001_gene-level

source_name: QBL


title: Tumor in Ptenf/f; p53f/f mice (1ptenp53 8)

description:
1ptenp53 8.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Tumor in Ptenf/f mice (1pten 3)

description:
1pten 3.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: QBL_0003_gene-level


title: Control 3

description: Replicate 3


title: Piperaquine-resistant_clone1

description: Genomic DNA hybridization of piperaquine-resistant clone 1

scan_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).

source_name: Genomic DNA from piperaquine-resistant clone 1 derived in vitro from Dd2


title: Ssa_H5Rc_41d_replicate 5


title: Ssa_H5Rc_29d_replicate 5


title: Piperaquine-resistant_clone2

description: Genomic DNA hybridization of piperaquine-resistant clone 2

source_name: Genomic DNA from piperaquine-resistant clone 2 derived in vitro from Dd2


title: Ssa_H5Rc_41d_replicate 2


title: QBL_0002_gene-level


title: Dd2_parental_clone

description: Genomic DNA hybridization of Dd2

source_name: Genomic DNA from Dd2 parental clone

value: Dd2 parental clone


title: PGF_0002_gene-level


title: Tumor in Ptenf/f mice (1pten 1)

description:
1pten 1.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_H5Rc_29d_replicate 4


title: PGF_0001_gene-level


title: Otocyst_EGFP-positive

city: Bunkyo-ku Tokyo

first: Chisato

last: Fujimoto

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

description: EGFP is mainly expressed in the ventral and dorsomedial otocyst.

hyb_protocol: The biotin-labeled cRNA was then hybridized to a high-density oligonucleotide array (GeneChip Mouse Genome 430 2.0 array; Affymetrix, Santa Clara, CA, USA). After washing, arrays were stained with streptavidin-phycoerythrin.

scan_protocol: Image data were collected and analyzed with an Affymetrix GeneChip Scanner 3000 (Affymetrix).

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference for each gene probe set, shown as the gene expression intensity value. The signal intensities were normalized so that the average of all of the genes on a GeneChip would be 100.

source_name: EGFP-positive otocyst epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA. The sample preparation protocol from the Affymetrix GeneChip Expression Analysis Manual (Affymetrix) was used.

growth_protocol: The mice were  housed with 12 hours of light and 12 hours of darkness in a controlled temperature (23 °C).

extract_protocol: Homogenization of cell lysates was performed using QIAshredder homogenizers (QIAGEN, Hilden, Germany). Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturers’ protocol.

treatment_protocol: Otocysts dissected from heterozygous embryos were dissociated to a single-cell suspension by trypsin treatment (200 μl of 0.25% trypsin/ EDTA solution). 1 ml of Dulbecco’s Modified Eagle Medium (DMEM) and 10% fetal calf serum (FCS) was added to the single-cell suspension. After centrifugation, the cells were resuspended in 0.5 ml of PBS and 5% FCS. Propidium iodide (PI) was added to a final concentration of 1 μg/ml. By FACS experiment, the otocyst epithelial cells were sorted into EGFP-positive and EGFP-negative cells.

value: otocyst

value: Tg(ETAR-EGFP)14Imeg heterozygous

tag: gfp status

value: positive


title: Ssa_H5Rc_29d_replicate 3

value: Head-kidney


title: Ssa_H5Rc_29d_replicate 2


title: Ssa_H5Rc_23d_replicate 5


title: COX_0003_gene-level

source_name: COX


title: Otocyst_EGFP-negative

description: EGFP is not expressed in the dorsolateral otocyst.

source_name: EGFP-negative otocyst epithelial cells

value: negative


title: Tumor in Ptenf/f mice (1pten 2)

description:
1pten 2.CEL
Gene expression data from tumor. The strain of mouse used in generating the tumors are on mixed background.


title: Ssa_H5Rc_20d_replicate 6


title: Ssa_H5Rc_23d_replicate 4


title: Ssa_H5Rc_29d_replicate 1


title: DC_3

city: Edinburgh

first: Adrian

last: Bird

address: Mayfield Road

department: WTCCB

country: United Kingdom

institute: The University of Edinburgh

description:
wt DC 3
replicate 3

hyb_protocol: 1.5ug cRNA was brought up to a total volume of 10ul with RNase free water. 20ul of HYB (hybridisation buffer) was then added to each crna sample. The assay sample was preheated at 65C for 5 minutes and then cooled to room temperature. 200ul of HCB (humidity control buffer) was added to the reservoirs within the hyb chambers and the beadchips were then placed in their holders within the chambers (both HYB and HCB reagents provided by Illumina with Gene Expression (GEX) kits). The assay sample was loaded onto the beadchip (sample order as per lab tracking sheet). The hyb chamber was then sealed and placed in the oven for 18 hours at 58C. Beadchips were washed with High-Temp Wash buffer and Wash E1BC (both reagents provided by Illumina with GEX kits). A 100% Ethanol wash was carried out prior to chips being blocked using Block E1 buffer (also provided in GEX kits) and detected with Block E1/streptavidin Cy-3 mix (streptavidin Cy-3 is supplied by Amersham – Product No. 389830). Beadchips were dried in a centrifuge (speed 275g for 4 minutes).

scan_protocol: The chips were scanned immediately on the Illumina Beadarray Reader using the Direct Hyb protocol. During the scan process, the Beadchip barcode is scanned, ensuring effective data management. The resulting images are then available for registration, extraction, and analysis using Illumina’s GenomeStudio software.

data_processing:
The GenomeStudio project was created by importing the image files (direct from the Beadarray scanner) into the project, alongside the sample sheet (sample order from previously referred to lab tracking sheet) and the manifest file (as supplied by Illumina). The manifest file denotes where the snps are placed on the arrays.    The controls were checked to ensure sample quality, sample processing and reagents, arrays and scanning worked optimally. The raw data (no normalisation, no background subtraction) was created by exporting the Sample Probe Profile direct from GenomeStudio with fields: Probe ID, Avg, Signal and Detection pvalue for all samples (excluding null samples). The normalised data was produced with average normalisation method and no background subtraction. The Sample Probe Profile was exported directly from GenomeStudio with the same fields as the raw data.
Raw Data - all samples GenomeStudio computed, no normalisation, no background subtracted.
Normalised Data - all samples GenomeStudio computed, average normalisation, no background subtracted.

source_name: Dendritic cells

label_protocol: Biotinylated cRNA were prepared using the TotalPrep RNA Amplification kit (Ambion) kit

extract_protocol: Total RNA was extracted with TRI reagent. Quality control was performed with Agilent Bioanalyser.

tag: Sex

value: Male+female

value: Dendritic cells


title: Ssa_H5Rc_23d_replicate 1


title: COX_0002_gene-level


title: Ssa_H5Rc_20d_replicate 5


title: Ssa_H5Rc_23d_replicate 2


title: COX_0001_gene-level


title: DC_2

description:
wt DC 2
replicate 2


title: Brain_2

description:
brain 2
replicate 2

source_name: Brain (whole)

value: Male

value: Brain


title: Brain_1

description:
brain 1
replicate 1


title: Brain_3

description:
brain 3
replicate 3


title: Ssa_H5Rc_20d_replicate 4


title: 3xFlag-HoxB4_Promoter 2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: ChIP-on-chip data from mouse ES cells-derived hematopoietic progenitor cells overexpressing 3xFLAG-HoxB4

hyb_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2505C using Agilent Scan Control software Ver. A.8.4.1 (Protocol: ChIP-v1_10_Apr08).

data_processing: Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

source_name: Input

extract_protocol: Chromain immunoprecipitation (ChIP) was carried out as previously described (Endoh et al., 2008). Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008).

tag: cell line

value: ES cell line B6N-22UTR

source_name: Flag-IP


title: Ssa_H5Rc_23d_replicate 3


title: DC_1

description:
wt DC 1
replicate 1

tag: strain


title: B cell_3

description:
wt B cell 3
replicate 3

source_name: B cells

value: B cells


title: CD11cLO dMϕs, patient 8

city: Cambridge

first: Brandy

middle: Lynn

last: Houser

address: 52 Oxford St.

department: Stem Cell and Regenerative Biology

institute: Harvard University

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Human U133 2.0 Plus array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data was normalized using the Broad's GenePattern program that utilizes the RMA algorithm.

source_name: fetal_gestation:  9 weeks gestation

label_protocol:
amplification_protocol:  Purified RNA was subjected to one round of amplification and biotinylation using Ambion's® MessageAmp™III RNA Amplification kit.
Biotinylated aRNA were prepared according to the standard Affymetrix protocol.

extract_protocol:
macrophage_release_protocol: Cells were sorted into CD11cHI and CD11cLO dMϕ by MoFlo cell sorting following digestion release from human decidual tissue.
Total RNA was extracted using Stratagene®s Absolutely RNA™ microprep kit protocol.

value: first trimester human decidua

tag: group

value: CD11cLO dMϕs


title: Ssa_H5Rc_20d_replicate 2


title: B cell_1

description:
wt B cell 1
replicate 1


title: B cell_2

description:
wt B cell 2
replicate 2


title: CD11cLO dMϕs, patient 7


title: Ssa_H5Rc_20d_replicate 1


title: QBL_unstimulated_rep1

hyb_protocol: Samples were hybridized to the custom MHC array (Affymetrix) for 16 hours at 45°C following manufacturer’s instructions. Hybridized arrays were then washed and stained on a GeneChip Fluidics 450 workstation (Affymetrix) using the FS450_0001 protocol.

data_processing:
A GC-based background-correction was performed using antigenomic control probes before processing and normalising the data using the VSN package in R/Bioconductor. Data from tiling probes and junction probes were analysed separately using probes specific for each path. Tiling data were smoothed using a moving window (100 bases) averaging method, followed by a Gaussian smoothing weighting for the distance from the centre of the window. Transcriptionally active regions (TARs) were determined by a permutation method. To this end, we generated 1,000 random datasets of 1,000 consecutive probes with a randomly attributed intensity. We then considered 51-base (25 bases on each side of the tested position) windows with at least 3 probes (corresponding to the 18 bp average resolution of the tiling) above background and computed their median intensities. We used the 99th (FDR 1%) and 95th (FDR 5%) percentiles of the generated distributions as the significance thresholds. Junction probes were present in four technical replicates on the array, which were first averaged to obtain a more accurate estimate of intensities. Junction intensities were next computed as the median of all probes in the junction metaprobeset and normalized against the gene level intensity.
Results file descriptions: Track files for tiling data showing smoothed signal intensities, TARs at a FDR of 5% and TARs at a FDR of 1%, are provided for each sample, on each strand of the shared and alternate paths (shared and haplotypic-specifc probes).

growth_protocol: Lymphoblastoid cell lines COX, PGF and QBL were grown in triplicate at a minimum density of 6x105 cells/mL in RPMI 1640 (Sigma, lot 16K2379) supplemented with 10% Fetal Calf Serum Gold (PAA, lot A64095-0537) and 2mM L-glutamine (PAA, lot M00406-0102) at 37oC in a 5% CO2 wet environment.

treatment_protocol: Cultures were stimulated or not for 6 hours with 200nM phorbol 12-myristate 13 acetate (PMA) (Sigma) and 125nM ionomycin (Sigma) and harvested at 8x105-1x106 cells/mL in log growth phase.


title: Naive CD4_3

description:
wt naive 3
replicate 3

source_name: Naïve CD4 T cells

value: Naïve CD4 T cells


title: Th2_3

description:
wt th2 3
replicate 3

source_name: Th2 cells

value: Th2 cells


title: Th1_3

description:
wt th1 3
replicate 3

source_name: Th1 cells

value: Th1 cells


title: QBL_stimulated_rep1

value: Lymphoblastoid cell line

value: Stimulated for 6 hours with 200nM PMA and 125nM ionomycin


title: Ssa_H5Rc_20d_replicate 3


title: CD11cLO dMϕs, patient 6

source_name: fetal_gestation:  7 weeks gestation


title: QBL_unstimulated_rep3

value: Unstimulated


title: QBL_stimulated_rep2


title: CD11cLO dMϕs, patient 5


title: QBL_stimulated_rep3


title: CD11cLO dMϕs, patient 4


title: Ssa_H5R_0h_replicate 6

value: oh


title: Ssa_H5R_0h_replicate 5

value: Head-kidney


title: Ssa_H5R_0h_replicate 4


title: QBL_unstimulated_rep2


title: PGF_stimulated_rep2


title: Ssa_H5R_0h_replicate 3


title: Naive CD4_2

description:
wt naive 2
replicate 2


title: Ssa_H5R_0h_replicate 2


title: CD11cLO dMϕs, patient 3

source_name: fetal_gestation:  6 weeks gestation


title: Th2_2

description:
wt th2 2
replicate 2


title: PGF_stimulated_rep3


title: PGF_stimulated_rep1


title: CD11cLO dMϕs, patient 2

source_name: fetal_gestation:  8 weeks gestation


title: PGF_unstimulated_rep1


title: Th1_2

description:
wt th1 2
replicate 2


title: COX_stimulated_rep3


title: CD11cLO dMϕs, patient 1


title: Ssa_H5R_0h_replicate 1


title: Naive CD4_1

description:
wt naive 1
replicate 1


title: CD11cHI dMϕs, patient 7

value: CD11cHI dMϕs


title: CD11cHI dMϕs, patient 6


title: iHoxB4_rep2

description: c-Kit+CD41+ hematopoietic progenitor cells at day 8 of coculture with OP9 stromal cells in the presence of doxycyclin

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the GeneChip ST array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 17 hours ± 1 hour. Please refer to the GeneChip® Expression Wash, Stain and Scan User Manual (P/N  702731) for the washing and staining steps required immediately after completion of  hybridization.

scan_protocol: GeneChip Scaner 3000 was used . The core software was used AGCC for image processing.

data_processing: The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.

source_name: c-Kit+CD41+ cells/iHoxB4

label_protocol: A master mix using the 5X TdT  Buffer, TdT and DNA Labeling reagent can be prepared just before aliquoting 15 μL  into the 0.2 mL strip tubes containing the 45 μL of Fragmented Single-Stranded  DNA. Incubate the reactions at 37°C for 60 minutes, 70°C for 10 minutes and 4°C for at least 2 minutes

tag: cell type

value: Hematopoietic stem/progenitor cells


title: CD11cHI dMϕs, patient 8


title: CD11cHI dMϕs, patient 5


title: Th2_1

description:
wt th2 1
replicate 1

value: Male+female


title: Th1_1

description:
wt th1 1
replicate 1


title: PGF_unstimulated_rep3

tag: treatment


title: COX_stimulated_rep1


title: COX_stimulated_rep2


title: QBL_0003_exon-level

description: exon-level analysis carried out with custom CDF (HuEx10stv2_Hs_VEGAE.cdf (v10))

data_processing:
CEL files were processed in Affymetrix Power Tools (APT) to generate probe, exon and gene level intensities. Probe-level data were extracted using apt-cel-extract with a GC-based background correction and then normalised using VSN in R/BioConductor, allowing direct comparison with the data for the same samples hybridised to our custom MHC array. Exon and gene level intensities were generated using the RMA algorithm and VEGA probeset definitions (alternative CDFs from the Microarray Lab (v10), University of Michigan)
exon analysis CDF: HuEx10stv2_Hs_VEGAE.cdf (v10)

source_name: QBL


title: COX_unstimulated_rep2


title: CD11cHI dMϕs, patient 2


title: CD11cHI dMϕs, patient 4


title: COX_unstimulated_rep3


title: HoxB4_rep1

description: c-Kit+CD41+ hematopoietic progenitor cells transduced with a HoxB4 control retrovirus cocultured with OP9 stromal cells for 8 days in the absence of doxycyclin

source_name: c-Kit+CD41+ cells/HoxB4


title: CD11cHI dMϕs, patient 3


title: iHoxB4_rep1


title: CD11cHI dMϕs, patient 1


title: COX_unstimulated_rep1


title: PGF_unstimulated_rep2


title: MigR1_rep2

description: c-Kit+CD41+ hematopoietic progenitor cells transduced with a MIGR1 control retrovirus cocultured with OP9 stromal cells for 8 days in the absence of doxycyclin

source_name: c-Kit+CD41+ cells/MigR1


title: QBL_0001_exon-level


title: QBL_0002_exon-level


title: PGF_0003_exon-level

source_name: PGF


title: HoxB4_rep2


title: 1st pulse only_510min

status: Public on May 22 2011

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description: One EGF pulse time course experiment, see Figure 3 in the paper for experiment design

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
Normalized expression signals were calculated from Affymetrix CEL files using Affymetrix's Expression Console by RMA (Irizarry et al., 2003).
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na28.hg18.transcript.csv

source_name: 1st pulse only_510min

label_protocol: Affymetrix protocol

growth_protocol: DMEM:F12HAM, 1:1 mixture supplemented with 2mM L-glutamine, 100unit/ml Penicilin/Streptomycin, 10mM HEPES pH8.0, 10nM tri-iodothyronine, 2nM beta-estradiol, 1ug/ml insulin, 2.8uM hydrocortison, 0.1mM ethanolamine, 10ug/ml transferrin, 15nM sodium selenite, 1ng/ml cholera toxin, 12.5ng/ml EGF, 1% heat-inactivated FBS (Gibco BRL, Grand Island, N.Y), and 35ug/ml bovine pituitary extract

extract_protocol: PerfectPure RNA isolation kit

treatment_protocol: 184A1 human mammary cells were GF-starved for 16 hours. They were then either pulsed with EGF at time 0 for 1 hour, washed and incubated in starvation medium for 7 hours, followed by a second, one hour long pulse of EGF. Samples are taken at the time point indicated;  For the 1st-pulse-only samples, they were then either pulsed with EGF at time 0 for 1 hour, washed and incubated in starvation medium for 7 hours, followed by a mock pulse. Samples are taken at the time point indicated.

value: Human mammary epithelial cells


title: MigR1_rep1


title: 1st pulse only_600min

source_name: 1st pulse only_600min


title: 1st pulse only_540min

source_name: 1st pulse only_540min


title: 1st+2nd pulses_540min

description: Two EGF pulses time course experiment, see Figure 3 in the paper for experiment design

source_name: 1st+2nd pulses_540min


title: 1st+2nd pulses_660min

source_name: 1st+2nd pulses_660min


title: PGF_0002_exon-level


title: PGF_0001_exon-level


title: 1st+2nd pulses_300min

source_name: 1st+2nd pulses_300min


title: 1st+2nd pulses_420min

source_name: 1st+2nd pulses_420min


title: 1st+2nd pulses_480min

source_name: 1st+2nd pulses_480min


title: 1st pulse only_660min

source_name: 1st pulse only_660min


title: 1st+2nd pulses_510min

source_name: 1st+2nd pulses_510min


title: 3xFlag-HoxB4_Promoter 1

source_name: Input

label_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

source_name: Flag-IP


title: COX_0003_exon-level

source_name: COX


title: 1st+2nd pulses_600min

source_name: 1st+2nd pulses_600min


title: 1st+2nd pulses_60min

source_name: 1st+2nd pulses_60min


title: 1st+2nd pulses_360min

source_name: 1st+2nd pulses_360min


title: 1st+2nd pulses_120min

source_name: 1st+2nd pulses_120min


title: 1st+2nd pulses_0min

source_name: 1st+2nd pulses_0min


title: macrophage_TrifKO_E.coli_3h_rep2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
KO_Ecoli3h_2
G004_G07_15_114-7_KO_Ecoli3h.CEL

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.14.0).

source_name: bone marrow derived macrophages from Trif knockout mice, stimulated with E.coli for 3hrs

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Murine macrophages, derived from the bone marrow of either C57BL/6J, or Trif-/- mice, were cultured in RPMI 1640 supplemented with macrophage colony-stimulating factor (M-CSF) and 10% FBS, plus 100μg/ml penicillin, 100μg/ml streptomycin, 10mM HEPES and 1nM sodium pyruvate (all obtained from Sigma-Aldrich).

extract_protocol: Total RNA was extracted from the BMMs using the RNeasy kit (QIAGEN). RNA from  RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: The cultured bone marrow derived macrophages (BMMs) were detached and re-plated 4 hours prior to the experiment. At the start of the experiment, BMMs were incubated with viable E. coli for the 1, 3 or 6 hours. Bacteria were used at a multiplicity of infection (MOI) of 20. All experiments were carried out in antibiotic free 'complete medium'. One hour after addition of viable bacteria, penicillin (100μg/ml) and streptomycin (100μg/ml) were added to the media in order to kill any remaining extracellular bacteria. For transcriptional analysis three independent experiments were performed. We compared this approach to washing the cells and replacing the antibiotic free medium with penicillin/streptomycin containing medium after one hour and found no differences with regards to the cellular responses measured.

tag: gender

value: Female

value: 5-6 weeks

tag: genotype/variation

value: Trf1 knock out

value: bone marrow macrophage (BMM)

tag: protocol

value: E.coli stimulation


title: macrophage_TrifKO_E.coli_6h_rep2

description:
KO_Ecoli6h_2
G004_H07_16_114-8_KO_Ecoli6h_2.CEL

source_name: bone marrow derived macrophages from Trif knockout mice, stimulated with E.coli for 6hrs

tag: time


title: 1st+2nd pulses_30min

source_name: 1st+2nd pulses_30min


title: macrophage_TrifKO_E.coli_6h_rep1

description:
KO_Ecoli6h_1
G004_H05_08_113-8_KO_Ecoli6h.CEL

tag: age


title: macrophage_TrifKO_E.coli_3h_rep3

description:
KO_Ecoli3h_3
G004_G09_23_117-7_KO_Ecoli3h.CEL


title: 1st+2nd pulses_180min

source_name: 1st+2nd pulses_180min


title: COX_0001_exon-level


title: Forafac®1157N _1.5mg/l3_0.5mg/l3

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

hyb_protocol: The hybridization was performed according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Two probe volumes (Cy3 vs. Cy5) corresponding with 300 ng cRNA were mixed and applied onto every microarray. The hybridization design comprised one separate n+2 A-optimal design for each of the Forafac® mixtures (Knapen et al., 2009). The microarray slides were incubated at 65°C for 17 hours in a hybridization chamber which was placed in a rotating (10 rpm) Agilent hybridization oven. The slides were washed with Agilent wash buffers and acetonitrile and finally submersed in Agilent stabilization and drying solution to protect against ozone-induced degradation of the cyanine dyes.

scan_protocol: Microarrays were scanned at 532 and 635 nm using the Genepix Personal 4100A confocal scanner (Axon instruments, Union City, USA) at a resolution of 5 µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing: The resulting images were analyzed using the Genepix Pro software 4.1 (Axon Instruments, Union City, USA) for spot identification and for quantification of the fluorescent signal intensities. Statistical analysis was performed in the open source statistical programming environment R, using the Bioconductor package limma (Linear Models for Microarray Data; Smyth, 2005). Spots for which the mean foreground signal was lower than the mean local BG+2SD (BG: background signal, SD: standard deviation of the background) on every array in the design were removed before analysis, requiring that the foreground intensities lie outside the 97.5% confidence interval of the background intensities (Allemeersch, 2006). Median intensity data were background corrected using a normal-exponential convolution model (Ritchie et al., 2007) and normalized using the lowess method (Smyth and Speed, 2003). An empirical Bayes method was used to estimate contrasts of interest from the normalized and linear model-fitted data (Smyth, 2004). The different exposure concentrations were contrasted against the control. Gene transcripts were considered significantly different if both the log2 ratio of a gene in a contrast was ≤ -0.75 or ≥ +0.75 and the p-value was <0.05.

organism: Scophthalmus maximus

source_name: Forafac®1157N _1.5mg/l3

label_protocol: Fluorescently labelled cRNA was constructed using the Quick Amp labelling kit (Agilent Technologies, Diegem, Belgium) according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Briefly, total RNA was reverse transcribed into first and second strand cDNA. Using T7 RNA polymerase, the second strand cDNA was converted in cRNA while either Cy3-CTP or Cy5-CTP was incorporated. The labelled cRNA was purified using the Qiagen RNeasy mini spin column kit (Qiagen, Venlo, The Netherlands) and labelling efficiency was determined by spectrophotometry at 550nm (Cy3) and 650 nm (Cy5) (NanoDrop, NanoDrop Technologies, Rockland, USA).

extract_protocol: Total liver RNA was extracted applying the Trizol-RNA extraction procedure (Gibco BRL, Life Technologies, Merelbeke, Belgium). The extracted RNA was purified using Dnase I and RNase inhibitor (Fermentas, St. Leon-Rot, Germany) followed by a phenol/chloroform extraction. RNA integrity was checked by denaturing formaldehyde-agarose gel electrophoresis. RNA quality was measured using spectrophotometry (NanoDrop, NanoDrop Technologies, Rockland, DE, USA): absorbance at 260 nm (RNA), 280 nm (proteins) and 230 nm (organic contaminants and solvents) was determined and all RNA samples had 260/280 and 260/230 ratios >1.8.

value: liver

tag: agent

tag: dose

source_name: Forafac®1157N _0.5mg/l3


title: macrophage_TrifKO_E.coli_6h_rep3

description:
KO_Ecoli6h_3
G004_H09_24_117-8_KO_Ecoli6h.CEL


title: Forafac®1157N _control 3_0.5mg/l3

source_name: Forafac®1157N _control 3

value: control


title: Forafac®1157N _0.5mg/l2_1.5mg/l3

source_name: Forafac®1157N _0.5mg/l2


title: Self2

city: Beltsville

first: George

last: Liu

state: MD

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

description: Self-to-self hybridization of the second founder cell line.

hyb_protocol: Performed by NimbleGen standard protocol

data_processing: Spacial corrected and normalized by standard NimbleGen methods

organism: Bos taurus

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, founder cell line

label_protocol: Labeled by NimbleGen.

extract_protocol: Qiagen QIAamp DNA Mini Kit

tag: breed

value: Jersey and Holstein mix

value: female

value: fetal fibroblasts

tag: sample type

value: founder cell line


title: COX_0002_exon-level

tag: biological source

value: Lymphoblastoid cell line

tag: haplotype

value: Unstimulated


title: Self3

description: Self-to-self hybridization of the third founder cell line.

scan_protocol: Performed by NimbleGen standard protocol

value: male


title: Forafac®1157N _1.5mg/l2_0.5mg/l1

source_name: Forafac®1157N _1.5mg/l2

tag: tissue


title: N-003_5

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human normal donor N-003

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.

source_name: Human normal donor N-003

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: legend

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); N:Normal donor sample; MGUS:Monoclonal Gammopathy of Undetermined Significance sample; PCL:Plasma Cell Leukemia sample.

value: purified plasma cells (PCs)

value: N


title: macrophage_TrifKO_E.coli_1h_rep3

description:
KO_Ecoli1h_3
G004_F09_22_117-6_KO_Ecoli1h.CEL

source_name: bone marrow derived macrophages from Trif knockout mice, stimulated with E.coli for 1hr

tag: strain

value: Female


title: Forafac®1157N _control 3_control1

source_name: Forafac®1157N _control1


title: Low3

description: Hybridization of the third founder cell line (reference) and the corresponding derived cell line (test) with low transgenic success rate.

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, derived cell line, low efficiency

value: derived cell line

tag: cloning efficiency

value: low


title: macrophage_TrifKO_E.coli_1h_rep2

description:
KO_Ecoli1h_2
G004_F07_14_114-6_KO_Ecoli1h.CEL

value: 5-6 weeks

value: Trf1 knock out

tag: cell type

value: bone marrow macrophage (BMM)


title: macrophage_TrifKO_E.coli_3h_rep1

description:
KO_Ecoli3h_1
G004_G05_07_113-7_KO_Ecoli3h.CEL

value: E.coli stimulation


title: Forafac®1157N _0.5mg/l1_control3

source_name: Forafac®1157N _0.5mg/l1

value: liver

source_name: Forafac®1157N _control3

value: control


title: macrophage_TrifKO_E.coli_1h_rep1

description:
KO_Ecoli1h_1
G004_F05_06_113-6_KO_Ecoli1h.CEL


title: macrophage_TrifKO_control_rep3

description:
KO_ctr0h_3
G004_E09_21_117-5_KO_ctr0h.CEL

source_name: bone marrow derived macrophages from Trif knockout mice, not stimulated


title: Forafac®1157N _1.5mg/l3_1.5mg/l2


title: High3

description: Hybridization of the third founder cell line (reference) and the corresponding derived cell line (test) with high transgenic success rate.

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, derived cell line, high efficiency

value: Jersey and Holstein mix

value: fetal fibroblasts

value: high


title: Self1

description: Self-to-self hybridization of the first founder cell line.

value: female

value: founder cell line


title: Forafac®1157N _control 2_1.5mg/l3

source_name: Forafac®1157N _control 2


title: macrophage_TrifKO_control_rep1

description:
KO_ctr0h_1
G004_E05_05_113-5_KO_ctr0h.CEL


title: macrophage_wildtype_E.coli_6h_rep3

description:
WT_Ecoli6h_3
G004_D09_20_117-4_WT_Ecoli6h.CEL

source_name: bone marrow derived macrophages from WT (C57BL6/J) mice, stimulated with E.coli for 6hrs

value: wild type


title: macrophage_wildtype_E.coli_6h_rep2

description:
WT_Ecoli6h_2
G004_D07_12_114-4_WT_Ecoli6h.CEL


title: macrophage_TrifKO_control_rep2

description:
KO_ctr0h_2
G004_E07_13_114-5_KO_ctr0h.CEL


title: macrophage_wildtype_E.coli_6h_rep1

description:
WT_Ecoli6h_1
G004_D05_04_113-4_WT_Ecoli6h_2.CEL


title: Forafac®1157 _control 3_control1

source_name: Forafac®1157 _control 3

source_name: Forafac®1157 _control1


title: macrophage_wildtype_E.coli_3h_rep3

description:
WT_Ecoli3h_3
G004_C09_19_117-3_WT_Ecoli3h.CEL

source_name: bone marrow derived macrophages from WT (C57BL6/J) mice, stimulated with E.coli for 3hrs


title: Forafac®1157N _control 3_1.5mg/l1

source_name: Forafac®1157N _control 3

source_name: Forafac®1157N _1.5mg/l1


title: High2

description: Hybridization of the second founder cell line (reference) and the corresponding derived cell line (test) with high transgenic success rate.

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, founder cell line


title: macrophage_wildtype_E.coli_3h_rep2

description:
WT_Ecoli3h_2
G004_C07_11_114-3_WT_Ecoli3h.CEL


title: Forafac®1157 _control 1_0.5mg/l2

source_name: Forafac®1157 _control 1

source_name: Forafac®1157 _0.5mg/l2


title: Forafac®1157 _0.5mg/l3_control3

source_name: Forafac®1157 _0.5mg/l3

source_name: Forafac®1157 _control3


title: macrophage_wildtype_E.coli_3h_rep1

description:
WT_Ecoli3h_1
G004_C05_03_113-3_WT_Ecoli3h.CEL


title: In vivo matured cumulus cells VVM-CC-4

city: Philadelphia

first: Young

middle: Shin

last: Lee

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: Gene expression data from cumulus cells isolated from COC matured in vivo (FSH stimulation + in vivo maturation with hCG stimulation)

hyb_protocol: The biotin-labeled cRNA samples were fragmented and 10 µg were hybridized onto Affymetrix Rhesus Genome GeneChip arrays at the University of Pennsylvania Microarray Core Facility. GeneChips were washed and stained in an automated fluidics station (Affymetrix).

scan_protocol: GeneChips were scanned using GCS3000 laser scanner.

data_processing: Probe hybridization intensity data were imported into the Affymetrix Expression Console Software and summarized using the Robust Multichip Analysis (RMA) algorithm with a global background correction and a quantile normalization.

organism: Macaca mulatta

source_name: Cumulus cells from COC matured in vivo (FSH stimulation + in vivo maturation with hCG stimulation)

label_protocol: 50 ng of total RNA from each sample were subjected to two rounds of cDNA synthesis and in-vitro transcription labeling to achieve a linear amplification (Eukaryotic Small Sample Target Labeling Assay, Affymetrix GeneChip Expression Analysis Technical Manual) with minor modifications (initial 5 µl volume for annealing and reverse transcription for 30 min at 42°C followed by 30 min at 45°C).

extract_protocol: Total RNA was extracted from cumulus cells using PicoPure RNA purification kit (MDS Analytical Technologies)

value: cumulus cells

tag: maturation

value: In vivo maturation


title: Forafac®1157 _0.5mg/l2_1.5mg/l3

source_name: Forafac®1157 _1.5mg/l3


title: Forafac®1157N _control 1_0.5mg/l2

source_name: Forafac®1157N _control 1


title: Forafac®1157 _0.5mg/l1_control3

source_name: Forafac®1157 _0.5mg/l1


title: Forafac®1157 _1.5mg/l1_0.5mg/l3

source_name: Forafac®1157 _1.5mg/l1


title: macrophage_wildtype_E.coli_1h_rep3

description:
WT_Ecoli1h_3
G004_B09_18_117-2_WT_Ecoli1h_2.CEL

source_name: bone marrow derived macrophages from WT (C57BL6/J) mice, stimulated with E.coli for 1hr

tag: gender

value: Female


title: Forafac®1157 _1.5mg/l2_0.5mg/l1

source_name: Forafac®1157 _1.5mg/l2


title: macrophage_wildtype_E.coli_1h_rep2

description:
WT_Ecoli1h_2
G004_B07_10_114-2_WT_Ecoli1h.CEL

tag: genotype/variation


title: In vivo matured cumulus cells VVM-CC-3


title: Forafac®1157N _1.5mg/l1_control 2

source_name: Forafac®1157N _control 2


title: Forafac®1157 _1.5mg/l3_1.5mg/l2


title: macrophage_wildtype_E.coli_1h_rep1

description:
WT_Ecoli1h_1
G004_B05_02_113-2_WT_Ecoli1h.CEL

tag: protocol


title: Low1

description: Hybridization of the first founder cell line (reference) and the corresponding derived cell line (test) with low transgenic success rate.

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, derived cell line, low efficiency

value: derived cell line


title: In vivo matured cumulus cells VVM-CC-1


title: Low2

description: Hybridization of the second founder cell line (reference) and the corresponding derived cell line (test) with low transgenic success rate.

value: low


title: In vivo matured cumulus cells VVM-CC-2


title: Forafac®1157 _control 3_1.5mg/l1

source_name: Forafac®1157 _control 3


title: Forafac®1157 _1.5mg/l1_control2

source_name: Forafac®1157 _control2


title: Forafac®1157 _control 2_1.5mg/l3

source_name: Forafac®1157 _control 2


title: In vitro matured cumulus cells IVM-CC-3

description: Gene expression data from cumulus cells isolated from COC matured in vitro (FSH stimulation + in vitro maturation)

source_name: Cumulus cells from COC matured in vitro (FSH stimulation + in vitro maturation)

value: In vitro maturation


title: Pre-maturation cumulus cells PM-CC-4

description: Gene expression data from cumulus cells isolated from immature COC (FSH-stimulation only)

source_name: Cumulus cells from immature COC (FSH-stimulation only)

value: Pre-maturation


title: In vitro matured cumulus cells IVM-CC-1


title: macrophage_wildtype_control_rep1

description:
WT_ctr0h_1
G004_A05_01_113-1_WT_ctr0h.CEL

source_name: bone marrow derived macrophages from WT (C57BL6/J) mice, not stimulated

value: 5-6 weeks

value: bone marrow macrophage (BMM)

tag: time


title: In vitro matured cumulus cells IVM-CC-2


title: Pre-maturation cumulus cells PM-CC-1


title: Pre-maturation cumulus cells PM-CC-2


title: macrophage_wildtype_control_rep2

description:
WT_ctr0h_2
G004_A07_09_114-1_WT_ctr0h_2.CEL

tag: age


title: macrophage_wildtype_control_rep3

description:
WT_ctr0h_3
G004_A09_17_117-1_WT_ctr0h.CEL


title: Pre-maturation cumulus cells PM-CC-3


title: High1

description: Hybridization of the first founder cell line (reference) and the corresponding derived cell line (test) with high transgenic success rate.

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, derived cell line, high efficiency

source_name: Bovine transgenic fetal fibroblasts derived from breeding cloned Jersey and Holstein cattle, founder cell line


title: array44: U20S synchronized by double thymidine block: 4 hr

status: Public on May 21 2011

city: Stanford

first: Tiffany

last: Hung

address: 371 SERRA MALL

institute: Stanford University

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: RMA normalized raw signals followed by peak calling analysis

label_protocol: RT to cDNA, standard Nimblegen protocol

growth_protocol: dmem 10% FBS

extract_protocol: Trizol extraction

tag: cell line

value: osteosarcoma


title: array51: Human ES (H9) rep3 (control)

source_name: Human ES (H9)

value: differentiated ES


title: array53: Primary human keratinocytes transduced with Sox2

growth_protocol: keratinocyte media + 10% fbs

value: Primary human keratinocytes


title: array53: Primary human keratinocytes transduced with Sox2 (control)

source_name: Primary human keratinocytes


title: array51: Human ES (H9) rep3

value: passage5 differentiated from ES


title: array48: U20S synchronized by double thymidine block: 16 hr (control)

source_name: U20S asynchronous


title: array50: Human ES (H9) rep2 (control)


title: array45: U20S synchronized by double thymidine block: 6 hr (control)


title: array47: U20S synchronized by double thymidine block: 14 hr (control)


title: array52: Primary human keratinocytes transduced with IkB (control)


title: array43: U20S synchronized by double thymidine block: 4 hr


title: array40: Primary human keratinocytes transduced with SOX2, RAS, and IkB (control)


title: array42: U20S synchronized by double thymidine block: 2 hr


title: array47: U20S synchronized by double thymidine block: 14 hr

source_name: U20S synchronized by double thymidine block: 10 hr


title: array46: U20S synchronized by double thymidine block: 8 hr (control)


title: array50: Human ES (H9) rep2

value: passage76 differentiated from ES


title: array43: U20S synchronized by double thymidine block: 4 hr (control)


title: array44: U20S synchronized by double thymidine block: 4 hr (control)


title: array49: Human ES (H9) rep1 (control)


title: array42: U20S synchronized by double thymidine block: 2 hr (control)


title: array46: U20S synchronized by double thymidine block: 8 hr


title: array40: Primary human keratinocytes transduced with SOX2, RAS, and IkB

source_name: keratinocytes


title: array52: Primary human keratinocytes transduced with IkB

source_name: Primary human keratinocytes transduced with IKB


title: array49: Human ES (H9) rep1

value: passage152 differentiated from ES


title: array41: U2OS synchronized by double thymidine block: 0 hr

source_name: U20S synchronized by double thymidine block: 0 hr


title: array41: U2OS synchronized by double thymidine block: 0 hr (control)


title: array48: U20S synchronized by double thymidine block: 16 hr

source_name: U20S synchronized by double thymidine block: 12 hr


title: array45: U20S synchronized by double thymidine block: 6 hr


title: array39: Primary human keratinocytes transduced with MYC


title: array39: Primary human keratinocytes transduced with MYC (control)

source_name: Primary human keratinocytes transduced with LacZ


title: array38: E2F3-RAS-IkB tumor 2 (control)

source_name: GFP-RAS-IkB tumor pool

value: GFP-RAS-IkB tumor pool


title: array37: E2F3-RAS-IkB tumor 1

source_name: tumor

value: E2F3-RAS-IkB tumor 1


title: array38: E2F3-RAS-IkB tumor 2

value: E2F3-RAS-IkB tumor 2


title: array35: MYC-RAS-IkB tumor 1 (control)


title: array37: E2F3-RAS-IkB tumor 1 (control)


title: array36: MYC-RAS-IkB tumor 2

value: MYC-RAS-IkB tumor 2


title: array36: MYC-RAS-IkB tumor 2 (control)


title: array34: Invasive ductal breast carcinoma P10 (control)

source_name: normal breast

value: normal breast tissue


title: array32: Invasive ductal breast carcinoma P7 (control)


title: array33: Invasive ductal breast carcinoma P9 (control)


title: array28: Invasive ductal breast carcinoma P3

source_name: Invasive ductal breast carcinoma

value: Invasive ductal breast carcinoma P3


title: array32: Invasive ductal breast carcinoma P7

value: Invasive ductal breast carcinoma P7


title: array33: Invasive ductal breast carcinoma P9

value: Invasive ductal breast carcinoma P9


title: array27: Invasive ductal breast carcinoma P2

value: Invasive ductal breast carcinoma P2


title: array29: Invasive ductal breast carcinoma P4 (control)


title: array26: Primary human keratinocytes transduced with myc (control)

source_name: keratinocytes + lacZ


title: array30: Invasive ductal breast carcinoma P5

value: Invasive ductal breast carcinoma P5


title: array28: Invasive ductal breast carcinoma P3 (control)


title: array34: Invasive ductal breast carcinoma P10

value: Invasive ductal breast carcinoma P10


title: array31: Invasive ductal breast carcinoma P6 (control)


title: array24: Primary human keratinocytes transduced with sox (control)

source_name: keratinocytes + gfp


title: array27: Invasive ductal breast carcinoma P2 (control)


title: array31: Invasive ductal breast carcinoma P6

value: Invasive ductal breast carcinoma P6


title: array25: Primary human keratinocytes transduced with myc


title: array25: Primary human keratinocytes transduced with myc (control)


title: array24: Primary human keratinocytes transduced with sox


title: array29: Invasive ductal breast carcinoma P4

value: Invasive ductal breast carcinoma P4


title: array30: Invasive ductal breast carcinoma P5 (control)


title: array26: Primary human keratinocytes transduced with myc

value: Primary human keratinocytes


title: array35: MYC-RAS-IkB tumor 1

value: MYC-RAS-IkB tumor 1


title: array23: Primary human keratinocytes transduced with sox (control)


title: array22: Primary human keratinocytes transduced with myc (control)


title: array23: Primary human keratinocytes transduced with sox


title: array21: Primary human keratinocytes transduced with myc (control)


title: array21: Primary human keratinocytes transduced with myc


title: array20: Primary human keratinocytes transduced with ras (control)


title: array22: Primary human keratinocytes transduced with myc


title: array20: Primary human keratinocytes transduced with ras


title: array19: Primary human keratinocytes transduced with E2F3


title: array19: Primary human keratinocytes transduced with E2F3 (control)


title: array18: Primary human keratinocytes transduced with ras


title: array14: Primary human keratinocytes treated with Ca2+ for 48 hours


title: array18: Primary human keratinocytes transduced with ras (control)


title: array13: Primary human keratinocytes transduced with p63 shRNA


title: array17: Primary human keratinocytes transduced with IkB (control)


title: array11: HeLa synchronized by double thymidine block: 10 hr (control)

source_name: HeLa asynchronous

value: hela


title: array17: Primary human keratinocytes transduced with IkB


title: array10: HeLa synchronized by double thymidine block: 8 hr

value: HeLa


title: array10: HeLa synchronized by double thymidine block: 8 hr (control)


title: array8: HeLa synchronized by double thymidine block: 4 hr (control)


title: array15: Primary human keratinocytes transduced with E2F3 (control)


title: array8: HeLa synchronized by double thymidine block: 4 hr


title: array12: HeLa synchronized by double thymidine block: 12 hr (control)


title: array13: Primary human keratinocytes transduced with p63 shRNA (control)

source_name: empty vector


title: array16: Primary human keratinocytes transduced with myc (control)


title: array7: HeLa synchronized by double thymidine block: 2 hr


title: array15: Primary human keratinocytes transduced with E2F3


title: array11: HeLa synchronized by double thymidine block: 10 hr


title: array6: HeLa synchronized by double thymidine block: 0 hr (control)


title: array16: Primary human keratinocytes transduced with myc


title: array9: HeLa synchronized by double thymidine block: 6 hr


title: array6: HeLa synchronized by double thymidine block: 0 hr


title: array14: Primary human keratinocytes treated with Ca2+ for 48 hours (control)

source_name: untreated


title: array5: Human fetal lung fibroblasts transduced with HRAS

value: fetal lung fibroblasts


title: array3: Human fetal lung fibroblasts transduced with HPV-E7 (control)

treatment_protocol: empty vector


title: array5: Human fetal lung fibroblasts transduced with HRAS (control)


title: KIT BL6 WT rep2

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

institute: Center for Genomic Regulation

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome 4x44k 60-mer oligo microarray using stnadard Agilent protocol.

scan_protocol: The arrays were scanned on an Agilent G2565CA microarray scanner at 110% PMT and 5 μm resolution.

data_processing: Intensity data was extracted using the Feature Extraction v 10.7.3.1 software (Agilent) and corrected for background noise using the normexp method [Ritchie ME etal. 2007. Bioinformatics]. To assure comparability across samples we use quantile normalization [Bolstad, B. (2001). Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf].

source_name: Sorted KIT+ cells from WT animals

label_protocol: cDNA from 25 ng of RNA was transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labelled cRNA using the standard Agilent labelling protocol.

growth_protocol: BM cells were pooled from 4 Msi2Gt/Gt females (aged 6-7 weeks) or 4 C57/Bl6 females (aged 6-7 weeks) and subjected to lineage depletion. Cells from each pool were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells (defined as Lineage- Sca-1+ c-kit+) and Kit+ (defined as Lineage-, Sca-1-, c-kit+) and sorted by FACS into PBS+5%FBS.

extract_protocol: Cells were pelleted and RNA was extracted using the RNeasy Mini Kit (Qiagen) by the manufacturer's instructions.

tag: marker phenotype

tag: marker phenotype short name

value: KIT+

tag: genotype

value: KIT

tag: genetic background


title: KIT BL6 Msi2Gt rep1

source_name: Sorted KIT+ cells from Msi2 null animals


title: KIT BL6 Msi2Gt rep2