title: Wild type + exogenous C12-HSL_logarithmic growth phase_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng/ml exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Comparison between hypothalami from freely feeding animals and tumor-bearing rats

status: Public on Apr 10 2010

type: RNA

city: Bordeaux

first: Jan Pieter

last: Konsman

address: 146, rue Léo Saignat

country: France

institute: CNRS

hyb_protocol: Agilent oligo microarray hybridation protocol

scan_protocol: Dual-laser microarray scanner agilent technologies, 10µm resolution, 100% PMT

data_processing: Agilent Feature-extraction software version A.7.5.1. Spot analysis method using Cookie Cutter, pixel outlier rejection based on IQR, non-uniformity outlier flagging on, population outlier flagging on, no background subtraction, spatial detrend on, normalization feature selection by using rank consistency filter, normalization method linear and LOWESS, multiplicative errors of 0.15 for red and 0.25 for green, additive errors of 20 for both channels.

molecule: total RNA

organism: Rattus norvegicus

source_name: Tumor-bearing rats

label_protocol: Total RNA extracts from individual animals were purified (RNeasy MinElute Cleanup kit, Qiagen, Courtaboeuf, France) and treated with DNaseI (Ambion, Austin, TX, USA), after which 2.0 μg of purified RNA were retrotranscribed to double stranded cDNA. A pool of cDNA for each experimental group containing an equal amount of cDNA of each individual was used for in vitro transcription to yield multiple copies of amino-allyl-modified antisense RNA (aRNA) using amino-allyl-labeled UTP (Ambion, Austin, TX, USA). Subsequently, aimine groups of the fluorescent Cy3 or Cy5 dyes (Amersham Biosciences, GE Healthcare, Munich, Germany ) were coupled to the a RNA amino allyl groups following manufacturer’s instructions.

extract_protocol: RNA was extracted using 500 ul Trizol following manufacturer’s protocol (Invitrogen, Carlsblad, CA, USA)

treatment_protocol: Subcutaneous injection between scapulae with ten million Morris hepatoma 7777 cells. Tumor-bearing rats had ad libitum access to food.

tag: sample type

value: Hypothalamus of 160-230g Buffalo rats

tag: tissue

value: hypothalamus

tag: strain

value: Buffalo

source_name: Freely feeding animals

treatment_protocol: Subcutaneous injection between scapulae with phosphate buffered saline (PBS). Animals had ad libitum access to food for the duration of the experiment.


title: Diploid Col-0 vs diploid Ler-0 seedlings Replicate 1

status: Public on May 01 2010

city: Freising

first: Ramon

middle: Angel

last: Torres-Ruiz

address: Emil-Ramann-Str. 8

department: Genetik

country: Germany

institute: Technische Universität München, WZW

description: Biological replicate 1a

hyb_protocol: cRNA (835ng) mixed with blocking agent and fragmentation buffer was incubated at RT (30 min) and fragmentation stopped with 2X hybridisation buffer. The mix was immediately loaded onto the microarray. Hybridization was performed at 65ºC for 17 hrs. The slides were subjected to three washing steps.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner G2565 (resolution: 5µm; channels: red & green; XDR: yes).

data_processing: Feature extraction and further processing was performed with the supplied Agilent feature extraction software (v.9.5.).  Probe sequences of the Agilent Chip were realigned to cDNA sequences of the TAIR7 gene annotation requiring a complete match (100% identity) of the probe sequences to the respective transcript sequence. Normalization and analysis of differential gene expression was restricted to probes uniquely matching one particular TAIR7 gene locus. These probes are indicated by flag=1 in the sheet of the processed expression values of the matrix sheet. TAIR7 transcript names for each probe are shown in the 'name' column of the matrix sheet if one probe mapped uniquely and specifically one alternative splice variant of the respective  locus, otherwise the TAIR7 locus identifier is reported for probes completely matching at least two alternative splice variants of the respective gene locus. Using the R/LIMMA package mean background intensities were subtracted from median red and green signals. M-values were normalized by the loess method for each array separately (“within array normalization”) and are shown as log2 Cy5/Cy3 ratios in the sample data tables.

organism: Arabidopsis thaliana

source_name: Total RNA from diploid Col-0

label_protocol: RNA (500ng) without detectable degradation and impurities was mixed with a spike-in mix, T7-promoter primer and denatured for 10 min followed by 2 hrs at 40ºC after addition of the cDNA master mix. The reaction was stopped at 65ºC for 15 min. The resulting cDNA was mixed with transcription master mix (with Cy3- or Cy5-label respectively) and incubated at 40ºC for additional 2 hrs. cRNA quantity and Cy3/Cy5-labelling efficiency was determined using a ND-1000 NanoDrop® spectrophotometer.

growth_protocol: Seeds were stratified for two days at 4ºC (on 0.8% agar) and transferred to a test chamber (HAEREUS) with constant light (~75 µmol photons/m2 sec) and 22ºC. About 100 seedlings per microarray analysis were harvested on the fifth day when root tips had penetrated the seed coat. Plants were grown on quartz sand and peaty mould (1:2 mixture) under constant light (~70 µmol photons/m2 sec), 40% relative humidity and 18º C in a Heareus (HEMZ 20/240/S) walk-in growth chamber equipped with OSRAM L58W-lamps (865-“LUMILUX Cool Daylight”, 530-“Warm White”, 77-“FLUORA”).

extract_protocol: Total RNA was isolated using SVtotalRNA-System (Promega) as recommended by the supplier.

treatment_protocol: Seeds without recognizable emerging roots or which appeared to have germinated prematurely were discarded (less than 1%). The 6-8th leaves were harvested when the bud of the eleventh leaf was recognizable.

tag: generation

value: established line

tag: cell ploidy

value: diploid

tag: cell line

value: seedlings

source_name: Total RNA from diploid Ler-0


title: wild-type_glycerolM9_mid-log_rep3

status: Public on Apr 01 2010

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

country: USA

institute: UCSD

description: The purpose of the experiment was to observe gene expression differences in mid-log phase growth of E. coli K-12 in glycerol M9 minimal media resulting from certain RNA polymerase (rpoC) mutations which had appeared during adaptive evolution in glycerol M9 minimal media.

hyb_protocol: Hybridization was performed using an Affymetrix Hybridization Oven 320.  Chip washing and staining was performed using a GeneChip Fluidics Station 450.

scan_protocol: The microarray was scanned at 500nm pixel resolution to get an image file by the GeneChip Scanner 3000 (Affymetrix).

data_processing: The twelve .cel files representing the expression measurements for triplicates of wild-type E. coli K-12 MG1655 and three related RNAP mutants were normalized together using RMAExpress and written to file using log-scale.  Gene names were assigned to results by mapping the gene probe ID to annotation using the Probe Set Data provided by Affymetrix.  Only probes which mapped to a gene synonym (three or four letters, such as hfq or rpoC) or a Blattner number (a "b" followed by a four-digit number, such as b1234) were considered in further analysis.  There were 4070 such probes.  Therefore, the VALUEs in the processed file are RMA-normalized log-scale values for the signal of probes on the GeneChip that corresponded to a gene synonym or Blattner number in the Probe Set Data file.

label: GeneChip DNA Labeling Reagent (Affymetrix, P/N 900542)

organism: Escherichia coli

source_name: Escherichia K-12 MG1655 (wild-type)

label_protocol: Approximately 10 ug of total RNA extract was used for cDNA synthesis (SuperScript II).  RNA was then removed by addition of NaOH and heat.  cDNA was purified using QIAquick PCR Purification kit and then fragmented using DNase I.  Fragments were visualized on a 2% agarose gel to confirm most fragments were 50-200 bp.  cDNA was 3'-terminal labeled using the GeneChip DNA Labeling Reagent.

growth_protocol: A small amount of frozen stock was inoculated into a flask of glycerol (2g/L) M9 minimal media and incubated at 30 degrees C.  After the culture reached stationary phase, it was diluted 1:100 into three separate flasks containing glycerol minimal media -- again these were incubated @ 30 degrees C.  These cultures were the three replicates used to extract mRNA for hybridization to the GeneChips.  mRNA was extracted when the cultures reached an OD of 0.3 (mid-log phase)

extract_protocol: Three mL of culture was mixed with 6 mL of RNAprotect reagent (Qiagen).  After sitting for 5 minutes at room temperature the tubes are centrifuged.  The pellets are frozen at -80 C.  mRNA is extracted from the pellets using an RNeasy kit (Qiagen) and using the recommended protocol.

value: wild type MG1655

tag: mutation

value: no rpoC mutation


title: wild-type_glycerolM9_mid-log_rep2


title: high passage HASM

city: NOTTINGHAM

first: SHAILENDA

last: SINGH

address: QUEEN'S MEDICAL CENTRE, DERBY ROAD

department: DIVISION OF THERAPEUTICS AND MOLECULAR MEDICINE

country: United Kingdom

institute: UNIVERSITY OF NOTTINGHAM

description:
Biological & technical replicate for affymetrix samples
Primary human airway smooth muscle cells obtained from the bronchi of patients (with no previous history of asthma) undergoing surgery with the requisite patient and ethical approval from the Nottingham local ethical research committee (Ethics Committee of City Hospital, Nottingham, United Kingdom). Lung fibroblasts cell line established from normal lung tissue of a 14-week-old male foetus was obtained from the European Collection of Cell Cultures (ECACC no. 84101801).

hyb_protocol: Microarray slides were prehybridized in buffer containing 5X SSC, 1% Bovine Serum Albumin and 0.1% SDS at 42-50 °C for 1 h and washed by dipping five times in distilled water. The slides were then dipped in isopropanol and centrifuged at 1000 rpm for 2 min to dry in 50 ml un-capped centrifuge tubes. The aminoallyl indirect labeled targets were mixed with 0.5 µl Fragmentation Buffer and incubated at 70º C (in Thermo Cycler) for 2 minutes. The labeled aRNA was then hybridized to Human 40K A OciChip™ array consisting of 20,000 genes (Ocimum biosolutions) and incubated for 16-17 hours in a humid environment (42°C)

scan_protocol: Gene Chips were then scanned in an Axon Genepix 4000b scanner (CBS) using appropriate gains on the photomultiplier tube (PMT) to obtain the highest intensity without saturation. A 16-bit TIFF image was generated for each channel, Cy3 and Cy5.

data_processing: Global LOWESS scale normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. J-express Pro software used.

organism: Homo sapiens

source_name: primary cultured human airway smooth muscle cells Passage 9

label_protocol: RNA isolated from different cell populations was amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Applied Biosystems, Warrington, U.K., Cat #1753, 1795, 1796, 1797) as per the manufacturer instructions. The next step was cDNA purification and in vitro transcription to synthesise aRNA for which the following components:  (14 ml of double-stranded cDNA, 3 ml aaUTP (amino allyl UTP) 50 mM solution, 12 ml of ATP, CTP, GTP 25mM mix, 3 ml of UTP 50 mM solution,  4 ml of T7 10X Reaction Buffer, 4 ml of T7 Enzyme mix) were mixed, briefly centrifuged and incubated  for 6-16 hr at 37oC. This was followed by aRNA purification and aminoallyl-aRNA pellet was resuspended in coupling buffer and coupled with Cy3 or Cy5 monoreactive dye (Amersham) prepared in DMSO for 30 minutes at room temperature in the dark.

growth_protocol: All  cell types used were cultured in 75 cm2 cell culture flasks in DMEM medium supplemented with 10% v/v heat-inactivated foetal calf serum, 100 U/ml penicillin, 100 ug/ml streptomycin, 2% L-glutamine at 37 C in a humidified atmosphere consisting of 95% air - 5% CO2.

extract_protocol: Total RNA was isolated and purified from the relevant cell types using a RNeasy mini kit and QIAshredders (Qiagen) as per the manufacturers protocol.

tag: cell type

source_name: lung fibroblasts cell line Passage 4

value: lung fibroblasts cell line


title: lung fibroblasts


title: bcereus 170966

status: Public on Apr 08 2010

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_5; R_6; bcereus 170966

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

scan_protocol: Images were acquired with 4200AL Molecular Devices

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
In the Data table, A=CH1 and B=CH2.

organism: Bacillus cereus ATCC 14579

source_name: Bacillus cereus ATCC14579, control

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: protocol

value: untreated (control)

source_name: Bacillus cereus ATCC14579, treated with target

value: Enterocin AS-48 challenge


title: Comparison between hypothalami from food-restricted weight-matched animals and tumor-bearing rats

source_name: Food-restricted weight-matched animals

treatment_protocol: When the difference in body weight gain between ad libitum fed tumor-bearing rats and PBS-injected animals reached 10%, eight rats were subjected to a 33% food restriction until they reached the same body weight as the former.


title: bcereus 170969

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_11; R_12; bcereus 170969


title: bcereus 170964

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_1; R_2; bcereus 170964


title: bcereus 170967

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_7; R_8; bcereus 170967


title: Comparison between hypothalami from freely feeding animals and food-restricted weight-matched animals


title: bcereus 170968

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_9; R_10; bcereus 170968


title: low passage HASM

source_name: primary cultured human airway smooth muscle cells Passage 3


title: bcereus 170965

description:
Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.
R_3; R_4; bcereus 170965


title: Comparison between hypothalami from tumor-bearing rats and freely feeding animals


title: Comparison between ventral striati from freely feeding animals and food-restricted weight-matched animals

value: Ventral striatum of 160-230g Buffalo rats

value: ventral striatum


title: Comparison between ventral striati from tumor-bearing rats and food-restricted weight-matched animals

treatment_protocol: Subcutaneous injection between scapulae with ten million Morris hepatoma 7777 cells. Tumor-bearing rats had ad libitum access to food


title: eBOP42_glycerolM9_mid-log_rep3

source_name: Escherichia K-12 rpoC mutant: eBOP42

value: isogenic to MG1655

value: deletion in the rpoC gene at base positions 3120 through 3143

tag: rnap mutant


title: Comparison between ventral striati from food-restricted weight-matched animals and freely feeding animals


title: wild-type_glycerolM9_mid-log_rep1


title: del27_glycerolM9_mid-log_rep1

source_name: Escherichia K-12 rpoC mutant: del27

value: deletion in the rpoC gene at base positions 3132 through 3158


title: Zymolyase MagExtractor rep2

status: Public on Mar 31 2010

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

description: Gene expression data from yeast

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: CEL file MAS5 normalized

label: biotin

organism: Saccharomyces cerevisiae

source_name: Zymolyase rep2

label_protocol: Approximately 4 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

growth_protocol: Parental 4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) was grown in YPD medium with low concentration of SDS at 25C for 2 days.

extract_protocol: Total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US),  or MagExtractor RNA kit (TOYOBO, Osaka, Japan) according to the manufacturer’s instructions.

treatment_protocol: Mag samples were preprocessed by zymolyase at 25C for 20 min before RNA extraction.


title: Zymolyase MagExtractor rep1

description: Gene expression data from yeast

source_name: Zymolyase rep1


title: Comparison between hypothalami from tumor-bearing rats and food-restricted weight-matched animals


title: Comparison between ventral striati from tumor-bearing rats and freely feeding animals


title: eBOP42_glycerolM9_mid-log_rep2


title: eBOP42_glycerolM9_mid-log_rep1


title: Comparison between ventral striati from freely feeding animals and tumor-bearing rats


title: Comparison between hypothalami from food-restricted weight-matched animals and freely feeding animals


title: del27_glycerolM9_mid-log_rep3


title: var2_green_leaf_rep1

city: Okayama

first: Eiko

last: Miura

address: 2-20-1 Chuo, Kurashiki

department: Research Institute for Bioresources

institute: Okayama University

description: US82800151_252116910194_S01_GE1-v5_10_Apr08_1_3.txt

hyb_protocol: The 2x cRNA target solution was prepared in a reaction volume of 52.8 ul containing 1.65 ug of Cy3-labeled cRNA and 10x Agilent blocking agent. 2.2 ul of 25x fragmentation buffer was added to 2x cRNA target solution. The solution was incubated in water bath at 60°C for 30 minutes . On completion of the fragmentation reaction, 55 ul of 2x hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis Oligo Microarray (barcode that begin with 2521169) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The slide was scanned at resolution of 5 μm using the Microarray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software V10 (Agilent) using default parameters (GE1-v5_10_Apr08) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Leaves from var2 green sectors

label_protocol: Microarray experiment was performed by custom service at Hokkaido System Science (Sapporo, Japan). cDNA was synthesized from 500ng total RNA samples and then cRNA was labeled with Cyanin3 (Cy3) using Quick Amp Labeling Kit (Agilent Technologies). Cy3-labeled cRNA was purified using RNeasy mini spin columns (QIAGEN).

growth_protocol: All plants were grown on MS medium supplemented with Gamborg’s vitamins (Sigma-Aldrich). MS medium was supplemented with 1.5% (w/v) sucrose and 0.7% (w/v) agar. Plants were maintained under a 12 h light (70 μmol•m-2•s-1)/12 h dark cycle at 22°C.

extract_protocol: Total RNAs were extracted by using RNeasy Plant Mini Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: ecotype

value: Col

tag: genotype

value: var2 (nonsense mutation with a nucleotide substitution)

value: rosette leaf

tag: developmental stage

tag: leaf color

value: green


title: Control Pro Red rep3

description: Gene expression data from yeast

source_name: Control rep3


title: var2_white_leaf_rep3

description: US82800151_252116910195_S01_GE1-v5_10_Apr08_1_1.txt

source_name: Leaves from var2 white sectors

value: white


title: Zymolyase MagExtractor rep3

description: Gene expression data from yeast

source_name: Zymolyase rep3


title: var2_white_leaf_rep1

description: US82800151_252116910194_S01_GE1-v5_10_Apr08_1_2.txt


title: Diploid vs tetraploid Col-0 (line 1326-28) leaves sibling4 Replicate 4

description: Biological replicate 12

source_name: Total RNA from diploid Col-0

value: established line

value: diploid

value: leaves

source_name: Total RNA from 1326-28 sibling4

value: tetraploid


title: Wild type_stationary growth phase_rep2

status: Public on Apr 23 2010

type: mixed

city: College Station

first: Jenni

last: Weeks

state: TX

address: 4467 TAMU

institute: Texas A&M University

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

hyb_protocol: Printed slides were submerged in 0.2 % SDS (Ambion, Austin, TX) for 2 minutes and washed three times in containers with ample ddH2O.  The microarray slides were placed in a prehybridization solution (5X SSC (Ambion, Austin, TX), 0.1 % SDS (Ambion, Austin, TX), and 1 % (w/v) BSA (Sigma, St. Louis, MO)) pre-warmed to 45°C for a minimum of 45 minutes.  Following prehybridization, the slides were washed five times in containers containing ample ddH2O, submerged once in isopropanol, and then immediately dried by centrifugation at 207 x g for 2 minutes at room temperature in a Jouan CR422 table top centrifuge.  The resuspended labeled RNA was combined with 1 µg of labeled genomic DNA from B. melitensis 16M to a total volume of 35 µl.  The sample was heated at 95°C for 5 minutes and held at 45°C until hybridization to the microarray slide.  The labeled cDNA was combined with 1X hybridization buffer (25 % (v/v) formamide (Sigma, St. Louis, Mo), 1X SSC (Ambion, Austin, TX) and 0.1 % (v/v) SDS (Ambion, Austin, TX)) and applied to the microarray with a 22 x 60 mm LifterSlip (Erie Scientific Company, Portsmouth, NH).  The microarray was incubated in a water bath for approximately 21 hours at 42°C in a sealed hybridization chamber (Corning, Corning, NY).    After hybridization, microarray slides were washed three times with agitation at room temperature.  The first wash buffer (2X SSC (Ambion, Austin, TX) and 0.2 % (v/v) SDS (Ambion, Austin, TX)) was pre-heated to 42°C and the microarray was washed for 10 minutes, followed by a 5 minute wash in 2X SSC (Ambion, Austin, TX).  The microarray was subsequently washed a third time in 0.2X SSC (Ambion, Austin, TX) for 5 minutes.  Immediately after the last wash, the arrays were dried by centrifugation for 2 minutes at 207 x g at room temperature in a Jouan CR422 tabletop centrifuge.

scan_protocol: Slides were scanned using a commercial laser scanner GenePix 4100A (Molecular Devices, Sunnyvale, CA) and Genepix 6.1 Pro software.  The auto-PMT (photomultiplier tube) function was used to determine the optimal gain for each laser channel with each slide.

data_processing: Spots that were flagged as bad or absent were removed from the analysis and background values were subtracted.  Raw Alexa 555 signals were normalized against the mean of the baseline Cy5 gDNA reference.  GeneSifter (VizX Labs, Seattle, WA) was used to perform global mean normalization on the signal values already normalized to the reference channel.  Genes were retained if their signals were altered by at least a 1.5-fold change between conditions and a p value of 0.05 or less was obtained applying a Student’s t-test.  To further filter data based on biological relevance, individual pairwise comparisons were also performed on signal values after global mean normalization using Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).  Any fold-change observed between test conditions were expected to be at least 50 % greater in magnitude (e.g., 1.5-fold greater) than the fold-change observed between any two biological replicate samples.  Genes that did not meet the criteria were removed from the analysis.  For the samples extracted during the exponential growth phase, the analysis was modified to account for variation revealed by scatter plots fitted with a trend line using the normalized signal values in the wild type samples.  In addition to the analysis described above, a separate comparison was performed that included only the two similar wild type samples.  The resulting fold-change values were expected to be greater than 50% of the value obtained for wild type 1 versus wild type 2.  A Student’s t-test was performed, retaining genes that had a p value of less than 0.05.  Genes that passed the conditions in either analysis method were considered statistically significant.

label: Alexa 555

organism: Brucella melitensis bv. 1 str. 16M

source_name: Brucella melitensis 16M, stationary phase of growth.

label_protocol: Total RNA extracted from B. melitensis 16M was transcribed into cDNA incorporating 5-(3-aminoallyl)-dUTP (aha-dUTP) for indirect labeling with Alexa Fluor 555 (Invitrogen, Carlsbad, CA), a Cy3-like fluorescein.  The cDNA synthesis combined 10 µg of total RNA, 6 µg random primers (Invitrogen, Carlsbad, CA), 1X first strand buffer (Invitrogen, Carlsbad, CA), 10 mM DTT, 0.5 mM each dATP, dTTP and dGTP, 0.3 mM dTTP (PCR grade, Invitrogen, Carlsbad, CA), 0.2 mM aha-dUTP (Invitrogen, Carlsbad, CA), 400 units SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) and 20 units protector RNAse inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 23°C for one minute and then at 46°C overnight.  The reaction was then treated with 0.4 M NaOH and incubated at 65°C for 15 minutes to stop the reaction and remove residual RNA.    The pH was brought back to neutral with the addition of 0.2M HCl, then the cDNA was purified to remove unincorporated aha-dUTP and free amines using PCR Purification columns (Qiagen, Valencia, CA) with the modified wash (5 mM KPO4 (pH 8.0) and 80 % (v/v) ethanol) and elution buffers (4 mM KPO4 (pH 8.5)).  The manufacturer’s instructions were modified to include 2 washes with the substituted phosphate wash buffer, and the elution was carried out in 2 steps: 50 µl each elution (yielding 100 µl total) with a one minute incubation of the elution buffer in the column at room temperature before centrifugation.  Alexa-Fluor 555 (Invitrogen, Carlsbad, CA) was coupled to the aha-dUTP incorporated into the cDNA following the coupling procedure outlined in the BioPrime® Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Carlsbad, CA) and purified using PCR purification columns (Qiagen, Valencia, CA) following manufacturer’s instructions.  Concentration and labeling efficiency of the labeled cDNA was examined using the Nanodrop® ND-1000 (Nanodrop, Wilmington, DE).  Labeled RNA samples were dried completely (Eppendorf Vacufuge, Westbury, NY) and resuspended in ddH2O immediately before hybridization to the microarrays.

growth_protocol: Brucella melitensis 16M Bv. 1 was obtained from ATCC and re-isolated from an aborted goat fetus by this lab.  B. melitensis 16M Bv. 1 and its genetically modified derivatives were maintained as frozen glycerol stocks.  Strains were plated for isolation on TSA and incubated at 37°C with 5% CO2 for 3 days.  Individual 50 ml conical tubes with 5 ml of Brucella Broth (Difco Laboratories, Becton, Dickinson and Company, Franklin Lakes, NJ) were inoculated from an isolated single colony and incubated at 37ºC with agitation for 48 hours.  Cultures were then inoculated 1:1000 in Brucella Broth and grown at 37°C with agitation.  50 ng/ml exogenous C12-HSL (Sigma) was added to some cultures at inoculation. Growth curves of cultures were determined by the optical density (OD) of the culture at 600nm with bacterial colony forming units (CFU).  For cells at logarithmic phase of growth, OD600=0.4; for cells at stationary phase of growth, OD600=1.5.

extract_protocol: At harvest time, 14 % (v/v) of a cold ethanol solution containing 5 % (v/v) acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added to the bacterial culture and immediately centrifuged at 10900 x g for 3 minutes.  The supernatant was removed and the bacterial pellet was frozen in liquid nitrogen and stored at -80°C.  RNA was collected by re-suspending the bacterial pellets in 0.5 mg/ml lysozyme (Amresco, Solon, OH) dissolved in TE, followed by the addition of 0.97 % (v/v) SDS.  The cells were then incubated at 64°C for 2 minutes.  Next, 0.5 M sodium acetate (pH 5.2) was added, mixed gently by inversion and an equal volume of acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added and mixed well by inversion.  The bacteria-phenol mix was incubated at 64°C for 6 minutes and mixed by inversion several times every 40 seconds.  The bacteria-phenol mix was chilled on ice for 30 minutes and the layers were separated by centrifugation at 28900 x g for 13 minutes.  The aqueous layer was removed and placed in a clean tube.  An equal volume of chloroform (Sigma, St. Louis, MO) was added to the aqueous layer and mixed well by inversion.  The layers were separated by centrifugation at 20700 x g for 7 minutes.  This aqueous layer was placed into a clean tube and total RNA was precipitated by adding an equal volume of cold isopropanol and 0.1 volumes of 3M sodium acetate (pH 5.4).  RNA was precipitated for one hour at -80°C and then pelleted by centrifugation at 19000 x g for 30 minutes, washed with 80 % (v/v) ethanol, centrifuged for 5 minutes at 19000 x g, and the resulting pellets were air-dried for 20 minutes.  The dried pellets were resuspended in RNAse-free water, and subjected to DNAseI treatment.  The DNA was degraded and removed by incubation with 5X DNAseI buffer (50 mM MgCl2, 50 mM Tris-Cl pH 7.5, 5 mM EDTA, 5 mM dithiothreitol (DTT)), 10 units of DNAseI (Qiagen, Valencia, CA) and 10 units of RNAse Inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 37°C for one hour.  Following the DNAseI digestion, the total RNA was further purified using the HighPure RNA isolation kit (Roche, Indianapolis, IN), following manufacturer’s instructions and included the optional (second) DNAseI incubation.  The RNA was eluted with the provided elution buffer, precipitated with 3 volumes of cold 95 % (v/v) ethanol and 0.1 volumes 3 M sodium acetate (pH 5.2) and washed with 80 % (v/v) ethanol.  The pellet was air dried for 15 minutes and then resuspended in The RNA Storage Solution (Ambion, Austin, TX).

tag: 16M bv.1 strain.


title: low passage HASM

description: primary human airway smooth muscle cells  obtained from the bronchi of patients (with no previous history of asthma) undergoing surgery with the requisite patient and ethical approval from the Nottingham local ethical research committee (Ethics Committee of City Hospital, Nottingham, United Kingdom).

hyb_protocol: Following fragmentation, Hybridization was performed using 5 micrograms of biotinylated target, which was then incubated with the GeneChip® Human Gene 1.0 ST array (Affymetrix) at 45°C for 17 hours.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) using GeneChip® Operating Software (GCOS).

data_processing: Raw data was extracted from the scanned images using robust multichip average (RMA) method and then analyzed with GeneSpring, version 9.0.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual Version 4).

value: primary cultured human airway smooth muscle cells


title: Wild-type_leaf_rep2

description: US82800151_252116910235_S01_GE1-v5_10_Apr08_1_1.txt

source_name: Leaves from wild-type


title: var2_green_leaf_rep2

description: US82800151_252116910235_S01_GE1-v5_10_Apr08_1_3.txt


title: var2_green_leaf_rep3

description: US82800151_252116910195_S01_GE1-v5_10_Apr08_1_2.txt


title: Wild-type_leaf_rep3

description: US82800151_252116910235_S01_GE1-v5_10_Apr08_1_4.txt


title: Control Pro Red rep2

description: Gene expression data from yeast

source_name: Control rep2


title: A5

status: Public on Mar 01 2010

city: New Orleans

first: Laura

middle: S

last: Levy

state: LA

address: 1430 Tulane Ave SL38

department: Microbiology & Immunology

institute: Tulane University

description: 3D assembly

hyb_protocol: 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® array.  The array was hybridized overnight at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.4. Analysis of the results using Bayesian Analysis of Variance model (BAM) identified genes highly likely to be differentially expressed under 3D growth conditions as compared to conventional culture.

label: biotiin

source_name: UMCL01-101 cell, cultured in RWV Bioreactor

label_protocol: Biotinylated cRNA was prepared using the standard Affymetrix T7 oligo(dT) primer protocol starting with 5 µg total RNA.

growth_protocol: UMCL01-101 cells were grown as conventional suspension cultures or in RWV bioreactor.

extract_protocol: Total cellular RNA was isolated and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).  Integrity and purity of the RNA were verified using an Agilent Bioanalyzer (Palo Alto, CA).

treatment_protocol: For growth in the RWV Bioreactor (Model RCCS-4D, Synthecon, Inc., Houston, TX), cells were seeded at 1 x 10e7 per ml in disposable 50-ml vessels and were grown for 15 days at a rotation speed of 12 rpm through day 10 and 14 rpm thereafter.

tag: culture

value: 3D assembly


title: del27_glycerolM9_mid-log_rep2

description: The purpose of the experiment was to observe gene expression differences in mid-log phase growth of E. coli K-12 in glycerol M9 minimal media resulting from certain RNA polymerase (rpoC) mutations which had appeared during adaptive evolution in glycerol M9 minimal media.


title: A2

description: 3D assembly


title: B3

description: Conventional cuture

source_name: UMCL01-101 cell, grown in suspension culture

value: conventional cuture


title: B4

description: Conventional cuture


title: high passage HASM

source_name: primary cultured human airway smooth muscle cells Passage 9


title: 1378: MT1-MMP -/-, MT2-MMP+/-

city: Bethesda

first: Kenn

last: Holmbeck

state: MD

address: 30 Convent Drive

institute: NIDCR

description: US45103093_251486818937_S01_GE1-v5_95_Feb07_1_2.txt

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 4x44K Whole Mouse Genome Microarrays (Cat. # G4122F Agilent Technologies, Santa Clara, CA) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately on air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807) with No Background Method and Background Detrend On.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions. To provide a positive control for monitoring the microarray workflow, RNA samples were spiked with control RNA from Agilent One Color RNA Spike-In Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. Labeled and amplified RNA was purified using Qiagen RNeasy mini spin columns (Qiagen, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: DNase-free RNA was prepared using an RNAqueous-4PCR kit (Ambion, Inc., TX) according to the manufacturer’s protocol.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fetal parts of the freshly isolated mouse placentas were snap frozen on dry ice.

value: placenta

tag: age


title: 1394: MT1-MMP -/-, MT2-MMP-/-

description: US45103093_251486818938_S01_GE1-v5_95_Feb07_1_1.txt


title: 1289: MT1-MMP -/-, MT2-MMP-/-

description: US45103093_251486818939_S01_GE1-v5_95_Feb07_1_1.txt


title: 1377: MT1-MMP +/-, MT2-MMP-/-

description: US45103093_251486818937_S01_GE1-v5_95_Feb07_1_3.txt


title: 1391: MT1-MMP -/-, MT2-MMP+/-

description: US45103093_251486818938_S01_GE1-v5_95_Feb07_1_2.txt


title: var2_white_leaf_rep2

description: US82800151_252116910235_S01_GE1-v5_10_Apr08_1_2.txt


title: lung fibroblasts

description: lung fibroblasts cell line established from normal lung tissue of a 14-week-old male foetus was obtained from the European Collection of Cell Cultures (ECACC no. 84101801).

source_name: lung fibroblasts cell line Passage 4

value: lung fibroblasts cell line


title: 1396: MT1-MMP +/-, MT2-MMP-/-

description: US45103093_251486818939_S01_GE1-v5_95_Feb07_1_3.txt


title: 1392: MT1-MMP +/-, MT2-MMP-/-

description: US45103093_251486818938_S01_GE1-v5_95_Feb07_1_3.txt


title: A6

description: 3D assembly


title: Common bean root, biological rep3

city: St Paul

first: Sam

last: Yang

state: MN

address: 411 Upper Buford Circle

department: ARS

institute: USDA

description: Gene expression data from leaf nodule, root of soybean and common bean.

hyb_protocol: RNA labeling, hybridization, washing and scanning were conducted in the Microarray Facility, Biomedical Genomics Center, University of Minnesota, following standard Affymetrix procedures. Briefly, 10 µg of total RNA was used to synthesize cDNA using SuperScriptTM Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). Biotinylated cRNA was generated via in vitro transcription using the Enzo BioArrayTM High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY). Fifteen micrograms of labeled RNA was chemically fragmented and used for hybridization.  The Affymetrix GeneChip Sample Cleanup Module was used for cDNA, biotinylated cRNA purification and chemical fragmentation. The integrity of total RNA and fragmented biotin-labeled cRNA was verified with RNA600 Nano LabChip using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA).

data_processing: After scanning the GeneChips, the exported files with probe signal intensities (cel files) were quantile-normalized  and background corrected by RMA (Irizarry et al., 2003) using the affy package from Bioconductor (http://bioconductor.org). To improve the quality of common bean CSH GeneChip data, we employed a methodology that masked putative probes targeting ISV regions. A signal intensity threshold 80 was selected that optimized both sensitivity and specificity. For each common bean tissue sample, three biological replicates were collected producing a total of 9 data points per probe (3 tissue types x 3 replicates). For a particular probe (9 data points), all data points were kept if three or more probes were above the signal intensity threshold. Otherwise, all 9 probes were masked. Next, the signal intensities of retained probes were quantile-normalized and condensed into probe set expression values by Robust Multi-array Average algorithm (RMA: Irizarry et al., 2003).

organism: Phaseolus vulgaris

source_name: Common bean root

growth_protocol: The common bean (Phaseolus vulgaris) Mesoamerican cv Negro Jamapa 81 and the Minsoy line of soybean (Glycine max) were used in this study. Plants were grown in a growth chamber (27/24 0C; 14/10 h photoperiod and 60% of humidity). Surface-sterilized seeds were germinated at 25 0C over sterile, wet filter paper. Three day-old seedlings were sown in pots containing Turface MVP (Profile Products LLC, Buffalo Grove, IL). Plants were watered three times per week with Summerfield nutrient solution (Summerfield et al., 1977). After three weeks, leaves and roots were harvested and immediately frozen in liquid nitrogen (N) and stored at -80 0C until used for RNA isolation.

extract_protocol: Total RNA was purified from three replicates of leaves, roots or nodules from common bean or soybean plants, using LiCl precipitation protocol as reported in (Valdes-Lopez et al., 2008). Contaminating genomic DNA was removed from each sample using the DNA-free™ kit following the manufacturer’s recommendations (www.ambion.com).

treatment_protocol: To evaluate the transcriptional profile of common bean nodules vs soybean nodules, three day-old seedlings were sown in pots containing Turface MVP and inoculated with Rhizobium tropici CIAT899 for common bean, or Bradirhizobium japonicum USDA110. Plants were watered three times per week with N-free Summerfield nutrient solution (Summerfield et al., 1977). After three weeks post-inoculation, nodules were harvested and immediately frozen in liquid N and stored until used for RNA isolation.

value: root

tag: cultivar

value: Mesoamerican cv Negro Jamapa 81


title: Control Pro Red rep1

description: Gene expression data from yeast

source_name: Control rep1


title: B1

description: Conventional cuture


title: Common bean root, biological rep2

scan_protocol: RNA labeling, hybridization, washing and scanning were conducted in the Microarray Facility, Biomedical Genomics Center, University of Minnesota, following standard Affymetrix procedures. Briefly, 10 µg of total RNA was used to synthesize cDNA using SuperScriptTM Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). Biotinylated cRNA was generated via in vitro transcription using the Enzo BioArrayTM High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY). Fifteen micrograms of labeled RNA was chemically fragmented and used for hybridization.  The Affymetrix GeneChip Sample Cleanup Module was used for cDNA, biotinylated cRNA purification and chemical fragmentation. The integrity of total RNA and fragmented biotin-labeled cRNA was verified with RNA600 Nano LabChip using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA).

tag: tissue


title: 1374: MT1-MMP +/-, MT2-MMP+/-

description: US45103093_251486818937_S01_GE1-v5_95_Feb07_1_4.txt


title: 1282: MT1-MMP +/-, MT2-MMP+/-

description: US45103093_251486818938_S01_GE1-v5_95_Feb07_1_4.txt


title: Wild-type_leaf_rep1

description: US82800151_252116910194_S01_GE1-v5_10_Apr08_1_1.txt


title: 1287: MT1-MMP +/-, MT2-MMP+/-

description: US45103093_251486818939_S01_GE1-v5_95_Feb07_1_4.txt


title: Common bean root, biological rep1

label_protocol: RNA labeling, hybridization, washing and scanning were conducted in the Microarray Facility, Biomedical Genomics Center, University of Minnesota, following standard Affymetrix procedures. Briefly, 10 µg of total RNA was used to synthesize cDNA using SuperScriptTM Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). Biotinylated cRNA was generated via in vitro transcription using the Enzo BioArrayTM High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY). Fifteen micrograms of labeled RNA was chemically fragmented and used for hybridization.  The Affymetrix GeneChip Sample Cleanup Module was used for cDNA, biotinylated cRNA purification and chemical fragmentation. The integrity of total RNA and fragmented biotin-labeled cRNA was verified with RNA600 Nano LabChip using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA).


title: Common bean nodule, biological rep3

source_name: Common bean nodule

value: nodule


title: 1390: MT1-MMP -/-, MT2-MMP+/-

description: US45103093_251486818939_S01_GE1-v5_95_Feb07_1_2.txt


title: Common bean nodule, biological rep1


title: Common bean nodule, biological rep2


title: 1373: MT1-MMP -/-, MT2-MMP-/-

description: US45103093_251486818937_S01_GE1-v5_95_Feb07_1_1.txt


title: Common bean leaf, biological rep3

source_name: Common bean leaf

value: leaf


title: Common bean leaf, biological rep1


title: Soybean root, biological rep3

organism: Glycine max

source_name: Soybean root

value: the Minsoy


title: Soybean root, biological rep2


title: hsfb1 hsfb2b double knockout vs wild type #4

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate 4 of 4.

hyb_protocol: As described in manual supplied by Agilent.

data_processing: By using Feature Extraction version 9.1 supplied by Agilent.

source_name: hsfb1 hsfb2b seedling

label_protocol: By using Quick Amp Labeling Kit supplied by Agilent.

growth_protocol: Grown under long day (16hr light), 22 degree temprature in MS agar medium. Grown together with control plants in same dish.

extract_protocol: By using RNeasy plant mini kit supplied by QIAGEN.

treatment_protocol: No treatment

value: seedling

value: 7 days

tag: strain

value: hsfb1 hsfb2b

tag: mutation description

value: hsfb1 hsfb2b double knockout

tag: growth condition

value: normal

source_name: wild-type seedling

growth_protocol: Grown under long day (16hr light), 22 degree temprature in MS agar medium. Grown together with mutant plants in same dish.

value: wild-type


title: Common bean leaf, biological rep2


title: Soybean root, biological rep1


title: Soybean leaf, biological rep3

source_name: Soybean leaf


title: hsfb1 hsfb2b double knockout vs wild type #1

description: Biological replicate 1 of 4.

scan_protocol: As described in manual supplied by Agilent.


title: Soybean nodule, biological rep2

source_name: Soybean nodule


title: Soybean nodule, biological rep1


title: Soybean nodule, biological rep3


title: Soybean leaf, biological rep1


title: Soybean leaf, biological rep2


title: hsfb1 hsfb2b double knockout vs wild type #2

description: Biological replicate 2 of 4.


title: 35S:HSFB1 vs wild type #2

description: Biological replicate 2 of 3.

source_name: 35S:HSFB1 root

value: 22 days

value: over-expresses HSFB1

source_name: wild-type root

growth_protocol: Grown under long day (16hr light), 22 degree temprature in MS agar medium. Grown together with transgenic plants in same dish.


title: hsfb1 hsfb2b double knockout vs wild type #3

description: Biological replicate 3 of 4.


title: 35S:mutHSFB1 vs wild type #1

description: Biological replicate 1 of 3.

source_name: 35S:mutHSFB1 root

value: over-expresses mutHSFB1, which has a mutated repression domain


title: 35S:mutHSFB1 vs wild type #3

description: Biological replicate 3 of 3.


title: X1692272063_E

status: Public on Feb 28 2010

city: Cologne

first: Thomas

last: Zander

address: Kerpenerstr. 62

institute: University Hospital Cologne

description: Non Bronchial Carcinoma

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R

source_name: PAXgene stabilized blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Peripheral blood samples

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

value: PBMC


title: X1692272063_C

description: Non Bronchial Carcinoma


title: X1692272063_A

description: Non Bronchial Carcinoma


title: X1692272063_B

description: Non Bronchial Carcinoma


title: X1692272063_D

description: Non Bronchial Carcinoma


title: X1723260256_F

description: Non Bronchial Carcinoma


title: 35S:mutHSFB1 vs wild type #2

description: Biological replicate 2 of 3.


title: 35S:HSFB1 vs wild type #3

description: Biological replicate 3 of 3.


title: X1723260256_D

description: Non Bronchial Carcinoma


title: X1723260256_B

description: Non Bronchial Carcinoma


title: X1723260256_C

description: Non Bronchial Carcinoma


title: X1723260265_D

description: Non Bronchial Carcinoma


title: X1723260256_A

description: Non Bronchial Carcinoma


title: X1723260265_E

description: Non Bronchial Carcinoma


title: X1723260265_B

description: Non Bronchial Carcinoma


title: X1723260265_F

description: Non Bronchial Carcinoma


title: X4202996086_F

description: Non Bronchial Carcinoma


title: X1723260256_E

description: Non Bronchial Carcinoma


title: X1723260265_C

description: Non Bronchial Carcinoma


title: 35S:HSFB1 vs wild type #1

description: Biological replicate 1 of 3.


title: X1723260253_B

description: Non Bronchial Carcinoma


title: X1723260265_A

description: Non Bronchial Carcinoma


title: X4202996086_C

description: Bronchial Carcinoma


title: X4202996086_E

description: Non Bronchial Carcinoma


title: X1692272063_F

description: Non Bronchial Carcinoma


title: X4202996086_A

description: Bronchial Carcinoma


title: X4202996086_D

description: Bronchial Carcinoma


title: X4202996064_D

description: Bronchial Carcinoma


title: X4202996064_C

description: Bronchial Carcinoma


title: X4202996068_E

description: Bronchial Carcinoma


title: X4202996064_E

description: Bronchial Carcinoma


title: X4202996064_B

description: Bronchial Carcinoma


title: X4202996068_C

description: Bronchial Carcinoma


title: X4202996068_B

description: Bronchial Carcinoma


title: X4202996068_A

description: Bronchial Carcinoma


title: X4202996068_F

description: Bronchial Carcinoma


title: X4202996086_B

description: Bronchial Carcinoma


title: X4202996067_D

description: Bronchial Carcinoma


title: X4202996067_E

description: Bronchial Carcinoma


title: X4202996064_A

description: Bronchial Carcinoma


title: X4202996067_C

description: Bronchial Carcinoma


title: X4202996068_D

description: Bronchial Carcinoma


title: X4202996067_A

description: Bronchial Carcinoma


title: X4202996067_B

description: Bronchial Carcinoma


title: X4320028042_C

description: Non Bronchial Carcinoma


title: X4320028042_B

description: Bronchial Carcinoma


title: X4320028040_E

description: Non Bronchial Carcinoma


title: X4320028042_D

description: Bronchial Carcinoma


title: X4320028040_D

description: Non Bronchial Carcinoma


title: X4320028042_A

description: Non Bronchial Carcinoma


title: X4202996064_F

description: Bronchial Carcinoma


title: X4320028040_C

description: Bronchial Carcinoma


title: X4320028059_F

description: Bronchial Carcinoma


title: X4320028040_B

description: Non Bronchial Carcinoma


title: X4202996067_F

description: Bronchial Carcinoma


title: X4320028046_F

description: Bronchial Carcinoma


title: X4320028059_E

description: Non Bronchial Carcinoma


title: X4320028046_E

description: Non Bronchial Carcinoma


title: X4320028046_C

description: Bronchial Carcinoma


title: X4320028046_D

description: Non Bronchial Carcinoma


title: X4320028046_B

description: Bronchial Carcinoma


title: X4320028046_A

description: Non Bronchial Carcinoma


title: X4320028059_B

description: Bronchial Carcinoma


title: X4320028039_D

description: Bronchial Carcinoma


title: X4320028039_C

description: Non Bronchial Carcinoma


title: X4320028039_B

description: Non Bronchial Carcinoma


title: X4320028020_F

description: Non Bronchial Carcinoma


title: X4320028025_E

description: Bronchial Carcinoma


title: X4320028025_D

description: Non Bronchial Carcinoma


title: X4320028039_A

description: Bronchial Carcinoma


title: X4320028020_E

description: Bronchial Carcinoma


title: X4320028025_B

description: Non Bronchial Carcinoma


title: X4320028017_D

description: Non Bronchial Carcinoma


title: X4320028020_D

description: Non Bronchial Carcinoma


title: X4320028025_A

description: Bronchial Carcinoma


title: X4320028056_E

description: Bronchial Carcinoma


title: X4320028020_C

description: Bronchial Carcinoma


title: X4320028055_D

description: Non Bronchial Carcinoma


title: X4320028020_B

description: Non Bronchial Carcinoma


title: X4320028025_C

description: Bronchial Carcinoma


title: X4320028017_B

description: Non Bronchial Carcinoma


title: X4320028059_C

description: Bronchial Carcinoma


title: X4320028017_A

description: Bronchial Carcinoma


title: X4320028055_F

description: Non Bronchial Carcinoma


title: X4320028056_F

description: Non Bronchial Carcinoma


title: X4320028056_D

description: Non Bronchial Carcinoma


title: X4320028017_C

description: Bronchial Carcinoma


title: X4320028055_E

description: Bronchial Carcinoma


title: X4320028056_A

description: Bronchial Carcinoma


title: X4320028056_B

description: Non Bronchial Carcinoma


title: X4320028056_C

description: Bronchial Carcinoma


title: X4320028055_C

description: Bronchial Carcinoma


title: X4320028020_A

description: Bronchial Carcinoma


title: X4320028055_B

description: Non Bronchial Carcinoma


title: X4320028025_F

description: Non Bronchial Carcinoma


title: X4320028041_D

description: Non Bronchial Carcinoma


title: X4320028041_E

description: Bronchial Carcinoma


title: X4320028055_A

description: Bronchial Carcinoma


title: X4320028041_B

description: Non Bronchial Carcinoma


title: X4320028041_F

description: Non Bronchial Carcinoma


title: X4320028041_A

description: Bronchial Carcinoma


title: X4320028053_F

description: Non Bronchial Carcinoma


title: X4320028053_B

description: Non Bronchial Carcinoma


title: X4320028053_A

description: Bronchial Carcinoma


title: X4320028053_E

description: Bronchial Carcinoma


title: X4320028052_A

description: Bronchial Carcinoma


title: X4320028041_C

description: Bronchial Carcinoma


title: X4320028049_F

description: Non Bronchial Carcinoma


title: X4320028053_C

description: Bronchial Carcinoma


title: X4320028047_B

description: Non Bronchial Carcinoma


title: X4320028047_A

description: Bronchial Carcinoma


title: X4320028052_D

description: Non Bronchial Carcinoma


title: X4320028053_D

description: Non Bronchial Carcinoma


title: X4320028049_B

description: Non Bronchial Carcinoma


title: X4320028047_E

description: Bronchial Carcinoma


title: X4320028049_D

description: Non Bronchial Carcinoma


title: X4320028052_C

description: Bronchial Carcinoma


title: X4320028047_F

description: Non Bronchial Carcinoma


title: X4320028057_E

description: Bronchial Carcinoma


title: X4320028049_E

description: Bronchial Carcinoma


title: X4320028049_A

description: Bronchial Carcinoma


title: X4320028051_E

description: Bronchial Carcinoma


title: X4320028052_F

description: Non Bronchial Carcinoma


title: X4320028051_D

description: Non Bronchial Carcinoma


title: X4320028051_C

description: Bronchial Carcinoma


title: X4320028049_C

description: Bronchial Carcinoma


title: X4320028051_B

description: Non Bronchial Carcinoma


title: X4252483011_D

description: Non Bronchial carcinoma

source_name: Snap frozen blood


title: X4320028057_B

description: Non Bronchial Carcinoma


title: X4320028051_F

description: Non Bronchial Carcinoma


title: X4252483011_C

description: Non Bronchial carcinoma


title: X4320028051_A

description: Bronchial Carcinoma


title: X4252483002_E

description: Non Bronchial carcinoma


title: X4252483002_D

description: Non Bronchial carcinoma


title: X4252483009_D

description: Non Bronchial carcinoma


title: X4252483002_C

description: Non Bronchial carcinoma


title: X4252483009_B

description: Non Bronchial carcinoma


title: X4252483009_C

description: Non Bronchial carcinoma


title: X4252483008_E

description: Non Bronchial carcinoma


title: X4252483011_E

description: Non Bronchial carcinoma


title: X4252483002_F

description: Non Bronchial carcinoma


title: X4252483009_F

description: Non Bronchial carcinoma


title: X4252483008_F

description: Non Bronchial carcinoma


title: X4252483011_F

description: Non Bronchial carcinoma


title: X4252483009_A

description: Non Bronchial carcinoma


title: X4252483011_B

description: Non Bronchial carcinoma


title: X4252483009_E

description: Non Bronchial carcinoma


title: X4252483011_A

description: Non Bronchial carcinoma


title: X4252483002_B

description: Non Bronchial carcinoma


title: X4252483008_D

description: Non Bronchial carcinoma


title: X4252483008_C

description: Non Bronchial carcinoma


title: X4252483001_D

description: Non Bronchial carcinoma


title: X4252483001_E

description: Non Bronchial carcinoma


title: X4252483008_B

description: Non Bronchial carcinoma


title: X4252483001_C

description: Non Bronchial carcinoma


title: X4252483001_A

description: Non Bronchial carcinoma


title: X4252483008_A

description: Non Bronchial carcinoma


title: X4252483001_F

description: Non Bronchial carcinoma


title: EPIC control #6: control

description: All samples were taken from smokers. EPIC cases were taken from the EPIC trial (a large prospective epidemiological trial in Europe, and are incident cases), Cosmos and BC cases are prevalent cases from a Cologne, Germany based epidemiological trial.

hyb_protocol: For hybridization samples were applied to the arrays and assembled into HybCartridges (Illumina). BeadChips were hybridized for 16h at 55°C on the BeadChip Hyb Wheel. 1.5 μg biotin labeled cRNA was hybridized to Sentrix® whole genome bead chips 6 x 2 V1 and V2 (Illumina, USA) according to the manufacturers instruction. Arrays were washed according to Illumina Wash BeadChip 6 x 2 protocol. Signals were developed with streptavidin Cy3.

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x.

data_processing: BeadStudio raw data were normalized using R

source_name: peripheral blood

label_protocol: Biotin labeled cRNA preparation was performed using the Ambion® Illumina RNA amplification kit (Ambion, UK). Quality was controlled using a PCR based system1.

extract_protocol: weWe used snap frozen PBMC enriched blood (~ 300 µl) from the EPIC study for RNA extraction. Blood samples were directly thawed in 5ml of TRI Reagent BD (Molecular Research Center, Inc, USA). RNA was extracted according to the manufactures instruction and stored in 70% ethanol until finalization of preparation and dilution in H2O. For further RNA purification we applied Qiagen MinElute columns (Qiagen, Germany). By this method we extracted 960ng RNA (mean; range 120 – 2500ng). One sample contained no RNA. The OD ratio 260/280 was 2.01 in mean (range 1.76-2.06). For the LC-group, we drew 2.5 ml blood directly into PAXgene vials providing stabilization of the gene expression profile. Samples were rested over night at room temperature and then stored at -80°C until further preparation. RNA was extracted according to the manufactures instruction (Qiagen, Hilden, Germany).

tag: control


title: EPIC control #5: control


title: EPIC control #3: control


title: EPIC control #2: control


title: EPIC control #4: control


title: EPIC control #11: control


title: EPIC control #12: control


title: EPIC control #10: control


title: EPIC control #9: control


title: EPIC control #13: control


title: EPIC control #1: control


title: EPIC control #8: control


title: EPIC case #6: bronchial carcinoma

tag: bronchial carcinoma


title: EPIC case #9: bronchial carcinoma


title: EPIC case #7: bronchial carcinoma


title: EPIC case #8: bronchial carcinoma


title: EPIC case #5: bronchial carcinoma


title: EPIC case #1: bronchial carcinoma


title: EPIC case #11: bronchial carcinoma


title: EPIC case #3: bronchial carcinoma


title: EPIC case #4: bronchial carcinoma


title: Patient without BC #25: control


title: EPIC case #12: control


title: EPIC case #10: bronchial carcinoma


title: Patient without BC #23: control


title: Patient without BC #26: control


title: Patient without BC #18: control


title: Patient without BC #21: control


title: Patient without BC #16: control


title: Patient without BC #20: control


title: X4252483001_B

description: Non Bronchial carcinoma

tag: cell type


title: Patient without BC #24: control


title: Patient without BC #22: control


title: Patient without BC #13: control


title: Patient without BC #15: control


title: Patient without BC #19: control


title: Patient without BC #17: control


title: Patient without BC #12: control


title: Patient without BC #14: control


title: Patient without BC #11: control


title: Patient with BC #34: bronchial carcinoma


title: Patient with BC #35: bronchial carcinoma


title: Patient with BC #29: bronchial carcinoma


title: Patient with BC #33: bronchial carcinoma


title: Patient without BC #9: control


title: Patient with BC #23: bronchial carcinoma


title: Patient with BC #32: bronchial carcinoma


title: Patient with BC #26: bronchial carcinoma


title: Patient with BC #25: bronchial carcinoma


title: Patient with BC #30: bronchial carcinoma


title: Patient with BC #27: bronchial carcinoma


title: Patient with BC #20: bronchial carcinoma


title: Patient with BC #22: bronchial carcinoma


title: Patient with BC #24: bronchial carcinoma


title: Patient with BC #21: bronchial carcinoma


title: EPIC control #7: control


title: Patient with BC #31: bronchial carcinoma


title: Patient with BC #19: bronchial carcinoma


title: Patient with BC #17: bronchial carcinoma


title: Patient with BC #28: bronchial carcinoma


title: Patient without BC #8: control


title: Patient with BC #18: bronchial carcinoma


title: Patient with BC #16: bronchial carcinoma


title: Patient with BC #15: bronchial carcinoma


title: Patient with BC #2: bronchial carcinoma


title: Patient with BC #11: bronchial carcinoma


title: Patient without BC #4: control


title: Patient without BC #5: control


title: Patient with BC #6: bronchial carcinoma


title: Patient with BC #14: bronchial carcinoma

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x

extract_protocol: We used snap frozen PBMC enriched blood (~ 300 µl) from the EPIC study for RNA extraction. Blood samples were directly thawed in 5ml of TRI Reagent BD (Molecular Research Center, Inc, USA). RNA was extracted according to the manufactures instruction and stored in 70% ethanol until finalization of preparation and dilution in H2O. For further RNA purification we applied Qiagen MinElute columns (Qiagen, Germany). By this method we extracted 960ng RNA (mean; range 120 – 2500ng). One sample contained no RNA. The OD ratio 260/280 was 2.01 in mean (range 1.76-2.06). For the LC-group, we drew 2.5 ml blood directly into PAXgene vials providing stabilization of the gene expression profile. Samples were rested over night at room temperature and then stored at -80°C until further preparation. RNA was extracted according to the manufactures instruction (Qiagen, Hilden, Germany). Biotin labeled cRNA preparation was performed using the Ambion® Illumina RNA amplification kit (Ambion, UK). Quality was controlled using a PCR based system1.


title: Patient without BC #2: control


title: Patient with BC #3: bronchial carcinoma


title: Patient without BC #1: control


title: Patient with BC #4: bronchial carcinoma


title: Patient with BC #12: bronchial carcinoma


title: Patient without BC #6: control


title: Patient with BC #10: bronchial carcinoma


title: Patient with BC #9: bronchial carcinoma


title: Patient with BC #7: bronchial carcinoma


title: Patient with BC #13: bronchial carcinoma


title: Patient with BC #8: bronchial carcinoma


title: epic sample 32: control

extract_protocol: We used snap frozen PBMC enriched blood (~ 300 µl) from the EPIC study for RNA extraction. Blood samples were directly thawed in 5ml of TRI Reagent BD (Molecular Research Center, Inc, USA). RNA was extracted according to the manufactures instruction and stored in 70% ethanol until finalization of preparation and dilution in H2O. For further RNA purification we applied Qiagen MinElute columns (Qiagen, Germany). By this method we extracted 960ng RNA (mean; range 120 – 2500ng). One sample contained no RNA. The OD ratio 260/280 was 2.01 in mean (range 1.76-2.06). For the LC-group, we drew 2.5 ml blood directly into PAXgene vials providing stabilization of the gene expression profile. Samples were rested over night at room temperature and then stored at -80°C until further preparation. RNA was extracted according to the manufactures instruction (Qiagen, Hilden, Germany).


title: epic sample 29: bronchial carcinoma


title: Patient with BC #5: bronchial carcinoma


title: epic sample 41: bronchial carcinoma


title: epic sample 25: control


title: Patient with BC #1: bronchial carcinoma


title: epic sample 27: bronchial carcinoma


title: epic sample 38: control


title: epic sample 19: control


title: epic sample 39: bronchial carcinoma


title: epic sample 11: bronchial carcinoma


title: epic sample 33: bronchial carcinoma


title: epic sample 9: control


title: epic sample 5: control


title: epic sample 3: bronchial carcinoma


title: TinoDeltaRING-his Filter Binding

city: Firenze

first: martino

last: donnini

state: Firenze

address: viale GB Morgagni

department: Pathology and Oncology

country: Italy

institute: University of Florence

description: For the in vitro approach, cRNAs were prepared from a human placenta cDNA library and incubated with TinoRING-his. This deleted form of Tino-his protein conserves its mRNA binding activity. mRNAs directly bound to Tino?RING-his protein were subsequently isolated using a nitrocellulose RNA-protein binding assay.

hyb_protocol: Hybridization mix for target dilution (100 mM MES, 1 M [Na +], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 150µg/ml and denatured at 99°C prior to introduction into the GeneChip cartridge. Each GeneChipHU-U133A v2.0 was then hybridized with each biotin-labeled target.   Hybridizations were performed for 16 hours at 45°C in a rotisserie oven. GeneChip cartridges were washed and stained in the Affymetrix fluidics station following the EukGE-WS2 standard protocol (including Antibody Amplification).

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner3000 7G, using default parameters. The resulting images were analysed using GeneChip Operating Software v1.4 (GCOS1.4).

data_processing: “Absolute analysis” was performed for each chip with GCOS1.4 software using default parameters, scaling signal intensity global trimmed mean of all images to a value of 500.   Report files were extracted for each chip, and performance of labelled targets was evaluated on the basis of several values (scaling factor, background and noise values, % present calls, average signal value, etc).   Further data analysis was performed using GeneSpring GX v.7.3.1 (Agilent Technologies) a commercial software for analysis of microarrays data

source_name: Co-fractionated mRNA from human placenta

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

growth_protocol: HEK293 cell line was purchased from Interlab Cell Line Collection (ICLC; http://www.iclc.it). HEK293 cells were cultured in Dulbecco's modified Eagle’s medium (Euroclone) supplemented with 10% fetal bovine serum, 2 mM L-Glutamine and 0.1 g/ml penicillin/streptomycin. cDNA expression vectors were transiently transfected with Lipofectamine 2000 (Invitrogen), according to the manufacturer’s instructions. Transfected cells were harvested 2 to 3 days after transfection, as indicated

extract_protocol: QIAGEN extraction of co-precipitated or  co-fractionated RNA was performed according to the manufacturer's instructions.


title: epic sample 26: control


title: epic sample 24: bronchial carcinoma


title: epic sample 22: bronchial carcinoma


title: Tino-his HEK293 overespressing

description: In the in vivo approach, we have transiently transfected HEK293 cells with a His-tagged Tino expressing construct and isolated Tino target mRNAs by immunoprecipitation (IP) assays carried out under conditions preserving mRNA-protein complex integrity.

source_name: Co-precipitated mRNA from HEK293 cells

tag: Co-precipitated mRNA from HEK293 cells


title: epic sample 1: bronchial carcinoma


title: epic sample 8: bronchial carcinoma


title: cosmos sample 20: control


title: cosmos sample 19: bronchial carcinoma


title: epic sample 14: control


title: cosmos sample 18: control


title: epic sample 20: control


title: cosmos sample 24: control


title: epic sample 13: control


title: epic sample 10: bronchial carcinoma


title: epic sample 23: control


title: cosmos sample 15: bronchial carcinoma


title: epic sample 6: control


title: cosmos sample 16: bronchial carcinoma


title: cosmos sample 13: bronchial carcinoma


title: epic sample 4: bronchial carcinoma


title: No protein Filter Binding

description: Negative control

tag: Co-fractionated mRNA from human placenta


title: epic sample 2: control


title: mock HEK293 overexpressing

description: This sample is the negative control using mock HEK293 cells.

source_name: Co-fractionated mRNA from HEK293 cells

tag: Co-fractionated mRNA from HEK293 cells


title: cosmos sample 23: control


title: cosmos sample 17: control


title: cosmos sample 22: control


title: cosmos sample 21: bronchial carcinoma


title: cosmos sample 11: bronchial carcinoma


title: EPIC case #2: bronchial carcinoma


title: cosmos sample 14: control


title: cosmos sample 12: bronchial carcinoma


title: Fall-Winter cDNA pool replicate 2

status: Public on Jan 31 2010

city: Halifax

first: Kathryn

middle: Vanya

last: Ewart

state: NS

address: 1411 Oxford St.

department: Marine Bioactives Group

country: Canada

institute: NRC Institute for Marine Biosciences

description:
technical replicate 2 of 3
For each replicate chip (47d1, 48d2 and 49d3) lowess normalized background subtracted median spot intensities are presented as well as Ch2/Ch1 ratios (Winter/Fall) as both arithmetic and log base 2 transformed values.

hyb_protocol: Pre-hybridization of the arrays was performed in O-ring sealed aluminum chambers using a solution of final concentration 5X SSC, 0.1% SDS and 0.2% BSA (fraction V) aliquoted beneath a spaced coverslip (Lifterslip) at 49°C for 45 min, after which the arrays were washed in water twice, and then dried by centrifugation.  A cDNA hybridization solution consisting of the two cDNA reactions described above, a GFP gridding assist spike, LNA dT blocker and 2X formamide hybridization buffer #7 was introduced (after denaturation at 80°C for 10 min and cooling to 49°C) beneath a fresh Lifterslip placed over the prepared, pre-warmed (to 49°C) arrays, which were then sealed in a humidified chamber for incubation at 49°C overnight.

scan_protocol: Microarrays were scanned at 532 and 635 nm using the ScanArray 5000XL (Packard BioChip Technologies) at a resolution of 10 μm with channels balanced based on line scans through representative groups of spots.

data_processing: Spot intensity values were obtained and normalized using the QuantArray (Packard) microarray analysis software and data were exported to Excel for further analysis.  Genes with intensity values ≥ 325 fluorescence units, with a coefficient of variation ≤ 30% within all like-named spots on the array and based upon data from a minimum of two technical replicates, were considered as suitable for inclusion in the analysis.  In the set of genes meeting the criteria, those for which the mean January expression value was 2-fold or greater or 0.5-fold or less of their October values were identified as differentially regulated (log base 2 ratios greater than 1 or less than -1).

label: Alexa 546

organism: Osmerus mordax

source_name: pooled Fall total RNA

label_protocol: Labelling of cDNAs employing the 3DNA Array 900 chemistry (Genisphere) for two colour analysis using the Alexa Fluor 546 and 647 kits was followed essentially as described by the manufacturers, with minor modifications.  For each pool of total RNA, 2 µg of RNA was combined with 1 µL of the fluor-specific RT primer and nuclease-free water to make 6 µL, after denaturing at 80°C for 5 min and cooling on ice, 4.5 µL of a master mix consisting of 5 µL 5x Superscript first strand buffer, 2.5 µL DTT, 1.25 µL Superase-in RNase inhibitor and 1.25 µL Superscript III enzyme (200 units) was added and after mixing and brief centrifugation, the reaction was incubated at 50°C for 2 h.  The reaction was stopped by the addition of 1 µL 1 M NaOH and after incubation at 65°C for 10 min to hydrolyse the RNA, the reaction was neutralized by adding 1.2 µL of 2 M Tris-HCl, pH 7.5, for a final reaction volume of 12.7 µL for each fluor.

growth_protocol: Rainbow smelt were wild-caught in Newfoundland, Canada, and maintained at the Memorial University of Newfoundland Ocean Sciences Centre (OSC) on flow-through water at ambient temperature.

extract_protocol: Liver (30-50 mg) was homogenized in 1 mL TRIzol reagent following the manufacturer’s protocol (Invitrogen) using an RNaseZap (Ambion)-treated Polytron homogenizer (Brinkmann) for 15-20 s on high speed.  The tip was rinsed between samples with a series of washes beginning with 0.1% SDS in DEPC water and ending with DEPC water. After air-drying, the total RNA pellet was re-dissolved in nuclease-free water (Sigma-Aldrich) and treated with RNAsecure reagent (Ambion).  RNA quality was assessed by electrophoresis on 2% agarose gels in TBE buffer and quantified using a NanoDrop Spectrophotometer (Thermo Fisher).

treatment_protocol: Livers were obtained from three male rainbow smelt held at the OSC on October 20th, 2000, when the water temperature was 10ºC and from three male smelt on January 23rd, 2001, when the temperature was 1ºC.  Excised livers were treated with RNALater (Ambion) and subsequently stored on dry ice for transport and for the long-term at -80°C

tag: gender

value: male

value: liver

tag: collection month

value: October

tag: water temperature

label: Alexa 647

source_name: pooled Winter total RNA

value: January


title: cosmos sample 6: bronchial carcinoma


title: Fall-Winter cDNA pool replicate 3

description:
technical replicate 3 of 3
For each replicate chip (47d1, 48d2 and 49d3) lowess normalized background subtracted median spot intensities are presented as well as Ch2/Ch1 ratios (Winter/Fall) as both arithmetic and log base 2 transformed values.


title: cosmos sample 9: bronchial carcinoma


title: cosmos sample 4: control


title: J5RH_2 with array type Medicago from Affymetrix

status: Public on Jan 29 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: The biological question is the study of root development adaptation to external nitrogen availability. One of the typical responses to low N provision consists on an increased root branching which promotes soil exploration. In order to differentiate between genes specifically involved in nitrate response and genes of root development, we had performed experiments on both a wild type and a mutant affected in root architecture, both supplied with two different levels of nitrate. Global gene expression profiling of root cells using microarray analysis will be conducted to identify genes expressed during root branching. First, analysing the differential gene expression between the wild type and the mutant both at low and high level of nitrate, we will identify genes of root development but also genes specifically involved in nitrate response. Then, additional comparisons will concern the modifications of wild type and mutant gene expression between the two levels of nitrate. These genes will be compared to those found to be expressed in the wild type roots under submitted to various nitrogen sources (Ruffel et al., 2008). All together these results will allow us to determine which genes, among the firstly underlined, are specifically involved in root development. The kinetics of expression in different tissues of the most relevant of these genes will be further analysed by qRT-PCR.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

source_name: J5, 10mM KNO3

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: root - Seeds are cold-treated at 4°C in agar-agar for 4 days, then placed in growth chamber in the dark at 20°C for germination during another 4 days. Individual seedlings are then transferred onto hydroponic culture tanks. Seedlings growing conditions: 8h/16h light/dark cycle, 300 µmol m-2 s-1 PAR light intensity; 23°C/19°C day/night temperature, 60% hygrometry

treatment_protocol: Name: HN - growth conditions - azote concentration, kno3 concentration:quantity 10mM time 10day.

value: Jemalong

tag: genotype

value: J5 (WT)

value: root

value: 10 days

tag: treatment

value: 10mM KNO3


title: Fall-Winter cDNA pool replicate 1

description:
technical replicate 1 of 3
For each replicate chip (47d1, 48d2 and 49d3) lowess normalized background subtracted median spot intensities are presented as well as Ch2/Ch1 ratios (Winter/Fall) as both arithmetic and log base 2 transformed values.


title: cosmos sample 2: control


title: 185H_2 with array type Medicago from Affymetrix

source_name: tr185, 10mM KNO3

value: tr185 (mutant)

tag: age


title: cosmos sample 1: control


title: cosmos sample 5: bronchial carcinoma


title: cosmos sample 3: bronchial carcinoma


title: cosmos sample 10: bronchial carcinoma


title: cosmos sample 7: control


title: cosmos sample 8: bronchial carcinoma


title: Patient without BC #3: control


title: Laer, pretreat with water, control, Biological Rep 1

status: Public on Jan 15 2010

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

institute: The Sainsbury Laboratory

description: Gene expression data from Arabidopsis leaves pre-treated with water

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: background corrected using RMA, quantile normalized, values summarised by median-polish

source_name: leaf discs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in SANYO cabinets under short day conditions (8h light, 16h dark), 120μE light intensity.

extract_protocol: RNA was extracted using Qiagen Rneasy plant mini kit according to the manufacturer's instructions.

treatment_protocol: Five weeks old short day grown Arabidopsis leaf discs were used to treat with 100nM flg22 and samples were collected after 1 hour and 2 hour time points. For Alternaria brassicicola, five weeks old plants were drop inoculated with 4x 5µl droplets of Alternaria brassicicola spores (5x105 spores/ml) and samples were collected 3 days post inoculation. Five weeks old plants were infiltrated with Pst DC3000 (2x105cfu/ml) bacteria and samples were collected after 12 hours post infiltration. For methyl jasmonate treatments, five weeks old plants were sprayed with 10µM Methyl Jasmonate solution, covered with plastic bags and samples were collected after one hour.

value: leaf discs


title: Laer, pretreat with GA, Flg22, 2h, Biological Rep 1

description: Gene expression data from Arabidopsis leaves pre-treated with GA and induced with flg22


title: Laer, pretreat with GA, Flg22, 2h, Biological Rep 2


title: Laer, pretreat with GA, Flg22, 1h, Biological Rep 2


title: Fat_LowRFI_calorierestricted_rep5

status: Public on Jan 10 2010

city: Ames

first: Sender

last: Lkhagvadorj

state: IA

address: 2255 Kildee

department: Animal Science

institute: Iowa State University

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

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

data_processing: Values are probe level measures that were summarized into probe set level expression measures using the "affy" package in R according to the MAS 5.0 algorithm

organism: Sus scrofa

source_name: Subcutaneous adipose tissue from low RFI pigs that went under caloric restriction for 8 days

label_protocol: cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: The pigs were fed ad libitum and contained at the Lauren Christian swine facility of Iowa State University. The animal was genotyped for MC4R variant and pigs with heterozygous genotypes were transferred to a clean animal facility for experiment.

extract_protocol: Total RNA was isolated from tissues by using the RNeasy Midi kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) based on the manufacturer's protocol.

treatment_protocol: Pigs with low RFI was fed at 80% of maintenance feed for 8 days.

tag: residual feed intake

value: low

tag: feed efficiency

value: high

value: 10th rib middle layer backfat

value: 6 months old

tag: breed

value: Yorkshire


title: Laer, pretreat with GA+JA, Flg22, 2h, Biological Rep 2

description: Gene expression data from Arabidopsis leaves pre-treated with GA+JA and induced with flg22

tag: tissue


title: Fat_HighRFI_calorierestricted_rep5

source_name: Subcutaneous adipose tissue from high RFI pigs that went under caloric restriction for 8 days

treatment_protocol: Pigs with high RFI was fed at 80% of maintenance feed for 8 days.


title: Laer, pretreat with GA, Flg22, 2h, Biological Rep 3


title: Laer, pretreat with GA, Flg22, 0h, Biological Rep 3


title: J5RH_3 with array type Medicago from Affymetrix

tag: cultivar


title: Fat_LowRFI_adlibitum_rep5

source_name: Subcutaneous adipose tissue from low RFI pigs that were fed ad libitum

treatment_protocol: Pigs with low RFI was fed ad libitum for 8 days.


title: Fat_HighRFI_adlibitum_rep5

source_name: Subcutaneous adipose tissue from high RFI pigs that were fed ad libitum

treatment_protocol: Pigs with high RFI was fed ad libitum for 8 days.


title: 185BN_2 with array type Medicago from Affymetrix

source_name: tr185, 1mM KNO3

treatment_protocol: Name: BN - growth conditions - azote concentration, kno3 concentration:quantity 1mM time 10day.

value: 1mM KNO3


title: 185H_1 with array type Medicago from Affymetrix


title: Patient without BC #7: control

tag: control


title: Laer, Flg22(Agrobacterium), 2h, Biological Rep 3

description: Gene expression data from Arabidopsis leaves treated with flg22


title: Laer, treat with paclobutrazol (PAC), Biological Rep 1

description: Gene expression data from Arabidopsis leaves treated with paclobutrazol


title: 185H_3 with array type Medicago from Affymetrix


title: Laer, pretreat with JA, Flg22, 0h, Biological Rep 2

description: Gene expression data from Arabidopsis leaves pre-treated with JA and induced with flg22


title: Laer, pretreat with GA+JA, Flg22, 2h, Biological Rep 1


title: 185BN_3 with array type Medicago from Affymetrix


title: J5RBN_2 with array type Medicago from Affymetrix

source_name: J5, 1mM KNO3


title: J5RBN_1 with array type Medicago from Affymetrix


title: Laer, pretreat with GA, Flg22, 1h, Biological Rep 3


title: 185BN_1 with array type Medicago from Affymetrix


title: J5RBN_3 with array type Medicago from Affymetrix


title: J5RH_1 with array type Medicago from Affymetrix


title: Liver_LowRFI_calorierestricted_rep5

source_name: Liver from low RFI pigs that went under caloric restriction for 8 days

value: Liver


title: Liver_LowRFI_adlibitum_rep5

source_name: Liver from low RFI pigs that were fed ad libitum


title: Liver_HighRFI_adlibitum_rep5

source_name: Liver from high RFI pigs that were fed ad libitum


title: Fat_HighRFI_adlibitum_rep4


title: Fat_LowRFI_adlibitum_rep4


title: Liver_HighRFI_adlibitum_rep4


title: Fat_LowRFI_calorierestricted_rep3


title: Fat_HighRFI_calorierestricted_rep4


title: Fat_LowRFI_calorierestricted_rep4


title: Liver_LowRFI_adlibitum_rep3


title: Liver_HighRFI_calorierestricted_rep4

source_name: Liver from high RFI pigs that went under caloric restriction for 8 days


title: Liver_LowRFI_calorierestricted_rep4


title: Fat_LowRFI_adlibitum_rep3


title: Fat_HighRFI_adlibitum_rep3


title: Liver_HighRFI_calorierestricted_rep3


title: Liver_LowRFI_adlibitum_rep2

growth_protocol: The pigs were fed ad libitum and contained at the Lauren Christian swine facility of Iowa State University. The animal was genotyped for MC4R variant and pigs with specific genotypes were transferred to a clean animal facility for experiment.


title: Liver_HighRFI_adlibitum_rep2

growth_protocol: The pigs were fed ad libitum and contained at the Lauren Christian swine facility of Iowa State University. The animal was genotyped for MC4R D298N variant and pigs with heterozygous genotypes were transferred to a clean animal facility for experiment.


title: Liver_HighRFI_adlibitum_rep3


title: Liver_LowRFI_adlibitum_rep4


title: Liver_LowRFI_calorierestricted_rep2


title: Fat_HighRFI_calorierestricted_rep2


title: Liver_HighRFI_calorierestricted_rep5


title: Liver_LowRFI_calorierestricted_rep3


title: Liver_HighRFI_calorierestricted_rep2


title: Fat_HighRFI_calorierestricted_rep3


title: Fat_LowRFI_adlibitum_rep2


title: Fat_LowRFI_calorierestricted_rep1


title: Fat_HighRFI_adlibitum_rep2


title: Fat_LowRFI_calorierestricted_rep2


title: Fat_LowRFI_adlibitum_rep1


title: Fat_HighRFI_calorierestricted_rep1


title: Fat_HighRFI_adlibitum_rep1


title: Liver_HighRFI_adlibitum_rep1

data_processing: Values are probe level measures that were summarized into probe set level expression measures using the "affy" packagein R according to the MAS 5.0 algorithm


title: Liver_LowRFI_adlibitum_rep1


title: Liver_HighRFI_calorierestricted_rep1


title: Liver_LowRFI_calorierestricted_rep1


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 2

status: Public on Jan 09 2010

city: Huntington

first: Yulia

last: Dementieva

state: WV

address: One John Marshall Drive

department: Mathematics

institute: Marshall University

description: Biological replicate 2 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP

hyb_protocol: 825 ng of each Cy3- and Cy5- labeled cRNAs were combined and hybridized onto Agilent Whole Mouse Genome Array for 17 hours at 65 degrees C

scan_protocol: Scanned on Agilent DNA Microarray Scanner

data_processing: Feature intensities, lowess-normalized, were extracted using Agilent Feature Extraction Software

source_name: Activated Murine CD4 T cells without VIP

label_protocol: 250 ng of total RNA was used as a starting material with QuickAmp labeling kit (Agilent) and Cy3-Ctp and Cy5-CTP from Perkin Elmer using modified QuickAmp protocol (Syed and Threadgill, Biotechniques 41:685-686, 2006)

growth_protocol: Mouse splenic CD4 T cells were isolated from 6-32 weeks old males and females by mincing five to ten spleens (per sample) in PBS at RT and passing through 30 um sieve.  Erythrocytes were lysed and cells resuspended in 93 ul of PBS / 0.5% BSA with 7 ul of anti-mouse CD4 magnetic beads at 4-8 degrees C for 20 min and than were purified on Miltenyia Auto-MACS instrument

extract_protocol: Total RNA was isolated using Rneasy mini columns (Qiagen) with on-column DNAse I treatment

value: VIP untreated

tag: strain

value: splenic CD4 T cells

source_name: Activated Murine CD4 T cells with VIP

value: VIP treated


title: WCFS1_Wt (glc) vs Wt (glc)

status: Public on Jan 01 2010

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

description: Wt (glc) vs Wt (glc)

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used

organism: Lactiplantibacillus plantarum WCFS1

source_name: Wt

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer 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 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: A defined medium for lactobacilli (DML) (36; Møretrø et al 1998) was used in the growth experiments, with the following modification: The succinate buffer was replaced with 0.1 M MES buffer, and 12 mM glucose or 12 mM ribose was used as carbon source. Gro

extract_protocol: Total RNA was extracted from exponentially growing L. plantarum strains (OD600 of 0.65) using the RNeasy Protect Bacteria Mini Prep Kit (Qiagen). Samples (3 ml) were collected and added to RNA Protect Bacteria Reagent (Qiagen) (6 ml), vortexed for 5 s, in

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

value: wild-type

tag: strain duplicate (a or b)

value: B

tag: carbon source

value: Glucose

value: A


title: WCFS1_Wt (rib) vs cggRKO (rib)

description: Wt (rib) vs cggRKO (rib)

value: Ribose

source_name: cggRKO

value: cggR-mutant


title: WCFS1_cggRKO (rib) vs cggRKO (rib)

description: cggRKO (rib) vs cggRKO (rib)


title: WCFS1_Wt (rib) vs Wt (rib)

description: Wt (rib) vs Wt (rib)


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 1

description: Biological replicate 1 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 4

description: Biological replicate 4 of 6, resting splenic CD4 T cells with and without VIP

source_name: Resting Murine CD4 T cells without VIP

source_name: Resting Murine CD4 T cells with VIP


title: WCFS1_Wt (rib) vs cggR+ (rib)

description: Wt (rib) vs cggR+ (rib)

source_name: cggR+


title: WCFS1_cggRKO (rib) vs Wt (rib)

description: cggRKO (rib) vs Wt (rib)


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 6

description: Biological replicate 6 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 5

description: Biological replicate 5 of 6, resting splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 3

description: Biological replicate 3 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 1

description: Biological replicate 1 of 6, resting splenic CD4 T cells with and without VIP


title: WCFS1_cggRKO (glc) vs cggRKO (rib), B

description: cggRKO (glc) vs cggRKO (rib)


title: WCFS1_cggR+ (rib) vs cggRKO (rib)

description: cggR+ (rib) vs cggRKO (rib)


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 3

description: Biological replicate 3 of 6, resting splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 4

description: Biological replicate 4 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Activated, Replicate 5

description: Biological replicate 5 of 6, acivated (PMA/ionomycin) splenic CD4 T cells with and without VIP


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 6

description: Biological replicate 6 of 6, resting splenic CD4 T cells with and without VIP


title: WCFS1_cggRKO (glc) vs cggRKO (glc)

description: cggRKO (glc) vs cggRKO (glc)


title: spleenocytes with VIP vs. spleenocytes without VIP, Resting, Replicate 2

description: Biological replicate 2 of 6, resting splenic CD4 T cells with and without VIP


title: WCFS1_cggR+ (rib) vs cggR+ (glc)

description: cggR+ (rib) vs cggR+ (glc)


title: WCFS1_cggRKO (glc) vs Wt (glc), B

description: cggRKO (glc) vs Wt (glc)


title: WCFS1_Wt (glc) vs cggR+ (glc)

description: Wt (glc) vs cggR+ (glc)


title: WCFS1_cggRKO (glc) vs Wt (glc), A

description: cggRKO (glc) vs Wt (glc)


title: Lactate_R_60

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. Normalization across samples was performed by total signal correction

organism: Lactiplantibacillus plantarum

source_name: Lactate_R t=0

growth_protocol: Cultures were grown in batch fermentation on a chemically defined medium untill an optical density of 1.0 before being stressed with Na-L-lactate

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction

tag: time point

source_name: Lactate_R t=60 min

value: 60 min


title: Lactate_R_15

source_name: Lactate_R t=15 min

value: 15 min


title: WCFS1_cggR+ (glc) vs cggRKO (glc)

description: cggR+ (glc) vs cggRKO (glc)


title: Lactate_L_30

source_name: Lactate_L t=0

source_name: Lactate_L t=30 min

value: 30 min


title: NC8_Wt (glc) vs cggRKO (glc)

description: Wt (glc) vs cggRKO (glc)


title: NC8_cggRKO (glc) vs cggRKO (glc)

description: cggRKO (glc) vs cggRKO (glc)


title: NC8_cggR+ (glc) vs Wt (glc)

description: cggR+ (glc) vs Wt (glc)


title: NC8_Wt (rib) vs Wt (glc)

description: Wt (rib) vs Wt (glc)


title: WCFS1_Wt (rib) vs Wt (glc)

description: Wt (rib) vs Wt (glc)


title: NC8_Wt (rib) vs Wt (rib)

description: Wt (rib) vs Wt (rib)


title: NC8_Wt (glc) vs Wt (glc)

description: Wt (glc) vs Wt (glc)


title: Lactate_L_15

source_name: Lactate_L t=15 min


title: NC8_cggRKO (rib) vs cggRKO (rib)

description: cggRKO (rib) vs cggRKO (rib)


title: NC8_cggRKO (rib) vs Wt (rib)

description: cggRKO (rib) vs Wt (rib)


title: WCFS1_cggRKO (glc) vs cggRKO (rib), A

description: cggRKO (glc) vs cggRKO (rib)


title: Lactate_L_60

source_name: Lactate_L t=60 min


title: NC8_cggRKO (rib) vs cggRKO (glc)

description: cggRKO (rib) vs cggRKO (glc)


title: NC8_Wt (rib) vs cggRKO (rib)

description: Wt (rib) vs cggRKO (rib)


title: NC8_cggRKO (glc) vs Wt (glc)

description: cggRKO (glc) vs Wt (glc)


title: Lactate_R_30

source_name: Lactate_R t=30 min


title: NC8_cggRKO (glc) vs cggRKO (rib)

description: cggRKO (glc) vs cggRKO (rib)