title: FR-si221-3

source_name: MCF7 fulvestrant-resistant cell line transfected by antisense hsa-miR-221


title: Spleen MZB cells from CD19:KLF3 mouse #92751

status: Public on Jan 29 2011

type: RNA

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina MouseRef-8 BeadChips V2  at 58oC for 20 hrs

scan_protocol: Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using  Illumina BeadStudio v3.

data_processing: Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed. The R software was used to quantile-normalized the probe intensities, and to minimun replace (surrogate-replacement policy) values below backround using the mean backround value of the built-in Illumina probe controls as an alternative to background substraction (which may introduce negative values) to reduce ‘over inflated’ expression ratios in subsequent steps.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CD19:KLF3 Spleen MZB

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.

growth_protocol: Viable spleen follicular B cells and MZB cells were sorted based on C19, CD21 and CD23 expression (sytox_blue_neg, CD19_pos, CD21_int, CD23_pos and sytox_blue_neg, CD19_pos, CD21_high, CD23_neg respectively)

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Cells were obtained from control B6 mice or mice transgenic for KLF3 (CD19:KLF3)

tag: animal id

value: CD19:KLF3 mouse #92751

tag: cell type

value: Spleen MZB

tag: genetic background

tag: genotype

value: CD19:KLF3 transgenic


title: FR-si221-2

city: Bloomington

first: Meng

last: Li

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

country: USA

institute: Indiana University

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using R default settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: MCF7-FR cells were growing in phenol red-free medium with 10% charcoal-stripped fetal bovine serum (FBS) and 10E-7 mol/L fulvestrant

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

treatment_protocol: For transfection assays, cells were plated in antibiotic-free media and transfected with Lipofectamine 2000 (Invitrogen, Carlasbad, CA) according to the manufacturer's instructions.  Antagomirs were transfected at 100nM concentrations.

tag: treatment

tag: cell line


title: BNE_AD_Control_A06-140a

city: London

first: Pascal

middle: Francis

last: Durrenberger

address: hammersmith hospital, Du cane road

department: Infectious disease and immunity

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The BeadChips were scanned using the Illumina BeadArray Reader according to standard Illumina scan protocol.

data_processing: The data was extracted using BeadStudio 3.2 (Illumina). Data normalisation and gene differential expression analyses were conducted using the Rosetta error models available in the Rosetta Resolver® system v7.0 (Rosetta Biosoftware, Seattle, Wa, USA).

label: Biotin

source_name: Entorhinal cortex

label_protocol: RNA samples were prepared for array analysis using the Illumina TotalPrep™-96 RNA Amplification Kit.

extract_protocol: Total RNA was extracted from dissected snap-frozen tissue by the individual laboratories according to a BNE optimised common protocol using the RNeasy® tissue lipid mini kit. Quality was assessed using Bioanalyzer.

tag: disease

value: Alzheimer's disease

tag: gender

value: M

tag: age at death (in years)

tag: post-mortem delay (in hours)

tag: post-mortem delay


title: Nonlesional Epithelium Nonatopic Control rep1

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description: Nonatopic Control biological replicate 1

hyb_protocol: cRNA was hybridized to Illumina Sentrix HumanRef-8 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

scan_protocol: All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction.  Two types of processed data were used for analysis: 1. Data was Z-transformed based on probes which were Present for at least one sample (the Illumina Detection Pvalue was < 0.01).  Specifically, for each sample, define m to be the mean of the expression values for that sample taken over all probes present in at least 1 sample, and define s to be the corresponding standard deviation. Then for all  the probes on the array, for that sample the Z-transformed expression value corresponding to an expression value e is (e-m)/s. 2. For use in calculating correlations of gene expression levels with the values of clinical variables; the expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed. For the data matrices, the ID_REF is the Illumina probe identifier, and the Detection Pval is the Illumina call for whether the measured expression level is Present (above background).  Detection Pvalues near 0 indicate Present.  In our analysis we considered expression values with a Detection Pvalue below 0.01 to be Present. Z-transformed data (item 1) provided as a supplementary file on GSE26952. Data median scaled (to median = 256) and then log base 2 transformed (item 2) included in Sample table.

source_name: Full-thickness epidermis

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

extract_protocol:
Tissue samples were obtained and prepared as described in the Methods section of the paper cited in the overall design section of this GEO submission. Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany).
The quality of total RNA samples was assessed using
an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease group

value: Nonatopic Control

tag: Sex

value: m

tag: age

tag: race

value: Caucasian

tag: easi/pasi

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:0

tag: ar or asthma

value: YES, subject has history of AR (allergic rhinitis), asthma or both:no

tag: eosinophil level (cells/ml)

value: normal (120-300 cells/ml):90

tag: ige (kiu/l)

tag: rast (radioallergosorbent test)

value: detects IgE that reacts specifically with suspected or known allergens:negative

tag: s. aureus

value: Skin culture positive or negative for S. Aureus:neg


title: FR-control-3

source_name: MCF7 fulvestrant-resistant cell line

tag: treatment

value: control


title: Nonlesional Epithelium Nonatopic Control rep2b

description: Nonatopic Control biological replicate 2 technical replicate b

value: f

value: YES, subject has history of AR (allergic rhinitis), asthma or both:YES

value: normal (120-300 cells/ml):50


title: FR-si221-1

tag: cell line


title: Spleen Follicular B cells from B6 mouse #92750

source_name: B6 Spleen Follicular B cells

tag: animal id

tag: cell type

value: Spleen Follicular B cells

tag: genetic background

tag: genotype

value: wild type


title: Spleen MZB cells from B6 mouse #92750

description: Spleen MZB cells from B6 mouse #92750

source_name: B6 Spleen MZB

value: Spleen MZB


title: BNE_AD_Control_A03-086

tag: disease

value: Alzheimer's disease

tag: gender

value: F

tag: age at death (in years)

tag: post-mortem delay (in hours)

tag: post-mortem delay


title: Nonlesional Epithelium Psoriasis rep3

description: Psoriasis biological replicate 3

tag: disease group

value: Psoriasis

tag: Sex

tag: age

tag: race

tag: easi/pasi

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:9.1

value: normal (120-300 cells/ml):10

value: detects IgE that reacts specifically with suspected or known allergens:positive


title: Nonlesional Epithelium Psoriasis rep4

description: Psoriasis biological replicate 4

value: Caucasian

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:6.6

tag: ar or asthma

value: YES, subject has history of AR (allergic rhinitis), asthma or both:no

tag: eosinophil level (cells/ml)

tag: ige (kiu/l)

tag: rast (radioallergosorbent test)

tag: s. aureus


title: FR-control-2

tag: treatment

tag: cell line


title: Spleen Follicular B cells from B6 mouse #92748

tag: animal id

tag: cell type

tag: genetic background

tag: genotype


title: WT#4_Cy3 vs EtrA7-1#4_Cy5

city: Atlanta

first: Claribel

last: Cruz-Garcia

state: Georgia

address: 311 Ferst Dr

department: Civil and Environmental Engineering

institute: Georgia Institute of Technology

description: Biological replicate #4 of 3, no biological replicate #1.

hyb_protocol: Labeled samples of the experimental (etrA deletion mutant) and the reference (wild type) with similar specific activities were used to hybridized on the array slides using a fresh hyb soln (50% Formamide, 5X SSC buffer, 0.2% SDS, 1 mg/ml Salmon Sperm DNA, 12.5 mM EDTA, and spiking controls) at room temperature. Before hybridization slides were prehyb for 45 min using a soln [5X SSC buffer, 0.1% SDS, 5g BSA (Sigma A9418), 0.01 M EDTA) at 42ºC. Slides were hyb for 16-18 h at 42ºC. After hyb, slides were washed four times for 4 min each, first wash on a 1X SSC, 0.2% SDS soln at 42ºC, the rest at room temp. Second wash was in a 0.1X SSC, 0.2% SDS soln and third and fourth washes were in a 0.1 X SSC soln.

scan_protocol: Slides were scanned in an Axon 4000B scanner and GenePix Pro 5.0 software.

data_processing:
Data analysis was performed using the GeneSpring 6.0 software.
The data was normalized per chip per gene (Lowess Normalization) and the spots with less than 55% of pixels greater than the background plus two standard deviations were not included in the analysis. The data was filtered using the Benjamini and Hochberg false discovery rate with 95% confidence and only those genes with a 2>-fold change in magnitude were considered significant.

organism: Shewanella oneidensis MR-1

source_name: etrA deletion strain_replicate #4_grown anerobically with nitrate

label_protocol: cDNA preparation and labeling were performed using the SuperScriptII (Invitrogen) and a 2:3 ratio of 5-(3-aminoallyl)-dUTP and dTTP following the manufacturer's manual. Reactions were incubated at 42ºC for 16 h. 20 ul of NaOH (1N) and 20 ul of 0.5 M EDTA pH 8 were added to the mixture, followed by a 15 min incubation at 65ºC. Reaction was neutralized adding 50 ul of HEPES Buffer (pH 7). cDNA was purified using Qiagen PCR purification Kit columns and Phosphate Buffers. Samples were dried in a SpeedVac and resuspended in 4.5 ul of a fresh solution of 0.1 M Na2CO3.HCl (pH 9) and 4.5 ul of either Cy3 or Cy5 dyes. Samples incubated for 60 min at 25 ºC followed by purification after addition of 0.1 M sodium acetate with the Qiagen PCR purification kit. Samples of the experimental (etrA deletion mutant) and the reference (wild type) with similar specific activities were used t

growth_protocol: Cultures were grown in 250 ml serum bottles containing 100 ml of HEPES minimal medium prepared anaerobically and supplemented with 2 mM KNO3 and 20 mM lactate.

extract_protocol: Total RNA was extracted from cultures at mid-log phase and concentrated by centrifuging at 4ºC for 30 min at 7,500 rpm. The pellets were washed with 1ml of an ice-cold 1X DEPC-treated PBS solution. The RNA was extracted with The RNAwiz Solution following the instructions of the manufacturer (Ambion, Inc.). The RNA extraction was followed by an isopropanol precipitation and its resuspension in the RNA storage solution (Ambion, Inc.). Samples were treated with DNaseI (Roche) to eliminate residual DNA and were later purified by phenol, phenol:chloroform (1:1) and chloroform extractions, and stored in ethanol at -80ºC until ready for use. Quality of RNA was observed using the RNA 6000 PicoLab Chip kit and the 2100 Bioanalyzer (Agilent Technologies). RNA concentration was determined with OD measurements at 260 nm using a Varian Cary 50 BIO UV-Vis spectrophotometer (Varian, Zug, Switzerland).

treatment_protocol: Cultures were incubated at 30ºC without shaking.

value: etrA deletion strain

source_name: MR-1 wild type strain_replicate #4_grown anerobically with nitrate

value: wild type strain


title: Nonlesional Epithelium Psoriasis rep1

description: Psoriasis biological replicate 1

value: m

value: African American

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:34

value: Skin culture positive or negative for S. Aureus:neg


title: Spleen Follicular B cells from CD19:KLF3 mouse #92747

source_name: CD19:KLF3 Spleen Follicular B cells

value: CD19:KLF3 mouse #92747

value: Spleen Follicular B cells

value: CD19:KLF3 transgenic


title: FR-control-1

value: control


title: BNE_AD_Control_A03-065

tag: disease

value: Alzheimer's disease

tag: gender

value: M

tag: age at death (in years)

tag: post-mortem delay (in hours)

tag: post-mortem delay


title: Nonlesional Epithelium Atopic Dermatitis rep5

description: Atopic Dermatitis biological replicate 5

tag: disease group

value: Atopic Dermatitis

tag: Sex

value: f

tag: age

tag: race

tag: easi/pasi

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:4.5

value: YES, subject has history of AR (allergic rhinitis), asthma or both:YES


title: soleus, biological rep3

city: Wuhan

first: Bo

last: Zuo

address: Shizishan Street

country: China

institute: HZAU

description: Gene expression data from SE muscle.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Porcine Genechip. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The probe arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1). Natural logarithms were then taken on quantile normalization (GeneSpring 10.0). Identification of DE genes was conducted using SAS (Ver.8.1, T-test). The p value cutoff for DE genes was set at 0.05.

organism: Sus scrofa

source_name: soleus of 150 day Meishan pig

label_protocol: Biotinylated cRNA were prepared according to the GeneChip® IVT Labeling Kit (Affymetrix) protocol.

growth_protocol: The pigs were fed twice daily with diets formulated according to age under a standardized feeding regimen and free access to water.

extract_protocol: TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN) were used for RNA extractions and purifications respectively followed by manufacturer’s instructions.

treatment_protocol: Two muscles with different locations, functions, and biochemical properties of three Meishan pigs were sampled: the longissimus at the last rib level, a fast twitch glycolytic muscle involved in voluntary movements of the back, and the deep portion of the SE, a oxydolytic muscle.

tag: tissue type

value: muscle

tag: muscle type

value: soleus

tag: biological replicate


title: Spleen MZB cells from B6 mouse #92748

description: Spleen MZB cells from B6 mouse #92748

tag: animal id

value: Spleen MZB

value: wild type


title: WT#2_Cy3 vs EtrA7-1#2_Cy5

description: Biological replicate #2 of 3, no biological replicate #1.

source_name: etrA deletion strain_replicate #2_grown anerobically with nitrate

value: etrA deletion strain

source_name: MR-1 wild type strain_replicate #2_grown anerobically with nitrate

value: wild type strain


title: longissimus dorsi, biological rep3

description: Gene expression data from LD muscle.

source_name: longissimus dorsi of 150 day Meishan pig

value: longissimus dorsi


title: WT#3_Cy3 vs EtrA7-1#3_Cy5

description: Biological replicate #3 of 3, no biological replicate #1.

source_name: etrA deletion strain_replicate #3_grown anerobically with nitrate

source_name: MR-1 wild type strain_replicate #3_grown anerobically with nitrate


title: Spleen MZB cells from CD19:KLF3 mouse #92747

value: CD19:KLF3 mouse #92747

tag: cell type


title: Spleen MZB cells from CD19:KLF3 mouse #92759

value: CD19:KLF3 mouse #92759

tag: genetic background


title: soleus, biological rep2

description: Gene expression data from SE muscle.


title: Nonlesional Epithelium Atopic Dermatitis rep3

description: Atopic Dermatitis biological replicate 3

value: African American

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:15.2

tag: ar or asthma

tag: eosinophil level (cells/ml)

tag: ige (kiu/l)

tag: rast (radioallergosorbent test)

value: detects IgE that reacts specifically with suspected or known allergens:positive

tag: s. aureus

value: Skin culture positive or negative for S. Aureus:neg


title: Nonlesional Epithelium Psoriasis rep2

description: Psoriasis biological replicate 2

value: Psoriasis

value: m

value: Caucasian

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:3

value: YES, subject has history of AR (allergic rhinitis), asthma or both:no

value: detects IgE that reacts specifically with suspected or known allergens:negative

value: Skin culture positive or negative for S. Aureus:neg / positive to Strep. Viridans


title: WT#3_Cy5 vs EtrA7-1#3_Cy3

tag: genotype


title: Spleen Follicular B cells from CD19:KLF3 mouse #92759

value: Spleen Follicular B cells

value: CD19:KLF3 transgenic


title: longissimus dorsi, biological rep1

description: Gene expression data from LD muscle.

value: muscle


title: soleus, biological rep1

description: Gene expression data from SE muscle.

value: soleus


title: Nonlesional Epithelium Atopic Dermatitis rep4

description: Atopic Dermatitis biological replicate 4

tag: disease group

value: Atopic Dermatitis

value: f

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:11.3

value: YES, subject has history of AR (allergic rhinitis), asthma or both:YES

value: Skin culture positive or negative for S. Aureus:pos


title: Spleen Follicular B cells from B6 mouse #92758

value: wild type


title: Nonlesional Epithelium Atopic Dermatitis rep2

description: Atopic Dermatitis biological replicate 2

tag: Sex

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:34.6

value: detects IgE that reacts specifically with suspected or known allergens:positive

value: Skin culture positive or negative for S. Aureus:neg


title: Nonlesional Epithelium Atopic Dermatitis rep1

description: Atopic Dermatitis biological replicate 1

value: m

tag: age

value: Native American

value: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis:11.6


title: WT#4_Cy5 vs EtrA7-1#4_Cy3

value: wild type strain

value: etrA deletion strain


title: Spleen MZB cells from B6 mouse #92758

description: Spleen MZB cells from B6 mouse #92758

value: Spleen MZB


title: longissimus dorsi, biological rep2

description: Gene expression data from LD muscle.

value: muscle

value: longissimus dorsi


title: WT#2_Cy5 vs EtrA7-1#2_Cy3


title: cells treatment with HY and irradiation then cultured for 6 h

status: Public on Jan 28 2011

city: shanghai

first: shu

last: yang

address: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science

institute: Fudan University

description: cells treatment with HY only

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Cubic spline normalization using Illumina BeadStudio Version BSGX Version3.2.3

label: botin

source_name: human nasopharyngeal carcinoma cell line CNE-2

label_protocol: As described in the illumina sentrix human WG-6_V2 expression BeadChip arrays processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)

tag: strain


title: cells treatment with HY and irradiation then cultured for 20 h

description: cells treatment with HY only

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: cells treatment with HY and irradiation then cultured for 2 h

description: cells treatment with HY only


title: cells treatment with HY and irradiation

description: cells treatment with HY only


title: cells treatment with HY and irradiation then cultured for 12 h

description: cells treatment with HY only


title: cells treatment with HY only then cultured for 20 h

description: cells treatment with HY only


title: COL2_625

city: Marseille

first: Sylviane

last: Olschwang

address: 232 boulevard Sainte-Marguerite

department: Centre de Recherches en Cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: gene expression data from stage II primary colon adenocarcinoma after surgery only

hyb_protocol: Expression profiles were established with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays

scan_protocol: Scanning was done with an Affymetrix GeneArray scanner and quantification with the Affymetrix GeneChip Operating Software (Affymetrix, Paris France).

data_processing:
CEL files were processed in the R/Bioconductor environment. Pre-processing steps (background adjustment, normalization and summarization) were performed with the GCRMA package
Expression measures were handled on log2 scale for statistical computations as well as for display purposes. Genes with overall low intensity were removed from further analysis. All remaining genes had an expression value greater than log2 (100) in at least 10% of the samples. As tumor samples and/or RNA samples were provided by 4 different centres, genes were then median-centred within each centre individually.

source_name: colon adenocarcinoma stage II

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Enriched tumor zones were selected from frozen material on HE-stained cryosections to ensure a 60% minimum of tumor cells. Nucleic acids were extracted using QIAamp and RNeasy kits (Qiagen, Courtaboeuf France) according to the manufacturer's instructions. Quantification of samples was done with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Illkirch France). RNA integrity was controlled on an Agilent Bioanalyzer (Agilent Technologies, Massy France).

treatment_protocol: Tissue samples were collected on fresh surgical specimens by pathologists within one hour after surgery from patients who underwent curative colonic resection, then flash frozen in liquid nitrogen and stored at -80°C until nucleic acids extraction.

tag: tissue

value: colon adenocarcinoma stage II

tag: age at diagnosis

tag: gender

value: M

tag: localisation

value: Left

tag: metastasis

tag: first apc mutation

tag: second apc mutation

tag: 5q loh


title: COL2_95


title: COL2_386


title: COL2_533


title: COL2_684

value: Right


title: COL2_538


title: COL2_426

value: F


title: COL2_92

value: LIVER


title: COL2_8336


title: COL2_363


title: COL2_512


title: COL2_7225


title: COL2_26


title: PFA Treated, biological rep3

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

description: Gene expression data from PFA-treated yeast cells

hyb_protocol: Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol were used. Yeast Genome 2.0 arrays were used.

scan_protocol: Affymetrix GenChip Scanner 3000 default parameters were used.

data_processing: Image analysis, scaling (TGT = 500), and probeset-level data analysis was performed using default parameters in GCOS v1.1

organism: Saccharomyces cerevisiae S288C

source_name: S. cerevisiae Strain S288C cells treated with plakortide F acid (PFA) at IC50 concentration (0.62 ug/ml)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Yeast cells were grown in synthetic dextrose medium MOPS buffered, pH 7.0.

extract_protocol: Qiagen RNeasy Midi-kit was used for total RNA extraction.

treatment_protocol: Yeast cells at OD 0.2 were treated with either plakortide F acid (PFA) at IC50 concentration (0.62 ug/ml), or solvent (0.25% DMSO), allowed to grow to OD 0.5, then harvested and frozen.

tag: agent

value: plakortide F acid (PFA)


title: COL2_211


title: COL2_284


title: COL2_225


title: COL2_241


title: COL2_7094


title: COL2_519


title: COL2_315


title: PFA Treated, biological rep1


title: PFA Treated, biological rep2


title: DMSO Control, biological rep3

description: Gene expression data from DMSO-treated yeast cells

source_name: S. cerevisiae Strain S288C cells treated with solvent (0.25% DMSO)

value: control


title: COL2_21


title: COL2_208


title: DMSO Control, biological rep2


title: BNE_AD_Control_A04-065

source_name: Entorhinal cortex

tag: disease

value: Alzheimer's disease

tag: age at death (in years)

tag: post-mortem delay (in hours)

tag: post-mortem delay


title: DMSO Control, biological rep1


title: VD, 72h

city: Tampa

first: Xiaohui

last: Zhang

state: FL

address: 12901 Bruce B. Downs Blvd.

department: Pathology and Lab Medicine

institute: University of South Florida College of Medicine

description: Gene expression data from ovarian cancer cells OVCAR3 treated with 1,25(OH)2D3 for 72 h (time point: 72h)

hyb_protocol: The cRNA was hybridized to GeneChip probe arrays according to the manufacturer's protocol. The chips were then washed, and the remaining biotinylated RNA was stained and scanned.

scan_protocol: The arrays were scanned using the HP ScanArray 5000 scanner according to the manufacturer's protocol.

data_processing: The .cel files were analyzed using Affymetrix MAS 5.0 and were scaled to an average intensity of 500.

source_name: OVCAR3 cells treated with 1,25(OH)2D3 for 72 h

label_protocol: RNA was converted to doublestranded cDNA using an oligo(dT)24 primer. The resulting double-stranded cDNA was transcribed into biotin-labeled cRNA using T7 RNA polymerase.

growth_protocol: OVCAR3 cells was cultured in RPMI 1640 medium supplemented with 15% fetal bovine serum (FBS), 2 mM Lglutamine, penicillin (50 U/ml), streptomycin (50 μg/ml), 10 mM HEPES, 1 mM sodium pyruvate, 4.5 g/L glucose, 1.5 g/L sodium bicarbonate and 10 μg/ml bovine insulin.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and purified using Qiagen Rneasy kit as recommended by Affymetrix.

treatment_protocol: 1,25(OH)2D3 was dissolved in ethanol, diluted to the desired concentration in culturing medium and added to the cells.

tag: cell line

tag: cell type

value: ovarian cancer

tag: treatment


title: VD, 8h

description: Gene expression data from ovarian cancer cells OVCAR3 treated with 1,25(OH)2D3 for 8 h (time point: 8h)

source_name: OVCAR3 cells treated with 1,25(OH)2D3 for 8 h


title: COL2_187


title: VD, 72h, biological replicate 3

scan_protocol: The arrays were scanned using the Affymetrix GCS3000 scanner according to the manufacturer's protocol.


title: COL2_12


title: COL2_206


title: COL2_200


title: Total RNA of M145 and wblA from 72 hour cultures and genomic DNA of M145

type: mixed

city: Norwich

first: Govind

last: Chandra

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

institute: John Innes Centre

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 72 hours of culturing on solid medium.

hyb_protocol: Pre-hybridisation: According to the protocol of the Pronto Universal Hybridisation Kit (Corning, 40026).  12 slides were processed at a time, and the slide staining troughs used had a 200 ml capacity.  Required volumes of Pronto Pre-Soak Solution and Pronto Pre-Hybridisation Solution were heated to 42C for 30 min.  2 ml of liquid borohydride was diluted in 198 ml (1:100 dilution) of 42C Pre-Soak Solution.  The resulting solution was used within 30 min of preparation to maximise its effectiveness.  Arrays were immersed in 42C Pre-Soak + liquid borohydride, and incubated at 42C for 20 min.  Arrays were transferred to Wash Solution 2 and incubated at room temperature for 30 s.  This step was repeated with fresh Wash Solution 2.  Arrays were transferred to 42C Universal Pre-Hybridisation Solution, and incubated at 42C for 15 min.  Arrays were transferred to fresh Wash Solution 2 and incubated at room temperature for 1 min.  Arrays were transferred to Wash Solution 3, and incubated at room temperature for 30 s.  This was repeated with fresh Wash Solution 3.  Arrays were transferred to nuclease-free dH2O and incubated at room temperature for 30 s.  Arrays were dried by centrifugation at 1600 xg for 5 min (Eppendorf 5810, A-4-62). Hybridisation: The concentration of Cy nucleotides was determined using the Nanodrop spectrophotometer.  An aliquot of Cy-cDNA containing 45pmol Cy3-dCTP was mixed with an aliquot of Cy-gDNA containing 20pmol of Cy5-dCTP.  The labelled target mixture was dried completely, in the dark, using a vacuum drier at room temperature.  The pellet was redissolved in 45 μl Pronto cDNA/LongOligo Hybridisation Solution (supplied with the Pronto Universal Microarray Hybridisation Kit; Corning, 40026), to give a final concentration of each cDNA-incorporated Cy dye of 1 pmol/μl.  From this point onwards, slides were processed one at a time.  The labelled target solution was denatured at 95C for 5 min in a PCR machine with a heated lid.  Whilst this was happening, the pre-hybridised slide was pre-heated on a slide heating block (Scientific Laboratory Supplies, MIC 4302) set to about 50C.  30 μl 3x SSC was placed in each well of the hybridisation chamber (CMT-Hybridisation Chambers, Corning, 2551) towards the end of incubation.  The target was applied to the arrayed area of the slide, avoiding bubbles.  The arrayed area was covered with a 24 x 60mm cover slip (HybriSlips, Sigma, H0784), and the array was sealed in the hybridisation chamber.  The arrays were incubated in a 42C waterbath for 16-20 h (overnight). Post-hybridisation: According to the protocol of the Pronto Universal Hybridisation Kit (Corning, 40026).  12 slides were processed at a time, and the slide staining troughs used had a 200 ml capacity.  The required volume of Wash Solution 1 was heated to 42C for 30 min.  Each hybridisation chamber was disassembled right side up and the array was immersed in Wash Solution 1 at 42C until the coverslip moved freely away from the slide.  The array was then transferred into fresh 42C Wash Solution 1.  Disassembly and coverslip removal were done one slide at a time.  Once all the slides had their coverslips removed and were immersed in fresh 42C Wash Solution 1, they were incubated at 42C for 5 min (NB. Slides processed first were incubated for longer than 5 min).  Arrays were transferred to Wash Solution 2 and incubated at room temperature for 2 min with gentle agitation (on an orbital shaker).  This step was repeated with fresh Wash Solution 2.  Arrays were transferred to Wash Solution 3 and incubated at room temperature for 2 min with gentle agitation.  This step was repeated with fresh Wash Solution 3.  Arrays were dried by centrifugation at 1600 xg for 5 min (Eppendorf 5810, A-4-62)

scan_protocol: The slides were scanned using a GenePix 4000A (Axon Instruments) scanner at 10 micron resolution.  Data was saved as multi-image .tif files. The multi-image .tif files were quantified using BlueFuse, and the outputs from BlueFuse were saved as .xls files.

data_processing: The .xls files output by Bluefuse were read into the limma package of the R platform and then processed as described in the documentation of the limma package. loess was used to normalise within arrays while scaling was used to normalise between arrays. Contrasts were defined as expression in wblA (mutant) minus expression in M145 (wild type) and coefficients re-calculated in terms of contrasts using the contrasts.fit() function. Finally the function eBayes() was used to compute (and rank genes by) the log-odds of differential expression.

organism: Streptomyces coelicolor

source_name: Total RNA from 72 hour culture labeled with Cyanine-5 (red).

label_protocol: Concentration of total RNA was determined using the Nanodrop spectrophotometer, and the quality of the RNA was assessed using the Agilent Bioanalyser.  For each labelling reaction, 5-7.5 μg total RNA (max. volume 7.6 μl) and 0.85 μl random primers (3 μg/μl; Invitrogen, 48190-011) were mixed, the volume adjusted to 8.45 μl with RNase-free dH2O, incubated at 70C for 10 min, and snap cooled on ice.  3 μl 5x First Strand Buffer (Invitrogen), 1.5 μl 100 mM DTT (Invitrogen), 0.3 μl dNTPs (25 mM each dA/G/TTP, 10mM dCTP; Invitrogen 100mM dNTP set, 10297-018), 1 μl SuperScript II (200U/μl; Invitrogen, 18064-014), and 0.75 μl Cy3-dCTP (GE Healthcare, PA55021) were added (if multiple labellings were done, a master mix was made up), and the reaction was incubated at 25C for 10 min, followed by 42C overnight.  All incubation steps were carried out in the dark, in a PCR machine with a heated lid.  10 μl 1N NaOH was added to each RNA labelling reaction, and incubated at 70C for 10 min, in order to hydrolyse the RNA.  The reactions were neutralised by adding 5 μl 1N HCl.  Labelled cDNA was purified using the MinElute PCR purification kit (QIAGEN, 28004) as follows.  To each labelling reaction, 125 μl (5 volumes) Buffer PB was added, and the mixture was applied to a MinElute column.  The column was centrifuged at 13,000 rpm for 1 min.  The flow-through was discarded, and 500 μl Buffer PE was added to the column, followed by centrifugation as before.  The flow-through was discarded, and 250 μl Buffer PE was added to the column, followed by centrifugation at 13,000 rpm for 2 min.  The column was transferred to a fresh 1.5 ml tube, and the labelled DNA was eluted from the column by adding 10 μl Buffer EB, incubating at room temperature for 1 min, and centrifuging at 13,000 rpm for 1 min.  This was done twice.

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 72 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.

extract_protocol: Typically 6 samples were handled at one time.  Frozen mycelium was ground in liquid nitrogen using a pestle and mortar, until a consistently uniform powder was obtained (~ 5 min).  The ground cells were transferred to an orange-capped 50 ml Corning tube, and 10 ml modified Kirby mix [1g N-lauroylsarcosine (Sigma, L-9150), 6g p-aminosalicylic acid sodium salt (Sigma, A-3505), 5ml 2M Tris-HCl pH8, 6ml buffered phenol pH8, dH2O to 100ml] was added.  Silica was also added (Sigma, S9887).  The suspension was vortexed for 2 min, and stored on ice.  The suspension was sonicated at full power for 6 cycles 30 s ON / 20 s OFF.  1 volume phenol/chloroform/isoamyl alcohol (25:24:1, pH8) was added, and vortexed for 30 s.  The suspension was centrifuged at 8500 rpm (Biofuge Primo, rotor Heraeus #7588) at 4C for 10 min.  The upper aqueous phase was transferred into a fresh tube, and 1 volume of phenol/chloroform/isoamyl alcohol was added, vortexed for 30 s, and centrifuged as before.  The upper aqueous phase was transferred to a fresh tube.  Phenol/chloroform/isoamyl alcohol extraction was repeated until there was a minimal amount of protein material in the interface.  The upper aqueous phase was transferred to a fresh tube, and 1 volume of chloroform was added, vortexed, and centrifuged as before.  The upper aqueous phase was transferred to a fresh tube and 0.1 volumes of 3M sodium acetate pH5.2, and 1 volume of isopropanol were added, and incubated at room temperature for 5 min.  The samples were centrifuged at 4C for 10 min.  The pellet of total nucleic acids (TNA) was washed with 1-2 ml 70% ethanol.  The pellet was then dried in a laminar flow hood at a 15-30˚ angle from the surface, towards the air flow, for 20-30 min. Once dry, the pellet was dissolved in 800μl RNase-free dH2O, transferred to a 2 ml tube, and 100μl 10x RQ1 buffer (Promega) and 100μl (100 units) RQ1 RNase-free DNase (Promega, M6101) were added.  DNase digestion was performed at 37C for at least 30 min.  Phenol/chloroform/isoamyl alcohol extractions, chloroform extraction, and isopropanol precipitation were done as before, centrifuging at 4C and 13000 rpm (Biofuge Fresco, rotor Heraeus #3288).  Genomic DNA contamination of the RNA samples was assayed using PCR using gene-specific primers.  Samples with significant genomic DNA contamination (all samples of biological replicate 1) were treated as follows, using RNeasy mini columns (QIAGEN, 74104):  350 μl Buffer RLT was added to 100 μl RNA sample (max. 100 μg) and mixed.  250 μl absolute ethanol was added to the diluted RNA, and mixed thoroughly by pipetting.  The sample (700 μl) was applied to an RNeasy mini column, which was then centrifuged for 1 min at ≥ 10,000 rpm.  The flow-through was discarded.  350 μl Buffer RW1 was added to the column, and centrifuged for 1 min to wash.  The flow-through was discarded.  On-column DNase I digestion was then carried out, using the RNase-free DNase Set (QIAGEN, 79254).  The DNase stock solution was prepared by dissolving solid DNase 1 (1500 Kunitz units) in 550 μl RNase-free dH2O, without vortexing.  60 μl aliquots were stored at -20C until use.  One DNase I aliquot was dissolved in 430 μl Buffer RDD, and mixed by pipetting.  78 μl was added to each column, directly into the RNeasy silica-gel membrane, and incubated at room temperature for 1 h.  350 μl Buffer RW1 was added to the column, and centrifuged for 1 min.  The flow-through was discarded, and 500 μl Buffer RPE was added to the column, and centrifuged for 1 min to wash the membrane.  The flow-through was discarded, and another 500 μl Buffer RPE was added, followed by centrifugation for 2 min to dry the membrane.  To eliminate any possible Buffer RPE carryover, the column was centrifuged for 1 min.  To elute the pure RNA from the column, 50 μl RNase-free dH2O was pipetted directly on to the membrane, and incubated at room temperature for 1 min, then centrifuged for 1 min.  The elution step was repeated with a second 50 μl volume of RNase-free dH2O.  For samples that would not label, this was attributed to polysaccharide contamination, and so these samples were treated as follows: the volume of an aliquot of RNA was adjusted to 500 μl with dH2O.  80 μl 5M NaCl was added so that the final NaCl concentration was 0.8M.  0.1 volumes CTAB/NaCl [10% CTAB (cetyltrimethylammonium bromide, Sigma H5882) in 0.7M NaCl; add CTAB slowly to 65C NaCl solution, autoclave]was added, and incubated at 55C for 10 min.  Once cooled, an equal volume of chloroform/isoamyl alcohol was added, and mixed by inversion at 4C for 30 min.  The phases were separated by centrifugation at 13,000 rpm for 15 min at 4C (Biofuge Fresco, rotor Heraeus #3288).  Chloroform/isoamyl alcohol extraction was repeated until a minimal amount of material was present in the interface.  The upper aqueous phase was transferred to a fresh tube, and 0.6 volumes isopropanol was added.  RNA was precipitated at room temperature for 5 min, and pelleted by centrifugation at 13000rpm for 10 min.  The RNA pellet was very clear and glassy, and was difficult to see.  The pellet was washed with 70% ethanol, and dried in a laminar flow hood as before.  The pellet was dissolved in 100 μl RNase-free dH2O.!Sample_molecule_ch1 = total RNA

tag: strain

value: M145 and strain J3900 (=wblA)

molecule: genomic DNA

source_name: Total genomic DNA labeled with Cyanine-3 (green).

label_protocol: Concentration of genomic DNA was determined using the Nanodrop spectrophotometer.  For each labelling reaction, 2-3 μg genomic DNA (max. volume 40.5 μl) and 1 μl random primers (3 μg/μl; Invitrogen 48190-011) were mixed, the volume adjusted to 41.5 μl with dH2O, and heated to 95C for 5 min in a PCR machine with heated lid, then snap cooled on ice.  5 μl Klenow buffer (10x, GE Healthcare), 1 μl dNTPs (5 mM each dA/G/TTP, 2 mM dCTP; Invitrogen 100 mM dNTP set 10297-018), 1.5 μl Cy5-dCTP (GE Healthcare, PA55021), and 1 μl Klenow fragment (5U/μl; GE Healthcare, E2141Y) were added, and the reaction was incubated at 37C overnight.  If multiple reactions were set up, they were combined into one tube, and the reaction components scaled up accordingly.  Labelled genomic DNA was purified using the MinElute PCR purification kit (QIAGEN, 28004) as follows.  To each labelling reaction, 250 μl (5 volumes) Buffer PB was added.  If multiple reactions were set up, the mixture was applied to an appropriate number of MinElute columns, such that the maximum binding capacity of the column was not exceeded (5 μg).  The column was centrifuged at 13,000 rpm for 1 min.  The flow-through was discarded, and 500 μl Buffer PE was added to the column, followed by centrifugation as before.  The flow-through was discarded, and 250 μl Buffer PE was added to the column, followed by centrifugation at 13,000 rpm for 2 min.  The column was transferred to a fresh 1.5 ml tube, and the labelled DNA was eluted from the column by adding 10 μl Buffer EB, incubating at room temperature for 1 min, and centrifuging at 13,000 rpm for 1 min.  This was done twice.

growth_protocol: Spores were inoculated into YEME medium supplemented with 0.5% glycine and 5mM MgCl2  and grown in a rotary shaker for 72 h at 30C before diluting with an equal volume of water and harvesting by centrifugation and washing once  with EDTA (10 mM, pH 8.0).

extract_protocol: Genomic DNA was extracted according to the protocol described in Kieser et al. (2000).  Mycelium was resuspended in 3 ml TE25S buffer (25mM Tris-HCl pH 8.0, 25mM EDTA, 0.3M sucrose), 100 μl lysozyme (60 mg/ml) solution was added, and the suspension was incubated at 37C for 10 min.  4 ml 2 x Kirby mix was added, and the suspension was vortexed for 1 min.  Phenol/chlorofom extraction was carried out using 8 ml phenol/chloroform/isoamyl alcohol, and centrifugation at 4000 rpm (Eppendorf 5810, A-4-62) for 10 min.  Phenol/chloroform extractions were repeated until a minimal amount of protein material remained in the interphase.  The upper phase was transferred to a fresh tube containing 3 ml phenol/chloroform/isoamyl alcohol and 600 μl 3M unbuffered sodium acetate.  The mixture was vortexed for 1 min, and centrifuged at 4000 rpm for 10 min.  The upper phase was transferred to a fresh tube, and 0.6 volumes of isopropanol was added and mixed.  Genomic DNA was spooled onto a sealed Pasteur pipette, and washed in 5 ml 70% ethanol.  The DNA was air dried and resuspended in 5 ml TE.  50 μl pre-boiled RNaseA (4 mg/ml) was added, and incubated at 37C for 30 min.  Phenol/chloroform extractions were repeated, followed by precipitation, spooling and washing.  The DNA was air dried and dissolved in 0.5-1 ml dH20.


title: COL2_112

tag: tissue


title: Total RNA of M145 and wblA from 84 hour cultures and genomic DNA of M145

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 84 hours of culturing on solid medium.

source_name: Total RNA from 84 hour culture labeled with Cyanine-5 (red).

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 84 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.

growth_protocol: Spores were inoculated into YEME medium supplemented with 0.5% glycine and 5mM MgCl2  and grown in a rotary shaker for 84 h at 30C before diluting with an equal volume of water and harvesting by centrifugation and washing once  with EDTA (10 mM, pH 8.0).


title: COL2_031424

tag: age at diagnosis


title: VD, 24h, biological replicate 3

description: Gene expression data from ovarian cancer cells OVCAR3 treated with 1,25(OH)2D3 for 24 h (time point: 24h)

source_name: OVCAR3 cells treated with 1,25(OH)2D3 for 24 h


title: COL2_011853

tag: gender


title: VD, 72h, biological replicate 2


title: COL2_174

tag: localisation


title: VD, 72h, biological replicate 1


title: VD, 24h, biological replicate 2


title: VD, 24h, biological replicate 1


title: COL2_197

tag: metastasis


title: VD, 0h

description: Gene expression data from ovarian cancer cells OVCAR3 treated with ethanol (time point: 0h, control)

source_name: OVCAR3 cells treated with ethanol

value: Vehicle Control


title: VD, 24h


title: VD, 8h, biological replicate 3


title: COL2_030625

tag: first apc mutation


title: VD, 8h, biological replicate 1


title: LNCaP + AR-shRNA rep1

city: Toledo

first: Robert

middle: J

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

description: Gene expression data from late passage LP50 cells treated with vehicle and AR shRNA

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing: Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

source_name: LP50 cells treated with vehicle and AR-shRNA

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

growth_protocol: Cells were routinely cultured at 37°C and in 5% CO2 in RPMI 1640 medium supplemented with FBS (10%), penicillin (100units/mL).  streptomycin (100 mg/mL), L-glutamine (2mM), and sodium pyruvate (1mM). To obtain hormone depletion, cells were grown in the same medium except with 10% Dextran charcoal-stripped FBS and transferrin (20 μg/mL),

extract_protocol: Total RNA was prepared using the RNeasy Mini kit (Qiagen).

treatment_protocol: LP50 cells were infected with AR shRNA lentivirus or non-target control lentivirus; 12h after infection the cells were grown in hormone-free media to deplete androgen. The cells were then treated for 6h with either vehicle or R1881 (1nM) and harvested to obtain total RNA.

value: late passage (LP50) LNCaP


title: LNCaP + AR-shRNA rep2


title: VD, 8h, biological replicate 2


title: Total RNA of M145 and wblA from 60 hour cultures and genomic DNA of M145

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 60 hours of culturing on solid medium.

source_name: Total RNA from 60 hour culture labeled with Cyanine-5 (red).

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 60 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.


title: Total RNA of M145 and wblA from 48 hour cultures and genomic DNA of M145

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 48 hours of culturing on solid medium.

source_name: Total RNA from 48 hour culture labeled with Cyanine-5 (red).

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 48 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.


title: VD, 0h, biological replicate 2


title: Total RNA of M145 and wblA from 24 hour cultures and genomic DNA of M145

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 24 hours of culturing on solid medium.

source_name: Total RNA from 24 hour culture labeled with Cyanine-5 (red).

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 24 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.


title: VD, 0h, biological replicate 3


title: LNCaP + R1881 rep2

description: Gene expression data from late passage LP50 cells treated with R1881 and control shRNA


title: Total RNA of M145 and wblA from 36 hour cultures and genomic DNA of M145

description: Two technical replicates each of three biological replicates of the wild type (M145) and wblA mutant harvested after 36 hours of culturing on solid medium.

source_name: Total RNA from 36 hour culture labeled with Cyanine-5 (red).

growth_protocol: Spores were pregerminated for 6 h at 30C in 50 ml 2xYT.  After pregermination, cultures were pelleted at 3000 rpm for 10 min.  Pellets were resuspended in 10 ml sterile H2O and sonicated in a sonic bath for 10 min to disrupt clumps.  The OD450nm was read, and the concentration of pregerminated spores was adjusted so that 100 μl (3x106 pregerminated spores) was inoculated on to each 9cm diameter plate overlaid with a sterile cellophane disc.  Medium used was minimal medium (Kieser et al., 2000) made with 1% Iberian agar and 0.5% mannitol as carbon source.  Strains were grown for a maximum of 84 h at 30C.  Plates were harvested after 36 h growth, using single-bladed razor blades.  Mycelium was immediately frozen in liquid nitrogen, and stored at -80C in orange-capped 50ml Corning tubes, with holes punctured in the lid to allow venting.


title: LNCaP + vehicle rep2

description: Gene expression data from late passage LP50 cells treated with vehicle and control shRNA


title: LNCaP + R1881 rep1

source_name: LP50 cells treated with R1881 and control shRNA


title: LNCaP + vehicle rep1

source_name: LP50 cells treated with vehicle and control shRNA


title: VD, 0h, biological replicate 1


title: Lung tumor Ctnnb1ex3flox:LSL-KrasG12D double mutant rep2

city: Philadelphia

first: Eugenia

middle: Cristina

last: Pacheco-Pinedo

state: PA

address: 421 Curie Boulevard

department: Department of Medicine - Cardiovascular Institute - Institute for Regenerative Medicine

institute: University of Pennsylvania

hyb_protocol: Hybridization for 16-18 hours at 45 C. Fluidics (wash, stain) was done on the Affymetrix Fluidics 450 station. More detailed information on protocols and so on can be found at www.affymetrix.com

scan_protocol: Scanning was done with an Affymetrix 3000 series scanner controlled by AGCC (used for CEL generation). More detailed information on protocols and so on can be found at www.affymetrix.com

data_processing: Affymetrix Expression Console was used for normalization.  More detailed information on protocols and so on can be found at www.affymetrix.com. RMA was applied to cel files using Partek Genomics Suite 6.5

source_name: Lung tumor Ctnnb1ex3flox:LSL-KrasG12D 5 month old double mutant rep2

label_protocol: Synthesis of Biotin-labeled cRNA  using Affymetrix Kit IVT reaction

growth_protocol: Animals were bred & kept in the ASU animal facility at the University of Pennsylvania From the moment of their birth to the moment of their sacrifice (5 months old) Animals were kept under regular husbandry conditions, no particular food or medicines were administered to induce the growth of the tumors. The tumors are product of the induction of LSL-KrasG12D mutation with or without Ctnnb1ex3flox mutation in the clara cells of CC10-cre+ animals. As controls littermates lacking the CC10-cre and LSL-KrasG12D alleles were used.

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

treatment_protocol: Animals were euthanized with CO2 prior their sacrifice. During dissection the lungs were Perfused with PBS to facilitate visualitation of the tumors. During dissection of the tumors the tissues were kept in ice cold PBS. Once dissected the tumors were stored in Trizol at -80oC until RNA extraction

tag: Sex

value: Female

value: Mixed background

tag: genotype

tag: age

value: 5 months old

value: lung tumor


title: Normal Lung rep2

source_name: Normal Lung 5 month old rep2

value: Normal Lung Ex3flox+

value: normal lung


title: Lung tumor CC10-cre:KrasG12D single mutant rep1

source_name: Lung tumor CC10-cre:KrasG12D 5 month old  single mutant rep1

value: CC10-cre+:KrasG12D+ (single mutant)


title: Lung tumor Ctnnb1ex3flox:LSL-KrasG12D double mutant rep1

source_name: Lung tumor Ctnnb1ex3flox:LSL-KrasG12D 5 month old double mutant rep1


title: Lung tumor CC10-cre:KrasG12D single mutant rep2

source_name: Lung tumor CC10-cre:KrasG12D 5 month old single mutant rep2


title: ODN2395 treated group 5

status: Public on Jan 27 2011

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

description:
5120221010_D
ODN2395 treated

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3.  Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group.

source_name: 2h treatment of MLE-15 cells

label_protocol: cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.

growth_protocol: MLE-15s grown in monolayer to approximately 80% confluence in 6 well plates

extract_protocol: total RNA extracted using Qiagen Rneasy per manufacturers instructions.  cRNA amplification using Ambion total prep kit per manufacturers instructions.

treatment_protocol: MLE-15 cells were treated with PBS, ODN2395 (0.4 ug), Pam2CSK4 (0.2 ug) or ODN2395+Pam2CSK4 for 2 hours. For each, a 20 ul volume of the treatment was added to a 500 ul volume of RPMI for each well of 6-well tissue culture plates.

tag: treatment time


title: Normal Lung rep1

source_name: Normal Lung 5 month old rep1


title: Combination treated group 6

description:
5120221010_F
Combination treated


title: ODN2395 treated group 6

description:
5120221010_H
ODN2395 treated


title: Sham treated group 5

description:
5120221010_G
Sham treated


title: Sham treated group 4

description:
5120221010_C
Sham treated


title: liver2 [gene-level]

city: Palo Alto

first: Weihong

last: Xu

state: CA

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

hyb_protocol: Follow Affymetrix Standard Protocol

scan_protocol: Affymetrix Gene ChIP Scanner 30007G

data_processing:
Data processing using Affymetrix Power Tools (APT). Arrays were RMA-background-corrected, quantile-normlized and summarized into exon/gene expression using median-polish
probe group file: hGlue2_0.r1.pgf
meta-probeset file: hGlue2_0.r1.TC.mps

source_name: Human Liver Total RNA (Ambion)

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit, refer to http://gluegrant1.stanford.edu/~DIC/GGHarray/GGHprotocol.html for details

extract_protocol: Ambion/Applied Biosystems WT Expression Kit, refer to http://gluegrant1.stanford.edu/~DIC/GGHarray/GGHprotocol.html for details

value: Liver


title: muscle3 [gene-level]

source_name: Human Skeletal Muscle Total RNA (Ambion)

value: Muscle


title: muscle4 [gene-level]


title: muscle1 [gene-level]


title: Combination treated group 5

description:
5120221010_B
Combination treated


title: muscle2 [gene-level]


title: liver3 [gene-level]


title: liver1 [gene-level]


title: Combination treated group 4

description:
5109275027_H
Combination treated


title: Pam2CSK4 treated group 5

description:
5120221010_A
Pam2CSK4 treated


title: ODN2395 treated group 4

description:
5109275027_F
ODN2395 treated


title: Sham treated group 3

description:
5109275027_E
Sham treated


title: Pam2CSK4 treated group 3

description:
5109275027_C
Pam2CSK4 treated


title: muscle4 [exon-level]


title: liver4 [gene-level]


title: Combination treated group 3

description:
5109275027_D
Combination treated


title: ODN2395 treated group 3

description:
5109275027_B
ODN2395 treated


title: Pam2CSK4 treated group 4

description:
5109275027_G
Pam2CSK4 treated


title: Pam2CSK4 treated group 2

description:
5109275002_F
Pam2CSK4 treated


title: Combination treated group 2

description:
5109275002_G
Combination treated


title: Gfp(3)

city: madrid

first: Ana

last: Dopazo

address: Melchor Fdez Almagro

department: Genomics Unit

country: Spain

institute: CNIC

hyb_protocol: Hybridization is performed from 10 μg of cRNA, overnight and at 37ºC in a shaking incubator, according to array manufacturers. Post-hybridization processing includes a stringent wash to remove unbound and nonspecifically hybridized target molecules, a staining step with a Cy™5-Streptavidin conjugate, and several non-stringent washing steps to remove unbound conjugate.

scan_protocol: Hybridized arrays were scanned on an Agilent Microarray Scanner (G2565BA, Agilent Technologies)

data_processing: CodeLink Expression Analysis software was used for primary data extraction from bioarray images. Microarray data were analyzed using the R language and packages from the Bioconductor project (http://www.bioconductor.org/). The codelink (Diez et al, 2007) package was used for preprocessing the arrays, genefilter (Gentleman et al, 2007) for data filtering and limma (Smyth, 2004) for statistical analysis. For preprocessing, background was corrected using the normexp method and quantile normalization was performed

source_name: Cultured hippocampal neurons lysate

label_protocol: The biotin-labelled cRNA target is prepared by a linear amplification method. The poly(A)+ RNA is primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA.

growth_protocol: Neurons were plated on 6-wells plates coated with poly-L-lysine at a density of 150–300 neurons/mm2, and they were cultured in Neurobasal supplemented with B-27 and GlutaMAX I.

extract_protocol: Cells were lysed and total RNA was extracted using illustra RNAspin Mini RNA isolation kit from GE Healthcare. RNA quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Neurons were transduced at 5 DIV using Sindbis virus bearing myc-tagged Ngn3 or GFP as control. After 1h viral particles were removed and proteins were allowed to express during 16h.

value: hippocampal neuron

tag: div

tag: genotype/variation


title: Gfp(2)


title: Gfp(1)


title: muscle1 [exon-level]


title: muscle3 [exon-level]


title: Gfp(4)


title: Sham treated group 2

description:
5109275002_H
Sham treated


title: muscle2 [exon-level]


title: liver2 [exon-level]


title: Ngn3(4)

value: Ngn3 overexpression


title: liver4 [exon-level]


title: Sham treated group 1

description:
5109275002_D
Sham treated


title: liver1 [exon-level]


title: Combination treated group 1

description:
5109275002_C
Combination treated


title: Ngn3(1)


title: Ngn3(3)


title: Ngn3(2)


title: liver3 [exon-level]


title: CXCR1- human effector CD8+ T cells U46

city: Port St. Lucie

first: Hiroshi

last: Takata

address: 9801 SW Discovery Way

institute: Vaccine & Gene Therapy Institute of Florida

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix HG-U133 plus 2.0 arrays for 18 hours at 45°C according to the manufacturer’s instruction.  The arrays were washed (Fluidics protocol FS450_0004) with an Affymetrix 7G system.

scan_protocol: The arrays were scanned with an Affymetrix 7G system. Scanning and initial analysis were performed by using Affymetrix GeneChip Operating Software (GCOS) 1.4.

data_processing: GeneChip data analysis was performed by using GeneSpring GX 9.0 (Agilent Technologies) as follows: Scanned CEL files were imported into GeneSpring software, and they were normalized with RMA (Robust Multichip Average). The probes showing the lowest 20% signals among the total probes were excluded.

source_name: ex vivo CD8+ T cells

label_protocol: The amplified cDNA (5 μg) was fragmented and then labeled with biotin by use of FL-Ovation cDNA Biotin Module V2 (NuGEN) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from FACS-sorted CXCR1+ and CXCR1- subsets by using an RNeasy Plus Micro kit (Qiagen). FACS-sorted CXCR1+ and CXCR1- subsets were first lysed in a guanidine-isothiocyanate-containing buffer, and then the lysate was then passed through a gDNA Eliminator spin column. Ethanol added samples were applied to an RNeasy MinElute spin column, and then total RNA was eluted with water. We amplified 16-50 ng of total RNA (RNA Integrity Number >8.5) as single-strand cDNA by using a WT-Ovation Pico RNA Amplification System (NuGEN) according to the manufacturer’s protocol. Amplified cDNA yields were 6.3-10.1 μg with A260:A280 ratios of >1.9.

treatment_protocol: CD8+ T cells were isolated from PBMCs by using anti-CD8-coated (clone: BW135/80) magnetic beads (Miltenyi Biotec). The isolated CD8+ T cells (>98%) were further purified by staining with anti-CD8 mAb (clone: RPA- T8) for FACS sorting. CXCR1+ and CXCR1- cells in the CD27-CD28- CD8+CD3+ subset were sorted.

value: male

tag: individual number

value: Peripheral CD8+ T cells from PBMCs

tag: phenotype of the cells


title: ODN2395 treated group 2

description:
5109275002_E
ODN2395 treated

tag: cell type


title: CXCR1+ human effector CD8+ T cells U25


title: CXCR1+ human effector CD8+ T cells U46


title: CXCR1+ human effector CD8+ T cells U36


title: Pam2CSK4 treated group 1

description:
5109275002_B
Pam2CSK4 treated


title: Equine Tissue Comparison: Cartilage/Spleen

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588378_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Spleen: Alexa Fluor 647

GSM588378_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Spleen: Alexa Fluor 555

hyb_protocol: Samples were hybridized 48 hours at 42C.

scan_protocol: DyeSaver2 was applied to each slide with one dip. Slides were scanned with a Molecular Devices GenePix Personal 4100A Scanner using GenePix Pro 5.0.

data_processing: Data was analyzed by Lowess normalization (Acuity Microarray Informatics Software, Molecular Devices), followed by quantile regression modeling using mean M and A values.

label: Alexa Fluor 647, Alexa Fluor 555

organism: Equus caballus

source_name: Adult Articular Cartilage

label_protocol: Samples were labeled with Invitrogen Indirect PLUS Labeling using amino-allyl dUTP.

extract_protocol: Total RNA was isolated using variations of acid guanidinium thiocyanate/phenol/chloroform extraction with alcohol and salt precipitations.[(1) Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987; 162: 156-159. (2) MacLeod JN, Burton-Wurster N, Gu DN, Lust G. Fibronectin mRNA splice variant in articular cartilage lacks bases encoding the V, III-15, and I-10 protein segments. J Biol Chem 1996; 271: 18954-18960].  The RNA was further cleaned up through a final RNeasy silica gel column (Qiagen Inc., Valencia, CA, #74104) purification and ethanol precipitation, and solubilized in nuclease-free water (Ambion, Applied Biosystems, Foster City, CA, #AM9937). Total RNA (2 micrograms) from each tissue sample received one round of linear amplification primed with oligo-dT (Invitrogen - SuperScript RNA Amplification System).

tag: breed

value: Thoroughbred

value: articular cartilage

tag: developmental stage

value: adult

label: Alexa Fluor 555, Alexa Fluor 647

source_name: Adult Spleen

value: spleen


title: CXCR1- human effector CD8+ T cells U36


title: Equine Tissue Comparison: Cartilage/Testis

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588379_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Testis: Alexa Fluor 647

GSM588379_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Testis: Alexa Fluor 555

tag: tissue

source_name: Adult Testis

value: testis


title: Equine Tissue Comparison: Cartilage/Placental Villus

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588377_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Placental Villus: Alexa Fluor 647

GSM588377_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Placental Villus: Alexa Fluor 555

source_name: Placental Villus

value: placental villus


title: Equine Tissue Comparison: Cartilage/Lung

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588376_slide1.gpr
Adult Articular Cartilage: Alexa Fluor 647
Adult Lung: Alexa Fluor 555

GSM588376_slide2.gpr
Adult Articular Cartilage: Alexa Fluor 555
Adult Lung: Alexa Fluor 647

source_name: Adult Lung

value: lung


title: Equine Tissue Comparison: Cartilage/LymphNode

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588375_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Lymph Node: Alexa Fluor 647

GSM588375_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Lymph Node: Alexa Fluor 555

source_name: Adult Lymph Node

value: lymph node


title: CXCR1+ human effector CD8+ T cells U14


title: CXCR1- human effector CD8+ T cells U25


title: CXCR1- human effector CD8+ T cells U13


title: Equine Tissue Comparison: Cartilage/Liver

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588374_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Liver: Alexa Fluor 647

GSM588374_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Liver: Alexa Fluor 555

source_name: Adult Liver

value: liver


title: 368T1E1-un

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.

data_processing:
Data processing was done using Partek Genomics Suite 6.5 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps

growth_protocol: Tumours were initiated by intratracheal infection of KrasLSL-G12D/+;p53flox/flox mice with a lentiviral vector expressing Cre-recombinase.  The MIT Institutional Animal Care and Use Committee approved all animal studies and procedures. Cell lines were created from individual lung tumours and metastases harvested from mice 8-14 months after tumour initiation. Tumours were cut into small pieces and then digested for 30 minutes at 37°C in 2ml of HBSS-free containing Trypsin, Collagenase IV, and Dispase in a 15ml conical tube. Following digestion, 4mL of Quench Solution (L15 media with 400μl of FBS and 15μl of 5mg/ml DNase) was added. Digested tumour samples were then pressed through 40μm cell strainers (BD). Finally, samples were centrifuged at 1,000 r.p.m. for 5 minutes, resuspended in culture media (DMEM, 10% FBS, pen/strep, glutamine), and plated in a 12-well plate. Cells were washed and culture media was changed every day for a week until stable cell lines were formed. In general we were able to derive cell lines from approximately 50% of tumours and metastases without a noticeable difference in the frequency of cell line generation from metastases from different site relative to the primary lung tumours.

extract_protocol: RNA was extracted using Trizol (Invitrogen)

treatment_protocol: To determine gene expression alterations induced by Nkx2-1 knockdown in TnonMet cells  Array analyses were performed on 368T1-control (bc37), 368T1-shNkx2-1 (E1), 394T4-control (bc37), and 394T4-shNkx2-1(E1) cells. The 394T4 samples were run in duplicate using either the Affymetrix GeneChip® WT Sense Target Labeling (A9242, A9244, A9245, A9247) or the Nugene Ovation® Systems Target Preparation kits (A9248 and A9249).  Thus, a pairwise comparison between the three control and their corresponding shNkx2-1 datasets was used to determine the potential Nkx2-1 regulated genes

value: lung adenocarcinoma shNkx2-1 infected tumor derived cell line


title: 394T4E1_un

source_name: shNkx2-1 infected tumor derived cell line

label_protocol: Nugene Ovation® Systems Target Preparation


title: 394T4bc37_un

value: lung adenocarcinoma control infected tumor derived cell line


title: Equine Tissue Comparison: Cartilage/Bladder

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588371_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Bladder: Alexa Fluor 647

GSM588371_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Bladder: Alexa Fluor 555

source_name: Adult Bladder

value: bladder


title: CXCR1- human effector CD8+ T cells U14


title: CXCR1+ human effector CD8+ T cells U13


title: 368T1bc37-un

source_name: control infected tumor derived cell line

label_protocol: Affymetrix GeneChip® WT Sense Target Labeling


title: 802T4

source_name: primary tumor derived cell line

value: lung adenocarcinoma primary tumor derived cell line


title: 394T4E1-un


title: ODN2395 treated group 1

description:
5109275002_A
ODN2395 treated

source_name: 2h treatment of MLE-15 cells


title: Equine Tissue Comparison: Cartilage/Cerebellum

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588372_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Cerebellum: Alexa Fluor 647

GSM588372_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Cerebellum: Alexa Fluor 555

source_name: Adult Cerebellum

value: cerebellum


title: Equine Tissue Comparison: Cartilage/Kidney

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588373_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Kidney: Alexa Fluor 555

GSM588373_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Kidney: Alexa Fluor 647

source_name: Adult Kidney

value: kidney


title: Equine Tissue Comparison: Cartilage/Muscle (Tongue)

description:
This "sample" represents an average of two dye-swap slides. For each raw data file, the samples are labeled as follows:

GSM588297_slide1.gpr:
Adult Articular Cartilage: Alexa Fluor 555
Adult Tongue Muscle: Alexa Fluor 647

GSM588297_slide2.gpr:
Adult Articular Cartilage: Alexa Fluor 647
Adult Tongue Muscle: Alexa Fluor 555

source_name: Adult Tongue Muscle

value: tongue muscle


title: 2691M1

value: lung adenocarcinoma metastasis derived cell line (from liver metastasis)


title: 2691N1

value: lung adenocarcinoma metastasis derived cell line (from lymph node metastasis)


title: Cell culture from patient11 untreated

city: Barcelona

first: Joan

last: Seoane

address: Vall d'Hebron 119-129

institute: VHIO

description:
07SE209HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma

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

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

data_processing: The data were analyzed with GeneSpring GX v7.3

source_name: Primary culture of human glioblatoma

label_protocol: Biotinylated cRNA was synthesized with the IVT Labeling kit (Affymetrix)

growth_protocol: Patient derived cells were grown in culture in the presence of DMEM+10%FBS

extract_protocol: RNA was extracted using Rneasy kit (QIAGEN)

treatment_protocol: Cells were treated with 2microM LY2109761 for 3 hours

tag: treatment group

value: untreated

value: Primary culture of human glioblatoma

tag: tumor type

value: Glioblastoma


title: Cell culture from patient11 treated with LY2109761

description:
07SE210HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma

value: treated with LY2109761


title: 394T4bc37-un


title: Cell culture from patient9 treated with LY2109761

description:
07SE202HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma


title: 482M1

value: lung adenocarcinoma metastasis derived cell line (from kidney metastasis)


title: Cell culture from patient9 untreated

description:
07SE201HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma


title: Cell culture from patient10 treated with LY2109761

description:
07SE206HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma


title: colonic epithelium_BL-infection_day7_rep2

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description: Isolation Protocol: Small pieces of colon were dissected from mouse large intestine and soaked in Hank's balanced salt solution (HBSS) containing 30 mM EDTA. After incubation on ice for 20 min, IECs were isolated by manipulation with a fine needle under stereomicroscopic monitoring.

hyb_protocol: Affymetrix standard procedures

scan_protocol: using GeneChip Scanner 3000

source_name: colonic epithelium

label_protocol: One-Cycle Target Labeling and Control Reagents

extract_protocol: using commercial kit

tag: Source Type isolated cell

tag: Organism Part large intestine

tag: Cell Type epithelial cell

tag: Cell Purification n/a

tag: Strain[background] BALB/c

tag: Developmental Stage adult

tag: Age 16 weeks

tag: Sex male

tag: Microbial Condition gnotobiote

tag: Genetic Modification n/a

tag: Disease State healthy


title: Cell culture from patient8 treated with LY2109761

description:
07SE198HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma

tag: cell type


title: Cell culture from patient10 untreated

description:
07SE205HGU133Plus_2.0_230207.CEL
Gene expression of primary culture glioblastoma


title: 482N1

source_name: metastasis derived cell line (from lymph node metastasis)

tag: genotype


title: 482T1


title: colonic epithelium_BA-infection_day7_rep3


title: colonic epithelium_BL-infection_day7_rep1


title: 404T1


title: Cell culture from patient8 untreated

description:
07SE197HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: Cell culture from patient7 treated with LY2109761

description:
07SE194HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: colonic epithelium_BL-infection_day7_rep3


title: Cell culture from patient7 untreated

description:
07SE193HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: colonic epithelium_BA-infection_day7_rep2


title: colonic epithelium_BA-infection_day7_rep1


title: 2557T1


title: Cell culture from patient6 untreated

description:
07SE189HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: Cell culture from patient6 treated with LY2109761

description:
07SE190HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: 482T2


title: colonic epithelium_BA+E-infection_day7_rep2

tag: Sex female


title: colonic epithelium_BA+E-infection_day7_rep1


title: Cell culture from patient5 treated with LY2109761

description:
07SE186HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma


title: 368T1


title: 389N1


title: colonic epithelium_BL+E-infection_day7_rep1


title: 389T9


title: Blastocyst from ICI treated uterus rep2

city: Montreal

first: yuefei

last: lou

state: QC

address: 687Pine Avenue

institute: Mcgill University

hyb_protocol: Samples were hybridized on 6 arrays using one Illumina MouseWG-6 v2.0 Expression BeadChips

scan_protocol: the array was sccanned at Illumina BeadStation 500 platform follwing standard Illumina scanning protocol

data_processing: The Illumina output (Excel files) was imported into GeneSpring 10.1 (Agilent Technologies) microarray analysis software for statistical analysis and presentation of the condition tree, the expression profiles and the average expression profiles. The normalization method was the standard method for Illumina array by GeneSpring software.

source_name: Blastocyst from ICI treated uterus

label_protocol: RNA was transcribed into cDNA, and biotin-labeled cRNA was produced by means of a linear amplification kit Illumina® TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Total RNA was extracted from pools of 100-120 embryos using PicoPure® RNA Isolation Kit (Molecular Devices)

treatment_protocol: CD-1 females were injected with 5 IU of Pregnant Mares Gonadotropin (PMSG, Sigma) and 44h later followed by 5 IU of Human Chrorionic Gonadotropin (hCG, Sigma). The females were mated as indicated by the presence of a vaginal plug (Dpc. 1) the following morning. Embryos at blastocyst stages were flushed from the uterus of normal pregnant mice and of the mice treated with ICI (0.5ug/mouse ) 70 hours after hCG injection. Blastocysts at dpc 4 were also collected from the oviducts which were ligated at dpc4.

tag: tissue

value: uterus

tag: embryo stage

value: blastocyst


title: colonic epithelium_BL+E-infection_day7_rep2


title: Blastocyst from uterus rep1

source_name: Blastocyst from uterus


title: Cell culture from patient5 untreated

description:
07SE185HGU133Plus_2.0_220207.CEL
Gene expression of primary culture glioblastoma

tag: treatment group

tag: tumor type


title: 389T5


title: Cell culture from patient4 treated with LY2109761

description:
07SE182HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: Blastocyst from uterus rep2


title: Blastocyst from ICI treated uterus rep1


title: 389T2


title: Blastocyst from oviduct rep2

source_name: Blastocyst from oviduct

value: oviduct


title: colonic epithelium_BL+E-infection_day1_rep1

tag: Source Type isolated cell

tag: Organism Part large intestine


title: colonic epithelium_BL+E-infection_day1_rep2

tag: Cell Type epithelial cell

tag: Cell Purification n/a


title: Cell culture from patient3 treated with LY2109761

description:
07SE178HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: Blastocyst from oviduct rep1


title: Cell culture from patient4 untreated

description:
07SE181HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: 393n1


title: Cell culture from patient3 untreated

description:
07SE177HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: 393m1

source_name: metastasis derived cell line (from liver metastasis)


title: 393T5


title: 393T3


title: colonic epithelium_E-infection_day1_rep2

tag: Strain[background] BALB/c

tag: Developmental Stage adult


title: Cell culture from patient2 treated with LY2109761

description:
07SE174HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: Cell culture from patient2 untreated

description:
07SE173HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma


title: P26AN13282 mock, technical rep.-extract 1

city: Galveston

first: Istvan

last: Boldogh

address: 301 University Blvd.

institute: University of Texas Medical Branch at Galveston

description: Gene expression data 12 hours after 8-oxoguanine exposure

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix HG-U133A 2.0 Arrays in an Affymetrix Hybridization Oven-640 according to the manufacturer's instructions.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mock treated MRC5 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: MRC5, human diploid fibroblasts were maintained at 37 oC, in 5% CO2, in EMEM medium, supplemented with 10% FBS, glutamine, penicillin, and streptomycin.

extract_protocol: Total RNA was isolated using Ambion's RNAqueous Kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 10µM 8-oxoguanine or mock treated with solvent for 6 hours.

value: human fibroblast

tag: cell line

tag: treatment

value: mock

tag: time


title: colonic epithelium_E-infection_day5_rep2

description: Isolation Protocol: Small pieces of colon were dissected from mouse large intestine and soaked in Hank's balanced salt solution (HBSS) containing 30 mM EDTA. After incubation on ice for 20 min, IECs were isolated by manipulation with a fine needle under stereomicroscopic monitoring.

tag: Age 16 weeks

tag: Microbial Condition gnotobiote

tag: Genetic Modification n/a

tag: Disease State healthy


title: 373N1

tag: cell type

tag: genotype


title: N13699 8oxoG 6h

description: Gene expression data 6 hours after 8-oxoguanine exposure

source_name: 8-oxoguanine treated MRC5 cells

value: 6 h


title: P26BN13282 mock, technical rep.-extract 2


title: P25CN13282 8oxoG, technical rep.-extract 3


title: P26CN13282 mock, technical rep.-extract 3


title: N13699 SOL 6h


title: 393T1

value: lung adenocarcinoma primary tumor derived cell line


title: P25BN13282 8oxoG, technical rep.-extract 2


title: Cell culture from patient1 untreated

description:
07SE169HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma

tag: treatment group


title: H322c 1μM Gefitinib

city: Aurora

first: Kathryn

last: Ware

state: CO

department: Craniofacial Biology

institute: University of Colorado Denver

description: Gene expression data from H322c cells treated with EGFR TKI, gefitinib

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: H322c after 4 days cultured with 1μM gefitinib

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: H322c cells were plated 24 hrs prior to DMSO or gefitinib addition to allow cells to adhere

extract_protocol: RNA was extracted from cells using the RNAeasy Mini Kit from Qiagen according to manufacteur's protocol

treatment_protocol: 10μL of 1mM gefitinib or 10μL of DMSO was added to 10mL of RPMI 10% FBS media to give a final concentration of 1μM gefitinib or 0.1% DMSO

value: Gefitinib


title: colonic epithelium_E-infection_day5_rep1

tag: Sex male


title: P25AN13282 8oxoG, technical rep.-extract 1


title: colonic epithelium_GF_rep1

tag: Source Type isolated cell

tag: Microbial Condition germ free


title: 373b1

value: lung adenocarcinoma metastasis derived cell line (from pleural fluid)


title: colonic epithelium_E-infection_day1_rep1

tag: Organism Part large intestine

tag: Cell Type epithelial cell


title: 373T2


title: colonic epithelium_GF_rep2

tag: Cell Purification n/a

tag: Strain[background] BALB/c

tag: Sex female


title: Cell culture from patient1 treated with LY2109761

description:
07SE170HGU133Plus_2.0_210207.CEL
Gene expression of primary culture glioblastoma

tag: tumor type


title: 373T1


title: colonic epithelium_BA+E-infection_day1_rep1

source_name: colonic epithelium_BAE_1_a

extract_protocol: Using commercial kit

tag: Developmental Stage adult


title: Placenta3

status: Public on Jan 26 2011

type: genomic

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

description: Placenta 3

hyb_protocol: Standard Illumina protocol for DNA methylation.

scan_protocol: Standard Illumina protocol for DNA methylation using the Bead Array Scanner.

data_processing: The data was generated using the BeadStudio 2.0 software provided by Illumina by following their analytical matrix. Average normalization was performed.

label: Cy3, Cy5

source_name: Placenta

growth_protocol: Placenta samples were stored in RNAlater prior to DNA extraction, WBC samples are collected in ACD tubes, AnCHMs and MCT DNA were extracted from snap frozen tissues.

extract_protocol: DNA extraction was performed using standard protocols.

treatment_protocol: All samples were bisulfite modified using kits from Qiagen and Sigma

tag: tissue

value: Placenta


title: colonic epithelium_BA+E-infection_day1_rep2

tag: Age 16 weeks

tag: Microbial Condition gnotobiote


title: H322c DMSO

description: Gene expression data from H322c cells not treated with EGFR TKI, gefitinib

source_name: H322c after 4 days cultured with 0.1% DMSO

tag: cell line

tag: treatment

value: DMSO


title: Placenta4

description: Placenta 4

label_protocol: Standard Illumina protocol for DNA methylation.


title: 10192_2_2134GG_vs_2129AA-Replicate 2

city: Yangzhou

first: Lan

last: Ye

state: Jiangsu

address: Daxue Road  NO 88

department: animal science and technology

institute: Yangzhou university

description: Biological replicate 2 of 4. a pair of full-sib with GG and AA genotype at M307 positionof FUT2 gene

hyb_protocol: Cy3 cRNA,Cy5 cRNA,10×Blocking Agent , 25 × Fragmentation Buffer (Gene Expression Hybridization Kit, Agilent,5188-5242 ) were added, and plus with 2×GEx Hybridization Buffer, samples were applied to microarrays for hybridization 65℃ 17h 10rpm. After hybridization, slides were washed sequential(Gene Expression Wash Buffer Kit (including wash buffer 1 & 2) Agilent 5188-5327),

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Agilent Feature Extraction was used for reading the data, Scan resolution 5μm, PMT 100%, 10% and LOWESS normalization

source_name: 2134 piglet with GG genotype of FUT1 gene

label_protocol: 2 µg of total RNA were primed with 5 µl of T7 Promotor primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h ,synthesized cRNA accroding to the instrction of aaUTP(Ambion AM8436) labeled by Cy3/Cy5(Cy3 NHS ester,GE healthcare,PA13105;Cy5 NHS ester,GE healthcare,PA15100 )

growth_protocol: The pig resource populations of the Sutai breed, either resistant or sensitive to the ETEC F18 strain, were housed under the same conditions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The animals were sacrificed to collect duodenal tissues, which were immediately preserved in liquid nitrogen and subsequently stored in a -70℃ freezer.

tag: breed

value: Sutai

tag: genotype/variation

value: GG genotype of FUT1 gene

value: duodenal

source_name: 2129 piglet with AA genotype of FUT1 gene

value: AA genotype of FUT1 gene


title: 10193_2_5152AG_vs_302AA-Replicate 2

description: Biological replicate 2 of 4. a pair of full-sib with AG and AA genotype at M307 positionof FUT6 gene

source_name: 5152 piglet with AG genotype of FUT1 gene

value: AG genotype of FUT1 gene

source_name: 302 piglet with AA genotype of FUT1 gene


title: MCT

description: Mature cystic ovarian teratoma

source_name: Mature cystic ovarian teratoma

value: Mature cystic ovarian teratoma


title: 10192_3_2383GG_vs_2385AA-Replicate 3

description: Biological replicate 3 of 4. a pair of full-sib with GG and AA genotype at M307 positionof FUT3 gene

source_name: 2383 piglet with GG genotype of FUT1 gene

source_name: 2385 piglet with AA genotype of FUT1 gene


title: pUPD4

description: Paternal UPD4 lymphoblastoid cell line

source_name: Lymphoblastoid Cell Line

value: Lymphoblastoid Cell Line


title: Placenta5

description: Placenta 5


title: 10192_4_2383GG_vs_2387AA-Replicate 4

description: Biological replicate 4 of 4. a pair of full-sib with GG and AA genotype at M307 positionof FUT4 gene

source_name: 2387 piglet with AA genotype of FUT1 gene


title: Placenta1

description: Placenta 1


title: 10193_3_5377AG_vs_5156AA-Replicate 3

description: Biological replicate 3 of 4. a pair of full-sib with AG and AA genotype at M307 positionof FUT7 gene

source_name: 5377 piglet with AG genotype of FUT1 gene

source_name: 5156 piglet with AA genotype of FUT1 gene


title: 10193_4_5381AG_vs_5379AA-Replicate 4

description: Biological replicate 4 of 4. a pair of full-sib with AG and AA genotype at M307 positionof FUT8 gene

source_name: 5381 piglet with AG genotype of FUT1 gene

source_name: 5379 piglet with AA genotype of FUT1 gene


title: WBC11

description: White blood cells 11

source_name: White blood cells

value: White blood cells


title: WBC6

description: White blood cells 6


title: WBC16

description: White blood cells 16


title: WBC13

description: White blood cells 13


title: 10193_1_2381AG_vs_2391AA-Replicate 1

description: Biological replicate 1 of 4. a pair of full-sib with AG and AA genotype at M307 positionof FUT5 gene

source_name: 2381 piglet with AG genotype of FUT1 gene

source_name: 2391 piglet with AA genotype of FUT1 gene


title: Placenta2

description: Placenta 2

source_name: Placenta


title: WBC15

description: White blood cells 15


title: WBC8

description: White blood cells 8


title: WBC7

description: White blood cells 7


title: WBC12

description: White blood cells 12


title: WBC14

description: White blood cells 14


title: 10192_1_512GG_vs_524AA-Replicate 1

description: Biological replicate 1 of 4. a pair of full-sib with GG and AA genotype at M307 positionof FUT1 gene

source_name: 512 piglet with GG genotype of FUT1 gene

source_name: 524 piglet with AA genotype of FUT1 gene


title: WBC10

description: White blood cells 10


title: WBC9

description: White blood cells 9


title: WBC2

description: White blood cells 2


title: WBC5

description: White blood cells 5


title: WBC1

description: White blood cells 1


title: AnCHM2

description: Androgenetic complete hydatidiform mole 2

source_name: Androgenetic complete hydatidiform mole

value: Androgenetic complete hydatidiform mole


title: WBC4

description: White blood cells 4


title: AnCHM3

description: Androgenetic complete hydatidiform mole 3


title: WBC3

description: White blood cells 3