title: First Experiment of MeJA-induced gene expression in rice plants

city: Seoul

first: Ju-Seok

last: Seo

department: Dept. of Applied Biology & Chemistry

institute: Seoul National University

description:
Two-week old seedlings after 100 uM MeJA treatment for 6 hrs
Microarray_Name: Wt_Meja_012605_A
Microarray_DB_ID: AXON487706

hyb_protocol: Hybridization was performed with 3DNA Array 900 (USA) The 2X hybridization Buffer (vial 6) and Nuclease Free Water (vial 10) was thawed and resuspended by heating to 65℃. For each array, a 3DNA Hybridization Mix was prepared according to the below: 1㎕ 3DNA Capture Reagent #1 (Vial 1), 1㎕ 3DNA Capture Reagent #2 (Vial 1), 30㎕ Nuclease Free Water (Vial 10), 32㎕(-1㎕) 2X Hybridization Buffer (Vial 6). The 3DNA Hybridization Mix is gently mixed and briefly microfuged. The 3DNA Hybridization Mix was incubated at 80℃ for 10 minutes with covered foil. And then further incubated at 55℃ for 5 minutes covered foil. The 3DNA Hybridization was gently vortexed and briefly microfuged. Each 28㎕ the 3DNA Hybridization Mix was added to a prewarmed microarray on heat block at 55℃. A glass coverslip was applied to the array and the array was incubated for 4 hours in a dark humidified chamber at 55℃.

scan_protocol: Themicroarray was scanned with Genepix 4000 B (Axon Instruments).

data_processing: Noncorrelation of signal and background intensities was confirmed by plotting base 2 log background intensity on the x axis and base 2 log intensity subtracted from background intensity on the y axis. Before normalization, the normal distribution and linear relations of Cy3 and Cy5 intensities were tested by qqplot and a linear regression model, respectively, in R statistical language. The spatial effects on the chip during the hybridization process were checked with spatial.func in the sma package. The variance differences between Cy3 and Cy5 intensities within the microarray were tested with the t test under the assumption of both uniform and nonuniform variances. One- and two-way analyses of variance of the signal intensity differences between microarrays were performed. Median pixel intensities were transformed as log ratios with base 2 and then adjusted by block-by-block Lowess normalization for each slide (Yang et al., 2002). Multiple analysis was performed with limma package in R computing environment (Smyth, G. K. (2004). Linear models and empirical Bayes methods were adopted for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3).  The package adopts the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes. Genes of which adj.P.Value or false discovery below 0.1 were collected and further selected for those gene expressions were higher than .67 or less than -.67 at least at one stage compared to that at stage1. To improve the specificity of our statistical hypothesis in low-intensity regions, we adopted the following empirical criteria: a spot was selected if it was not flagged for its morphology, the diameter was larger than 51 pixels, and the inn tensities of both signals were higher than 500. Multivariate statistical tests such as clustering, principal component analysis, and multidimensional scaling were performed with Acuity 3.1 (Axon Instruments).

label_protocol:
Poly A+ mRNA was isolated from total RNA using Oligotex mRNA Spin-Column (QIAGEN, USA). Briefly, 200 ug total RNA was applied into an RNase-free 1.5ml microcentrifuge, and adjust to 250 ul with RNase-free water. The same amount volume of Buffer OBB was added and mixed the contents thoroughly by pipetting of flicking the tube and subsequently, inverted 10 times. The tube was centrifuged for 5min at maximum speed and the supernatant was transferred to a new microcentrifuge tube. 15 ul of Oligotex Suspension was added and mixed the contents thoroughly by pipetting of flicking the tube. The tube was incubated for 3min at 70℃ in a heating block with inverting the tube 10 times. The sample was removed from the heating block, and placed at 20 to 30℃ for 10min. Pellet of the Oligotex:mRNA comlex was collected by centrifugation for 2min at maximum speed and cafully the supernantant was removed by pepetting. The Oligotex:mRNA pellet was resuspended  in 400㎕ buffer OW2 by vortexing and pipetted onto a small spin column placed in a 1.5ml microcentrifuge tube. The tube was centrifuged for 1 min at maximum speed.  The spin column was transferred to a new RNase-free 1.5ml microcentrifuge tube, and 400㎕ Buffer OW2 was applied to the column. The tube was centrifuged for 2 min at maximum speed and the flow-through was discarded. Spin column was transferred to a new RNase-free 1.5ml microcentrifuge tube. 50㎕ OEB buffer was pippeted onto the column and the resin was resuspended by pipetting up and down 3 or 4 times. The column was incubated for 5min at 70℃ and centrifuge for 1 minute. To concentrate mRNA, 1/10 volume of mRNA of 3M NaOAc was added and the mixture was gently invertted and briefly microcentrifuged. 250㎕ of cold 100% EtOH was added and inverted sevral times. The tube was incubate on ice for 30 minutes and then centrifuged for one hour at 4℃. The supernantant was carefully removed by pipetting. 200㎕ 70% EtOH  was added and centrifuged for 5 minutes at 4℃. The supernantant was carefully removed by pipetting. The tube was incubated for 5 minutes at room temperature. The pellet was resuspended in 10㎕ RNase free water by tapping for 5minutes.
cDNA was synthesized in a 1.5mL RNase-free microcentrifuge tube by combining	 10㎕ poly(A)+RNA(25-100ng), 1㎕  RT Primer (5 pmole/㎕- cy3,  3DNA Array 900, USA ) and then adjusted to a final volume of 11㎕ with RNase free water.   The RNA-RT primer mix is centrifuged briefly to collect contents in the bottom of the tube. The tube is incubated at 80℃ for 10 minutes and immediately transferred to ice for 5 minutes. In a separate microtube, the reaction mixture of 4㎕  5×SuperscriptⅡ First Strand Buffer , 1㎕ dNTP mix, 2㎕ 0.1M dithiotreitol(DTT), 1㎕ Superase-In, and 1㎕ SuperscriptⅡ enzyme, 200Units are combined (invitrogen, USA). The reaction mix is incubated at 42℃ for one hour 30minutes. The reaction was stopped by adding 3.5㎕ of 0.5M NaOH and gently mixed to. The tube is incubated at 65℃ for 10 minutes to denature the DNA/RNA hybrids and degrade RNA. The mixture was neutralized by adding 5㎕ of 1M Tris-HCl, pH 7.5.

growth_protocol: Wild-type rice (O.sativa cv. Nakdong) seeds were germinated in Murashige-Skoong solid medium in a growth chamber in the dark at 28 °C for 3days, transplanted to soil pots, and grown in a greenhouse (16 h light/8 h dark cycle) at 28-30 °C. Each pot (10 X 10 X 10 cm) was filled with rice nursery soil (Bio-media, Kyoungju, Korea).

extract_protocol: TriZol and Qiagen oligotex column procedure

treatment_protocol: Non treated control

tag: reference

value: Non treated control

label_protocol:
Poly A+ mRNA was isolated from total RNA using Oligotex mRNA Spin-Column (QIAGEN, USA). Briefly, 200 ug total RNA was applied into an RNase-free 1.5ml microcentrifuge, and adjust to 250 ul with RNase-free water. The same amount volume of Buffer OBB was added and mixed the contents thoroughly by pipetting of flicking the tube and subsequently, inverted 10 times. The tube was centrifuged for 5min at maximum speed and the supernatant was transferred to a new microcentrifuge tube. 15 ul of Oligotex Suspension was added and mixed the contents thoroughly by pipetting of flicking the tube. The tube was incubated for 3min at 70℃ in a heating block with inverting the tube 10 times. The sample was removed from the heating block, and placed at 20 to 30℃ for 10min. Pellet of the Oligotex:mRNA comlex was collected by centrifugation for 2min at maximum speed and cafully the supernantant was removed by pepetting. The Oligotex:mRNA pellet was resuspended  in 400㎕ buffer OW2 by vortexing and pipetted onto a small spin column placed in a 1.5ml microcentrifuge tube. The tube was centrifuged for 1 min at maximum speed.  The spin column was transferred to a new RNase-free 1.5ml microcentrifuge tube, and 400㎕ Buffer OW2 was applied to the column. The tube was centrifuged for 2 min at maximum speed and the flow-through was discarded. Spin column was transferred to a new RNase-free 1.5ml microcentrifuge tube. 50㎕ OEB buffer was pippeted onto the column and the resin was resuspended by pipetting up and down 3 or 4 times. The column was incubated for 5min at 70℃ and centrifuge for 1 minute. To concentrate mRNA, 1/10 volume of mRNA of 3M NaOAc was added and the mixture was gently invertted and briefly microcentrifuged. 250㎕ of cold 100% EtOH was added and inverted sevral times. The tube was incubate on ice for 30 minutes and then centrifuged for one hour at 4℃. The supernantant was carefully removed by pipetting. 200㎕ 70% EtOH  was added and centrifuged for 5 minutes at 4℃. The supernantant was carefully removed by pipetting. The tube was incubated for 5 minutes at room temperature. The pellet was resuspended in 10㎕ RNase free water by tapping for 5minutes.
cDNA was synthesized in a 1.5mL RNase-free microcentrifuge tube by combining	 10㎕ poly(A)+RNA(25-100ng), 1㎕  RT Primer (5 pmole/㎕-cy5; 3DNA Array 900, USA) and then adjusted to a final volume of 11㎕ with RNase free water.   The RNA-RT primer mix is centrifuged briefly to collect contents in the bottom of the tube. The tube is incubated at 80℃ for 10 minutes and immediately transferred to ice for 5 minutes. In a separate microtube, the reaction mixture of 4㎕  5×SuperscriptⅡ First Strand Buffer , 1㎕ dNTP mix, 2㎕ 0.1M dithiotreitol(DTT), 1㎕ Superase-In, and 1㎕ SuperscriptⅡ enzyme, 200Units are combined (invitrogen, USA). The reaction mix is incubated at 42℃ for one hour 30minutes. The reaction was stopped by adding 3.5㎕ of 0.5M NaOH and gently mixed to. The tube is incubated at 65℃ for 10 minutes to denature the DNA/RNA hybrids and degrade RNA. The mixture was neutralized by adding 5㎕ of 1M Tris-HCl, pH 7.5.

treatment_protocol: Two-week old seedlings were harvested after 100 uM MeJA treatment for 6 hrs.

value: two-week old seedling

value: MeJA


title: Second Experiment of MeJA-induced gene expression in rice plants

status: Public on Jan 01 2011

type: RNA

country: South Korea

description:
Two-week old seedlings after 100 uM MeJA treatment for 6 hrs
Microarray_Name: Wt_MeJa_021705_A
Microarray_DB_ID: AXON571712

molecule: total RNA

organism: Oryza sativa

tag: developmental stage

tag: agent


title: 30 minutes bile exposure replicate D

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

department: R&D

country: Finland

institute: Valio Ltd

hyb_protocol: The labeled cDNA samples were hybridized to microarrays following Agilent’s procedure titled “Two-Color Microarray-Based Gene Expression Analysis.” For each microarray, 825 ng of cyanine 3-labeled cDNA and 825 ng of cyanine 5-labeled cDNA were mixed with 11 µl of 10X GE Blocking Agent and 2.2 µl of 25X Fragmentation Buffer. Volume of this fragmentation mix was brought to 55 µl with nuclease-free water and mix was incubated at 60 °C for exactly 30 minutes. After incubation, fragmentation reaction was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer, mixed gently and centrifuged for one minute at RT at 15800 × g. 100 µl of hybridization sample was loaded onto an array and hybridized at 65 °C for 17 hours at 10 rpm with Agilent hybridization oven. Microarrays were washed twice with GE Wash Buffer 1 for one minute at RT and once with prewarmed (37 °C) GE Wash Buffer 2 for one minute.

scan_protocol: Immediately after washing, microarrays were scanned at 5 µm resolution with a GenePix 4200 AL scanner (Axon Instruments) and stored as TIFF images. The fluorescence intensities were quantified and addressed to genomic ORFs with GenePix Pro 6.0 software (Axon Instruments / Molecular Devices Corp.). Microarray image analysis and feature detection were performed using GenePix Pro 6.0 software with default parameters, and results were further improved manually.

data_processing: Data analysis was performed using Bioconductor for the R statistical software. Background correction and normalization were done using the limma package, and the statistical significance was assessed using cyberT. The data set contained 12 two-color microarrays, with each condition measured four times, and was analyzed as an entity. The foreground and background median intensity estimates were used, and the data were background corrected using the normexp-function (offset set to 50), normalized within arrays using loess (100 iterations, suspicious spots and probe sequences deleted, matching multiple hits or borders of the coding regions downweighted to zero and intergenic probe sequences downweighted to 0.1) and normalized between arrays using quantile normalization. Expression ratios for genes were obtained by taking the averages of the log2-transformed expression ratios of probes describing the same gene and matching a single genetic coding region locus. The gene expression ratios were calculated for 2798 genes out of the total 2944 (95% coverage) genes in the genome. The statistical significance of the expression ratio of a gene between two conditions was analyzed using a paired t-test method implemented in CyberT (Bayesian prior estimate of within-treatment variance was set to five, and the window size was set to 101). P-values were Bonferroni adjusted by the number of performed t-tests in total (8394). The analysis showed that 248, 133, and 9 genes had significant differences in expression between the zero and 10 min conditions, the zero and 30 min conditions, and zero and 120 min conditions, respectively, when using 0.01 as the threshold for statistical significance and when requiring at least two-fold changes in expression ratio.

organism: Lacticaseibacillus rhamnosus

source_name: Total RNA before bile exposure

label_protocol: Five micrograms of RNA were reverse transcribed to cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s protocol except that 6 µg of random primers (Invitrogen, 48190-011) were used instead of anchored oligo(dT)20 primers and random hexamers. The cDNA was fluorescently labeled using Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences) and purified with a column included in the SuperScript Indirect cDNA Labeling System kit.

growth_protocol: Bacterial cells were grown in MRS broth at bioreactor at 37 °C. pH was maintained constant at 6.0.

extract_protocol: One to three milliliters of bacterial culture were mixed with 2–6 mL of RNAprotect Bacteria reagent (Qiagen) and handled according to the manufacturer’s instructions. The cell pellets were stored at –70 °C for subsequent RNA extraction. Cells were lysed with 10 mg/mL lysozyme (Amresco), 3 mg/mL proteinase K (Sigma-Aldrich), and 100 U of mutanolysin (Sigma-Aldrich) at 37 °C for 30 minutes. The suspension was supplemented with 1 mL of preheated (65 °C) TRIzol reagent (Invitrogen) and vortexed for 3 minutes. After incubation at RT for 5 minutes, the cell lysate was homogenized in a MagNA Lyser instrument (Roche) with <106 µm glass beads (Sigma-Aldrich) for four 30 s cycles at 6000 rpm. Between each cycle, the cells were chilled on ice for 1 minute. Cell debris was removed by centrifugation (12000 × g at 4 °C for 15 min), and the lysate was extracted with 200 µl of chloroform by vortexing for 15 s. After incubation at RT for 3 min, the phases were separated by centrifugation (12000 × g at 4 °C for 15 min). The aqueous phase was mixed with 500 µl of 80% ethanol for total RNA purification with an RNeasy Mini Kit (Qiagen). During RNA purification, DNA was removed using RNase-Free DNase (Qiagen) as described in the manual.

tag: strain

value: GG

source_name: Total RNA 30 minutes after bile exposure


title: 120 minutes bile exposure replicate B

source_name: Total RNA 120 minutes after bile exposure


title: J1-null trypomastigotes sample 2

city: Athens

first: Dilrukshi

middle: K

last: Ekanayake

state: GA

address: 120, Green Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Georgia

hyb_protocol: Microarrays were obtained from the Pathogen Functional Genomic resource center, and contained an array of 12,288 70mer oligonuclotides, each with complementarity to an individual T. cruzi open reading frame. Microarray was prehybridized immediately before hybridization. Three hybridizations were performed for each life stages as previously

scan_protocol: Arrays were scanned on a ScanArray 4000(GSI Lumonics, Wilmington, MA) to obtain tagged Image File format (TIFF) images.

data_processing: Background subtracted intensities were normalized by lowess, log2 transformed ratio of medians (ProScanArray Express version 4.0 (Perkin Elmer)).

organism: Trypanosoma cruzi

source_name: wild type

label_protocol: cDNA was synthesis using superscript II reverse transcriptase (Life technologies, Grand Island, NY) and Cy3 or Cy5-dUTP (Amersham Phamacia Biotech) included in the reaction mix. Unincorporated fluorescence nucleotide was removed using GFX columns per manufacture’s instructions

growth_protocol: Trypomasigotes were then grown in monolayer of Vero cells/myoblast in Modified Eagle’s Media containing 20% fetal bovine serum. Emergent trypomastigotes were harvested daily and examined by light microscopy. Preparations containing >95% of trypomasigotes were used in the subsequent assays.

extract_protocol: Briefly, total RNA was isolated using TRIZOL and cleaned up with RNAeasy kit (QIAGEN, Valencia, CA) per the manufacture’s instruction

tag: stage

value: trypomastigotes

value: Y

value: J1-null Y


title: 30 minutes bile exposure replicate C


title: MeJA-induced gene expression in rice plants

description:
Two-week old seedlings after 100 uM MeJA treatment for 6 hrs
Microarray_Name: Wt_MeJaTotal_021805_A
Microarray_DB_ID: AXON576917


title: 30 minutes bile exposure replicate A


title: 30 minutes bile exposure replicate B


title: 10 minutes bile exposure replicate D

source_name: Total RNA 10 minutes after bile exposure


title: 120 minutes bile exposure replicate A


title: 10 minutes bile exposure replicate B


title: 10 minutes bile exposure replicate A


title: 10 minutes bile exposure replicate C


title: J1-null trypomastigotes sample 1


title: Pam + TSA 4hours stimulation rep2

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description:
Mus musculus BMDM cRNA12 vs cRNA pool UMRR after 4 hours cell growth in presence of Pam + TSA replicate 2/2
cRNA24

hyb_protocol: A mixture of sample cRNA and pool RNA was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

organism: Mus musculus

source_name: BMDM Pam + TSA 4hours stimulation rep2

label_protocol: First cDNA Synthesis from Total RNA then fluorescent cRNA Syntesis: in vitro transcription and incorporation of cyanine 5-CTP

extract_protocol: Fixation followed by RNeasy purification

tag: gender

value: female

value: BALB/c

tag: cell type

value: BM-derived macrophage

tag: age

value: 12 weeks

value: Pam + TSA

tag: time

source_name: Universal mouse RNA mixture (UMRR)

tag: reference pool

value: Universal mouse RNA mixture


title: LPS + TSA 4hours stimulation rep1

description:
Mus musculus BMDM cRNA7 vs cRNA pool UMRR after 4 hours cell growth in presence of LPS + TSA replicate 1/2
cRNA19

source_name: BMDM LPS + TSA 4hours stimulation rep1

value: LPS + TSA


title: LPS 4hours stimulation rep2

description:
Mus musculus BMDM cRNA6 vs cRNA pool UMRR after 4 hours cell growth in presence of LPS replicate 2/2
cRNA18

source_name: BMDM LPS 4hours stimulation rep2

value: LPS


title: TSA 4hours stimulation rep1

description:
Mus musculus BMDM cRNA3 vs cRNA pool UMRR after 4 hours cell growth in presence of TSA replicate 1/2
cRNA15

source_name: BMDM TSA 4hours stimulation rep1

value: TSA


title: Pam 4hours stimulation rep1

description:
Mus musculus BMDM cRNA9 vs cRNA pool UMRR after 4 hours cell growth in presence of Pam replicate 1/2
cRNA21

source_name: BMDM Pam 4hours stimulation rep1

value: Pam


title: WKS938_expo_rep3

type: genomic

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

hyb_protocol: Samples were hybridized as described in Auchtung et al. 2005 PNAS 102:12554-9 [PMID 16105942].

scan_protocol: Arrays were scanned and analyzed with GenePix Pro 3.0 (Axon Instruments).

data_processing: GPR files were loaded and processed in Prep+07 (BMC Bioinformatics 2009, 10:16 [PMID 19134227; doi:10.1186/1471-2105-10-16]). Lowess normalization was performed and spots for which signal was 90% within 2SD above background were removed. Results from the Prep+07 analysis were manually curated in Microsoft Excel for spots that had <2 datapoints with quality data.

molecule: genomic DNA

organism: Bacillus subtilis subsp. subtilis str. 168

label_protocol: Samples were prepared for microarray analysis by labelling aliquots of the resuspended immunoprecipitated DNA or total control DNA with aminoallyl-dUTP using 13 U Sequenase (USB) and 5 μg random nonamer. The labelled samples were purified, conjugated to Cy3 or Cy5, and hybridized to microarrays.

growth_protocol: Cells were grown in minimal 1% glucose medium until OD600 reached approximately 0.6.

extract_protocol: Chromatin immunoprecipitation (ChIP) of DNA bound to epitope-tagged proteins was done essentially as described (1998, Lin and Grossman, Cell, 92:675-685 [PMID 9506522]; Breier and Grossman, Molecular Microbiology, 64:703-718 [PMID 17462018]).

tag: genotype

value: 168 hbs::pWKS913 (spc) (hbs-myc)

tag: growth phase

value: exponential

tag: isolation

value: anti-myc IP-associated DNA

tag: antibody

value: Zymed mouse monoclonal anti-cMyc

tag: antibody vendor

value: Invitrogen

tag: antibody catalog #

value: total chromosomal DNA


title: WKS895_expo_rep1

value: 168 rok::pWKS516 (spc) (rok-myc)


title: Pam 4hours stimulation rep2

description:
Mus musculus BMDM cRNA10 vs cRNA pool UMRR after 4 hours cell growth in presence of Pam replicate 2/2
cRNA22

source_name: BMDM Pam 4hours stimulation rep2

value: female


title: LPS + TSA 4hours stimulation rep2

description:
Mus musculus BMDM cRNA8 vs cRNA pool UMRR after 4 hours cell growth in presence of LPS + TSA replicate 2/2
cRNA20

source_name: BMDM LPS + TSA 4hours stimulation rep2

value: BALB/c


title: WKS895_expo_rep2


title: WKS938_expo_rep2


title: LPS 4hours stimulation rep1

description:
Mus musculus BMDM cRNA5 vs cRNA pool UMRR after 4 hours cell growth in presence of LPS replicate 1/2
cRNA17

source_name: BMDM LPS 4hours stimulation rep1

value: BM-derived macrophage


title: WKS895_expo_rep3


title: control 4hours stimulation rep2

description:
Mus musculus BMDM cRNA2 vs cRNA pool UMRR after 4 hours cell growth in absence of TSA replicate 2/2
cRNA14

source_name: BMDM control 4hours stimulation rep2

value: 12 weeks

value: control


title: Pam + TSA 1hour stimulation rep2

description:
Mus musculus BMDM cRNA12 vs cRNA pool UMRR after 1 hour cell growth in presence of Pam + TSA replicate 2/2
cRNA12

source_name: BMDM Pam + TSA 1hour stimulation rep2

value: Pam + TSA

value: Universal mouse RNA mixture


title: control 4hours stimulation rep1

description:
Mus musculus BMDM cRNA1 vs cRNA pool UMRR after 4 hours cell growth in absence of TSA replicate 1/2
cRNA13

source_name: BMDM control 4hours stimulation rep1


title: Pam 1hour stimulation rep1

description:
Mus musculus BMDM cRNA9 vs cRNA pool UMRR after 1 hour cell growth in presence of Pam replicate 1/2
cRNA9

source_name: BMDM Pam 1hour stimulation rep1


title: TSA 4hours stimulation rep2

description:
Mus musculus BMDM cRNA4 vs cRNA pool UMRR after 4 hours cell growth in presence of TSA replicate 2/2
cRNA16

source_name: BMDM TSA 4hours stimulation rep2


title: LPS + TSA 1hour stimulation rep2

description:
Mus musculus BMDM cRNA8 vs cRNA pool UMRR after 1 hour cell growth in presence of LPS + TSA replicate 2/2
cRNA8

source_name: BMDM LPS + TSA 1hour stimulation rep2

value: LPS + TSA


title: LPS + TSA 1hour stimulation rep1

description:
Mus musculus BMDM cRNA7 vs cRNA pool UMRR after 1 hour cell growth in presence of LPS + TSA replicate 1/2
cRNA7

source_name: BMDM LPS + TSA 1hour stimulation rep1


title: WKS938_expo_rep1


title: LPS 1hour stimulation rep1

description:
Mus musculus BMDM cRNA5 vs cRNA pool UMRR after 1 hour cell growth in presence of LPS replicate 1/2
cRNA5

source_name: BMDM LPS 1hour stimulation rep1

value: LPS


title: Pam + TSA 1hour stimulation rep1

description:
Mus musculus BMDM cRNA11 vs cRNA pool UMRR after 1 hour cell growth in presence of Pam + TSA replicate 1/2
cRNA11

source_name: BMDM Pam + TSA 1hour stimulation rep1


title: TSA 1hour stimulation rep2

description:
Mus musculus BMDM cRNA4 vs cRNA pool UMRR after 1 hour cell growth in presence of TSA replicate 2/2
cRNA4

source_name: BMDM TSA 1hour stimulation rep2

value: TSA

source_name: Universal mouse RNA mixture (UMRR)


title: Pam 1hour stimulation rep2

description:
Mus musculus BMDM cRNA10 vs cRNA pool UMRR after 1 hour cell growth in presence of Pam replicate 2/2
cRNA10

source_name: BMDM Pam 1hour stimulation rep2

value: Pam


title: control 1hour stimulation rep1

description:
Mus musculus BMDM cRNA1 vs cRNA pool UMRR after 1 hour cell growth in absence of TSA replicate 1/2
cRNA1

source_name: BMDM control 1hour stimulation rep1


title: control 1hour stimulation rep2

description:
Mus musculus BMDM cRNA2 vs cRNA pool UMRR after 1 hour cell growth in absence of TSA replicate 2/2
cRNA2

source_name: BMDM control 1hour stimulation rep2


title: TSA 1hour stimulation rep1

description:
Mus musculus BMDM cRNA3 vs cRNA pool UMRR after 1 hour cell growth in presence of TSA replicate 1/2
cRNA3

source_name: BMDM TSA 1hour stimulation rep1


title: Wt_elev_gen4_5_vs_Wt_amb_gen4_5

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

hyb_protocol: Three µg of labeled aRNA were subsequently used for hybridization onto Arabidopsis slides printed with Operon v 3.1, 70 mer oligos obtained from the laboratory of David Galbraith at the University of Arizona. A formamide-based (50%) hybridization solution was applied at 42 ˚C for 14 h and then washed according to Galbraith protocols www.cals.arizona.edu/microarray.

scan_protocol: Arrays were imaged with a Scan Array 5000 system (Perkin Elmer, Wellesley, MA) and the resultant image files were imported into GenePix Pro 6.0 for data extraction and initial data diagnostics.

data_processing:
Quality of the hybridization was assessed with the Bioconductor packages arrayMagic v.1.14.0 and arrayQuality v.1.12.0.  Log-fold (M) over variance (A) plots (M-A plots) were used to determine the most appropriate background correction method.  We used basic normexp (offset=16) for background correction and print-tip loess for within slide normalization. Using limma, a linear model was fitted to compare control to all treatment conditions as contrasts and empirical Bayes was used to compute a moderated t-statistic.  Multiple testing errors were accounted for by using a false discovery rate (FDR) correction.

GSM tables contain raw gpr data. The published normalized signal intensity data is linked as a supplementary file to GSE16068.

organism: Arabidopsis thaliana

source_name: wild-type mutant Arabidopsis thaliana, leaves from mesocosm, elevated CO2, generation 4

label_protocol: Six µg of each amplified RNA (aRNA) sample was coupled to either CY3 or CY5 monochromeric dye (Amersham) also according to the Chandler protocols.  Three µg of labeled aRNA were subsequently used for hybridization onto Arabidopsis slides printed with Operon v 3.1, 70 mer oligos obtained from the laboratory of Dr. David Galbraith at the University of Arizona (www.cals.arizona.edu/microarray).

growth_protocol: Samples were derived from 100 leaves collected within mesocosms (50 x 50 x 45 cm) during generation 2 grown on Loamy Sand soil with pH 6.9 and the equilivant of 55 lbs/Acre NO3 and 7.64 lbs/Acre NH4. Samples were collected during maximum leaf area just prior to flower initiation, which was 45 days after germination under these conditions.

extract_protocol: Total RNA was isolated and labeled from control and treatment shoot tissue using methods from the Chandler Lab (http://www.maizearray.org/maize_protocols_factsheet.shtml).  Briefly, the TRIZOL reagent procedure was initially used to isolate total RNA that was further purified with RNA clean-up spin columns (Qiagen).  This two-step process ensured for high quality RNA determined spectrophotometircally (Nanodrop) and as determined with denaturing agarose gels.

treatment_protocol: Plants were subjected to 800 ppm CO2 fumigation

value: wild-type

tag: tissue

value: leaves from mesocosm

tag: ecotype

value: Columbia

value: 45 days of growth

source_name: wild-type mutant Arabidopsis thaliana, leaves from mesocosm, ambient CO2, generation 4

treatment_protocol: Plants were subjected to ambient CO2


title: nia_elev_gen4_6_vs_Wt_amb_gen4_4

source_name: nia2 mutant Arabidopsis thaliana, leaves from mesocosm, elevated CO2, generation 4

value: nia2 mutant


title: nia_amb_gen4_6_vs_Wt_elev_gen4_2

source_name: nia2 mutant Arabidopsis thaliana, leaves from mesocosm, ambient CO2, generation 4


title: Wt_amb_gen4_6_vs_Wt_elev_gen4_6


title: nia_elev_gen2_6_vs_Wt_amb_gen2_4

source_name: nia2 mutant Arabidopsis thaliana, leaves from mesocosm, elevated CO2, generation 2

growth_protocol: Samples were derived from 100 leaves collected within mesocosms (50 x 50 x 45 cm) during generation 2 grown on Loamy Sand soil with pH 6.9 and the equilivant of 55 lbs/Acre NO3 and 7.64 lbs/Acre NH4. Samples were collected during maximum leaf area just prior to flower initiation, which was 42 days after germination under these conditions.

value: 42 days of growth

source_name: wild-type mutant Arabidopsis thaliana, leaves from mesocosm, ambient CO2, generation 2


title: Nia_elev_gen2_4_vs_Wt_elev_gen2_4

source_name: wild-type mutant Arabidopsis thaliana, leaves from mesocosm, elevated CO2, generation 2


title: Wt_elev_gen2_1_vs_nia_amb_gen2_5

source_name: nia2 mutant Arabidopsis thaliana, leaves from mesocosm, ambient CO2, generation 2


title: Wt_amb_gen4_1_vs_nia_amb_gen4_3


title: 13912820 - Col0 RB2 vs ZF1 814 RB2

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Etude transcriptomique de mutants d’une nouvelle protéine de type AGO-hook chez Arabidopsis thaliana

hyb_protocol: ZF1 814 RB2 Cy5 / Col0 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

source_name: Col0 ZF1 814

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

growth_protocol: rosette - Media: Soil Temperature: 20°C Light: 16 Hours

treatment_protocol: no treatment

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)

source_name: Col0 wild-type

extract_protocol: Col0 RB1:100mg.


title: 13912821 - ZF1 814 RB2 vs Col0 RB2

hyb_protocol: Col0 RB2 Cy5 / ZF1 814 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: nia_amb_gen4_4_vs_Wt_amb_gen4_2


title: 13912521 - Col0 RB1 vs ZF1 814 RB1

hyb_protocol: ZF1 814 RB1 Cy5 / Col0 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Wt_amb_gen4_3_vs_nia_elev_gen4_5


title: Wt_elev_gen4_3_vs_nia_elev_gen4_3


title: nia_elev_gen4_1_vs_nia_amb_gen4_1


title: nia_amb_gen4_2_vs_nia_elev_gen4_2


title: Wt_elev_gen2_5_vs_Wt_amb_gen2_5


title: nia_amb_gen2_6_vs_Wt_elev_gen2_2


title: 13912819 - ZF1 404 RB2 vs Col0 RB2

hyb_protocol: Col0 RB2 Cy5 / ZF1 404 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 ZF1 404


title: Wt_amb_gen2_3_vs_nia_elev_gen2_5


title: 13912818 - Col0 RB2 vs ZF1 404 RB2

hyb_protocol: ZF1 404 RB2 Cy5 / Col0 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Wt_elev_gen4_1_vs_nia_amb_gen4_5


title: nia_elev_gen4_4_vs_Wt_elev_gen4_4


title: 13912520 - ZF1 404 RB1 vs Col0 RB1

hyb_protocol: Col0 RB1 Cy5 / ZF1 404 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Wt_elev_gen2_3_vs_nia_elev_gen2_3


title: Wt_amb_gen2_6_vs_Wt_elev_gen2_6


title: Nia_amb_gen2_4_vs_Wt_amb_gen2_2


title: WM3_40

city: Montreal

first: Martineau

last: Christine

state: Qc

address: 6100 Royalmount Ave.

department: Environmental Microbiology

country: Canada

institute: NRC-BRI

hyb_protocol: Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.

scan_protocol: Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10µm

data_processing: Spot presence-absence was scored by visual examination of the gridded microarray images. If a spot was visible by eye, it was scored as present (1), if not it was scored as absent (0). For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).

organism: environmental samples

source_name: Axel Heiberg Island

label_protocol: Total DNA extracted from all soil samples was submitted to a PCR procedure with eubacterial 16S rRNA gene primers F1-R13, with a touchdown PCR protocol from 65°C to 55°C. PCR products were then chemically labelled using the Label IT nucleic acid labelling kit (Mirus Bio, Madison, WI).

extract_protocol: DNA was co-extracted with RNA from 3 g of soil samples using the MoBio RNA PowerSoil Total RNA Isolation Kit and eluted from the purification column using the RNA PowerSoil DNA Elution Accessory Kit (MoBio Laboratories, Carlsbad, CA)

tag: soil type

value: wet meadow

tag: treatment

value: 2009 (winter conditions)

tag: sampling depth

value: 40 cm


title: 13912522 - ZF1 814 RB1 vs Col0 RB1

hyb_protocol: Col0 RB1 Cy5 / ZF1 814 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WM4_top

value: top 15 cm


title: WM4_40


title: WM3_top


title: WM2_40

value: 2008 (winter conditions)


title: 13912519 - Col0 RB1 vs ZF1 404 RB1

hyb_protocol: ZF1 404 RB1 Cy5 / Col0 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: UT3_40

value: upland tundra soil


title: WM1_top


title: Heat Shock 60 min replicate 3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: Biological replicate 3 of 3; Control Vs Heat shock 60 min

hyb_protocol: Hybridizations were carried out using two samples of labeled cDNA (75 pmol of each) that were labeled with Cy3 or Cy5 d-CTP.  The pooled samples were hybridized using the GE hybridization kit (Agilent Technologies) as recommended by the manufacturer. The mixture was applied on a Surhyb 1 array (Agilent Technologies) and hybridized on the Coxiella burnetii array using the agilent hybridization chamber (Agilent Technologies). Microarrays were hybridized for 17h at 62°C in a rotative hoven. Microarrays were washed using the GE washing buffers (Agilent Technologies) with 5 min of Wash buffer 1 at room temperature followed by 1 min of Wash buffer 2 at 37°C. Microarrays were dried using a bath of acetonitrile (VWR, Fontenay sous Bois, France).

scan_protocol: The microarrays were scanned using the Agilent G2565C microarray scanner (Agilent Technologies) using XDR at 5µm resolution. Images were quantified using Agilent Feature Extraction Software.

data_processing:
The data filtering and normalization were performed using Midas from the TM4 suite (TIGR). Data normalizations were performed using global normalization and lowess normalization methods. All experiments were conducted three times, which yielded 12 measurements per gene (representing four technical replicates in three biological replicates). Gene expression level was determined by determining the mean of the 12 values obtained for each probes.
The mean of Normalized data were processed using the Tmev software from the TM4 suite (TIGR) with a t-test with a p-value of <0.05 and a cut-off of 2 for the fold change

organism: Coxiella burnetii

source_name: C.burnetii Heat Shock 60 min

label_protocol: RNA was retro-transcribed using M-MLV (Invitrogen, Cergy-Pontoise, France) and random hexamer primer (Invitrogen) as previously described (La MV 2007). cDNA were amplified by the processive polymerase phi29 using the GenomPhi illustrator V2 kit (GE HealthCare, Lifescience, Orsay, France) as described (La MV). The amplified cDNA were labeled with the Bioprime Labelling System (Invitrogen) using d-CTP Cy3/5 fluorochromes (GE HealthCare Lifescience). Labeled cDNA were purified using Qiaquick mini kit columns (Qiagen) and the level of incorporation was quantified using the NanoDrop (Thermo Scientific).

growth_protocol: All experiments were performed with mid-log cultures of C. burnetii grown at 35°C on L929 cells with MEM medium (GIBCO, Invitrogen, Cergy-Pontoise, France) supplemented with 4% SVF (GIBCO) and 1% of L-Glutamine (GIBCO).

extract_protocol: Infected cells were harvested using glass beads and centrifuged at 7.500 rpm for 10 min. Pellets were frozen using liquid nitrogen and stored at -80°C. Pellets were resuspended in 100 µl of TE supplemented with 10mg/ml of lyzozyme (Euromedex, Souffelweyersheim, France) and incubated for 10 min at room temperature. Total RNA was extracted and purified from resuspended pellets using the RNeasy mini Kit (Qiagen, Courtaboeuf, France) as recommended by the manufacturer. DNase treatment was performed using the DNA turbo free kit (Ambion, Applied Biosystems, Courtaboeuf, France). Total RNA integrity was checked using the 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) and the concentrations were quantified using the NanoDrop (Thermo, Wingmilton, USA). Eukaryotic RNA was depleted using the MicrobEnrich kit as described (La MV 2007). The integrity of bacterial RNA was checked using the 2100 BioAnalyzer (Agilent) and the concentrations were quantified using the NanoDrop (Thermo Scientific).

treatment_protocol: For temperature stress flasks containing L929 infected cells were incubated at 4°C and 42°C for 30 min and 1h with the Nine Mile I Strain.

tag: strain

value: RSA 493 phase I

value: 35°C 9 days and 42°C 60 min

tag: assayed molecule

value: bacteria mRNA

source_name: C.burnetii control 35°C

value: 35°C 9 days


title: WM2_top


title: WM1_40


title: nia_amb_gen2_2_vs_nia_elev_gen2_2

treatment_protocol: Plants were subjected to ambient CO2 fumigation

tag: age


title: Heat Shock 30 min replicate 3

description: Biological replicate 3 of 3; Control Vs Heat shock 30 min

source_name: C.burnetii Heat Shock 30 min

value: 35°C 9 days and 42°C 30 min


title: Wt_amb_gen2_1_vs_nia_amb_gen2_3

source_name: wild-type Arabidopsis thaliana, leaves from mesocosm, ambient CO2, generation 2

value: wild-type


title: Heat Shock 60 min replicate 1

description: Biological replicate 1 of 3; Control Vs Heat shock 60 min


title: UT1_40


title: UT2_top


title: UT2_40


title: UT3_top


title: Heat Shock 30 min replicate 1

description: Biological replicate 1 of 3; Control Vs Heat shock 30 min


title: Heat Shock 60 min replicate 2

description: Biological replicate 2 of 3; Control Vs Heat shock 60 min


title: Cold Shock 60 min replicate 3

description: Biological replicate 3 of 3; Control Vs Cold shock 60 min

source_name: C.burnetii Cold Shock 60 min

value: 35°C 9 days and 4°C 60 min


title: Heat Shock 30 min replicate 2

description: Biological replicate 2 of 3; Control Vs Heat shock 30 min


title: Cold Shock 60 min replicate 1

description: Biological replicate 1 of 3; Control Vs Cold shock 60 min


title: Cold Shock 60 min replicate 2

description: Biological replicate 2 of 3; Control Vs Cold shock 60 min


title: Nia_elev_gen2_1_vs_Nia_amb_gen2_1

value: leaves from mesocosm

value: Columbia

treatment_protocol: Control [CO2]


title: Cold Shock 30 min replicate 3

description: Biological replicate 3 of 3; Control Vs Cold shock 30 min

source_name: C.burnetii Cold Shock 30 min

value: 35°C 9 days and 4°C 30 min


title: UT1_top


title: AC3_top

value: acidic soil


title: AC3_40


title: AC2_40


title: Cold Shock 30 min replicate 2

description: Biological replicate 2 of 3; Control Vs Cold shock 30 min


title: AC2_top


title: AC1_top


title: Cold Shock 30 min replicate 1

description: Biological replicate 1 of 3; Control Vs Cold shock 30 min


title: AC1_40


title: ST-Host Project_ST array_S2A6_(000vs180)

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Eight arrays are included in one slide (Agilent 8X44K platform)

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 8x44K microarrays. Arrays were incubated at 65 ℃ for 17 h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-µm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analysis.

data_processing:
The signal intensity of each gene was globally normalized using LOWESS by R program (Yang et al, 2002).

'REPEAT 1', 'REPEAT 2', and 'REPEAT 3' in the Sample data table represent three technical repeats of each probe.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella typhimurium. Heterophils encountered (180M-B3)

label_protocol: A 250 ng of aliquot of bacterial total RNA was polyadenylated to generate a poly(A) tail, and reverse transcribed into cDNA using MessageAmp II – Bacteria kit (Ambion Inc., Austin, TX). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

extract_protocol: Salmonella typhimurium were pelleted, re-suspended in lysis buffer (Ribopure-Bacteria kit, Ambion Inc., Austin, TX), and frozen. The lysed cells were transferred to Ambion homogenizer columns filled with bead and were vortexed for 10 min at highest speed. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 20 µl heated elution buffer and stored at -80°C.

treatment_protocol: Salmonella Typhimurium (300 μl of 1X10^9 colony forming units/ml) was incubated with Heterophils (1×10^7) for 3h at 39°C on a rotary shaker.

tag: heterophils encountered

value: yes

tag: time

value: 180 min

source_name: Salmonella typhimurium, No heterophils encountered (0M-ST)

value: no

value: 0 min


title: ST-Host Project_ST array_S2A1_(120vs000)

source_name: Salmonella typhimurium. Heterophils encountered (120M-B1)

treatment_protocol: Salmonella Typhimurium (300 μl of 1X10^9 colony forming units/ml) was incubated with Heterophils (1×10^7) for 2h at 39°C on a rotary shaker.

value: 120 min


title: ST-Host Project_ST array_S2A5_(180vs000)

source_name: Salmonella typhimurium. Heterophils encountered (180M-B1)


title: ST-Host Project_ST array_S2A2_(000vs120)

source_name: Salmonella typhimurium. Heterophils encountered (120M-B3)


title: ST-Host Project_ST array_S2A7_(180vs000)

source_name: Salmonella typhimurium. Heterophils encountered (180M-B2)


title: ST-Host Project_ST array_S2A8_(000vs180)

source_name: Salmonella typhimurium. Heterophils encountered (180M-B4)


title: ST-Host Project_ST array_S1A1_(030vs000)

source_name: Salmonella typhimurium, Heterophils encountered (30M-B1)

treatment_protocol: Salmonella Typhimurium (300 μl of 1X10^9 colony forming units/ml) was incubated with Heterophils (1×10^7) for 30 min at 39°C on a rotary shaker.

value: 30 min


title: ST-Host Project_ST array_S2A4_(000vs120)

source_name: Salmonella typhimurium. Heterophils encountered (120M-B4)


title: ST-Host Project_ST array_S1A6_(000vs060)

source_name: Salmonella typhimurium. Heterophils encountered (60M-B3)

treatment_protocol: Salmonella Typhimurium (300 μl of 1X10^9 colony forming units/ml) was incubated with Heterophils (1×10^7) for 60 min at 39°C on a rotary shaker.

value: 60 min


title: ST-Host Project_ST array_S1A5_(060vs000)

source_name: Salmonella typhimurium. Heterophils encountered (60M-B1)


title: non-infected vs high burden line B R3

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program.

organism: Gallus gallus

source_name: non-infected control

label_protocol: A 500 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

growth_protocol: Raised on the floor in isolated room

extract_protocol: A 20 mg sample was removed from RNAlater-stabilized spleen tissue, cut into pieces and placed in a 2 ml centrifuge tube containing 600 µl TRI Reagent (Ambion, Austin, TX). The PRO200 homogenizer (PRO Scientific, Oxford, CT) was used to homogenize the lysate. Total RNA was isolated from each homogenized sample using MagMaxTM-96 for Microarrays Kit (Ambion, Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: Orally inoculated with PBS on one day after hatch

value: spleen

value: one-week old broiler

tag: genetic line

value: B (susceptible)

source_name: high C. jejuni burden

treatment_protocol: Orally inoculated with 10^5 C. jejuni on one day after hatch


title: low burden Cy 5 vs non-infected line B R3

description: Four arrays are included in one slide

source_name: low C. jejuni burden


title: ST-Host Project_ST array_S1A4_(000vs030)

source_name: Salmonella typhimurium. Heterophils encountered (30M-B4)


title: low burden vs non-infected line B R2

description: Four arrays are included in one slide


title: high burden vs low burden line B R2

description: Four arrays are included in one slide


title: ST-Host Project_ST array_S2A3_(120vs000)

source_name: Salmonella typhimurium. Heterophils encountered (120M-B2)


title: ST-Host Project_ST array_S1A7_(060vs000)

source_name: Salmonella typhimurium. Heterophils encountered (60M-B2)


title: LPS 1hour stimulation rep2

description:
Mus musculus BMDM cRNA6 vs cRNA pool UMRR after 1 hour cell growth in presence of LPS replicate 2/2
cRNA6

source_name: BMDM LPS 1hour stimulation rep2

tag: gender

value: female

value: BALB/c

tag: cell type

value: BM-derived macrophage

value: 12 weeks

tag: agent

value: LPS

source_name: Universal mouse RNA mixture (UMRR)

tag: reference pool

value: Universal mouse RNA mixture


title: non-infected vs high burden line B R4

description: Four arrays are included in one slide

tag: tissue


title: low burden vs non-infected line B R4

description: Four arrays are included in one slide


title: ST-Host Project_ST array_S1A8_(000vs060)

source_name: Salmonella typhimurium. Heterophils encountered (60M-B4)

source_name: Salmonella typhimurium, No heterophils encountered (0M-ST)


title: ST-Host Project_ST array_S1A3_(030vs000)

source_name: Salmonella typhimurium. Heterophils encountered (30M-B2)


title: ST-Host Project_ST array_S1A2_(000vs030)

source_name: Salmonella typhimurium, Heterophils encountered (30M-B3)


title: non-infected vs high burden line B R1

description: Four arrays are included in one slide


title: high burden vs low burden line B R3

description: Four arrays are included in one slide


title: high burden vs low burden line B R4

description: Four arrays are included in one slide


title: non-infected vs high burden line B R2

description: Four arrays are included in one slide


title: low burden vs non-infected line B R1

description: Four arrays are included in one slide


title: Human fetal colon control: Biological replicate 2: Duplicate 1

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

description: Colon #2a

hyb_protocol: Arabidopsis cDNA and hybridization buffer (formamide 50%, SSC 5X, SDS 0.1%) were added, and samples were applied to microarrays enclosed in hybridization chambers overnight at 42°C. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on a ScanArray Express (Packard Bioscience).

data_processing: Images were quantified using Quantarray software (Packard Bioscience). Background-subtracted, LOWESS normalized, iterative log mean centerized data were obtained from log2 of processed Red signal/processed Green signal. TIGR package software was used.

organism: Homo sapiens

source_name: reference pool

label_protocol: Total RNA was amplified with TargetAmp 1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI) following manufacturer's instructions. 1 µg of aRNA was primed with 3 µl of 2 µg/µL hexamer random primers at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, 200µM dTTP and 300µM aa-dUTP.

extract_protocol: Total RNA from reference pool was isolated by phenol/chloroform extraction (Trizol, Invitrogen).

value: mixture of equimolar aliquots of RNA from Caco-2/15 cells (at -1, 10, and 25 days of confluence), proliferative HT-29 cells, SKOV3 cells, A549 cells

source_name: human fetal colonic explants

extract_protocol: Total RNA from human fetal colon tissue were isolated by phenol/chloroform extraction (Trizol, Invitrogen).

value: colon

tag: developmental stage

value: 20 weeks of gestation


title: Human fetal colon control: Biological replicate 2: Duplicate 2

description: Colon #2b


title: RIL_WN78

city: Haren(GN)

first: Yang

last: Li

address: Kerklaan 30

country: Netherlands

institute: Groningen Bioinformatics Center

description: Gene expression data from worm belonging to the L3 life stage

hyb_protocol: DNase I-treated and control samples were hybridized to the Affymetrix GeneChip® C. elegans Tiling 1.0R Array, which contains ~3.2 million perfect match/mismatch probe pairs tiled through the Watson strand of the entire non-repetitive C. elegans genome. The probes are tiled at an average distance of 25 bp, as measured from the central position of adjacent 25-mer oligonucleotide probes.

scan_protocol: GeneChip® Scanner 3000 Quick Reference Card or user’s manual

data_processing: The data has been quantile normalized.

label: biotin

organism: Caenorhabditis elegans

source_name: C. elegans Recombinant Inbred Lines

label_protocol: For the fragmentation and labeling we used GeneChip WT double stranded DNA Terminal Labeling Kit.

growth_protocol: All RILs were reared on NGM agar plates seeded with the OP50 strain of E. coli as a food source. Stock cultures of OP50 were stored at -80 C, and the bacterial cultures were grown in autoclaved LB medium (10 g peptone, 10 g yeast extract, 5 g NaCl/l water) for 16 h at 37 C and shaken at 150 rpm. RIL populations were started with only nonmated hermaphrodites and screened regularly to remove any occurring males. Experiments were carried out with nematodes belonging to the L3 life stage. To determine the entry into this stage, the size of the gonads and vulva were monitored. Populations of each of the RILs were bleached (0.5 M NaOH, 1% hypochlorite) to collect synchronized eggs, which were then inoculated onto fresh dishes.

extract_protocol: The frozen nematode samples were ground and RNA was extracted using the Trizol method, and cleaned up with the RNeasy Micro kit (Qiagen, http://www1.qiagen.com/). RNA concentration and quality was measured with a NanoDrop spectrophotometer (http://www.nanodrop.com). Ds-cDNA synthesis with Affymetrix GeneChip WT double-stranded cDNA Synthesis Kit. To clean the cDNA we used the GeneChip Sample Cleanup Module from Affymetrix.

treatment_protocol: Four replicate dishes of synchronized eggs for each RIL were kept at 24 C until L3 was reached. The nematodes were then collected and frozen in liquid nitrogen.

value: whole worm


title: Human fetal colon control: Biological replicate 3: Duplicate 2

description: Colon #3b


title: Human fetal ileum control: Biological replicate 3: Duplicate 1

description: Ileum #3a

source_name: human fetal ileal explants

extract_protocol: Total RNA from human fetal ileum tissue were isolated by phenol/chloroform extraction (Trizol, Invitrogen).

value: ileum


title: low burden Cy 5 vs non-infected line A R4

description: Four arrays are included in one slide

value: A (resistant)


title: non-infected vs high burden line A R4

description: Four arrays are included in one slide


title: low burden vs non-infected line A R3

description: Four arrays are included in one slide

treatment_protocol: Orally inoculated with 10^5 cfu on one day after hatch


title: high burden vs low burden line B R1

description: Four arrays are included in one slide


title: Human fetal ileum control: Biological replicate 2: Duplicate 2

description: Ileum #2b


title: high burden vs low burden line A R4

description: Four arrays are included in one slide


title: Human fetal colon control: Biological replicate 1: Duplicate 1

description: Colon #1a


title: Human fetal colon control: Biological replicate 3: Duplicate 1

description: Colon #3a


title: OsbHLH148_1

description: Two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants(line2)

hyb_protocol: Mix 13μg of DNA with 19.5μl of 2X hybridization buffer(Nimblegen, U.S.A.) and make the volume of 39μl with deionized water. Hybridize the sample solution with microarray (Nimblegen, U.S.A.) using MAUI chamber(Biomicro, U.S.A.) at 42°C for 16 hours. After the hybridization, remove chip from MAUI Hybridization Station and immerse in the shallow 250ml Wash I (Nimblegen, U.S.A.) at 42 °C. Agitate the chip in Wash I for 10-15 seconds and transfer the slide into the second dish of Wash I. Incubate 2 min with agitation. Transfer slide rack into dish of Wash II. Incubate 1 minute with agitation. Transfer slide rack into dish of Wash III. Incubate for 15 seconds with agitation. Remove slide rack from Wash III and spin dry in a centrifuge for 1 minute at 500g. Store the dried array in a dark desiccator.

scan_protocol: Scan the slide using GenePix scanner 4000B(Axon, U.S.A.) and analyze intensities of spots using Nimblescan(Nimblegen, U.S.A.).

data_processing: To assess the reproducibility of the microarray analysis, we repeated the experiment two times with independently prepared total RNA. The normal distribution of Cy3 intensities was tested by qqline. The data was nomalized and processed with cubic spline normalization using quantiles to adjust signal variations between chips and Rubust Multi-Chip Analysis (RMA) using a median polish algorithm implemented in NimbleScan (Workman et al., 2002. Genome Biol. 3: research0048.1 - research0048.16 ; Irizarry et al., 2003. Nucleic Acids Research 3:e15).

source_name: RNA from two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants(line2)

label_protocol: Combine 10μl(10μg) of total RNA with 1μl of oligo dT primer(100μM) and heat to 70 °C for 10 minutes. Briefly spin tubes in a microcentrifuge, and place the reaction(s) in an ice. Add 4μl of 5X First Strand Buffer, 2μl of 0.1M DTT, 1μl of 10mM dNTP mix and 2μl of SuperScript enzyme. Place sample(s) in a incubator of 42°C for 1 hour. Add 91μl of DEPC-Water, 30μl of 5X Second Strand Buffer, 3μl of 10mM dNTP mix, 1μl of 10U/μl DNA ligase, 4μl of 10U/μl DNA Polymerase I and 1μl of 2U/μl RNase H to the first strand reaction(s). Incubate at 16°C for two hours and add 2 μl of 5 U/ξ? T4 DNA polymerase to each reaction. To remove RNA strand, add 1A?Aμl of 10 mg/ml RNase A(Amresco, U.S.A.) solution to the tubes and incubate sample(s) at 37°C for 10 minutes. To precipitate cDNA, add 180μl of phenol/chloroform and centrifuge at maximum speed for 5 minutes. Transfer upper phase into new tube, add 16μl of 7.5 M Ammonium Acetate and 326μl of cold ethanol. Centrifuge at maximum speed for 20minutes and remove supernatant. Add 500μl of 80% ethanol and centrifuge again at maximum speed for 5 minutes. Remove supernatant and dry the pellet. Rehydrate samples with 20μl of water. For the synthesis of C3-labeled target DNA fragments, mix 1μg of double strand cDNA with 40μl(1OD) of Cy3-9mer primers(Sigma-Aldrich, U.S.A.), make the volume of 80μl with deionized water and then, heat to 98°C for 10 minute. Add 10μl of 50X dNTP mix (10mM each), 8μl of deionized water, 2μl of Klenow fragment(50 U/μl, NEB, U.S.A.) and incubate at 37°C for 2 hours. Finally, stop the reaction by addition of 10μl of 0.5M EDTA. Precipitate DNA fragments by adding 11.5μl of 5M NaCl and add 110μl of isopropanol to each tube. Vortex and incubate at room temperature for 10 minutes. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Add 500μl of 80% ethanol and centrifuge again at maximum speed for 5 minutes. Remove supernatant and dry the pellet. Rehydrate samples with 25μl of water. Determine the concentration of each sample uing spectrophotometer.

growth_protocol: Transgenic and wild-type rice (O.sativa cv. Nakdong) seeds were germinated in Murashige-Skoong solid medium in a growth chamber in the dark at 28 °C for 3days, transplanted to soil pots, and grown in a greenhouse (16 h light/8 h dark cycle) at 28-30 °C. Each pot (10 X 10 X 10 cm) was filled with rice nursery soil (Bio-media, Kyoungju, Korea). Two-week old seedlings were harvested for Rice 3'-Tiling Microarray.

extract_protocol: TriZol procedure

value: two-week old seedlings

tag: genotype/variation

value: oscc1:OsbHLH148 transgenic (line2)


title: high burden vs low burden line A R3

description: Four arrays are included in one slide

value: spleen


title: Human fetal ileum control: Biological replicate 3: Duplicate 2

description: Ileum #3b


title: non-infected vs high burden line A R2

description: Four arrays are included in one slide

source_name: non-infected control

value: one-week old broiler


title: low burden vs non-infected line A R1

description: Four arrays are included in one slide

treatment_protocol: Orally inoculated with PBS as controls on one day after hatch


title: Human fetal ileum control: Biological replicate 2: Duplicate 1

description: Ileum #2a


title: high burden vs low burden line A R 2

description: Four arrays are included in one slide

source_name: high C. jejuni burden

treatment_protocol: Orally inoculated with 10^5 cfu C. jejuni on one day after hatch


title: non-infected vs suscpetible line A R3

description: Four arrays are included in one slide


title: low burden Cy 5 vs non-infected line A R2

description: Four arrays are included in one slide

source_name: low C. jejuni burden


title: high burden vs low burden in line A R1

description: Four arrays are included in one slide


title: Human fetal ileum control: Biological replicate 1: Duplicate 2

description: Ileum #1b


title: Human fetal ileum control: Biological replicate 1: Duplicate 1

description: Ileum #1a


title: RIL_WN77


title: RIL_WN75


title: RIL_WN73


title: RIL_WN72


title: Human fetal colon control: Biological replicate 1: Duplicate 2

description: Colon #1b


title: RIL_WN67


title: RIL_WN69


title: RIL_WN70


title: RIL_WN66


title: RIL_WN68


title: RIL_WN60


title: non-infected vs high burden line A R1

description: Four arrays are included in one slide

treatment_protocol: Orally inoculated with 10^5 cfu C. jejuni as controls on one day after hatch


title: OsbHLH148

description: Two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants(line9)

source_name: RNA from two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants(line9)

value: oscc1:OsbHLH148 transgenic (line9)


title: RIL_WN59


title: Cow 28_Period II

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C with constant rotational mixing at 60 rpm on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneGhip Scanner 7G and Affymetrix GeneChip Operating Software version 1.4

data_processing: All microarray analysis including preprocessing, normalization and statistical analysis was carried out using R Software (version 2.10 and Bioconductor version 2.5). Data were quality assessed before and after normalization using a number of built-in quality control methods implemented in the Bioconductor affycoretools and associated packages to identify eventual irregularities of array hybridization, RNA degradation, and data normalization. Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA; (Wu et al., 2004), employing the empirical Bayes approach for background correction followed by quantile normalization.

organism: Bos taurus

source_name: Cow fed control diet

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

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

treatment_protocol: Twenty-eight Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), DIM (153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to treatment groups based to one of the four dietary treatments. The dietary treatments were a basal diet supplemented with either: 2.7% rapeseed oil as a source of cis-9-18:1 (oleic acid), 2.7% soybean oil as a source of cis-9, cis-12-18:2 (linoleic acid), 2.7% linseed oil as a source of ALA or 2.7% of a 1:1:1 mixture of the three oils. The oil supplements were included in the concentrate, which was fed, together with corn silage and grass silage, as a total mixed ration (TMR; Table 1). Corn silage, grass silage and concentrates comprised 52, 12 and 36% of the total TMR, respectively, on a DM basis. The cows were grazing on pasture composed of ryegrass (Lolium perenne L.), with approximately 20% white clover (Trifolium repens L.), during the day (from 8:00h until 16:00h) and were fed the TMR, indoors at night. The paddock was 5 ha in size and the stocking density was 16 cows/ha. Cows grazed the paddocks at an herbage allowance of approximately 5.5 kg of DM/cow per day, and were fed the TMR at a level of about 14.5 kg of DM/cow per day. After the first period of 23 days (Experimental period I, final DIM = 176 ± 32.8 days), all cows were switched to a control diet without oil supplementation for an additional 28 days (Experimental period II; final DIM= 204 ± 32.8 days).

value: Mammary gland


title: RIL_WN65


title: Cow 26_Period II


title: RIL_WN61


title: Cow 22_Period II


title: Cow 23_Period II


title: Cow 25_Period II


title: Cow 24_Period II


title: Cow 17_Period II


title: RIL_WN58


title: Cow 21_Period II


title: Cow 20_Period II


title: RIL_WN56


title: RIL_WN55


title: Nakdong_WT

description: Two-week old seedlings of wild type rice plants (O.sativa cv. Nakdong)

source_name: RNA from two-week old seedlings of wild type rice plants

value: wild type


title: RIL_WN53


title: Cow 19_Period II


title: RIL_WN52


title: Cow 15_Period II


title: RIL_WN57


title: Cow 18_Period II


title: RIL_WN49


title: Cow 27_Period II


title: Cow 16_Period II


title: Cow 14_Period II


title: Cow 12_Period II


title: Cow 13_Period II


title: Cow 10_Period II


title: Cow 11_Period II


title: Nakdong_WT_1

description: Two-week old seedlings of wild type rice plants


title: RIL_WN42


title: RIL_WN40


title: RIL_WN39


title: RIL_WN38


title: RIL_WN48


title: RIL_WN46


title: RIL_WN43


title: RIL_WN37


title: RIL_WN36


title: RIL_WN35


title: Cow 7_Period II


title: RIL_WN44


title: Cow 9_Period II


title: Cow 2_Period II


title: RIL_WN33


title: RIL_WN32


title: RIL_WN41


title: Cow 8_Period II


title: Cow 4_Period II


title: RIL_WN31


title: Cow 3_Period II


title: Cow 1_Period II


title: Cow 5_Period II


title: Cow 6_Period II


title: Cow 26_Period I

source_name: Cow fed soybean oil


title: Cow 27_Period I

source_name: Cow fed rapeseed oil


title: Cow 25_Period I

source_name: Cow fed linseed oil


title: RIL_WN30


title: RIL_WN29


title: RIL_WN27


title: RIL_WN26


title: Cow 23_Period I


title: RIL_WN25


title: RIL_WN22


title: Cow 21_Period I


title: Cow 20_Period I

source_name: Cow fed mix diet


title: RIL_WN24


title: Cow 19_Period I


title: Cow 18_Period I


title: RIL_WN21


title: Cow 22_Period I


title: Cow 24_Period I


title: RIL_WN13


title: RIL_WN11


title: RIL_WN15


title: RIL_WN17


title: RIL_WN19


title: RIL_WN8


title: RIL_WN5


title: Cow 16_Period I


title: RIL_WN4


title: Cow 15_Period I


title: Cow 17_Period I


title: Cow 10_Period I


title: Cow 12_Period I


title: Cow 8_Period I


title: Cow 9_Period I


title: Cow 13_Period I


title: Cow 14_Period I


title: RIL_WN3


title: Cow 11_Period I


title: Cow 7_Period I


title: RIL_WN2


title: RIL_WN1


title: Cow 6_Period I


title: RIL_WN80


title: Cow 28_Period I


title: RIL_WN76


title: RIL_WN62


title: Cow 2_Period I


title: RIL_WN20


title: RIL_WN9


title: Cow 4_Period I


title: Cow 5_Period I


title: SKOV3TRip2 collection 1

city: Birmingham

first: Charles

last: Landen

state: AL

address: 1825 University Blvd Rm 505

department: Obstetrics and Gynecology

institute: University of Alabama at Birmingham

description:
replicate 1
SKOV3TRip2 3A_4186640014_E.AVG_Signal

hyb_protocol: 750ng of labeled cRNA were hybridized on the Illumina Human Ref-8 V2.0 arrays according to Illumina instructions

scan_protocol: Standard Illumina scanning protocol

data_processing:
Using Beadstudio 3.1 software, raw data were normalized by the cubic spline method.
Authors were unable to retrieve raw data.

label_protocol: Biotinylated cRNA were prepared from 500ng total RNA using the Illumina Total Prep RNA Amplification Kit (Ambion) according the manufacturer's instructions

growth_protocol: 2-dimensional culture routine culture plates

extract_protocol: RNAeasy

treatment_protocol: No treatment

tag: growth protocol

value: in vitro culture

tag: taxane sensitivity

value: resistant


title: SKOV3TRip2 collection 3

description:
replicate 3
SKOV3TRip2 3C_4186640028_C.AVG_Signal


title: BALB/c+NC-Liverpool 6 hour

city: Sydney

first: John

last: Ellis

state: NSW

address: Broadway

department: Medical & Molecular Biosciences

country: Australia

institute: University of Technology Sydney

description: Average of 3 biological replicates. Infection of BALB/c mice with NC-Liverpool; 6 hour post infection time point

hyb_protocol: The hybridisation mix contained, per slide for hybridisation, 100µl DIG Easy Hyb (Roche, Germany) 2µl yeast tRNA (11mg/ml) (Sigma, USA) and 5µl calf thymus DNA (9.1mg/ml). 80µl of this mix was added to the probe sample, and loaded onto the microarray slide. . Slides were then incubated for 10-16 hrs at 37ºC in the dark.  Following hybridisation, the coverslip was removed by immersion of the slide in 1XSSC at room temperature. Slides were then washed in three 15-20 min washes, by placing them in a rotating hybridisation oven at 50ºC in a 50ml centrifuge tube filled with 1XSSC, 0.1% SDS at 50ºC. Residual SDS was removed by rinsing first in 1XSSC (room temperature) and then in MilliQ H2O (room temperature).

scan_protocol: Arrayworx microarray scanner

data_processing: Intensity data was log transformed and normalised using the Locfit (Lowess) normalisation algorithm. Normalized log2 ratio (Cy5/Cy3) representing infected/saline were first computed.

source_name: 6 hour infection of BALB/c with NC-Liverpool

label_protocol: 30 µg of total RNA were primed with 500ng T20VN DNA primer (Sigma) at 65°C for 10 min, then reversed transcribed at 42°C for 2.5 h in the presence of 400 U SuperScript II RTase (Invitrogen), and  dATP, dATP, dCTP, dTTP  and amino-allyl dUTP. After purification, the cDNA was conjugated to either Cy3 or Cy5 in NaHCO3

growth_protocol: Tachyzoites of Neospora caninum were grown in Vero cells using horse serum supplemented RPMI medium

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

treatment_protocol: Infected mice injected subcutaneously with tachyzoites of Neospora caninum; Control mice injected with saline

tag: mouse

value: BALB/c

tag: treatment

value: NC-Liverpool

tag: time post injection

value: 6 hours post infection

source_name: 6 hour post injection of BALB/c with saline

value: 0.9% sterile saline


title: SKOV3ip1 collection 3

description:
replicate 3
SKOV3ip1 1C_4186640006_C.AVG_Signal

value: sensitive


title: BALB/c+NC-Nowra 10 day

description: Average of 4 biological replicates. Infection of BALB/c mice with NC-Nowra; 10 days post infection time point

source_name: 10 day infection of BALB/c with NC-Nowra

value: NC-Nowra

value: 10 days post infection

source_name: 10 days post injection of BALB/c with saline


title: Qs+NC-Liverpool 10 day

description: Average of 4 biological replicates. Infection of Qs mice with NC-Liverpool; 10 days post infection time point

source_name: 10 day infection of Qs with NC-Liverpool

value: Qs

source_name: 10 days post injection of Qs with saline


title: BALB/c+NC-Nowra 6 hour

description: Average of 3 biological replicates. Infection of BALB/c mice with NC-Nowra; 6 hour post infection time point

source_name: 6 hour infection of BALB/c with NC-Nowra


title: Cow 1_Period I


title: SKOV3ip1 collection 2

description:
replicate 2
SKOV3ip1 1B_4186640014_G.AVG_Signal


title: BALB/c+NC-Liverpool 10 day

description: Average of 4 biological replicates. Infection of BALB/c mice with NC-Liverpool; 10 days post infection time point

source_name: 10 day infection of BALB/c with NC-Liverpool


title: WhiteSpruce_32C16_32A24_bark

city: Vancouver

first: Ilga

last: Porth

address: 2424 Main Mall

institute: University of British Columbia

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repA

hyb_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. Following pooling of the appropriate Cy3 and Cy5 cDNAs, samples were precipitated with linear acrylamide and resuspended in 17.7 μL nuclease-free water. A 27.3 μL hybridisation mixture containing 22.5 μL 2xSDS buffer, 4 μL LNA d(T) blocker, 2 μg sheared salmon testes DNA (Invitrogen) and 0.3 μL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech) was added to the cDNA probe. Immediately prior to use, arrays were pre-washed 2x in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80ºC for 10 min, then maintained at 65ºC prior to adding to a microarray slide heated to 55ºC, covered with a 22 x 60 x 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 60ºC. Arrays were washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, then three washes of 5 min in 2x SSC at room temperature, and three washes of 5 min in 0.2x SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 μL volume consisting of 22.5 μL 2x SDS buffer, 17.5 μL nuclease-free water, 2.5 μL Cy3 capture reagent and 2.5 μL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 60ºC, then washed and dried as before.

scan_protocol: Fluorescent images of hybridized arrays were acquired by using ScanArray Express (PerkinElmer, Foster City, USA). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively. All scans were performed at the same laser power (90%), but with the photomultiplier tube settings for the two channels adjusted such that the ratio of the mean signal intensities was ~1, and the percentage of saturated array elements was < 0.5% but > 0%, while minimizing background fluorescence. Fluorescent intensity data were extracted by using the ImaGene 6.0 software (Biodiscovery, El Segundo, USA).

data_processing: After quantification of the signal intensities in each array the local background was subtracted for each subgrid. Data were normalized to compensate for non-linearity of intensity distributions using the variance stabilizing normalization method (Huber, et al. 2002). A linear model was fit to the normalized intensities in the Cy3 and Cy5 channels to account for technical effects within the experiment (gene-specific ‘dye’ effect, replicate ‘block’, microarray fabrication ‘batch’, experimenter ‘person’ are all fixed effects). All statistical analyses were done using the R statistical package (www.r-project.org/). The residuals were used in the subsequent QTL analysis.

organism: Picea engelmannii x Picea glauca

label_protocol: 40 micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Trees were planted in 1995 and grown in the field in a complete randomized block design. Experimental spruce populations originated from a controlled-cross progeny trial that had been established in 1995 at Kalamalka Research Station in Vernon, BC, Canada {{Alfaro, 2004}). The respective sires and dams had been selected from individuals previously ranked for weevil-resistance in open-pollinated progeny tests conducted in north central BC in the late 1980’s ({Kiss, 1991}). Out of twenty crosses segregating for the resistance phenotype ({Alfaro, 2004}), we selected four families from the trial based on two important criteria: clear intermediate weevil resistance and shared parentage.

extract_protocol: Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824. Total RNA was quantified and quality checked by NanoDrop ND-1000 Spectrophotometer and agarose gel. RNA was also evaluated for integrity using the Agilent 2100 Bioanalyzer

treatment_protocol: During the seasonal onset of weevil attack, on May 16 to May 18, 2006, unaffected terminal leaders were cut , bark/phloem tissue detached from the cambium was harvested, immediately flash frozen in liquid nitrogen.

tag: origin

value: Twelve year old trees from a weevil screening trial

tag: cross

tag: replicate

value: C

tag: specimen

value: tree 16

value: from the leader of each tree, bark with attached phloem and cambium

tag: collection dates

tag: biomaterial provider

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: A

value: tree 24


title: Qs+NC-Liverpool 6 hour

description: Average of 3 biological replicates. Infection of Qs mice with NC-Liverpool; 6 hour post infection time point

source_name: 6 hour infection of Qs with NC-Liverpool

source_name: 6 hour post injection of Qs with saline


title: SKOV3TRip2 collection 2

description:
replicate 2
SKOV3TRip2 3B_4186640006_A.AVG_Signal

value: in vitro culture


title: Peripheral blood leukocyte_Obese mother_Sample 5

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

description:
column in raw data file: OBM_5
pair with OBC_3

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and BeadStudio (Gene expression Module)

data_processing: Raw data was log2 transformed and median-centered using JMP Genomics 4.0 (SAS Institute, Cary NC).

source_name: Peripheral blood leukocytes, Obese mother in third trimester of pregnancy

label_protocol: cDNA and cRNA labeling and amplification were all performed using a single kit : Ambion's Illumina TotalPrep RNA Aamplification kit.

extract_protocol: Total RNA was extracted from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: life stage

value: mother

value: peripheral blood

tag: cell type

value: leukocytes

tag: rna integrity score


title: Qs+NC-Nowra 10 day

description: Average of 4 biological replicates. Infection of Qs mice with NC-Nowra; 10 days post infection time point

source_name: 10 day infection of Qs with NC-Nowra


title: WhiteSpruce_32C13_32A21_bark

value: tree 13

tag: tissue

value: tree 21


title: Qs+NC-Nowra 6 hour

description: Average of 3 biological replicates. Infection of Qs mice with NC-Nowra; 6 hour post infection time point

source_name: 6 hour infection of Qs with NC-Nowra

value: 6 hours post infection

value: 0.9% sterile saline


title: Peripheral blood leukocyte_Obese mother_Sample 6

description:
column in raw data file: OBM_6
pair with OBC_8


title: SKOV3ip1 collection 1

description:
replicate 1
SKOV3ip1 1A_4186640028_F.AVG_Signal

value: sensitive


title: Cow 3_Period I

value: Mammary gland


title: WhiteSpruce_32C08_32A06_bark

value: Twelve year old trees from a weevil screening trial

value: tree 08

value: tree 06


title: Peripheral blood leukocyte_Obese mother_Sample 3

description:
column in raw data file: OBM_3
pair with OBC_6


title: WhiteSpruce_32C11_32A16_bark

value: C

value: tree 11

value: from the leader of each tree, bark with attached phloem and cambium

value: tree 16


title: Peripheral blood leukocyte_Obese mother_Sample 4

description:
column in raw data file: OBM_4
pair with OBC_5


title: WhiteSpruce_32C07_32B22_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repB

value: tree 07

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: B

value: tree 22


title: Peripheral blood leukocyte_Obese mother_Sample 1

description:
column in raw data file: OBM_1
pair with OBC_11

value: mother

value: peripheral blood

value: leukocytes


title: Peripheral blood leukocyte_Obese mother_Sample 2

description:
column in raw data file: OBM_2
pair with OBC_9


title: WhiteSpruce_32C03_32B08_bark

value: tree 03


title: Peripheral blood leukocyte_Normal wieght mother_Sample 11

description: column in raw data file: NMM_11

source_name: Peripheral blood leukocytes, Normal-weight mother in third trimester of pregnancy


title: WhiteSpruce_32C05_32A23_bark

value: tree 05

value: A

value: tree 23


title: WhiteSpruce_32B23_32C09_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repC

value: Twelve year old trees from a weevil screening trial

value: tree 09


title: WhiteSpruce_32B20_32C10_bark

value: tree 20

value: C

value: tree 10


title: WhiteSpruce_32C01_32B03_bark

value: tree 01

value: from the leader of each tree, bark with attached phloem and cambium


title: WhiteSpruce_32B21_32A04_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repA

value: tree 21

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: tree 04


title: WhiteSpruce_32C02_32A07_bark

value: tree 02

value: tree 07


title: Peripheral blood leukocyte_Normal wieght mother_Sample 6

description: column in raw data file: NMM_6

value: mother

value: peripheral blood

value: leukocytes


title: Peripheral blood leukocyte_Normal wieght mother_Sample 5

description:
column in raw data file: NMM_5
pair with NMC_7


title: Peripheral blood leukocyte_Normal wieght mother_Sample 10

description:
column in raw data file: NMM_10
pair with NMC_14


title: Peripheral blood leukocyte_Gestational diabetic mother_Sample 2

description:
column in raw data file: GSM_2
pair with GSC_2

source_name: Peripheral blood leukocytes, Gestational diabetic mother in third trimester of pregnancy


title: Peripheral blood leukocyte_Normal wieght mother_Sample 2

description:
column in raw data file: NMM_2
pair with NMC_12


title: WhiteSpruce_32A20_32B14_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repB

value: A

value: B

value: tree 14


title: Peripheral blood leukocyte_Normal wieght mother_Sample 7

description:
column in raw data file: NMM_7
pair with NMC_8


title: Peripheral blood leukocyte_Normal wieght mother_Sample 4

description:
column in raw data file: NMM_4
pair with NMC_9


title: WhiteSpruce_32B12_32C06_bark

value: Twelve year old trees from a weevil screening trial

value: tree 12

value: tree 06


title: Peripheral blood leukocyte_Gestational diabetic mother_Sample 1

description:
column in raw data file: GSM_1
pair with GSC_6


title: WhiteSpruce_32B16_32A22_bark

value: tree 16

value: tree 22


title: Cord blood leukocyte_Child of obese mother, Sample 12

description: column in raw data file: OBC_12

source_name: Cord blood leukocytes, Child from a obese mother

value: newborn baby

value: umbilical cord blood


title: Peripheral blood leukocyte_Normal wieght mother_Sample 1

description:
column in raw data file: NMM_1
pair with NMC_19


title: WhiteSpruce_32B09_32C22_bark

value: tree 09

value: from the leader of each tree, bark with attached phloem and cambium

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: C


title: WhiteSpruce_32A15_32B17_bark

value: tree 15

value: tree 17


title: Peripheral blood leukocyte_Normal wieght mother_Sample 9

description:
column in raw data file: NMM_9
pair with NMC_16

value: mother

value: peripheral blood

value: leukocytes


title: Peripheral blood leukocyte_Normal wieght mother_Sample 8

description:
column in raw data file: NMM_8
pair with NMC_1


title: Peripheral blood leukocyte_Normal wieght mother_Sample 3

description: column in raw data file: NMM_3


title: WhiteSpruce_32A17_32C19_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repC

value: A

value: tree 19


title: WhiteSpruce_32B11_32C12_bark

value: Twelve year old trees from a weevil screening trial

value: B

value: tree 11

value: tree 12


title: WhiteSpruce_32B06_32A13_bark

value: tree 06

value: tree 13


title: WhiteSpruce_32B15_32C24_bark

value: tree 24


title: WhiteSpruce_32A10_32B10_bark

value: tree 10

value: from the leader of each tree, bark with attached phloem and cambium


title: WhiteSpruce_29C05_29B19_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repB

value: C

value: tree 05

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: WhiteSpruce_32A11_32B25_bark

value: tree 25


title: WhiteSpruce_29C16_29A14_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repA

value: tree 16

value: tree 14


title: Cord blood leukocyte_Child of normal mother_Sample 19

description:
column in raw data file: NMC_19
pair with NMM_1

source_name: Cord blood leukocytes, Child from a normal-weight mother

value: newborn baby

value: umbilical cord blood

value: leukocytes


title: Cord blood leukocyte_Child of obese mother, Sample 4

description: column in raw data file: OBC_4


title: Cord blood leukocyte_Child of obese mother, Sample 13

description: column in raw data file: OBC_13


title: WhiteSpruce_32A09_32B18_bark

value: Twelve year old trees from a weevil screening trial

value: A

value: tree 09

value: B

value: tree 18


title: Cord blood leukocyte_Child of obese mother, Sample 10

description:
column in raw data file: OBC_10
pair with OBM_1


title: WhiteSpruce_29B22_29A18_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repA

value: tree 22


title: WhiteSpruce_32A14_32B24_bark

value: tree 24


title: WhiteSpruce_29B21_29A09_bark

value: tree 21

value: from the leader of each tree, bark with attached phloem and cambium


title: WhiteSpruce_29C14_29B25_bark

value: C


title: Cord blood leukocyte_Child of obese mother, Sample 5

description:
column in raw data file: OBC_5
pair with OBM_4


title: Cord blood leukocyte_Child of obese mother, Sample 11

description: column in raw data file: OBC_11


title: Cord blood leukocyte_Child of normal mother_Sample 17

description: column in raw data file: NMC_17


title: Cord blood leukocyte_Child of obese mother, Sample 3

description:
column in raw data file: OBC_3
pair with OBM_5


title: WhiteSpruce_29C09_29B11_bark

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: tree 11


title: Cord blood leukocyte_Child of normal mother_Sample 15

description: column in raw data file: NMC_15


title: WhiteSpruce_29C13_29A13_bark

value: tree 13


title: Cord blood leukocyte_Child of normal mother_Sample 16

description:
column in raw data file: NMC_16
pair with NMM_9


title: Cord blood leukocyte_Child of obese mother, Sample 6

description:
column in raw data file: OBC_6
pair with OBM_3


title: WhiteSpruce_32A05_32C14_bark

value: tree 05

value: tree 14