title: X514 50mM xylose vs. X514 200mM xylose

description:
total RNA/ genomic DNA
Cy5 dUTP for RNA, Cy3 dUTP for genomic DNA
Each oligonucleotide probe had two replicates on a single slide. Additionally, six different concentrations (11, 22, 45, 90, 180 and 360 ng/ul) of genomic DNA were spotted (eight duplicates for each of the six concentrations on a single slide) as positive controls.

label: Cy3, Cy5

organism: Thermoanaerobacter sp. X514

source_name: X514 samples grown on 50mM

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 50mM or 200 mM xylose as the sole carbon source.

extract_protocol: Total cellular RNA was isolated using Trizol Reagent (Invitrogen). RNA samples were treated with Rnase-free DNaseI and purifed using the total RNA Isolation Kit (NucleoSpin RNAII, Macherey-Nagel Inc. Genomic DNA was isolated and purified from Thermoanaerobacter sp. X514 by CTAB (hexadecyltrimethylammonium bromide)-NaCl method (Zhou et al., 1995).

tag: treatment

value: 50mM xylose

value: mid-log

source_name: X514 samples grown on 200mM xylose

value: 200mM xylose


title: E1_aerobic_a

status: Public on Nov 02 2011

type: RNA

city: Stanford

first: Jared

last: Wenger

state: CA

address: 300 Pasteur Drive

country: USA

institute: Stanford University Medical School

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79806.gif

hyb_protocol: not provided

scan_protocol: Agilent Feature Extraction

data_processing: Agilent Feature Extraction software

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: pooled reference (all 6 parental)

label_protocol: LRILAK labeling

extract_protocol: not provided

tag: reference

value: pool of 6 parental strains

growth_protocol: Wenger 2010 chemostat; Strains for chemostat cell cultures were grown 1% YPD cultures and 1mL aliquots were frozen in 15% glycerol at -80 oC. The entire contents of a single1mL frozen aliquot of evolved (E1-E5) or ancestral (CP1AB or simply P) isolates were used to inoculate an individual chemostat (ATR SixFors fermentation apparatus, ATR Biotechnologies) with working volume set to 400mL of minimal (SC) media defined by [1]. Batch cultures were then grown for 24 hours to achieve saturation. After saturation was achieved, chemostat pumps were turned on to the desired dilution rate and 2-3 vessel volumes of turnover were allowed so cultures could reach steady state. The dilution rate was set to 0.17hr-1 for aerobic (0.08% glucose) and anaerobic glucose limitation (0.08% glucose + 420mg mL-1 Tween 80 + 10mg L-1 ergosterol) and 0.05hr-1 for aerobic acetate limitation (10.9g/L sodium acetate). Aerobic conditions were achieved by sparging with 25 L h-1 of sterile air and anaerobic conditions by sparging cultures with 25 L hr-1 sterile-filtered, humidified N2 (g).

extract_protocol: To isolate total RNA, 100mL of sample was quickly filtered through 0.45 mm Nylon filters (Whatman) and flash frozen in liquid nitrogen. RNA for gene-expression measurements was isolated using the hot acid-phenol method described by [2].1. Adams J, Hansche PE (1974) Population studies in microorganisms. I.Evolution of diploidy in Saccharomyces cerevisiae. Genetics 76: 327-338.2. Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematicchanges in gene expression patterns following adaptive evolution in yeast.Proceedings of the National Academy of Sciences 96: 9721-9726

tag: strain name

tag: media

value: aerobic


title: B1 EB 14 days

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: dual color Nimblegen data

hyb_protocol: According to the Nimblegen hybridization user guide

scan_protocol: Slides were scanned using the Agilent 2505B with upgrade to C  High-Resolution Microarray  Scanner and Agilent Scan Control software (Version A.8.4.1) and intensities were extracted using Nimblegen NimbleScan software (Version 2.6.0.0)

data_processing: Calculations performed in R using bioconductor packages: 1) poor quality probes were flagged and removed, 2) the common reference was used for within slide loess normalization, 3) RMA (background subtraction, between slide quantile normalization and median polish). SIGNAL_MEAN#1 contains Cy3 data and SIGNAL_MEAN#2 contain Cy5 data in the raw data files.

organism: Homo sapiens

source_name: embryoid bodies derived from B at 14 days of suspension culture

label_protocol: RNA T7 amplification procedure

growth_protocol: Human testis derived ES-like cells were maintained in sulture conditions A (bFGF/Matrigel) (Mizrak S.C.et al.Hum Reprod. 2010 Jan;25(1):158-67),  B (bFGF/Mitomycine C inactivated MEFs feeder) and C (bFGF/CHIR99021/Matrigel)

extract_protocol: Total RNA extraction was performed using MagNa pure LC RNA isolation kit and MagNA Pure LC Instrument (Roche, The Netherlands).

treatment_protocol: Maintanance in medium A, B or C at 37C 5% CO2 and EB formation in ultra low attachment dishes in basic medium without bFGF

tag: cell type

value: embryoid bodies

tag: pluripotency

value: under study

tag: days of suspension culture

source_name: pooled from all samples, plus additional human ES cell lines, human dermal fibroblasts and testis derived ES-like cells from preburtal individuals and embryoid bodies derived from them at 4, 7, 10, 14 and 18 days of suspension culture.

tag: sample type

value: reference


title: B1 EB 10 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 10 days of suspension culture


title: B1 EB 18 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 18 days of suspension culture


title: X514 10mM xylose vs. X514 200mM xylose

city: Norman

first: Christopher

middle: L

last: Hemme

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

hyb_protocol: The Cy3 labeled genomic DNA was used as a common reference to co-hybridize the Cy5 labeled RNA samples on each slide. Hybridization was carried out using a TECAN HS4800 Pro Hybridization Station (Tecan, NC) by following the manufacturer’s instructions. This system automatically performs hybridization, washing and drying of arrays.

scan_protocol: slides were scanned using a ProScanArrayTM microarray analysis system (Perkin Elmer®, MA).

data_processing: To determine signal intensity of fluorescence for each spot, the 16-bit TIFF scanned images were analyzed by the software ImaGene 6.1 (Biodiscovery Inc., EI Segundo, CA). Microarray data were analyzed as previously described by Mukhopadhyay et al. (Mukhopadhyay et al., 2006; He et al., 2009b). Briefly, it includes the following major steps. (i) Empty spots with SNR <2.0 (SNR, signal-to-noise ratio), and bad spots were flagged and removed before normalization. (ii) The net signal of each spot was calculated by subtracting the background signal and adding a pseudo signal of 100 to obtain a positive value. For resulting net signals of <50, a value of 50 was used. (iii) The total signal intensity of all microarray (slides) in this experiment was normalized with the genomic DNA signal (Cy3 signal), and a normalization factor was calculated for each slide. (iv) Both Cy3 and Cy5 signal intensity of each spot were adjusted by multiplying the normalization factor calculated above. Therefore, the resultant Cy5 signal of each probe presents the normalized signal intensity for each gene. (v) A ratio R of Cy5/Cy3 signal was calculated for each spot on each array. (vi) To compare genomic analysis, the control and treatment conditions were defined respectively so as to identify the control (Rc) and treatment (Rt) ratios. And then log2 R value was calculated for each gene. (vii) Finally, to access the significant change between treatment and control, a Z score was calculated via following equation: , where 0.25 is a pseudovariance term. Typically, a cutoff |Log2R|?1.0 and |Z|? 2.0 was used to determine changes with significance.

source_name: X514 samples grown on 10mM

label_protocol: Ten microgram of total RNA was reverse-transcribed using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 1 mM Cy5 dUTP (Invitrogen) according to previous  description (He et al., 2006). The purified 500 ng genomic DNA was fluorescently labeled by random priming using Klenow fragment of DNA polymerase  in the presence of 1mM Cy3 dUTP as described elsewhere (He et al., 2005).

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 10mM or 200 mM xylose as the sole carbon source.

value: 10mM xylose

tag: growth phase

value: 200 mM xylose


title: E2_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79797.gif

value: anaerobic


title: P_aerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79812.gif


title: B1 EB 7 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 7 days of suspension culture


title: E5_aerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79810.gif


title: B1 EB 4 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 4 days of suspension culture


title: -2DPA inner ovule cells vs. -2DPA ovule epidermal cells

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Gossypium hirsutum L. cv. TM-1

hyb_protocol: One Cy3-dCTP reaction is mixed with one Cy5-dCTP reaction to make one probe. Therefore, two “identical” probes each containing an equal amount of Cy3- and Cy5-labeled cDNAs were hybridized with two slides, which constituted one dye-swap experiment. The dye-swap was repeated once as a technical replication. The large dye-swap (four slides) was repeated using another biological sample (e.g., RNAs isolated from different pools of 3-DPA ovules). Therefore, each experiment consists of four technical replications and two biological replications in a total of eight slides (Chen et al. 2004). Hybridization was performed overnight (∼14 h) at 65°C. After hybridization, the slides were washed twice for 4 min each in 2X SSC, 0.2% SDS, again twice for 2 min each in 0.2XSSC, and twice for 2 min each in 0.05X SSC.

scan_protocol: The slides were scanned using GenePix 4000B (Axon, Foster City, CA), and the images were captured by GenePix Pro 4.1 software.

data_processing: After the data were processed using log2 ratios of green and red hybridization signals, a robust and locally weighted linear regression (lowess) (Cleveland 1979) was used to remove non-linear components (e.g. dye and pin effects) (Quackenbush 2002). For the duplicate spots in each feature, we used an average value for data analysis. No additional steps for data normalization and background subtraction are needed for the AVONA model (Lee et al. 2004). The data were then subjected to the analysis of variance (ANOVA) test in a linear model to estimate the significant changes in gene expression caused by the two treatments (genotypes) (Black and Doerge 2002; Lee et al. 2004). A standard t-test statistic was used for this comparison based on the normality assumption for the residuals. The standard false discovery rate (FDR) (Hochberg and Tamhane 1987) was applied to control multiple testing errors using a significance level α= 0.05.

organism: Gossypium hirsutum

source_name: -2DPA inner ovule cells

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy5 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy5-labeled aRNA probes was used for hybridization.

extract_protocol: Captured cells were homogenized in 500 µl of RNA extraction buffer (200 mM sodium borate decahydrate (pH 9), 30 mM ethylene glycol bis-N,N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), 1% (w/v) sodium deoxycholate, 2% (w/v) polyvinylpyrrolidone (PVP), 0.5% (v/v) Nonidet-40 (NP-40), 10 mM dithiothreitol (DTT)). After 250 µl of ethanol was added to the captured cells, the sample was loaded onto a Qiagen RNeasy mini column (Qiagen, Valencia, CA) and washed as per the manufacturer’s recommendation.

tag: cultivar

tag: tissue

value: inner ovule cells

tag: developmental stage

value: -2 DPA

tag: capture technique

value: laser capture microdissection (LCM)

source_name: -2DPA ovule epidermal cells

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy3 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy3-labeled aRNA probes was used for hybridization.

value: ovule epidermal cells


title: A1 EB 10 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from A at 10 days of suspension culture


title: human urinary bladder grade 3 carcinoma cell line - permissive for MVwt - cultured - biol rep 1

city: Langen

first: Michael

last: Mühlebach

address: Paul-Ehrlich-Strasse 51-59

country: Germany

institute: Paul-Ehrlich-Institut

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (4x44K) using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: Feature Extraction Software derived output data files were further processed with Rosetta Resolver (v7.2); Rosetta Inpharmatics LLC

source_name: original cell source: ATCC (#CRL-1472) - normal culture under optimal culture conditions -> cells in exponential growth phase

label_protocol: 1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol:
Cell lines were grown in T175 flasks until sub-confluence under optimal growth conditions. The cells were detached from the culture vessel using PBS-EDTA (1 mM) + Trypsin, and pelleted at 500xg for 5 min at 4°C. Supernatants were removed, the cells were washed once with 1 ml ice-cold PBS and pelleted, again. Supernatants were aspirated and the cell pellets were snap-frozen by submersion in liquid nitrogen for approx. 1 min. Frozen cell pellets were stored at -80°C until shipment of samples for extraction and further analysis on dry ice.
Cell lines were cultured as instructed by ATCC. In brief: H23, H358, H441, and H522 were grown in RPMI 1640 + 10% FCS; HT1376 were grown in EMEM + 10% FCS; T24 were grown in McCoy´s 5a + 10% FCS; SCaBER were grwon in MEM (adjusted to contain 1.5 g/L sodium bicarbonate and 0.1 mM non-essentail amino acids) + 2 mM L-Gln + 10% FCS. All cell lines were grown at 37°C in a humidified atmosphere containing 5% carbon dioxide.

extract_protocol: RNA was isolated using the NucleoSpin® RNA II kit  (Macherey-Nagel) according to the manufacturer's instructions.

tag: disease

value: urinary bladder grade 3 carcinoma

tag: cell line

tag: virus permissive

value: yes


title: A1 EB 14 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from A at 14 days of suspension culture


title: human urinary bladder grade 3 carcinoma cell line - permissive for MVwt - cultured - biol rep 3


title: X514 10mM xylose vs. X514 50mM xylose

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 10mM or 50 mM xylose as the sole carbon source.

extract_protocol: Total cellular RNA was isolated using Trizol Reagent (Invitrogen). RNA samples were treated with Rnase-free DNaseI and purifed using the total RNA Isolation Kit (NucleoSpin RNAII, Macherey-Nagel Inc. Genomic DNA was isolated and purified from Thermoanaerobacter sp. X514by CTAB (hexadecyltrimethylammonium bromide)-NaCl method (Zhou et al., 1995).

source_name: X514 samples grown on 50mM xylose

value: 50 mM xylose


title: human lung papillary adenocarcinoma cell line - permissive for MVwt - cultured - biol rep 3

source_name: original cell source: ATCC (#HTB-174) - normal culture under optimal culture conditions -> cells in exponential growth phase

value: lung papillary adenocarcinoma


title: human urinary bladder grade 3 carcinoma cell line - permissive for MVwt - cultured - biol rep 2


title: A1 EB 7 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from A at 7 days of suspension culture


title: A1 EB 4 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from A at 4 days of suspension culture


title: WFS1 KO USHT_10_322_ko

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description: Gene expression data from hypothalamus of wfs1 deficient mice

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to standard protocols

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductir software based on R language

label: biotin

organism: Mus musculus

source_name: hypothalamus

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

growth_protocol: Frozen in liquid nitrogen

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

treatment_protocol: Hypothalami were dissected under dissection microscope

tag: genetic background

tag: genotype

value: WFS1 KO

value: hypothalamus


title: DFB2

description: dual color Nimblegen data

source_name: human dermal fibroblasts

value: terminally differentiated somatic cells


title: human lung bronchioalveolar carcinoma cell line - permissive for MVwt - cultured - biol rep 3

source_name: original cell source: ATCC (#CRL-5807) - normal culture under optimal culture conditions -> cells in exponential growth phase

value: lung bronchioalveolar carcinoma


title: E5_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79832.gif

source_name: pooled reference (all 6 parental)

tag: reference

value: pool of 6 parental strains

value: aerobic


title: BMMSC2

description: dual color Nimblegen data

source_name: human bone marrow derived MSC

value: adult progenitors restricted to mesodermal linage

source_name: pooled from all samples, plus additional human ES cell lines, human dermal fibroblasts and testis derived ES-like cells from preburtal individuals and embryoid bodies derived from them at 4, 7, 10, 14 and 18 days of suspension culture.

value: reference


title: human lung papillary adenocarcinoma cell line - permissive for MVwt - cultured - biol rep 1


title: X514 1mM xylose vs. X514 50mM xylose

source_name: X514 samples grown on 1mM

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 1mM or 50 mM xylose as the sole carbon source.

tag: treatment

value: 1mM xylose

value: mid-log


title: A1 EB 18 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from A at 18 days of suspension culture

value: embryoid bodies

value: under study


title: human lung papillary adenocarcinoma cell line - permissive for MVwt - cultured - biol rep 2


title: GFP- sample

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

hyb_protocol: standard protocol from the Affymetrix GeneChip Expression Analysis Manual using an Affymetrix GeneChip Fluidics Station 450 Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Affymetrix GCS 3000 7G scanner

data_processing: Default values of Affymetrix MAS5.0 were used.

source_name: Olfactory epithelium

label_protocol: biotin-labeled cRNA probes made using the standard protocol in the Affymetrix GeneChip Expression Analysis Manual

extract_protocol: Total RNA was isolated using the TriReagent protocol (Molecular Research Center Inc., Cincinnati, OH).

tag: strain

value: Tgn1-2G transgenic mice

tag: age

value: postnatal days 5 - 8

tag: number

tag: gender

value: both

value: Olfactory epithelium

tag: cell

value: 6.8 million GFP negative cells by FACS


title: X514 1mM xylose vs. X514 200mM xylose

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 1mM or 200 mM xylose as the sole carbon source.

tag: growth phase

source_name: X514 samples grown on 200mM xylose

value: 200 mM xylose


title: X514 1mM xylose vs. X514 10mM xylose

growth_protocol: Thermoanaerobacter sp. X514 was grown anaerobically in defined medium supplemented with 1mM or 10 mM xylose as the sole carbon source.

source_name: X514 samples grown on 10mM xylose

value: 10 mM xylose


title: human lung bronchioalveolar carcinoma cell line - permissive for MVwt - cultured - biol rep 2

value: yes


title: GFP+ sample

value: 1.3 million weakly GFP positive cells by FACS


title: human urinary bladder transitional cell carcinoma cell line - non-permissive for MVwt - cultured - biol rep 3

source_name: original cell source: ATCC (#HTB-4) - normal culture under optimal culture conditions -> cells in exponential growth phase

value: no


title: DFB1

description: dual color Nimblegen data

tag: cell type

tag: pluripotency

value: terminally differentiated somatic cells

tag: days of suspension culture

tag: sample type


title: GFP-hES-3-1

description: dual color Nimblegen data

source_name: pluripotent stem cells

value: pluripotent


title: MCF7 tumor bearing-mice treated with Letrozole+BMS-754807, biological rep2

city: Princeton

first: Fei

last: Huang

state: NJ

institute: Bristol-Myers Squibb Co

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix HT Human Genome HT_HG-U133A 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 normalized by RMA and log2 transformed using Bioconductor package.

source_name: MCF7 tumor bear-mice treated agent for 28 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: treatment group

tag: tissue

value: breast tumor


title: human urinary bladder transitional cell carcinoma cell line - non-permissive for MVwt - cultured - biol rep 2

tag: disease

tag: cell line

tag: virus permissive


title: GFP-hES-3-2

description: dual color Nimblegen data

value: reference


title: human urinary bladder transitional cell carcinoma cell line - non-permissive for MVwt - cultured - biol rep 1


title: human lung bronchioalveolar carcinoma cell line - permissive for MVwt - cultured - biol rep 1

value: lung bronchioalveolar carcinoma


title: MCF7 tumor bearing-mice treated with Tamoxifen+BMS-754807, biological rep2


title: GFP+++ immature OSN sample

value: 1 million highly GFP positive cells by FACS


title: MCF7 tumor bearing-mice treated with Letrozole+BMS-754807, biological rep1


title: C1 EB 18 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 18 days of suspension culture

value: embryoid bodies

value: under study


title: MCF7 tumor bearing-mice treated with Tamoxifen+BMS-754807, biological rep1


title: MCF7 tumor bearing-mice treated with Letrozole, biological rep1

value: Letrozole


title: MCF7 tumor bearing-mice treated with Letrozole, biological rep2


title: C1

description: dual color Nimblegen data

source_name: human testis derived ES-like cells

value: ES-like cells


title: human urinary bladder squamous carcinoma cell line - non-permissive for MVwt - cultured - biol rep 1

description: ScaBER

source_name: original cell source: ATCC (#HTB-3) - normal culture under optimal culture conditions -> cells in exponential growth phase

value: urinary bladder squamous carcinoma


title: A1

description: dual color Nimblegen data


title: HUES-1-1

description: dual color Nimblegen data


title: human urinary bladder squamous carcinoma cell line - non-permissive for MVwt - cultured - biol rep 2

description: ScaBER


title: BMMSC1

description: dual color Nimblegen data

value: adult progenitors restricted to mesodermal linage


title: MCF7 tumor bearing-mice treated with Tamoxifen, biological rep2

value: Tamoxifen


title: human lung adenocarcinoma cell line b - non-permissive for MVwt - cultured - biol rep 3

source_name: original cell source: ATCC (#CRL-5810) - normal culture under optimal culture conditions -> cells in exponential growth phase

value: lung adenocarcinoma


title: human urinary bladder squamous carcinoma cell line - non-permissive for MVwt - cultured - biol rep 3

description: ScaBER


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP positive replicate 1

city: Minneapolis

first: Fengli

last: Fu

state: MN

address: 312 Church Street SE

institute: University of Minnesota

description: amplified twice

hyb_protocol: Amplified aRNAs were hybridized to Affymetrix mouse 430 2.0 full genome array chips at the BioMedical Genomics Center of the University of Minnesota  BioMedical Genomics Center of the University of Minnesota

scan_protocol: GeneChip were scanned according to Affymetrix standard protocols

data_processing: The data were processed with affymetrix RMA method

source_name: ER71 EYFP; ER71 mutant, E8.0 embryo

label_protocol: MessageAmpII-Biotin Enhanced Kit

extract_protocol: trizol

treatment_protocol: digested with trypsin and sorted on a BD FACSAria

value: ER71 embryonic ER71 mutant EYFP positive cells

tag: eyfp

value: positive

tag: genotype

value: ER71 mutant

tag: genetic background

value: C57BL/6 and FVB mixed line


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP negative replicate 3

description: amplified twice

value: ER71 embryonic ER71 mutant EYFP negative cells

tag: age

value: negative


title: HUES-1-2

description: dual color Nimblegen data

value: pluripotent

value: reference


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP negative replicate 1

description: amplified twice


title: human lung adenocarcinoma cell line b - non-permissive for MVwt - cultured - biol rep 1

value: no


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP negative replicate 2

description: amplified twice


title: B1

description: dual color Nimblegen data


title: MCF7 tumor bearing-mice treated with Tamoxifen, biological rep1

value: breast tumor


title: MCF7 tumor bearing-mice treated with BMS-754807, biological rep2


title: ER71 EYFP E8.0 embryo wildtype EYFP negative replicate 3

description: amplified twice

source_name: ER71 EYFP; ER71 wildtype E8.0 embryo

value: ER71 embryonic wildtype EYFP negative cells

value: ER71 wildtype


title: human lung adenocarcinoma cell line a - non-permissive for MVwt - cultured - biol rep 3

source_name: original cell source: ATCC (#CRL-5800) - normal culture under optimal culture conditions -> cells in exponential growth phase


title: ER71 EYFP E8.0 embryo wildtype EYFP positive replicate 3

description: amplified twice

value: ER71 embryonic wildtype EYFP positive cells


title: MCF7 tumor bearing-mice treated with control, biological rep2

value: control


title: MCF7 tumor bearing-mice treated with control, biological rep1


title: Advanced cirrhosis vs Early cirrhosis 3

city: Pittsburgh

first: Taichiro

last: Nishikawa

state: PA

address: 530 45th Street

department: Surgery

institute: University of Pittsburgh

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 3 and Rat hepatocyte from early cirrhosis 3

hyb_protocol: Microarray slides were hybridized overnight, then washed

scan_protocol: Scanned with Agilent G2565BA Microarray Scanner. Images were analyzed with GenePix 5.0 software (Axon Instruments).

data_processing: Median foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which is used for all data input, diagnostic plots and normalization. The ratio of expression for each element on the array was calculated in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). These values were then normalized by the print tip loess method using the marray microarray processing package in R.

organism: Rattus norvegicus

source_name: Hepatocytes from Advanced cirrhosis 3

label_protocol: All RNA samples were amplified using the Ovation™ Aminoallyl RNA Amplification and Labeling System (Nugen Inc, CA). Flourescent label (Cy™Dye, Amersham Pharmacia Biotech Ltd, NJ) was coupled to 2 ug of amplified cDNA and hybridized to the Mouse PancChip 6.2 13K cDNA microarray.

extract_protocol: Total RNA was extracted from isolated rat hepatocytes using the RNeasy Mini Kit according to the manufacturer’s instructions.

value: hepatocytes

tag: disease state

value: Advanced cirrhosis 3

source_name: Hepatocytes from Early cirrhosis 3

treatment_protocol:
Total RNA was extracted from isolated rat hepatocytes using the RNeasy Mini Kit (QIAGEN, Valencia CA) according to the manufacturer’s instructions. cDNA was synthesized from 500ng hepatocyte RNA using oligo(4) and SuperScript II reverse transcriptase at 42 ºC for 1 h.
Hepatocytes were isolated from normal, early cirrhotic and advanced cirrhotic rat livers by in situ collagenase perfusion

value: Early cirrhosis 3


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP positive replicate 3

description: amplified twice

value: ER71 embryonic ER71 mutant EYFP positive cells


title: ER71 EYFP E8.0 embryo wildtype EYFP positive replicate 2

description: amplified twice

value: positive


title: human lung adenocarcinoma cell line a - non-permissive for MVwt - cultured - biol rep 2

value: lung adenocarcinoma


title: Advanced cirrhosis vs Control liver 3

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 3 and Rat hepatocyte from control liver 3

treatment_protocol: Total RNA was extracted from isolated rat hepatocytes using the RNeasy Mini Kit (QIAGEN, Valencia CA) according to the manufacturer’s instructions. cDNA was synthesized from 500ng hepatocyte RNA using oligo(4) and SuperScript II reverse transcriptase at 42 ºC for 1 h.

source_name: Hepatocytes from Control liver 3

value: Control liver 3


title: Advanced cirrhosis vs Control liver 4

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 4 and Rat hepatocyte from control liver 4

source_name: Hepatocytes from Advanced cirrhosis 4

value: Advanced cirrhosis 4

source_name: Hepatocytes from Control liver 4

value: Control liver 4


title: Advanced cirrhosis vs Early cirrhosis 2

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 2 and Rat hepatocyte from early cirrhosis 2

source_name: Hepatocytes from Advanced cirrhosis 2

value: Advanced cirrhosis 2

source_name: Hepatocytes from Early cirrhosis 2

value: Early cirrhosis 2


title: Advanced cirrhosis vs Early cirrhosis 4

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 4 and Rat hepatocyte from early cirrhosis 4

source_name: Hepatocytes from Early cirrhosis 4

value: Early cirrhosis 4


title: Macrolide-resistant Campylobacter cy3 slide 10

city: Ames

first: Qijing

last: Zhang

state: Iowa

address: 1600 Christensen Drive

department: Veterinary Microbiology and Preventive Medicine

institute: Iowa State University

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescence intensities of all spots were log2 transformed. The median of the three log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni

source_name: macrolide resistant Campylobacter

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: strain

value: isogenic Eryr transformant T.L.101


title: Advanced cirrhosis vs Early cirrhosis 5

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 5 and Rat hepatocyte from early cirrhosis 5

source_name: Hepatocytes from Advanced cirrhosis 5

tag: cell

value: Advanced cirrhosis 5

source_name: Hepatocytes from Early cirrhosis 5

value: Early cirrhosis 5


title: ER71 EYFP E8.0 embryo wildtype EYFP negative replicate 1

description: amplified twice

value: ER71 embryonic wildtype EYFP negative cells

value: negative

value: ER71 wildtype

value: C57BL/6 and FVB mixed line


title: human lung adenocarcinoma cell line b - non-permissive for MVwt - cultured - biol rep 2

value: no


title: MCF7 tumor bearing-mice treated with BMS-754807, biological rep1

source_name: MCF7 tumor bear-mice treated agent for 28 days

value: breast tumor


title: Macrolide-susceptible Campylobacter cy3 slide 09

source_name: macrolide susceptible Campylobacter


title: HOK-Adeno CMV (Cy3) Vs. Adeno EZH2 (Cy5)

city: ANN ARBOR

first: NISHA

middle: J

last: D'SILVA

state: MICHIGAN

address: 1011 N. UNIVERSITY AVE, ROOM 5217

department: PERIODONTICS AND ORAL MEDICINE/ SCHOOL OF DENTISTRY

institute: UNIVERSITY OF MICHIGAN SCHOOL OF DENTISTRY

description: Overexpression of EZH2.

hyb_protocol: 825 ng each of the test and reference channel purified labeled products were combined to put on the microarray slide in a hybridization reaction at 65 0C for 17 hours in rotating hybridization oven.  The washing of the disassembled array slides was done with a washing procedure to prevent ozone degradation of Cy5 signals: GE Wash Buffer-1 for 1 minute at room temperature, Buffer 2 for 1 minutes at 37 0C,  Acetonitrile wash for 10 sec at room temperature, and Stabilization and Drying solution for 30 sec at room temperature.

scan_protocol: Microarray image scanning was done on an Agilent scanner G2505B (5 um scan with software v7.0). Data extraction was performed with Agilent Feature Extraction software v9.5 using protocol GE-v5_95_Feb07.

data_processing: Processed values represent the gene expression fold change (treatment / control). For the siRNA treatment, the processed value represents siRNA EZH2 / siRNA Non-Targeting. Similarly, in the over-expression studies, the processed value represents Adeno EZH2 / Adeno CMV.

source_name: HOK-Adeno CMV

label_protocol: Cy5- or Cy3-labeled cRNA products were generated in a transcription reaction using T7 RNA polymerase and cyanine 3-CTP or cyanine-5 CTP nucleotides.  Test channel RNA samples were labeled with Cy5, and reference channel RNA with Cy3, for the normal polarity (with dye swap experiments, the Cy5 and Cy3 polarity were reversed).  The Cy5- or Cy3-labeled cRNA products were purified on the Qiagen’s RNeasy mini spin columns, and the purified products measured on NanoDrop spectrophotometer for RNA concentration and Cy5/Cy3 labeling specific activity.

growth_protocol: OSCC3 cells were grown in DMEM media with 10%  FBS in a humidified cell culture incubator with 5% carbon dioxide (CO2). HOK (Human Oral (Normal) Keratinocyte) cells were grown in OKM (ScienceCell) media supplemented with 1% OKGS (Oral Keratinocyte Growth Supplement) in a humidified cell culture incubator with 5% carbon dioxide (CO2).

extract_protocol: After appropriate treatment, cells were washed twice with cold PBS and were lysed by qiazol lysis reagent (Qiagen). The lysates were passed through an 18 gauge needle 5 times, and total RNA was isolated with the miRNeasy mini kit (Qiagen) following manufacturer's instructions with an in-column RNase-free DNase I digestion. Each RNA was passed through quality control of RIN value of 7.5 and higher.

treatment_protocol: OSCC3 cells were transfected for 48 hours with EZH2 siRNA or non-targeting siRNA (Dharmacon) by  oligofectamine (Invitrogen) reagent.  For overexpression studies, cells were infected with an adenoviral construct of control (Ad-CMV) or EZH2 (Ad-EZH2) gene (Open  Biosystems) in normal serum-containing medium for 48 hours.

value: primary normal human oral keratinocytes (HOK)

tag: treatment

value: control adenovirus

source_name: HOK-Adeno EZH2

value: EZH2 adenovirus


title: Macrolide-susceptible Campylobacter cy5 slide 10


title: Macrolide-resistant Campylobacter cy5 slide 09


title: ER71 EYFP E8.0 embryo wildtype EYFP negative replicate 2

description: amplified twice

source_name: ER71 EYFP; ER71 wildtype E8.0 embryo

tag: cell type


title: OSCC3-siRNA Non-Targeting (Cy3) Vs. siRNA EZH2 (Cy5)

description: Stable knockdown of EZH2.

source_name: OSCC3-siRNA Non-Targeting

value: squamous cell carcinoma of the head and neck (HNSCC)

value: control siRNA

source_name: OSCC3-siRNA EZH2

value: EZH2 siRNA


title: HIMEC ulcerative colitis TGFTNFIL1 12h

city: Cleveland

first: Florian

last: Rieder

state: OH

address: 9500 Euclid Avenue

department: Dept of Pathobiology

institute: Cleveland Clinic

description: The downstream statistical and functional analyses of gene expression data were performed by the Integrative Genomics Analysis Core facility {http://lerner.ccf.org/gmi/igac)

hyb_protocol: cRNA was hybridized to the Illumina HumanRef-8 v2 Expression BeadChip available at the Cleveland Clinic Genomics Core facility (http://lerner.ccf.org/services/gc) using the standard protocols provided by Illumina (San Diego, CA).

scan_protocol: Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA.

data_processing:
The raw gene expression datasets were processed to remove outliers, log2 transformed and quantile normalized using R lumi software.
Quality control analyses were applied to detect the outlier samples.

label: Biotin

source_name: human intestinal microvascular endothelial cells, ulcerative colitis patient, TGFbeta1/TNFalpha/IL-1beta, 12 hours

label_protocol: 250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX). cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel.

growth_protocol: Surgically resected specimens were used for isolation of human intestinal microvascular endothelial cells (HIMEC). All specimens were of colonic origin, and cells were isolated and cultured as previously reported (Binion DG, West GA, Ina K, et al. Enhanced leukocyte binding by intestinal microvascular endothelial cells in inflammatory bowel disease. Gastroenterology 1997;112:1895-907). Briefly isolation of HIMEC consisted of enzymatic digestion of intestinal mucosal strips followed by gentle compression to extrude endothelial cell clumps, which adhered to fibronectin-coated plates and were subsequently cultured in MCDB131 medium (Sigma, St. Louis, MO, USA) supplemented with 20% FBS, antibiotics, heparin, and endothelial cell growth factor (Lonza, Walkersville, MA, USA). HIMEC were used between passage 8 and 15. HIMEC cultures were maintained at 37°C in 5% CO2, fed twice a week, and subcultured at confluence. All diagnoses were confirmed by clinical, radiologic, endoscopic and histologic criteria. The Institutional Review Board of the Cleveland Clinic Foundation approved the study.

extract_protocol: Total RNA was isolated and purified with the RNeasy Mini kit (Quiagen).

treatment_protocol: HIMEC monolayers were cultured in 75cm2 tissue culture flasks coated with fibronectin (1µg/ml) (Roche, Basel, Switzerland). Cells were left untreated (unstimulated) or exposed to the combination of IL-1b 100 U/ml, TNF-a 100 U/ml and TGF-b1, 5ng/ml (TGFTNFIL1); all from Peprotech, Rocky Hill, NJ) for six days. HIMEC medium was changed every 3 days.

value: Intestinal mucosa

tag: gender

value: Female

value: 34 yrs

value: ulcerative colitis


title: HIMEC normal 1 TGFTNFIL1 12h

source_name: human intestinal microvascular endothelial cells, control patient 1, TGFbeta1/TNFalpha/IL-1beta, 12 hours

value: Male

value: 56 yrs

value: normal


title: Advanced cirrhosis vs Early cirrhosis 1

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 1and Rat hepatocyte from early cirrhosis 1

source_name: Hepatocytes from Advanced cirrhosis 1

value: hepatocytes

value: Advanced cirrhosis 1

source_name: Hepatocytes from Early cirrhosis 1

value: Early cirrhosis 1


title: HIMEC Crohn's disease TGFTNFIL1 12h

source_name: human intestinal microvascular endothelial cells, crohn’s disease patient, TGFbeta1/TNFalpha/IL-1beta, 12 hours

value: 37 yrs

value: Crohn's disease


title: Advanced cirrhosis vs Control liver 2

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 2 and Rat hepatocyte from control liver 2

source_name: Hepatocytes from Advanced cirrhosis 2

value: Advanced cirrhosis 2

source_name: Hepatocytes from Control liver 2

value: Control liver 2


title: OSCC3-siRNA Non-Targeting (Cy5) Vs. siRNA EZH2 (Cy3)

description: Stable knockdown of EZH2.

value: squamous cell carcinoma of the head and neck (HNSCC)


title: HIMEC normal 2 TGFTNFIL1 12h

source_name: human intestinal microvascular endothelial cells, control patient 2, TGFbeta1/TNFalpha/IL-1beta, 12 hours

value: 48 yrs


title: Advanced cirrhosis vs Control liver 1

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 1and Rat hepatocyte from control liver 1

source_name: Hepatocytes from Control liver 1

value: Control liver 1


title: Advanced cirrhosis vs Control liver 5

description: Biological replicate 1 of 5. Rat hepatocytes from advanced cirrhosis 5 and Rat hepatocyte from control liver 5

source_name: Hepatocytes from Advanced cirrhosis 5

value: Advanced cirrhosis 5

source_name: Hepatocytes from Control liver 5

value: Control liver 5


title: Macrolide-susceptible Campylobacter cy5 slide 08

source_name: macrolide susceptible Campylobacter


title: Limb_IgGChIP_rep1

status: Public on Nov 01 2011

type: genomic

city: Miami

first: Joy

last: Lincoln

address: 1600 NW 10th Ave.

institute: University of Miami

description: Sheared, ChIP-enriched DNA.

hyb_protocol: Microarrays were hybridized 17 hours at 45oC in the Affymetrix Hybridization Oven 645 according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned with the Affymetrix Scanner 3000 7G.

data_processing:
Image analysis was carried out using the Affymetrix Command Console Software (AGCC). Data analysis was performed with Tiling Analysis Software and Integrated Genome Browser (Affymetrix).  Enrichment of target genes was determined by setting a graph threshold for signal intensity (value ≥ 30) and minimum run (100 base pairs) in the Integrated Genome Browser (Affymetrix) based on a known Sox9-binding site in the Cartilage Link Protein  promoter.

Bar files: Output files following analysis comparing IgG control (1_IgG.CEL_intensity.bar) to Sox9 pull-down (2_SoA.CEL_intensity.bar) samples using Tiling Analysis Software.

molecule: genomic DNA

source_name: IgG ChIP limb DNA

label_protocol: DNA targets were amplified and labeled according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol. Briefly, DNA targets were PCR amplified with Sequenase DNA Polymerase (USB), fragmented, labeled and hybridized according to Affymetrix instructions.

extract_protocol: Neonate limbs were diced and cytoplasmic proteins were removed by treatment with hypotonic lysis buffer. Formaldehyde crosslinking, immunoprecipitation, and DNA purification were then performed according to instructions for the EZ-ChIP kit (Millipore) with the following adjustments: Hypotonic lysis of diced tissue samples was performed for 30 minutes on ice to remove cytoplasmic proteins, and DNA/Protein crosslinking was acheived with 0.5% formaldehyde treatment for 10 minutes at room temperature.

value: forelimb

tag: developmental stage

value: neonate

value: IgG control chromatin immunoprecipitation

tag: chip antibody

value: rabbit IgG

tag: antibody vendor

value: Santa Crux

tag: antibody catalog number

tag: antibody lot number


title: Limb_Sox9ChIP_rep1

description: Sheared, ChIP-enriched DNA.

source_name: Sox9 ChIP limb DNA

tag: tissue

value: Sox9 chromatin immunoprecipitation

value: pooled anti-Sox9

tag: antibody 1

value: affinity-purified anti-Sox9 generated by Dr. Michael Wegner (PMID 12842915)

tag: antibody 2

value: rabbit polyclonal anti-Sox9 (C-20)

tag: antibody 2 vendor

value: Santa Cruz

tag: antibody 2 catalog number

tag: antibody 2 lot number


title: human lung adenocarcinoma cell line a - non-permissive for MVwt - cultured - biol rep 1

source_name: original cell source: ATCC (#CRL-5800) - normal culture under optimal culture conditions -> cells in exponential growth phase

tag: disease

value: lung adenocarcinoma

tag: cell line

tag: virus permissive

value: no


title: HIMEC normal 2 unstimulated 12h

source_name: human intestinal microvascular endothelial cells, control patient 2, unstimulated, 12 hours

value: Intestinal mucosa

value: Male

tag: age

tag: disease state

value: normal


title: CN

city: Maastricht

first: Paula

last: da Costa Martins

address: P.Debyelaan 25

institute: Maastricht University

description: 3 pooled cardiac samples.

hyb_protocol: Overnight on mParaflo microfluidic chip using a micro-circulation pump and 100 ml 6xSSPE buffer containing 25% formamide overnight. Each detection probe on the microfluidic chip consisted of a chemically-modified nucleotide coding segment complementary to target microRNA or other RNA (control sequences), and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Images were acquired using an Axon GenePix 4000B Microarray Scanner. Intensity data were collected using Array-Pro image analysis software (Media Cybernetics) with a scan resolution of 10 microns and PTM between 480 and 540V.

data_processing: Analysis was conducted on background-subtracted signal intensities. Background was determined using a regression-based background mapping method. Spots yielding true signal (i.e., present) had signal intensities higher than 3×(background standard deviation) and standard deviation/signal intensity < 0.5. CV is calculated by (standard deviation)/(signal intensity). Probes repeated multiple times on an array were called present if the signals from at least 50% of the probes were above detection level. Raw data were normalized by the LOWESS method on the background-subtracted data. A Student t-test was performed to analyze the statistical significance of the signal differences between the two groups.

source_name: left ventricle, CnTg

label_protocol: After extraction, 1 mg of total reference RNA was fractionated using a YM-100 Microcon filter. Small RNAs, less than 300 nt in length, were extended with a poly(A) tail using poly(A) polymerase. Poly(A) tails were ligated with an oligonucleotide tag for subsequent dye staining.

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

tag: strain

tag: genotype

value: aMHC-Calcineurin transgenic (CnTg)

value: left ventricle

value: 6 weeks

tag: gender

value: male


title: ACD- bacteria root response replicate 2

city: Waterloo

first: Jennifer

last: Stearns

state: Ontario

address: 200 University Ave. W.

country: Canada

institute: University of Waterloo

description:
R_KO_2
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Axon GenePix 4200A scanner, 1 line average, scan power and PMTs adjusted for each scan, GenePix Pro 6.0.1.27 software, local feature background subtraction.

data_processing: Background correction and normalization done using the LIMMA library (Linear Models for Microarray Data, v 2.10.5) of the bioconductor package within R.  LOWESS normalization was used to correct for within-array dye and spatial effects then these values were quantile normalized across arrays. The two-replicate scans per slide (for shoots only) were used to maximize the robustness of each gene's differential expression measurement via the lmFit function within LIMMA. R_KO_2 (17-1.txt) was excluded as outlier data prior to normalization

organism: Brassica napus

source_name: ACD- bacteria treated

label_protocol: According to Agilent Fluorescent Direct Label Kit protocol: 10 µg of total RNA were primed with DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400U MMLV-RT, and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3 or Cy5-label.

growth_protocol: treated and untreated seeds (see below) grown for 6 days in nutrient solution soaked vermiculite. Growth chamber conditions with 12hr light cycle and 20C.

extract_protocol: Total RNA extracted from plant tissues in 4 M guanidine isothiocyanate, 3M NaOAc at pH 6.0 and 0.835%  B-mercaptoethanol  per liter, ultracentrifuged over 5.7 M CsCl at 116,000 xg for 23 hrs at 4C then washed with 70% ethanol and precipitated with 100% ethanol. Total RNA cleaned with Qiagen RNeasy Midi kit

treatment_protocol: Seeds surface-sterilized then either soaked in a control solution (untreated) or soaked in a suspension bacteria (ACD+ or ACD- bacterial genotype) at OD600 = 0.5 for 1 hr.

value: day 6 seedlings

value: root

source_name: untreated


title: HIMEC ulcerative colitis unstimulated 12h

source_name: human intestinal microvascular endothelial cells, ulcerative colitis patient, unstimulated, 12 hours

value: Female

value: 34 yrs

value: ulcerative colitis


title: WT

description: 3 pooled cardiac samples.

source_name: left ventricle, WT

value: WT


title: Macrolide-susceptible Campylobacter cy3 slide 07


title: SF126-tet-R175H-1

city: sendai

first: imai

last: hiroo

state: Miyagi

address: 4-1 seiryo-machi

department: clinical oncology

country: Japan

institute: tohoku university

description: Biological replicate 1 of 3. From the data (log2 cy5/ cy3), Change in the abundance of a particular shRNA barcode is tracked for 10 days by competitive hybridization between the Cy5 and Cy3 groups.

hyb_protocol: Barcode sequences labeled by Cy3 or Cy5 was hybridized on the barcode microarray in the hybridization oven (Agilent Technologies, Inc.) at 65°C for 17 h.

scan_protocol: After hybridization, the arrays were scanned with the Agilent DNA microarray scanner to quantify log2 Cy5/Cy3.

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal according agilent software manufacturer's instructions.

source_name: SF126 human glioblastoma cell

label_protocol: Barcode sequences corresponding to specific shRNAs were amplified by the following primers located outside the barcode sequence:  forward, 5′-caaggggctactttaggagcaattatcttg-3′  reverse, 5′-ggttgattgttccagacgcgt-3′.  Amplified PCR products were separated in 1.5% TAE agarose gel and extracted using Wizard SV Gel and PCR Clean-Up System (Promega, Madison WI, USA). Each purified PCR product was labeled with Cy5 (doxycycline-on group) or Cy3 (doxycycline-off group) using Agilent’s Genomic DNA Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA)

growth_protocol: The stable SF126 cell line expressing the doxycycline (Dox)-inducible p53 R175H mutant (SF126-tet-R175H) was constructed. Cells were cultured in RPMI1640 with 10% FBS at 37°C, 5% CO2.

extract_protocol: Genomic DNA was extracted from each group using the Blood & Cell Culture DNA Mini Kit (Qiagen), according to the manufacturer’s recommendation.

treatment_protocol: One million SF126-tet-R175H cells were seeded in 10-cm culture plates for 24 h. The medium was removed from the plates and the Decode RNAi Viral Screening Library (Thermo Scientific Open Biosystems, Huntsville, AL, USA) was added to the plate at the multiplicity of infection (MOI) of 0.3 with serum-free medium. After 6 h, the medium was replaced with virus-free medium. After 48 h, puromycin was added at a final concentration of 2 mg/ml to select the infected cells. Finally, 7 × 106 of lentivirus-infected SF126-tet-R175H cells were obtained. These cells theoretically contain 70,000 distinct shRNAs, and each cell should express a single shRNA product. These cells were divided into two groups, and each group was cultured with or without doxycycline for 10 days.

tag: genotype/variation

value: p53 R175H mutant

tag: cell name


title: Macrolide-resistant Campylobacter cy5 slide 07

source_name: macrolide resistant Campylobacter

value: isogenic Eryr transformant T.L.101


title: SF126-tet-R175H-3

description: Biological replicate 3 of 3. From the data (log2 cy5/ cy3), Change in the abundance of a particular shRNA barcode is tracked for 10 days by competitive hybridization between the Cy5 and Cy3 groups.


title: SF126-tet-R175H-2

description: Biological replicate 2 of 3. From the data (log2 cy5/ cy3), Change in the abundance of a particular shRNA barcode is tracked for 10 days by competitive hybridization between the Cy5 and Cy3 groups.


title: HIMEC Crohn's disease unstimulated 12h

source_name: human intestinal microvascular endothelial cells, crohn’s disease patient, unstimulated, 12 hours

value: 37 yrs

value: Crohn's disease


title: Macrolide-resistant Campylobacter cy3 slide 08


title: ACD+ bacteria root response replicate 3

description:
R_ACD_3
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues

source_name: ACD+ bacteria treated


title: ACD+ bacteria root response replicate 2

description:
R_ACD_2
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: ACD- bacteria root response replicate 3

description:
R_KO_3
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: NMuMG_Ex_TGF-beta

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: exon level data

hyb_protocol: Hybridization was performed according to the protocols provided by Affymetrix, using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: Scanning was performed according to the protocols provided by Affymetrix.

data_processing: CEL files were generated using Affymetrix GeneChip Command Console Software (AGCC).

source_name: normal murine mammary gland epithelial cell line (NMMuMG), treated with TGF-beta

label_protocol: Labeling was performed according to the protocols provided by Affymetrix.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA) supplemented with 4.5 g/l glucose, 10% fetal bovine serum (FBS), 10 ug/ml insulin, 50 U/ml penicillin, and 50 ug/ml streptomycin.

extract_protocol: Total RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were treated with 1 ng/ml recombinant human TGF-beta1 (R&D Systems, Minneapolis, MN) or left untreated.

value: NMuMG

tag: tissue origin

value: mammary gland


title: NMuMG_Ex_control

description: exon level data

source_name: normal murine mammary gland epithelial cell line (NMMuMG), untreated


title: ACD- bacteria root response replicate 1

description:
R_KO_1
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues

tag: tissue


title: ACD+ bacteria root response replicate 1

description:
R_ACD_1
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: ACD- bacteria shoot response replicate 1

description:
S_KO_1
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues

value: shoot


title: ACD- bacteria shoot response replicate 3

description:
S_KO_3
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: ACD+ bacteria shoot response replicate 3

description:
S_ACD_3
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: ACD+ bacteria shoot response replicate 1

description:
S_ACD_1
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: ACD- bacteria shoot response replicate 2

description:
S_KO_2
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues


title: TASC-MAT1

city: Singapore

first: Frank

middle: Daniel

last: McKeon

address: 60 Biopolis street

department: Stem cell and Developmental Biology 7

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Hybridization was done using standard Affymetrix protocols

scan_protocol: GeneChip® Scanner 3000,Affymetrix

data_processing:
To validate sample quality probe hybridization ratios were calculated using Affymetrix Expression Console software.  The intensity values were log2-transformed and imported into the Partek Genomics Suite 6.5(beta).  Exons were summarized to genes and a 1-way ANOVA was performed to identify differentially expressed genes.  P values and fold-change were calculated for each analysis.  Heatmaps were generated using Pearson’s correlation and Ward’s method and Principal Component Analysis was conducted using all probe sets.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: primary cell culture

label_protocol: RNA was amplified and labelled using WT Pico RNA Amplification System, WT-Ovation Exon Module and Encore Biotin Module (NuGEN Technologies)

growth_protocol: Human airway stem cells were cultured on feeder layer(3T3) or different differentiation systems namely ALI, MAT and SAS

extract_protocol: RNA was extracted using Pico pure RNA isolation kit from Arcturus

tag: clone

value: TASC airway stem cells

tag: growth protocol

value: MAT differentiation system


title: TASC-MAT2

treatment_protocol: Human airway stem cells were cultured on feeder layer(3T3) or different differentiation systems namely ALI, MAT and SAS


title: TASC-ALI1

value: ALI differentiation system


title: TASC-ALI3


title: TASC-3T3-3

value: 3T3 feeder layer


title: TASC-ALI2


title: TASC-3T3-2


title: TASC-3T3-1


title: ACD+ bacteria shoot response replicate 2

description:
S_ACD_2
Seeds inoculated with bacteria or left untreated, day 6 seedlings dissected into individual tissues

value: day 6 seedlings


title: NESC-MAT3

value: NESC airway stem cells


title: NESC-MAT2


title: HIMEC normal 1 unstimulated 12h

description: The downstream statistical and functional analyses of gene expression data were performed by the Integrative Genomics Analysis Core facility {http://lerner.ccf.org/gmi/igac)

source_name: human intestinal microvascular endothelial cells, control patient 1, unstimulated, 12 hours

value: Intestinal mucosa

value: Male

value: 56 yrs

value: normal


title: NESC-ALI1


title: NESC-SAS3

value: SAS differentiation system


title: NESC-SAS1


title: NESC-SAS2


title: NESC-3T3-3


title: NESC-ALI2


title: DASC-MAT1

value: DASC airway stem cells


title: DASC-MAT2


title: NESC-ALI3


title: NESC-3T3-1


title: NESC-3T3-2


title: NESC-MAT1


title: DASC-3T3-3


title: DASC-ALI2


title: DASC-ALI1


title: DASC-3T3-2


title: DASC-ALI3


title: Control 5 Technical Rep 1

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

institute: SA Pathology

description: RNA extracted from normal control

hyb_protocol: Performed by Australian Genomic Research Facility (AGRF)

data_processing:
CEL files were imported into Partek Genomic Suite Version 6.5 using robust multi array (RMA) normalisation, log 2 transformed then batch effect was removed. Gene expression was averaged from intensity values of all probesets comprising the genes. P value was caluclated using ANOVA-1-way assuming equal variances.
probe group file: HuEx-1_0-st-v2.na29.hg18.probeset
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core

source_name: Unrelated control

growth_protocol: The Epstein-Barr virus (EBV) immortalized B- cell lines (B-LCL) used in this study were established from peripheral blood lymphocytes of patients and controls. Once established the LCL cell lines were cultured in RPMI 1640 (Sigma) supplemented with 10% FCS, 2mM L-Glutamine, 0.017mg/ml benzylpenicillin and grown at 37 0 C with 5% CO2

extract_protocol: Trizol Reagent (Invitrogen) and RNeasy Mini Kit (QIAGEN)

tag: cell type

value: Lymphoblastoid cell line

tag: disease status

value: normal control


title: Control 5 Technical Rep 2

description: RNA extracted from normal control

scan_protocol: Performed by Australian Genomic Research Facility (AGRF)


title: Control 3 Technical Rep 2

description: RNA extracted from normal control

label_protocol: Performed by Australian Genomic Research Facility (AGRF)


title: Control 1 Technical Rep 1

description: RNA extracted from normal control


title: Control 4 Technical Rep 2

description: RNA extracted from normal control


title: Control 1 Technical Rep 2

description: RNA extracted from normal control


title: Control 2 Technical Rep 1

description: RNA extracted from normal control


title: Control 3 Technical Rep 1

description: RNA extracted from normal control


title: DASC-3T3-1


title: Control 4 Technical Rep 1

description: RNA extracted from normal control


title: Control 2 Technical Rep 2

description: RNA extracted from normal control


title: Patient 3 Technical Rep 2

description: RNA extracted from patient with UPF3B mutation

source_name: UPF3B patient

value: UPF3B mutation


title: Patient 4 Technical Rep 1


title: Patient 2 Technical Rep 1


title: Patient 2 Technical Rep 2


title: Patient 3 Technical Rep 1


title: Patient 5 Technical Rep 1


title: Skin_age_75_individual_1

first: Daniel

last: Haustead

state: WA

address: 35 stirling highway (M317)

institute: University Of Western Australia

description:
n/a
Sample_probe_group_file  HuEx-1_0-st-v2.r2.pgf
Sample_meta-probeset_file  HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA expression values were obtained for the core subsets of genes using Expression Console with default settings.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted from 3mm pounch biopsies of skin stored in RNALater (Qiagen), using manual dissection and hand-held rotor-stator homogenisation in Trizol reagent (Invitrogen), and purified using quick spin columns (Qiagen).  RNA quality was assessed using the Agilent BioAnalyzer (Agilent Technologies) and UV spectrophotometer for the presence of sharp peaks and 28S/18S RNA.

value: skin


title: Skin_age_74.5_individual_1


title: Skin_age_75_individual_3


title: Skin_age_77_individual_1


title: Skin_age_75_individual_2


title: Skin_age_72_individual_2


title: Skin_age_79_individual_1


title: Patient 1 Technical Rep 1


title: Patient 1 Technical Rep 2


title: Skin_age_72_individual_1


title: Skin_age_74_individual_1


title: Skin_age_86_individual_1


title: Skin_age_73_individual_2


title: Skin_age_73_individual_1


title: Skin_age_73_individual_4


title: Skin_age_77_individual_2


title: Skin_age_70_individual_2


title: Skin_age_73_individual_3


title: Skin_age_72_individual_3


title: Skin_age_78_individual_1


title: Skin_age_70_individual_1


title: Skin_age_69_individual_1


title: Skin_age_67_individual_1


title: Skin_age_67_individual_2


title: Skin_age_66_individual_4


title: asexual_rep1

city: Urbana

first: Phillip

middle: A

last: Newmark

state: IL

address: C609 CLSL, 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

description: Total RNA from whole asexual planarians starved for 1 week before extraction.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Expression data were received from Roche Nimblegen Inc. and EST calls were generated using the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, NAR; Irizarry et al., 2003, Biostatistics).

organism: Schmidtea mediterranea

source_name: whole animals

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Asexual strain of Schmidtea mediterranea was maintained in 1 X Montjuic salts at 21°C (Cebrià F and Newmark PA, 2005, Development).

extract_protocol: Total RNA was extracted from equivalent weights of asexual and sexual animals using Trizol (Invitrogen). RNA was treated with RNase-free DNAse (Promega), purified using RNeasy Mini Spin kit (Qiagen), and quantified with Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies) at the Roy J. Carver Biotechnology Center (University of Illinois at Urbana-Champaign, Urbana, IL USA).

value: asexual


title: Skin_age_66_individual_3


title: Skin_age_66_individual_1


title: 4QMT08242009A_WT2-Cu.Cy3_pafA2-Cu.Cy5_14017956_MDS.mev.refIsIA.out

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air, and scanned with an Axon GenePix 4000 scanner (http://intranet.jtc.jcvsf.org/sops/M008.pdf).  All wash buffers were supplemented with 1-ml of 0.1M DTT per liter of wash buffer.

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing to mid log

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: The wildtype cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5).

extract_protocol: RNA was extracted from Mtb as follows: an equal volume of 4 M guanidinium isothiocyanate (GTC), 0.5% sodium N-lauryl sarcosine, 25 mM trisodium citrate) was added to cultures to arrest transcription, and cells were collected by centrifugation at 2,885 x g. Bacterial were resuspended in 1 ml TRIzol reagent (Invitrogen) and bead beat with zirconia silica beads (BioSpec Products) in a BioSpec Mini Bead Beater two times for 30 s, with 1 min cooling on ice in between. Samples were either stored at -80 C degree or used immediately. Samples were centrifuged for 5 min at 16,100 5 g at 4 C degree to pellet cellular debris. 300 ml of chloroform was added to PhaseLock tubes (Heavy 2 ml, 5Prime) after which the TRIzol samples were added. Tubes were vigorously inverted for 15 s and allowed to rest at RT for 5 min. Tubes were centrifuged for 10 min at 10,500 g at 4 C degree. The aqueous phases were added to microfuge tubes containing 270 ml isopropanol and 270 ml high salt solution (0.8 M trisodium citrate, 1.2 M NaCl) and vortexed for 5 s. After a 10 min incubation at RT, tubes were microcentrifuged at 16,100 g for 10 min at 4 C degree to pellet RNA. RNA pellets were washed with 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4 C degree. Pellets were allowed to dry by air and resuspended in 50 µl of RNA storage buffer (Ambion). 2 µl were used for quantification and another 2 µl were added to 80% formamide/ 20% loading dye to check RNA integrity on an (1.6%) agarose gel. The purification process was repeated two times to obtain DNA-free RNA. RNA aliquots were stored at -80 C degree.

treatment_protocol: No copper sulfate treatment.

value: wildtype

source_name: M. tuberculosis pafA strain Cy5 cell culture growing to mid log

growth_protocol: The mutant cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5).

value: pafA mutation


title: Skin_age_63_individual_5

city: Perth


title: Skin_age_66_individual_2


title: Skin_age_68_individual_1


title: Skin_age_63_individual_4


title: 4QMT08242009A_WT1-Cu.Cy5_pafA1-Cu.Cy3_140179176_MDS.mev.refIsIB.out

source_name: M. tuberculosis pafA strain Cy3 cell culture growing to mid log

source_name: M. tuberculosis CDC1551 strain Cy5 cell culture growing to mid log


title: Skin_age_64_individual_1


title: 4QMT08242009A_WT2-Cu.Cy5_pafA2-Cu.Cy3_14017959_MDS.mev.refIsIB.out


title: Blood-fed salivary gland vs. unfed salivary gland, rep3

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

hyb_protocol: Probes prepared from the RNA of salivary glands from blood-fed mosquitoes (labeled with Cy5-dUTP fluorescent nucleotides) were co-hybridized with probes prepared from the RNA obtained from salivary glands of unfed mosquitoes (labeled with Cy3-dUTP fluorescent nucleotides).

scan_protocol: The slides were scanned using a GenePix 7000 autoloader scanner (Axon Instruments).

data_processing: TIGR

organism: Anopheles gambiae

source_name: Blood-fed salivary gland

label_protocol: The Cy5- and Cy3-labeled probes were synthesized using the Low RNA Input Fluorescent Linear Amplification Kit from Agilent Technologies (Santa Clara, California, USA).

growth_protocol: A. gambiae Keele strain mosquitoes were reared at 27°C in 70% humidity, and adults were maintained on a 10% sucrose solution on a 12-h light/dark cycle, according to standard rearing conditions.

extract_protocol: RNA was extracted from dissected salivary glands (~80-100) using an RNeasy kit (Qiagen, Valencia, California, USA) according to standard methodology.

treatment_protocol: A. gambiae mosquitoes were allowed to feed for 20 min on Swiss Webster strain mice that had been anesthetized with a ketamine solution. Salivary glands were dissected 2 h after blood feeding (from both blood-fed and unfed mosquitoes). The blood-fed mosquitoes were not provided sugar solution for 2 hrs after blood-feeding, after which the salivary glands were dissected. The control unfed mosquitoes were treated in the same way.

value: Keele

value: salivary gland

tag: treatment

value: blood feeding

source_name: Unfed salivary gland

value: no blood feeding


title: Skin_age_68_individual_2


title: Skin_age_65_individual_1


title: sexual_rep1

description: Total RNA from whole mature, sexual planarians starved for 1 week before extraction.

growth_protocol: Sexual strain of Schmidtea mediterranea was maintained in 0.75 X Montjuic salts at 18°C (Wang Y et al., 2007, PNAS).

value: sexual


title: 4QMT08242009A_WT1+Cu.Cy5_pafA2+Cu.Cy3_14017988_MDS.mev.refIsIB.out

source_name: M. tuberculosis pafA strain Cy3 cell culture growing in the suplemented with Cu

growth_protocol: The mutant cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours.

treatment_protocol: Exposed to 500uM copper sulfate

source_name: M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu

growth_protocol: The wildtype cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours.


title: 4QMT08242009A_WT2+Cu.Cy3_pafA2+Cu.Cy5_14017961_MDS.mev.refIsIA.out

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu

source_name: M. tuberculosis pafA strain Cy5 cell culture growing in the suplemented with Cu


title: Blood-fed salivary gland vs. unfed salivary gland, rep2


title: Skin_age_63_individual_1


title: 4QMT08242009A_WT2+Cu.Cy5_pafA1+Cu.Cy3_14017953_MDS.mev.refIsIB.out


title: Skin_age_63_individual_3


title: 4QMT08242009A_WT1-Cu.Cy3_pafA1-Cu.Cy5_14018004_MDS.mev.refIsIA.out

source_name: M. tuberculosis pafA strain Cy5 cell cell culture growing to mid log


title: 4QMT08242009A_WT2-Cu.Cy3_mpa1-Cu.Cy5_14017960_MDS.mev.refIsIA.out

source_name: M. tuberculosis mpA strain Cy5 cell culture growing to mid log

value: mpA mutantion


title: 4QMT08242009A_WT1-Cu.Cy5_mpa1-Cu.Cy3_14017975_MDS.mev.refIsIB.out

source_name: M. tuberculosis mpA strain Cy3 cell culture growing to mid log

source_name: M. tuberculosis CDC1551 strain Cy5 cell cell culture growing to mid log


title: 4QMT08242009A_WT2+Cu.Cy3_pafA1+Cu.Cy5_14017978_MDS.mev.refIsIA.out


title: Skin_age_65_individual_2


title: Skin_age_60_individual_3


title: Skin_age_63_individual_2


title: 4QMT08242009A_WT1-Cu.Cy3_mpa1-Cu.Cy5_14018006_MDS.mev.refIsIA.out

source_name: M. tuberculosis mpA strain Cy5 cell cell culture growing to mid log


title: Skin_age_60_individual_1


title: Skin_age_62_individual_1


title: 4QMT08242009A_WT1+Cu.Cy3_mpa2+Cu.Cy5_14017957_MDS.mev.refIsIA.out

source_name: M. tuberculosis mpA strain Cy5 cell culture growing in the suplemented with Cu


title: Foetal Gonad Male 1

city: Copenhagen

first: Henrik

last: Leffers

address: Universitetsparken 13

department: August Krogh Building

country: Denmark

institute: Dept. of Biology, Copenhagen University

hyb_protocol: Hybridization to the arrays was made according to Agilent's instructions.

scan_protocol: Array images were scanned using Agilent scanner G2565BA with scanner software version A. 7.0.1 with XDR function, and data obtained using Agilent Feature Extraction software version 9.5.3.1

data_processing:
The per-array lowess normalized signal (gProcessedSignal) from each array was normalized to each other by quantile normalization using the marray package in R/bioC version 2.7.2.
the values were background subtracted, normalized, negative values were set to 0, before all values were log2 transformed.

source_name: Human foetal male testis, week 10-11.

label_protocol: 100 ng of total RNA from each sample was labelled with CY3 according to the instructions from Agilent.

extract_protocol: RNA was extracted from frozen tissue by trizol, extracted with chloroform and precipitated with isppropanol, according to the standard trizol procedure.

treatment_protocol: All samples are untreated.

value: Human foetal male testis, week 10-11.


title: Foetal Gonad Female 1

source_name: Human foetal female gonad, week 12-13.

value: Human foetal female gonad, week 12-13.


title: 4QMT08242009A_WT1+Cu.Cy5_mpa2+Cu.Cy3_14017958_MDS.mev.refIsIB.out

source_name: M. tuberculosis mpA strain Cy3 cell culture growing in the suplemented with Cu


title: Foetal Gonad Male 2

source_name: Human foetal male testis, week 12. The sections used here contain only mesonephros, no germ cells present.


title: 4QMT08242009A_WT2+Cu.Cy5_mpa1+Cu.Cy3_14017954_MDS.mev.refIsIB.out


title: Skin_age_60_individual_2


title: Skin_age_59_individual_1


title: Skin_age_57_individual_1


title: Skin_age_54_individual_2


title: 4QMT08242009A_WT2+Cu.Cy3_mpa1+Cu.Cy5_14018003_MDS.mev.refIsIA.out


title: Testis RNA, Biochain

source_name: Human normal testis RNA from Biochain Institute. Contaminated with RNA from epididymis.


title: Blood-fed salivary gland vs. unfed salivary gland, rep1

source_name: Blood-fed salivary gland


title: Skin_age_55_individual_1


title: Skin_age_60_individual_4


title: CIS, patient 11

source_name: Biopsy with CIS in 50-90% of tubules.

value: Biopsy with CIS in 50-90% of tubules.


title: Skin_age_54_individual_1


title: Skin_age_53_individual_4


title: CIS, patient 9

source_name: Biopsy with CIS in 40-80% of tubules.

value: Biopsy with CIS in 40-80% of tubules.


title: CIS, patient 10

source_name: Biopsy with CIS in 5-50% of tubules.

value: Biopsy with CIS in 5-50% of tubules.


title: CIS, patient 6

source_name: Rest tissue from biopsy after removal of seminom. CIS in 40-50% of tubules.


title: Testis RNA, Ambion

source_name: Human normal testis RNA from Ambion. Contaminated with RNA from epididymis.


title: EC, patient 2

source_name: Embryonal carcinoma (EC), no normal germ cells or CIS.


title: CIS, patient 8

source_name: Biopsy with CIS in 70-100% of tubules.

value: Biopsy with CIS in 70-100% of tubules.


title: CIS, patient 2

source_name: Biopsy with CIS in 60-75% of tubules. Rest tissue after removal of EC.


title: Skin_age_53_individual_3


title: SEM patient 5

source_name: Seminom (SEM), no normal germ cells or CIS.


title: EC, patient 1

value: Embryonal carcinoma (EC), no normal germ cells or CIS.


title: Skin_age_53_individual_2

value: skin


title: Skin_age_52_individual_2


title: CIS, patient 5

source_name: Biopsy with CIS in 50-80% of tubules. Rest tissue after removal of SEM.


title: Skin_age_53_individual_1


title: Skin_age_50_individual_3


title: SEM patient 4

value: Seminom (SEM), no normal germ cells or CIS.


title: SEM patient 3


title: CIS, patient 7

source_name: Biopsy with CIS in 20-70% of tubules.

value: Biopsy with CIS in 20-70% of tubules.


title: Skin_age_49_individual_1


title: Skin_age_50_individual_4


title: Skin_age_50_individual_1


title: Skin_age_50_individual_2


title: Skin_age_52_individual_1


title: CIS, patient 3

source_name: Biopsy with CIS cells in 10-50% of tubules. Rest tissue after removal of SEM.


title: Skin_age_47_individual_4


title: SCO, patient 13

source_name: SCO  (no normal germ cells and no CIS).

value: SCO  (no normal germ cells and no CIS).


title: SCO, patient 14

source_name: SCO  (no normal germ cells but CIS cells found in testis).  Extra-gonadal germ cell tumour removed.


title: Skin_age_47_individual_3


title: SCO, patient 12

source_name: Sertoli cell only (SCO) (no normal germ cells and no CIS).


title: Skin_age_51_individual_1


title: Normal spermatogenesis, patient 16

source_name: Normal spermatogenesis, rest tissue after removal of leyiomyosarcoma. No tumour tissue present in sample.


title: Normal spermatogenesis, patient 15

source_name: Normal spermatogenesis, rest tissue after removal of leydig cell tumour. No tumour tissue present in sample.


title: Skin_age_47_individual_2


title: Skin_age_47_individual_1


title: Skin_age_45_individual_2


title: Skin_age_44_individual_1


title: Skin_age_45_individual_1


title: Skin_age_43_individual_1


title: Skin_age_43_individual_3


title: Skin_age_41_individual_1


title: SF6220V CIS100

data_processing: The per-array lowess normalized signal (gProcessedSignal) from each array was normalized to each other by quantile normalization using the marray package in R/bioC version 2.7.2.

source_name: Adult human testis with 99-100% CIS tubules.

extract_protocol: RNA was extracted from frozen tissue sections by trizol, extracted with chloroform and precipitated with isppropanol, according to the standard trizol procedure.

treatment_protocol: All human samples are untreated, Frozen tissue samples (biopsies) were cut in 20 µm sections, and every third section was stained with BCIP to reveal tubules with CIS. The percentage of tubules with CIS and tubules with normal spermatogenesis was determined.


title: Normal human testis RNA from Ambion

source_name: Adult human testis with normal spermatogenesis from Ambion. Contaminated with RNA from epididymis.


title: Skin_age_43_individual_2


title: SF6193H CIS50

source_name: Adult human testis with 50% CIS tubules. Normal spermatogenesis in rest.


title: SF6246H-II CIS30

source_name: Adult human testis with 30% CIS tubules. Normal spermatogenesis in rest.


title: Skin_age_38_individual_1


title: Skin_age_42_individual_3


title: Skin_age_42_individual_1


title: fib2_24H

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

country: France

institute: Institut Curie

description: immortalized fibroblasts 2 treated with H202 during 24 hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization

label: DASL

label_protocol: RNA was prepared according to the manufacturer instructions

extract_protocol: RNA was extracted wih miRNeasy Mini kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: time

value: immortalized fibroblast


title: Skin_age_42_individual_2


title: Skin_age_43_individual_4


title: Skin_age_34_individual_1


title: Skin_age_36_individual_1


title: Skin_age_39_individual_1


title: Skin_age_26_individual_2


title: Skin_age_27_individual_1


title: Skin_age_30_individual_1


title: fib2_8H

description: immortalized fibroblasts 2 treated with H202 during 8 hours

value: 8 h


title: fib2_4H

description: immortalized fibroblasts 2 treated with H202 during 4 hours

value: 4 h


title: fib2_2H

description: immortalized fibroblasts 2 treated with H202 during 2 hours

value: 2 h


title: fib2_0.5H

description: immortalized fibroblasts 2 treated with H202 during 0.5 hour


title: fib1_4H

description: immortalized fibroblasts 1 treated with H202 during 4 hours


title: fib1_8H

description: immortalized fibroblasts 1 treated with H202 during 8 hours


title: Skin_age_33_individual_1


title: Skin_age_24_individual_1


title: Skin_age_23_individual_2


title: Skin_age_31_individual_1


title: fib1_0.5H

description: immortalized fibroblasts 1 treated with H202 during 0.5 hour


title: fib1_NT

description: immortalized fibroblasts 1 untreated

value: untreated

value: 0 h


title: fib1_1H

description: immortalized fibroblasts 1 treated with H202 during 1 hour

value: 1 h


title: Skin_age_22_individual_5


title: CovR-R158C-2 grown to mid-exponential phase in THY

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

hyb_protocol: Per Affymetrix protocol

scan_protocol: Per Affymetrix protocol

data_processing: Probes corresponding to the serotype M3 strains were extracted from the total data set.  The total intensity for each sample was then calculated by adding the values for each of the probe sets.  The probe set values were then normalized such that the total intensity derived from each sample was equivalent.

organism: Streptococcus pyogenes

source_name: Strain CovR-R158C grown to mid-exponential phase in THY

label_protocol: Per Affymetrix protocol

extract_protocol: Strain was grown to mid-exponential phase in THY.  2x RNAprotect (Qiagen) was added for 5 mins and cells were pelleted.  Total RNA was extracted with RNeasy (Qiagen) and reverse transcribed to cDNA with SuperScriptIII (Invitrogen). cDNA was labeled and hybridized following Affymetrix insturctions.

value: CovR R158C

value: CovR C158

tag: growth

value: mid-exponential phase in THY


title: Skin_age_22_individual_4


title: Skin_age_22_individual_6


title: Skin_age_22_individual_2


title: Skin_age_22_individual_7


title: Skin_age_25_individual_1


title: Strain CovR-R158C-1 grown to mid-exponential phase


title: fib1_24H

description: immortalized fibroblasts 1 treated with H202 during 24 hours


title: fib2_1H

description: immortalized fibroblasts 2 treated with H202 during 1 hour


title: fib2_NT

description: immortalized fibroblasts 2 untreated


title: Skin_age_22_individual_1


title: Skin_age_22_individual_3


title: Skin_age_23_individual_1


title: fib1_2H

description: immortalized fibroblasts 1 treated with H202 during 2 hours


title: Strain CovR-R144C-2 grown to mid-exponential phase in THY

source_name: Strain CovR-R144C grown to mid-exponential phase in THY

value: CovR with C144

value: Mid-exponential phase in THY


title: Strain CovR-R144C-1 grown to mid-exponential phase in THY

value: CovR C144


title: Skin_age_21_individual_1

value: skin


title: CovR-N193I-2 grown to mid-exponential phase in THY

source_name: CovR-N193I growth to mid-exponential phase in THY

value: CovR with I193

value: mid-exponential in THY


title: Skin_age_21_individual_2


title: CovR knockout strain rep2 grown to mid-exponential phase in THY

source_name: Strain 10870-delta-covR grown to mid-expontial phase in THY

value: covR knockout


title: CovR knockout strain grown to mid-exponential phase in THY

source_name: Strain 10870-delta-covR growth to mid-exponential phase in THY

value: CovR knockout


title: CovR-N193I-1 grown to mid-exponential phase in THY

source_name: Strain CovR-N193I grown to mid-exponential phase in THY


title: MGAS10870_rep_1

source_name: Strain MGAS10870 growth to mid-exponential phase in THY

value: wild-type


title: T cells_OT-II_unstimulated

city: Aachen

first: Alma

last: Dr. Zernecke

address: Pauwelsstr. 30

institute: IMCAR

description: The JPG pictures of the scaned array membranes were evaluated with GEArray Expression Analysis Suite 2.0.

hyb_protocol: The array filters were hybridized with these biotin-labeled targets (5µg/array) at 60°C for 17 hours. Filters were first washed with 2 x SSC/1% SDS and then with 0.1 x SSC/1% SDS at 60°C for 15 minutes each. Chemilumilescent detection steps were performed by subsequent incubation of the filters with alkaline phosphatase– conjugated streptavidin and CDP-Star substrate.

scan_protocol: The images were captured using LAS 3000 (Fuji). One picture per 5 minutes was taken over a period of 60 minutes.With multi gauge 3.0 the pictures were converted into JPG.

data_processing: For quantification, intensity of signal was first measured using GEArray Expression Analysis Suite 2.0 (SuperArray) with a local background subtraction method. These subtracted intensities were then normalized via house-keeping genes and negative controls (e.g. Blanks) to obtain a relative intensity for each spot. A spot is considered "Present" if its stretched average is greater then its stretched local background, and the average density of the spot is greater than 1.5x of the mean value of the local backgrounds of the lower 75 percentile of all non-bleeding spots. All other spots are considered Absent.  A spot is considered "Bleeding" if the average density of the spot is greater than 75% of the maxim average value of all spots and its stretched average differs from its stretched local background value by less then 50%. These relative intensities were used to compare samples.

source_name: CD4+ OT-2 T cells, unstimulated

label_protocol: Biotin-labeled cRNAs, known as labeled cRNA targets, were generated using TrueLabeling-AMP Linear RNA Amplification Kit following manufacturer’s protocol (SuperArray Bioscience Corporation). Briefly, total RNA (5 µg/array) was first converted to cDNA at 42°C for 50 minutes. These cDNAs were then in vitro transcribed to cRNAs in the presence of biotin-16-UTP (Roche). Biotin-labeled cRNAs were purified using a RNeasy Mini Kit (Qiagen). The concentration of cRNAs was measured with a NanoDrop spectrometer.

extract_protocol: Total RNAs from indicated cells were isolated using QIAGEN RNeasy Mini Kit by following the manufacturer’s instructions.

tag: cd4+ t cells from ot-2 mice day

value: 0 without stimulation and DC interaction


title: T cells_OT-II_after interaction with Ccl17E/+ DCs

hyb_protocol: The array filters were hybridized with these biotin-labeled targets (5µg/array) at 60°C for 17 hours. Filters were first washed with 2 x SSC/1% SDS and then with 0.1 x SSC/1% SDS at 60°C for 15 minutes each. Chemilumilescent detection steps were performed by subsequent incubation of the filters with alkaline phosphatase– conjugated streptavidin and  CDP-Star substrate.

source_name: CD4+ OT-2 T cells, stimulated with Ccl17E/+ DCs

value: 3 after interaction with Ccl17E/+ DCs


title: T cells_OT-II_after interaction with Ccl17E/E DCs

source_name: CD4+ OT-2 T cells, after interaction with Ccl17E/E DCs

value: 3 after interaction with Ccl17E/E DCs


title: Skin_age_20_individual_1

description:
n/a
Sample_probe_group_file  HuEx-1_0-st-v2.r2.pgf
Sample_meta-probeset_file  HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

tag: age


title: Skin_age_19_individual_1


title: MGAS10870_rep_2

source_name: Strain MGAS10870 grown to mid-exponential phase in THY


title: OASM_Early_2

city: Chicago

first: Carla

middle: R

last: Scanzello

address: 1611 W. Harrison St., Ste. 510

department: Rheumatology

institute: Rush University Medical Center

hyb_protocol: aRNA was hybridized on to chips by incubating at 45 C for 16hr (60 rpm rotation).  The chips were washed and stained with the program EukGE-WS2V5_450 on Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The chips were scanned with Affymetrix GeneChip scanner 3000.

data_processing: Robust Multi-Array Analysi (RMA; Irizarry et al. Biostatistics 4: 249.) in the Matlab software package (v2009a The MathWorks Inc., Natick, MA) was first used to do background corrections of raw expression data (.cel files) from individual sample sets.  Then quantile normalization over multiple arrays was done across the 26 samples sets being compared, and median polishing was conducted to reduce the contribution of outlier probes to the single expression value derived from multiple probes for a given gene in a sample set.

source_name: Synovial Membrane, knee

label_protocol: Message Amp premier RNA amplification kit (Applied Biosystems, #AM1792) was used for labelling. The input total RNA was 150ng. Biotin was added during in Vitro transcription to synthesize biotin-modified aRNA.

extract_protocol: We extracted total RNA from homogenized samples of osteoarthritic synovial membranes by using the PerfectPure® RNA Fibrous Tissue kit (5Prime Inc.). All RNA was DNAse treated. RNA integrity was determined by electrophoresis on a microfluidics-based platform (Agilent Technologies).

value: Synovial Membrane, knee

tag: phenotype

value: early-stage osteoarthritis

value: M


title: OASM_Early_8


title: OASM_Early_10


title: OASM_Early_1


title: OASM_Early_3


title: OASM_Early_5

value: F


title: OASM_Early_6


title: OASM_Early_9


title: OASM_End_9

value: end-stage osteoarthritis


title: OASM_Early_4


title: OASM_Early_7


title: OASM_End_7


title: OASM_End_6


title: root, wildtype, replicate 1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.15.3) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

organism: Medicago truncatula

source_name: root (meristem, elongation and differentiation zone)

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug total RNA. The protocol was conducted using the reagents provided by Affymetrix, as the manufacturer's instructions.

growth_protocol: Medicago plants used for gene expression analysis were grown vertically on Färhaeus medium plates without nitrate. RNA was isolated from the Nod factor susceptible zone of 7-day-old roots samples snap-frozen in liquid N2.

extract_protocol: Total RNA was extracted and purified from root Nod factor suspension zone using the Qiagen RNeasy plant mini kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 25S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 9.0.

value: Wildtype (Jemalong A17)

value: 7 days old

value: root meristem


title: OASM_End_5


title: OASM_End_8