title: 0.1% BSA-treated SMCs rep2

status: Public on Dec 31 2012

type: RNA

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road

department: Molecular Physiology and Biological Physics

country: USA

institute: University of Virginia

description: Gene expression data from vehicle-treated rat aortic smooth muscle cells

hyb_protocol: 10 ug of cRNA was hybridized for 16 hours on Affymetrix rat 230 2.0 GeneChips and stained using Affymetrix Fluidics Station 450 according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and between-group fold changes were calculated using Affymetrix Data Mining Tool 3.0.  Local pooled error testing was performed by the University of Virginia Gene Expression Open Source System (GEOSS) software.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat aortic smooth muscle cells treated with vehicle (.1% BSA)

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

growth_protocol: Smooth muscle cells were grown in 10% serum-containing media for 5 days, then switched to serum-free media for 3 days prior to treatment for 24 hours.

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Cells treated with either vehicle (.1% BSA) or IL-1b (2.5 ng/mL) for 24 hours.

tag: genotype

value: Sprague-Dawley

tag: cell type

value: aortic smooth muscle cell

tag: agent

value: BSA


title: Yeast cells harboring specific members of the cytosolic Hsp70-Ssa family: Ssa3

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

country: Japan

institute: TORAY Industries, Inc.

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning with 100% laser power and PMT at which the brightest spot intensity would not be saturated.

data_processing: Array images were analyzed with GenePix ver5 (Molecular Device). The background value which is the average of blank spots are subtrated from each gene datum. Globally normalization was adapted to the whole series.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae strain G402

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: 1.5ml of an exponentially growing 5ml yeast culture was used to isolate total RNA. RNA was extracted using the Qiagen RNeasy mini kit exactly as recommended by the manufacturer.

tag: strain

value: quadruple ssa1/2/3/4 deletion expressing Ssa3 ectopically from plasmid


title: Yeast cells harboring specific members of the cytosolic Hsp70-Ssa family: Ssa1

value: quadruple ssa1/2/3/4 deletion expressing Ssa1 ectopically from plasmid


title: SJRH30 cells at time 6h, biological rep2

city: Bunkyo-ku

first: Soichi

last: Ogishima

state: Tokyo

address: Yushima 1-5-45

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Gene expression data from SJRH30 cells under hypoxia.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip HG U133A2.0 array (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R using Bioconductor packages and global scaling as normalization by RMA function. These data were then log2-transformed.

organism: Homo sapiens

source_name: SJRH30 cells at 6 h from starting 1 % hypoxia

label_protocol: Total RNA (10 µg) was used to synthesize double-stranded cDNA and cRNA using a MessageAmpTM II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: The human rhabdomyosarcoma cell line SJRH30 (ATCC, CRL-2061) was cultured and maintained in RPMI 1640 medium (Gibco BRL Life Technologies, Gaithersburg, MD) supplemented with 10% fetal bovine serum, penicillin (50 IU/ml), and streptomycin sulfate (50 μg/ml).

extract_protocol: Extraction of total RNA was performed by using RNeasy® Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: One percent hypoxia was delivered in a hypoxic chamber MCO-5U (SANYO, Gifu, Japan) gassed with 94% N2 and 5% CO2. To observe the temporal gene expression, we treated cells for 6, 12 and 24 h under a 1% hypoxic condition.

value: muscle fibroblasts

tag: cell line


title: 0.1% BSA-treated SMCs rep1


title: Yeast cells harboring specific members of the cytosolic Hsp70-Ssa family: Ssa2

value: quadruple ssa1/2/3/4 deletion expressing Ssa2 ectopically from plasmid


title: SJRH30 cells at time 6h, biological rep1


title: Yeast cells harboring specific members of the cytosolic Hsp70-Ssa family: Ssa4

value: quadruple ssa1/2/3/4 deletion expressing Ssa4 ectopically from plasmid.


title: SJRH30 cells at time 12h, biological rep2

source_name: SJRH30 cells at 12 h from starting 1 % hypoxia


title: IL-1b (2.5 ng/mL) treated SMCs rep2

description: Gene expression data from IL-1b-treated rat aortic smooth muscle cells

source_name: Rat aortic smooth muscle cells treated with IL-1b (2.5 ng/mL)


title: SJRH30 cells at time 0h, biological rep1

description: Gene expression data from SJRH30 cells before starting hypoxia.

source_name: SJRH30 cells before starting hypoxia


title: SJRH30 cells at time 24h, biological rep1

source_name: SJRH30 cells at 24 h from starting 1 % hypoxia


title: SJRH30 cells at time 12h, biological rep1


title: Laval_Rupert_hybrid individual_23

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

country: Canada

institute: Laval university

hyb_protocol: Microarray were hybridized using Cy3/Al647 dyes (Genisphere) as detailed in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray scanner (Packard BioScience). Spots were localized and quantified with the QuantArray 3.0 software, using the histogram quantification method and keeping the mean value of intensity for each spot.

data_processing: Data were exported in text format and were analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000)

organism: Salvelinus fontinalis

source_name: Frozen individual in toto

label_protocol: For each sample, 12µg total RNA was retro-transcribed and the cDNA samples labelled using Genisphere 3DNA Array 50 Kit, Invitrogen’s Superscript II retro-transcriptase and Cyanine3 and Alexa 647 fluorescent dyes (Genisphere), following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

growth_protocol: Whole individuals were stored at -80°C prior to any sampling

extract_protocol: Total RNA was extracted with PureLink TM Micro-to-Midi Total RNA Purification System Kit and then treated using DNase I, Amplification Grade (1 unit/μl) (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Total RNA were further purified by ultra-centrifugation using microcon (Millipore) spin columns. The 96 deep-frozen individuals were extracted in toto to obtain the expression of whole transcriptome. Quality and integrity of the total RNA was controlled with an Experion Automated Electrophoresis Station and RNA HighSens Chips (Biorad, Hercules, CA). Total RNA was stored in pure water supplemented with Superase-In™ RNase Inhibitor (Ambion) at -80°C.

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling

tag: hybrid

tag: hybrid individual

tag: developmental stage

value: One sexually undifferentiated individual - sampling at 15 weeks after exogenous feeding


title: IL-1b (2.5 ng/mL) treated SMCs rep1


title: Laval_Rupert_hybrid individual_24


title: SJRH30 cells at time 0h, biological rep2


title: Rupert_Laval_hybrid individual_24


title: SJRH30 cells at time 24h, biological rep2


title: Laval_Rupert_hybrid individual_22


title: Rupert_Laval_hybrid individual_23


title: Rupert_Laval_hybrid individual_20


title: Laval_Rupert_hybrid individual_21


title: Rupert_Laval_hybrid individual_21


title: Laval_Rupert_hybrid individual_20


title: Laval_Rupert_hybrid individual_19


title: Rupert_Laval_hybrid individual_19


title: Laval_Rupert_hybrid individual_16

value: One sexually undifferentiated individual - sampling at yolk sac resorption stage


title: Rupert_Laval_hybrid individual_17


title: Rupert_Laval_hybrid individual_16


title: Rupert_Laval_hybrid individual_15


title: Laval_Rupert_hybrid individual_15


title: Rupert_Laval_hybrid individual_12


title: Laval_Rupert_hybrid individual_12


title: Rupert_Laval_hybrid individual_14


title: Laval_Rupert_hybrid individual_10


title: Laval_Rupert_hybrid individual_14


title: Laval_Rupert_hybrid individual_11


title: Rupert_Laval_hybrid individual_13


title: Rupert_Laval_hybrid individual_11


title: Laval_Rupert_hybrid individual_9


title: Rupert_Laval_hybrid individual_10


title: Rupert_Laval_hybrid individual_18


title: Laval_Rupert_hybrid individual_17


title: Rupert_Laval_hybrid individual_22


title: Laval_Rupert_hybrid individual_18


title: Rupert_Laval_hybrid individual_9


title: Laval_Rupert_hybrid individual_13


title: Rupert_Laval_hybrid individual_8

value: One sexually undifferentiated individual - sampling at Hatching


title: Laval_Rupert_hybrid individual_8


title: Laval_Rupert_hybrid individual_7


title: Rupert_Laval_hybrid individual_6


title: Rupert_Laval_hybrid individual_7


title: Laval_Rupert_hybrid individual_5


title: Rupert_Laval_hybrid individual_4


title: Rupert_Laval_hybrid individual_5


title: Laval_Rupert_hybrid individual_3


title: Laval_Rupert_hybrid individual_4


title: Rupert_Laval_hybrid individual_3


title: Laval_Rupert_hybrid individual_6


title: Laval_Domestic_hybrid individual_23


title: Domestic_Laval_hybrid individual_24


title: Laval_Rupert_hybrid individual_1


title: Domestic_Laval_hybrid individual_22


title: Rupert_Laval_hybrid individual_2


title: Laval_Domestic_hybrid individual_22


title: Domestic_Laval_hybrid individual_21


title: Laval_Domestic_hybrid individual_21


title: Laval_Domestic_hybrid individual_20


title: Laval_Rupert_hybrid individual_2


title: Domestic_Laval_hybrid individual_20


title: Domestic_Laval_hybrid individual_23


title: Laval_Domestic_hybrid individual_24


title: Laval_Domestic_hybrid individual_17


title: Laval_Domestic_hybrid individual_16


title: Domestic_Laval_hybrid individual_19


title: Laval_Domestic_hybrid individual_15


title: Laval_Domestic_hybrid individual_19


title: Domestic_Laval_hybrid individual_15


title: Laval_Domestic_hybrid individual_18


title: Domestic_Laval_hybrid individual_13


title: Domestic_Laval_hybrid individual_17


title: Laval_Domestic_hybrid individual_9


title: Domestic_Laval_hybrid individual_16


title: Laval_Domestic_hybrid individual_13


title: Laval_Domestic_hybrid individual_12


title: Domestic_Laval_hybrid individual_12


title: Domestic_Laval_hybrid individual_9


title: Domestic_Laval_hybrid individual_7


title: Laval_Domestic_hybrid individual_10


title: Domestic_Laval_hybrid individual_8


title: Laval_Domestic_hybrid individual_14


title: Laval_Domestic_hybrid individual_8


title: Domestic_Laval_hybrid individual_6


title: Laval_Domestic_hybrid individual_7


title: Domestic_Laval_hybrid individual_14


title: Laval_Domestic_hybrid individual_5


title: Rupert_Laval_hybrid individual_1


title: Domestic_Laval_hybrid individual_10


title: Laval_Domestic_hybrid individual_6


title: Laval_Domestic_hybrid individual_4


title: Domestic_Laval_hybrid individual_5


title: Domestic_Laval_hybrid individual_11


title: Laval_Domestic_hybrid individual_3


title: Domestic_Laval_hybrid individual_2


title: Laval_Domestic_hybrid individual_11


title: Domestic_Laval_hybrid individual_4


title: Domestic_Laval_hybrid individual_3


title: Laval_Domestic_hybrid individual_2


title: Domestic_Laval_hybrid individual_18


title: Laval_Domestic_hybrid individual_1


title: RH9T testicular germ cell tumour

type: genomic

city: London

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: Hybridized to 10K SNP

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software: GOLF.

label: Biotin

molecule: genomic DNA

source_name: testicular germ cell tumour

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Fresh frozen samples were digested by Proteinase K and RNaseA. DNA was extracted from these samples using phenol/chroloform.

tag: comment

tag: tissue

value: testicular germ cell tumour


title: RH39T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 103T testicular germ cell tumour

description: Hybridized to 10K SNP


title: Domestic_Laval_hybrid individual_1


title: 93T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 104T testicular germ cell tumour

description: Hybridized to 10K SNP


title: RH48T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 106T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 38T testicular germ cell tumour

description: Hybridized to 10K SNP


title: RH26T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 109T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 80T testicular germ cell tumour

description: Hybridized to 10K SNP


title: RH30T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 29T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 23T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 40T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 107T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 86T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 19T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 30T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 46T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 94T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 105T testicular germ cell tumour

description: Hybridized to 10K SNP


title: RH53T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 56T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 18T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 15T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 9T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 79T testicular germ cell tumour

description: Hybridized to 10K SNP


title: Sc-2340-180-38-0308-3j_reanalysis

city: Castanet-Tolosan Cedex

first: Gwenola

last: Tosser-Klopp

address: Chemin de Borde-Rouge  BP 52627

country: France

institute: INRA

description: Reanalysis of GSM595692. A pig nylon micro-array is hybridized with a complex 33P labelled probe

hyb_protocol: A porcine microarray, published in GEO database as GPL3729, described by Bonnet et al. and produced by CRB-GADIE was used to hybridize the RNA samples. Micro-arrays were first hybridized with a 33P- labelled oligonucleotide sequence present in all PCR products to control the quality of the spotting process and to evaluate the amount of DNA in each spot. After stripping, the arrays were hybridized with 33P- labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H- reverse transcriptase (Invitrogen, Cergy-Pontoise, France). Each complex probe has been hybridized on membrane exposed 1, 3 or 7 days to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest, Courbevoie, France). The imaging plates were scanned thereafter with a phosphor imaging system at 25µm resolution (BAS-5000, Fujifilm, Raytest, Courbevoie, France).

scan_protocol: Hybridization images obtained from oligonucleotide and complex probes were quantified using the semi-automated AGScan software.

data_processing: Data exploration and analysis were performed using R software. The data coming from complex probes hybridization were analysed on the logarithmic scale. As a first step, negative spot with >7 intensity values were checked on images and replaced by the median of negative spots in case of obvious overshining effect or hybridization stain. Then, luciferase positive controls were removed and the correlations of the data from each membrane were examined intra condition. Hybridizations with a lower than 0.80 correlation coefficient were discarded. Spots with low signal value (below the average of empty spots + 3 standard deviations) were considered as unexpressed and were excluded from the analysis. Finally, the negative control spots were removed and the remaining data were centred for each membrane. Thereafter, a linear model was fitted on these data, using the lm procedure on follicle type factor and differentially expressed genes were selected with R statistical software. We tested the significance of the follicle class on the gene expression using t-test (Student test) followed by the Benjamini-Hochberg procedure controlling False Discovery Rate (FDR) for each cDNA. A set of predictive genes was identified using the balanced Random Forests approach (RFs). To obtain a stable selection of genes, fifty of balanced RFs were launched with each of 15000 trees. For each cDNA, the average value of its rank in the different random forest and was calculated for two criteria of importance calculated in the Random Forest procedure: Mean decrease Gini and Mean decrease accuracy. The average rank values were plotted in a decreasing order and groups of genes with homogeneous values were made. The most important cDNAs were selected as the group of genes having the higher average rank. Finally, the relevance of the two selections was evaluated via unsupervised hierarchical clustering using the Ward method and Euclidian distance with the R functions hclust and heatmap.

organism: Sus scrofa

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 61030

label_protocol: The arrays were hybridized with 33P-labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H-reverse transcriptase (Invitrogen, Cergy-Pontoise, France)

extract_protocol: Once ovaries collected, all visible antral follicles larger than 1 mm in diameter were isolated carefully using a binocular microscope. After dissection, follicle diameter was measured and each follicle was classified according to size, animal and follicular quality. Follicles measuring 1 to 2 mm were kept and granulosa cells were recovered from all individual follicles as described previously, and they were stored at -80°C until RNA extraction. For each follicle, a sample of granulosa cells was smeared on a histological slide, and then Feulgen stained to determine follicular quality by microscopic examination. Both healthy follicles (presence of mitosis and absence of pycnosis in granulosa cells), noted SHF, and atretic follicles (absence of mitosis and presence of pycnosis in granulosa cells), noted SAF, were kept for this study. RNA was extracted from granulosa cells according to the technique described by Chomczynski and Sacchi with minor modifications using pools of granulosa cells from the same follicle size class, status and the same animal. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies, Massy, France) and low-quality RNA preparations were discarded.

tag: annotation pf/mf/gf

value: PF

tag: date hybridation-genovul

tag: status

value: A


title: Sc-2327-180-32-0308-3j_reanalysis

description: Reanalysis of GSM595690. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52571


title: Bt-2333-180-34-0308-8j

description: A pig nylon micro-array is hybridized with a complex 33P labelled probe

hyb_protocol: A porcine microarray, published in GEO database as GPL3729, described by Bonnet et al. and produced by CRB-GADIE was used to hybridize the RNA samples. Micro-arrays were first hybridized with a 33P labelled oligonucleotide sequence present in all PCR products to control the quality of the spotting process, to evaluate the amount of DNA in each spot and the variations between membranes of the batch. After stripping, the arrays were hybridized with 33P labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H reverse transcriptase (Invitrogen, Cergy-Pontoise, France). Each complex probe has been hybridized onto one membrane exposed 1, 3 or 7 days to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest, Courbevoie, France). The imaging plates were scanned thereafter with a phosphor imaging system at 25µm resolution (BAS-5000, Fujifilm, Raytest, Courbevoie, France).

data_processing:
Data exploration and analysis were performed using R software. The data coming from complex probes hybridization were analysed on the logarithmic scale. As a first step, negative spot with >7 intensity values were checked on images and replaced by the median of negative spots in case of obvious overshining effect or hybridization stain. Then, luciferase positive controls were removed and the correlations of the data from each membrane were examined intra condition. Hybridizations with a lower than 0.80 correlation coefficient were discarded. Spots with low signal value (below the average of empty spots + 3 standard deviations) were considered as unexpressed and were excluded from the analysis. Finally, the negative control spots were removed and the remaining data were centred for each membrane.
Data exploration and analysis were performed using R software. The data coming from oligonucleotide probes were plotted and the correlation coefficients were calculated. The data coming from complex probes hybridization were analysed on the logarithmic scale. As a first step, negative spot with >7 intensity values were checked on images and replaced by the median of negative spots in case of obvious overshining effect or hybridization stain. Then, luciferase positive controls were removed and the correlations of the data from each membrane were examined intra condition. Hybridizations with a lower than 0.80 correlation coefficient were discarded. Spots with low signal value (below the average of empty spots + 3 standard deviations) were considered as unexpressed and were excluded from the analysis. Finally, the negative control spots were removed and the remaining data were centred for each membrane. This procedure was performed on different datasets:  - a global dataset, containing both species and all follicle stages membranes  - a pig dataset, containing pig species and all follicle stages membranes - a cattle dataset, containing cattle species and all follicle stages membranes. The normalised values coming from this procedure were used to generate: - an "atresia" normalised dataset, composed of Small atresia follicles noted SAF and Small healthy follicles noted SHF membranes for both species - a "development" normalised dataset, composed of Large healthy follicles noted LHF and SHF membranes for both species  - "pig-atresia" / "cattle-atresia" normalised datasets, composed of SAF and SHF membranes for pig/cattle species  - "pig-development" / "cattle-development" normalised datasets, composed of LHF and SHF membranes for pig/cattle species  - a global normalised dataset, composed of all the membranes. A linear model was fitted on the global normalised dataset, using the lm procedure on follicle type factor and differentially expressed genes were selected with R statistical software. We tested the significance of the follicle class on the gene expression using t-test (Student test) followed by the Benjamini-Hochberg procedure controlling False Discovery Rate (FDR) for each cDNA or the Bonferroni correction. Finally, the relevance of the selection was evaluated via unsupervised hierarchical clustering using the Ward method and Euclidian distance with the R functions hclust and heatmap. Thereafter, a linear model was fitted on each of the normalised datasets "atresia" and "development", using the lm procedure on follicle type and species factors and genes exhibiting a follicle type*species interactions were selected with R statistical software. We tested the significance of the interaction on the gene expression using F-test followed by the Benjamini-Hochberg procedure controlling False Discovery Rate (FDR) for each cDNA and the relevance of the selection was evaluated via unsupervised hierarchical clustering using the Ward method and Euclidian distance with the R functions hclust and heatmap. A set of predictive genes was identified using the balanced Random Forests approach (RFs) on the "pig-atresia",  "cattle-atresia" "pig- development" and "cattle-development" datasets. To obtain a stable selection of genes, fifty of balanced RFs were launched with each of 15000. For each cDNA, the average value of its rank in the different random forest and was calculated for two criteria of importance calculated in the Random Forest procedure: Mean decrease Gini and Mean decrease accuracy. The average rank values were plotted in a decreasing order and groups of genes with homogeneous values were made. The most important cDNAs were selected as the group of genes having the higher average rank. Finally, the relevance of the two selections was evaluated via unsupervised hierarchical clustering using the Ward method and Euclidian distance with the R functions hclust and heatmap.

organism: Bos taurus

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from cow abattoir1

extract_protocol: Once ovaries collected, all visible antral follicles larger than 1 mm in diameter for sows and 3 mm for cows were isolated carefully using a binocular microscope. After dissection, follicle diameter was measured and each follicle was classified according to its species and animal origins, its size, and follicular quality. Follicles were allocated to two size classes: small (noted SF, 1-2 mm for sows and 3-5mm for cows) and large (noted LF, 7-8 mm for sows and 15-20mm for cows). Granulosa cells were recovered from all individual follicles as described previously, and they were stored at -80°C until RNA extraction. For each follicle, a sample of granulosa cells was smeared on a histological slide, and then Feulgen stained to determine follicular quality by microscopic examination. Both healthy follicles (presence of mitosis and absence of pycnosis in granulosa cells) and atretic (absence of mitosis and presence of pycnosis in granulosa cells) were kept for this study. RNA was extracted from granulosa cells according to the technique described by Chomczynski and Sacchi with minor modifications using pools of granulosa cells from the same follicle size class and the same animal. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies, Massy, France) and low-quality RNA preparations were discarded.

tag: group

value: small follicles

value: A (atretic follicles)


title: Sc-2302-180-41-0308-3j_reanalysis

description: Reanalysis of GSM595687. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52495


title: Sc-2337-180-44-0308-3j_reanalysis

description: Reanalysis of GSM572689. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow60990

value: S


title: Sc-2337-180-44-0308-3j

hyb_protocol: Micro-arrays were first hybridized with a 33P-labelled oligonucleotide sequence present in all PCR products to control the quality of the spotting process and to evaluate the amount of DNA in each spot. After stripping, the arrays were hybridized with 33P-labelled complex probes synthesized from 5 µg of each RNA sample, using SuperScript II RNAse H-reverse transcriptase (Invitrogen, Cergy-Pontoise, France). Each complex probe has been hybridized on membrane exposed 1, 3 or 7 days to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest, Courbevoie, France).

scan_protocol: The imaging plates were scanned thereafter with a phosphor imaging system at 25µm resolution (BAS-5000, Fujifilm, Raytest, Courbevoie, France). Hybridization images obtained from oligonucleotide and complex probes were quantified using the semi-automated AGScan software.

data_processing: Data exploration and analysis were performed using R software. The data coming from complex probes hybridization were analysed on the logarithmic scale. As a first step, negative spot with >7 intensity values were checked on images and replaced by the median of negative spots in case of obvious overshining effect or hybridization stain. Then, luciferase positive controls were removed and the correlations of the data from each membrane were examined intra condition. Hybridizations with a lower than 0.80 correlation coefficient were discarded. Spots with low signal value (below the average of empty spots + 3 standard deviations) were considered as unexpressed and were excluded from the analysis. Finally, the negative control spots were removed and the remaining data were centred for each membrane.

extract_protocol: Once ovaries collected, all visible antral follicles larger than 1 mm in diameter for sows and 3 mm for cows were isolated carefully using a binocular microscope. After dissection, follicle diameter was measured and each follicle was classified according to size, animal and follicular quality. Follicles were allocated to two size classes: small (noted SF, 1-2 mm for sows and 3-5mm for cows) and large (noted LF, 7-8 mm for sows and 15-20mm for cows). Granulosa cells were recovered from all individual follicles and they were stored at -80°C until RNA extraction. For each follicle, a sample of granulosa cells was smeared on a histological slide, and then Feulgen stained to determine follicular quality by microscopic examination. Only healthy follicles (presence of mitosis and absence of pycnosis in granulosa cells) were kept for this study. RNA was extracted from granulosa cells according to the technique described by Chomczynski and Sacchi with minor modifications using pools of granulosa cells from the same follicle size class and the same animal. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies, Massy, France) and low-quality RNA preparations were discarded.

value: S (healthy follicles)


title: Sc-2303-180-07-0308-3j

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52568


title: Sc-2338-180-08-0308-3j_reanalysis

description: Reanalysis of GSM572690. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Bt-2345-0308_corr

source_name: Total RNA extracted from a pool of 15 to 20 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 401

value: GF

value: large follicles


title: Sc-2304-180-54-0308-3j


title: Bt-2321-180-36-0308-8j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 5868


title: Bt-2322-180-20-0308-7j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 9936


title: Sc-2302-180-41-0308-3j


title: Sc-2313-180-24-0308-3j_reanalysis

description: Reanalysis of GSM572682. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow52499


title: Sc-2339-180-03-0308-3j


title: Sc-2336-180-35-0308-3j_reanalysis

description: Reanalysis of GSM572688. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow61030


title: Bt-2335-0308_corr

source_name: Total RNA extracted from a pool of 15 to 20 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 5868


title: Sc-2289-180-43-0308-3j_reanalysis

description: Reanalysis of GSM572679. A pig nylon micro-array is hybridized with a complex 33P labelled probe

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow52495


title: Sc-2290-180-45-0308-3j

source_name: Total RNA extracted from a pool of 1 to 2 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52499


title: Sc-2325-180-40-0308-3j_reanalysis

description: Reanalysis of GSM572685. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Sc-2339-180-03-0308-3j_reanalysis

description: Reanalysis of GSM595691. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Sc-2338-180-08-0308-3j


title: Sc-2303-180-07-0308-3j_reanalysis

description: Reanalysis of GSM595688. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Sc-2340-180-38-0308-3j


title: Bt-2310-180-27-0308-8j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 1990


title: Sc-2304-180-54-0308-3j_reanalysis

description: Reanalysis of GSM595689. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Sc-2290-180-45-0308-3j_reanalysis

description: Reanalysis of GSM595686. A pig nylon micro-array is hybridized with a complex 33P labelled probe


title: Sc-2327-180-32-0308-3j


title: Bt-2297-180-37-0308-8j


title: Bt-2334-180-02-0308-8j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as atretic using microscopic examination after Feulgen staining of some granulosa cells, originating from cow abattoir3


title: Sc-2336-180-35-0308-3j


title: Sc-2330-180-30-0308-3j

source_name: Total RNA extracted from a pool of 7 to 8 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52571


title: Sc-2306-180-13-0308-3j

source_name: Total RNA extracted from a pool of 7 to 8 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52604


title: Bt-2344-180-26-0308-7j

source_name: Total RNA extracted from a pool of 15 to 20 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 400


title: Sc-2305-180-11-0308-3j

source_name: Total RNA extracted from a pool of 7 to 8 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52544


title: Sc-2313-180-24-0308-3j


title: Sc-2318-180-09-0308-3j

source_name: Total RNA extracted from a pool of 7 to 8 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from sow 52568


title: Sc-2316-180-15-0308-3j


title: Sc-2329-180-50-0308-3j


title: Bt-2331-180-48-0308-8j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow abattoir1


title: Bt-2307-180-42-0308-8j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow abattoir2


title: Sc-2325-180-40-0308-3j


title: Bt-2324-180-39-0308-8j

source_name: Total RNA extracted from a pool of 15 to 20 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 1990


title: Sc-2289-180-43-0308-3j


title: Bt-2319-180-55-0308-7j

source_name: Total RNA extracted from a pool of 3 to 5 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 7759


title: Bt-2294-180-10-0308-8j


title: Oryza Sativa Japonica C418 cold stress 6h rep3

city: Beijing

first: Fan

last: Zhang

state: Beijing

address: 12 South Zhong-Guan-Cun St.

country: China

institute: CAAS

description: A japonica restorer line, C418, which is the male parent of many elite japonica commercial hybrid cultivars widely grown in North China

hyb_protocol: cRNA was then hybridized to the Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences at 45 °C with rotation for 16h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained on the Affymetrix Fluidics Station 450 followed by scanning on Affymetrix GeneChip Scanner 3000. All above mentioned experiment steps were processed in CapitalBio Corporation in Beijing.

scan_protocol: GeneChip Operating Software (GCOS1.4) was used to analyze the hybridization data. The scanned images were firstly examined by visual inspection then satisfactory images were analyzed to generate raw data saved as CEL files using the default settings of GCOS1.4.

data_processing: MAS 5.0

organism: Oryza sativa Japonica Group

source_name: C418(Japonica), cold stress(4C), 6h

label_protocol: Biotin-tagged cRNA was generated from an in vitro transcription reaction using the MessageAmpTM II aRNA Amplification Kit and then fragmented into strands of 35 to 200 bases in length following the Affymetrix’s protocol.

growth_protocol: The sterilized seeds of C418 and K354 were allowed to germinate in distilled water for two days. Well germinated seeds were sown in 6 cm × 10 cm plastic pots with a hole at the bottom and filled with soil, which were placed 65 cm × 44 cm × 14 cm plastic case with nutrient solution following IRRI standard protocol in the growth chamber of Institute of Crop Science of Chinese Academy of Agricultural Science. Both cold stress treatment and control conditions were set with 24 replications for each line. ~15 strong seedlings each replication were allowed to grow until the 3-leaf stage in the growth chamber set at 25 °C constant day/night temperature, 12 h photoperiod and the relative humidity at 75-80%.

extract_protocol: RNA preparation was processed as recommended by the Instruction of Affymetrix (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix). Briefly total RNA was isolated from liquid nitrogen frozen sample using TRIZOL reagent and the following steps were then processed in the CapitalBio Corporation, Beijing.

treatment_protocol: At the 3-leaf stage, plastic cases with the seedlings were transferred to another growth chamber which the temperature was set to 4 °C constant day/night temperature. Shoot samples were collected at 2h, 6h, 12h, 24h and 48h during cold stress treatment and control. Three biological replicates (each from individual plastic pot) were prepared for microarray analysis. After collection, samples were snap frozen in liquid nitrogen and kept in a -80 °C freezer for total RNA extraction.

tag: treatment

value: cold stress (4C)

tag: time

value: Shoot

value: C418, a japonica restorer line

tag: age

value: 3-leaf seedling stage


title: Bt-2312-180-28-0308-7j

source_name: Total RNA extracted from a pool of 15 to 20 mm antral follicles, determined as healthy using microscopic examination after Feulgen staining of some granulosa cells, originating from cow 9936


title: Oryza Sativa Japonica C418 cold stress 48h rep2

source_name: C418(Japonica), cold stress(4C), 48h

tag: genotype


title: Oryza Sativa Japonica C418 control rep2

source_name: C418(Japonica), control

value: control


title: Oryza Sativa Japonica C418 cold stress 6h rep2


title: Oryza Sativa Japonica C418 control rep1


title: Oryza Sativa Japonica C418 cold stress 12h rep2

source_name: C418(Japonica), cold stress(4C), 12h


title: Oryza Sativa Japonica C418 cold stress 12h rep3


title: Oryza Sativa Japonica C418 control rep3


title: Oryza Sativa Japonica C418 cold stress 6h rep1


title: Oryza Sativa Japonica C418 cold stress 48h rep3


title: Oryza Sativa Japonica C418 cold stress 48h rep1


title: Oryza Sativa Japonica C418 cold stress 24h rep3

source_name: C418(Japonica), cold stress(4C), 24h


title: Oryza Sativa Japonica C418 cold stress 12h rep1


title: Oryza Sativa Japonica C418 cold stress 2h rep3

source_name: C418(Japonica), cold stress(4C), 2h


title: Oryza Sativa Japonica K354 cold stress 48h rep3

description: K354, a BC2F6 introgression line with cold tolance derived from a cross between recurrent parent C418 and Bg300 (an indica variety from Sri Lanka)

source_name: K354(cold tolerant introgression line under C418 genetic background), cold stress(4C), 48h


title: Oryza Sativa Japonica C418 cold stress 24h rep1


title: Oryza Sativa Japonica K354 control rep2

source_name: K354(cold tolerant introgression line under C418 genetic background), control

value: K354, a BC2F6 introgression line with cold tolance derived from a cross between recurrent parent C418 and Bg300 (an indica variety from Sri Lanka)


title: Oryza Sativa Japonica K354 cold stress 24h rep2

source_name: K354(cold tolerant introgression line under C418 genetic background), cold stress(4C), 24h


title: Oryza Sativa Japonica K354 control rep3


title: Oryza Sativa Japonica K354 cold stress 12h rep2

source_name: K354(cold tolerant introgression line under C418 genetic background), cold stress(4C), 12h


title: Oryza Sativa Japonica K354 cold stress 2h rep3

source_name: K354(cold tolerant introgression line under C418 genetic background), cold stress(4C), 2h


title: Oryza Sativa Japonica K354 cold stress 6h rep2

source_name: K354(cold tolerant introgression line under C418 genetic background), cold stress(4C), 6h


title: Oryza Sativa Japonica C418 cold stress 2h rep2


title: Oryza Sativa Japonica K354 cold stress 48h rep1


title: Oryza Sativa Japonica K354 cold stress 24h rep1


title: Oryza Sativa Japonica K354 control rep1


title: Oryza Sativa Japonica K354 cold stress 12h rep3


title: Oryza Sativa Japonica C418 cold stress 24h rep2


title: Oryza Sativa Japonica K354 cold stress 6h rep1


title: Oryza Sativa Japonica K354 cold stress 12h rep1


title: Oryza Sativa Japonica K354 cold stress 24h rep3


title: Oryza Sativa Japonica C418 cold stress 2h rep1


title: Oryza Sativa Japonica K354 cold stress 6h rep3


title: Oryza Sativa Japonica K354 cold stress 2h rep2


title: Oryza Sativa Japonica K354 cold stress 48h rep2


title: Dongjin 9_1

city: Shanghai

first: Wang

middle: Jie

last: Chen

state: Shanghai

address: 300 fenglin Road

institute: Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science

description: Gene expression data from 9 DAF endosperm of Dongjin

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45 Celsius degree on Affymetrix rice Genome array. GeneChips were washed and stained in the Fluidics Station 450(GeneChip® Hybridization, Wash and Stain Kit, Affymetrix, P/N  900720)

scan_protocol: Hybridized microarrays were scanned using a GeneChip® Scanner 3000(P/N 00-00212, Affymetrix), and raw data were read by Command Console Software 3.1(Affymetrix).

data_processing: The raw data was normalized using Gene Spring Software 11.0(Agilent).  MAS 5.0

organism: Oryza sativa

source_name: 9 DAF endosperm of Dongjin (wild type),biological rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (3' IVT Express Kit , Affymetrix, P/N 901229)

growth_protocol: Rice were grown during summer under natural environmental conditions in Songjiang experimental field

extract_protocol: Total RNA was extracted with the RNAplant plus reagent (DP437, Tiangen, China)

treatment_protocol: Developing endosperm that were harvested from both osbzip58-1 and wild-type Dongjin at 9 DAF

value: 9 DAF

value: endosperm

tag: genetic background

value: Dongjin

value: wild type


title: osbzip58-1  B20 9_4

description: Gene expression data from 9 DAF endosperm of osbzip58-1

source_name: 9 DAF endosperm of osbzip58-1 mutant,biological rep 3


title: osbzip58-1  B20 9_2

source_name: 9 DAF endosperm of osbzip58-1 mutant,biological rep 1


title: Lung 101M_E1

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

description: Lung 101M_MSC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with Bioconductor software (v.2.9).

organism: Mus musculus

source_name: Lung_Septic Mice_MSCs

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

growth_protocol: C57Bl/6J female mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by purification of mRNA using Qiagen purification kit.

treatment_protocol: A frozen vial of murine MSCs (isolated from male C57Bl/6J mice, courtesy of Dr. Darwin Prockop at Tulane University) was thawed and expanded according to previously published literature.  MSCs in all in vivo experiments were used between passages 8 to 11. Saline or cultured male MSCs (at 2.5 x 105 cells, 100uL total volume) was slowly infused via the inserted canula 6 hours following sham-operation or CLP.

tag: gender

value: female

tag: sample group

value: CLP-injured mice with MSCs (Cecum Ligation Perforation w/ Mesenchymal Stem Cells)

value: lung


title: Dongjin 9_2

source_name: 9 DAF endosperm of Dongjin (wild type),biological rep 2


title: Lung 61M_E1

description: Lung 61M_MSC

tag: strain


title: Oryza Sativa Japonica K354 cold stress 2h rep1


title: osbzip58-1  B20 9_3

source_name: 9 DAF endosperm of osbzip58-1 mutant,biological rep 2


title: Heart 44M_E1

description: Heart 44M_MSC

source_name: Heart_Septic Mice_MSCs


title: Lung 100M_E1

description: Lung 100M_MSC


title: Lung 44M_E1

description: Lung 44M_MSC

value: kidney


title: Lung 16M_E1

description: Lung 16M_MSC


title: Kidney 100M_E1

description: Kidney 100M_MSC

source_name: Kidney_Septic Mice_MSCs


title: Dongjin 9_3

source_name: 9 DAF endosperm of Dongjin (wild type),biological rep 3


title: Kidney 44M_E1

description: Kidney 44M_MSC


title: Liver 101M_E1

description: Liver 101M_MSC

source_name: Liver_Septic Mice_MSCs


title: Heart 101M_E1

description: Heart 101M_MSC


title: Kidney 16M_E1

description: Kidney 16M_MSC


title: Liver 61M_E1

description: Liver 61M_MSC

value: heart


title: Heart 16M_E1

description: Heart 16M_MSC


title: Liver 16M_E1

description: Liver 16M_MSC


title: Spleen_MSC8

source_name: Spleen_Septic Mice_MSCs


title: Spleen_MSC5

value: liver


title: Kidney 101M_E1

description: Kidney 101M_MSC


title: Liver 44M_E1

description: Liver 44M_MSC


title: Heart 100M_E1

description: Heart 100M_MSC


title: Liver 100M_E1

description: Liver 100M_MSC


title: Heart 61M_E1

description: Heart 61M_MSC


title: Kidney 61M_E1

description: Kidney 61M_MSC


title: Spleen_MSC7


title: Lung 37C_E1

description: Lung 37C_CLP

source_name: Lung_Septic Mice_placebo

value: CLP-injured mice with placebo (Cecum Ligation Perforation w/ saline)


title: Lung 107C_E1

description: Lung 107C_CLP


title: Lung 35C_E1

description: Lung 35C_CLP


title: Lung 24C_E1

description: Lung 24C_CLP


title: Kidney 35C_E1

description: Kidney 35C_CLP

source_name: Kidney_Septic Mice_placebo


title: Kidney 107C_E1

description: Kidney 107C_CLP


title: Lung 34C_E1

description: Lung 34C_CLP


title: Spleen_MSC4


title: Kidney 24C_E1

description: Kidney 24C_CLP


title: Kidney 34C_E1

description: Kidney 34C_CLP


title: Heart 107C_E1

description: Heart 107C_CLP

source_name: Heart_Septic Mice_placebo


title: Liver 37C_E1

description: Liver 37C_CLP

source_name: Liver_Septic Mice_placebo


title: Heart 37C_E1

description: Heart 37C_CLP


title: Heart 34C_E1

description: Heart 34C_CLP


title: Liver 34C_E1

description: Liver 34C_CLP


title: Heart 35C_E1

description: Heart 35C_CLP


title: Liver 35C_E1

description: Liver 35C_CLP


title: Lung 78S_E1

description: Lung 78S_Saline

value: sham Operated  (controls)


title: Liver 107C_E1

description: Liver 107C_CLP


title: Lung 22S_E1

description: Lung 22S_Saline


title: Spleen_CLP3

source_name: Spleen_Septic Mice_placebo


title: Liver 24C_E1

description: Liver 24C_CLP


title: Kidney 78S_E1

description: Kidney 78S_Saline


title: Lung 21S_E1

description: Lung 21S_Saline


title: Kidney 76S_E1

description: Kidney 76S_Saline


title: Kidney 21S_E1

description: Kidney 21S_Saline


title: Kidney 22S_E1

description: Kidney 22S_Saline


title: Heart 78S_E1

description: Heart 78S_Saline


title: Lung 77S_E1

description: Lung 77S_Saline


title: Lung 76S_E1

description: Lung 76S_Saline


title: Heart 24C_E1

description: Heart 24C_CLP


title: Kidney 37C_E1

description: Kidney 37C_CLP


title: Heart 77S_E1

description: Heart 77S_Saline


title: Heart 21S_E1

description: Heart 21S_Saline

value: Spleen


title: Kidney 77S_E1

description: Kidney 77S_Saline


title: Liver 77S_E1

description: Liver 77S_Saline


title: Liver 22S_E1

description: Liver 22S_Saline


title: Heart 22S_E1

description: Heart 22S_Saline


title: Liver 78S_E1

description: Liver 78S_Saline


title: Heart 76S_E1

description: Heart 76S_Saline


title: Spleen_s4


title: Spleen_s3


title: Liver 76S_E1

description: Liver 76S_Saline


title: Spleen-CLP8


title: Spleen_s2


title: Liver 21S_E1

description: Liver 21S_Saline


title: Lung 0mg silica 32 week post-exposure rep3

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description: The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA,), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc,) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc,). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconducter using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes genes undetected and resulting in a subset of genes detected on the array. A linear model analysis using ‘limma’ package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes.  Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

source_name: 0mg/m3 silica, 32 week post-exposure rat 123 Lung

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72 ± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the blood samples using Mouse RibopureTM Blood isolation kit (Ambion Inc, Austin, TX) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase and further purified using RNeasy Mini kit (Qiagen Inc, Valencia, CA) following the recommendations of the supplier. The globin mRNA present in abundance in the blood RNA samples was depleted using the GlobinclearTM – Mouse/Rat globin mRNA removal kit (Ambion Inc, Austin, TX).

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Rats were sacrificed at 32 weeks following the last silica exposure.

value: CDF Fisher 344

value: male

value: 3 mo

value: 0mg/m3 silica

value: 32 wk post exposure


title: Lung 15mg silica 32 week post-exposure rep5

institute: National Institute for Occupational Safety and Health

source_name: 15mg/m3 silica, 32 week post-exposure rat 119 Lung

value: 15mg/m3 silica


title: Lung 15mg silica 32 week post-exposure rep1

source_name: 15mg/m3 silica, 32 week post-exposure rat 113 Lung


title: Lung 15mg silica 32 week post-exposure rep6

source_name: 15mg/m3 silica, 32 week post-exposure rat 120 Lung


title: Lung 0mg silica 32 week post-exposure rep4

source_name: 0mg/m3 silica, 32 week post-exposure rat 124 Lung


title: Lung 15mg silica 32 week post-exposure rep2

source_name: 15mg/m3 silica, 32 week post-exposure rat 114 Lung


title: Lung 0mg silica 32 week post-exposure rep6

source_name: 0mg/m3 silica, 32 week post-exposure rat 126 Lung


title: Lung 0mg silica 32 week post-exposure rep5

source_name: 0mg/m3 silica, 32 week post-exposure rat 125 Lung


title: Lung 0mg silica 32 week post-exposure rep2

source_name: 0mg/m3 silica, 32 week post-exposure rat 122 Lung


title: Lung 15mg silica 32 week post-exposure rep3

source_name: 15mg/m3 silica, 32 week post-exposure rat 115 Lung


title: Lung 15mg silica 32 week post-exposure rep4

source_name: 15mg/m3 silica, 32 week post-exposure rat 117 Lung


title: Lung 0mg silica 32 week post-exposure rep1

source_name: 0mg/m3 silica, 32 week post-exposure rat 121 Lung


title: Blood 15mg silica 32 week post-exposure rep5

source_name: 15mg/m3 silica, 32 week post-exposure rat 119 Blood

value: blood


title: Blood 15mg silica 32 week post-exposure rep2

source_name: 15mg/m3 silica, 32 week post-exposure rat 114 Blood


title: Blood 0mg silica 32 week post-exposure rep4

source_name: 0mg/m3 silica, 32 week post-exposure rat 124 Blood


title: Blood 15mg silica 32 week post-exposure rep1

source_name: 15mg/m3 silica, 32 week post-exposure rat 113 Blood


title: Blood 15mg silica 32 week post-exposure rep4

source_name: 15mg/m3 silica, 32 week post-exposure rat 117 Blood


title: Blood 0mg silica 32 week post-exposure rep2

source_name: 0mg/m3 silica, 32 week post-exposure rat 122 Blood


title: Blood 15mg silica 32 week post-exposure rep6

source_name: 15mg/m3 silica, 32 week post-exposure rat 120 Blood


title: Blood 15mg silica 32 week post-exposure rep3

source_name: 15mg/m3 silica, 32 week post-exposure rat 115 Blood


title: Blood 0mg silica 32 week post-exposure rep5

source_name: 0mg/m3 silica, 32 week post-exposure rat 125 Blood


title: Blood 0mg silica 32 week post-exposure rep1

source_name: 0mg/m3 silica, 32 week post-exposure rat 121 Blood


title: Blood 0mg silica 32 week post-exposure rep3

source_name: 0mg/m3 silica, 32 week post-exposure rat 123 Blood


title: Blood 0mg silica 32 week post-exposure rep6

source_name: 0mg/m3 silica, 32 week post-exposure rat 126 Blood


title: MEF+mRPA1-shRNA_3

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

description: RPA1 knockdown.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5. RMA was used as the normalization method.

source_name: MEFs, RPA1 shRNA

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affimetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: DMEM containing 10% fetal bovine serum at 37C.

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Immortalized MEF cells were infected with an adenovirus expressing each shRNA (1 x 10^8 pfu/ml) for 2 h, and maintained with normal medium for 70 h.

tag: strain/background

value: ICR

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

tag: shRNA


title: MEF+mRPA1-shRNA_1

description: RPA1 knockdown.


title: MEF+mRPA1-shRNA_2

description: RPA1 knockdown.


title: MEF+mHSF1-shRNA_3

description: HSF1 knockdown.

source_name: MEFs, HSF1 shRNA


title: MEF+scr_3

source_name: MEFs, control shRNA

value: control


title: MEF+mHSF1-shRNA_2

description: HSF1 knockdown.


title: MEF+scr_1


title: DEREG x Ldlr-/-_PBS_DC_F

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: Gene expression data from liver at harvest

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

scan_protocol: An Affimetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affimetrix AGCC software.

data_processing: Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).

source_name: LIVER_DEREG x Ldlr-/-_PBS

label_protocol: cDNA was labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Chimeric DEREG x Ldlr-/- mice were kept on a high fat diet for 8 weeks

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

treatment_protocol: Treated with DT (vehicle) or PBS (placebo) i.p. for 8 weeks.

tag: genotype/varaiation

value: DEREG x Ldlr-/-

value: PBS


title: MEF+mHSF1-shRNA_1

description: HSF1 knockdown.


title: DEREG x Ldlr-/-_DT_DD_K

source_name: LIVER_DEREG x Ldlr-/-_DT

tag: tissue

value: diphteria toxin (DT)


title: DEREG x Ldlr-/-_DT_DD_L

value: liver


title: DEREG x Ldlr-/-_PBS_DC_B


title: MEF+scr_2


title: DEREG x Ldlr-/-_DT_DD_G


title: DEREG x Ldlr-/-_DT_DD_I


title: Spleen_CLP2

source_name: Spleen_Septic Mice_placebo

value: female

value: CLP-injured mice with placebo (Cecum Ligation Perforation w/ saline)

value: heart


title: Spleen-CLP10


title: DEREG x Ldlr-/-_PBS_DC_C


title: DEREG x Ldlr-/-_DT_DD_H


title: DEREG x Ldlr-/-_PBS_DC_E


title: p80HT transgenic 1

city: Augusta

first: Brian

middle: A

last: McCarthy

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Health Sciences University

description: p80HT Mutation

hyb_protocol: Hyb mix included Control Oligonucleotide B2, 20X Eukaryotic Hyb Controls and DMSO (Affymetrix, Santa Clara, CA).  200ul of mixed sample was hybridized for 18 hours at 45C.  The arrays are then washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.  Images were aquired with AGCC software.

data_processing: The arrays were nomalized (RMA) using Partek.  The sample groups were compared using ANOVA, from which genes with a 2-fold-change and significant p-values were isolated.

source_name: p80HT Mutation

label_protocol: Samples were labeled using the WT Terminal Labeling kit (Affymetrix, Santa Clara, CA) with using terminal deoxynucleotidyl transferase (TdT) in the presence of a  biotinylated compound

extract_protocol: Trizol extraction by manufacturer's protocol

treatment_protocol: B cells were isolated from the spleens of mice with EasySep (Stemcell Technologies, Vancouver, BC, Canada) using an anti B220 antibody (clone RA3-6B2, BD Pharmingen, San Diego, CA)

value: p80HT transgenic

value: C57BL/6J x SJL/J

value: B cell


title: p80HT transgenic 2

description: p80HT Mutation


title: p80HT transgenic 3

description: p80HT Mutation


title: DEREG x Ldlr-/-_PBS_DC_A


title: cultured for day 7, biological rep3

city: Hangzhou

first: Zonghui

last: Ding

state: Zhejiang

address: 88 Jiefang Road

institute: Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 7

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using a confocal laser GeneChip Scanner 3000 7G.

data_processing: Raw CEL files were imported into Affymetrix Expression Console Software (version 1.1), and analyzed with RMA normalization to remove between-array effects and to standardize the low-level data.

source_name: 4T1 cells cultured with 20mM lactic acid on day 7

growth_protocol: 4T1 cells were grown in a humidified CO2 incubator at 37C, and subcultured with 0.25% trypsin 0.02% EDTA.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 4T1 cells were cultured with 3mM glucose and 20mM lactic acid for 1 day, 3 days, 4 days, 5 days, 7 days, 9 days and 11 days, respectively. 4T1 cells were cultured with 3mM glucose  as control.

value: murine breast cancer cell line

tag: cell line


title: cultured for day 11, biological rep2

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 11

source_name: 4T1 cells cultured with 20mM lactic acid on day 11


title: cultured for day 5, biological rep3

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 5

source_name: 4T1 cells cultured with 20mM lactic acid on day 5


title: cultured for day 7, biological rep2


title: cultured for day 1, biological rep1

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 1

source_name: 4T1 cells cultured with 20mM lactic acid on day 1


title: cultured for day 3, biological rep2

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 3

source_name: 4T1 cells cultured with 20mM lactic acid on day 3


title: cultured for day 11, biological rep1


title: Wild-type 3

description: Wild Type

source_name: Wild Type

value: wild type


title: cultured for day 9, biological rep2

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 9

source_name: 4T1 cells cultured with 20mM lactic acid on day 9


title: cultured for day 5, biological rep2


title: cultured for day 3, biological rep1


title: cultured for day 3, biological rep3


title: cultured for day 9, biological rep1


title: cultured for day 5, biological rep1


title: cultured for day 4, biological rep3

description: Gene expression data from 4T1 cells with 20mM lactic acid on day 4

source_name: 4T1 cells cultured with 20mM lactic acid on day 4


title: DEREG x Ldlr-/-_PBS_DC_D


title: control, biological rep3

description: Gene expression data from 4T1 cells without 20mM lactic acid.

source_name: 4T1 cells cultured without lactic acid


title: Spleen_s1

value: sham Operated  (controls)

value: Spleen


title: cultured for day 4, biological rep1


title: control, biological rep1


title: cultured for day 1, biological rep3


title: cultured for day 1, biological rep2


title: cultured for day 7, biological rep1


title: cultured for day 4, biological rep2


title: Wild-type 1

description: Wild Type


title: cultured for day 9, biological rep3


title: 8HR BMP+ADR

city: Singapore

first: Shuet Theng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: GIS

description: replicate 1

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Illumina Inc. Genome Studio V2011.1. Data normalized with Shift to 75 percentile.

source_name: Mouse cell lines

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

value: MEF

tag: genotype/variation

value: control (passage 2 Primary MEFs)

tag: transformation

value: non-transformed

tag: agent

value: BMP2 and ADR

value: 8 hour


title: 16HR BMP

description: replicate 1

value: 16 hour


title: cre 12h Adr (0.3um)

description: replicate 1

value: RasV12/E1A- transformed MEFs

value: ADR

value: 12 hour


title: MEF p2 8hr BMP (100NG/ML)

description: replicate 1


title: 16HR Adr

description: replicate 1


title: 8HR ADR

description: replicate 1


title: control, biological rep2


title: Wild-type 2

description: Wild Type


title: 16HR BMP+ADR

description: replicate 1


title: 16HR

description: replicate 1

value: CTRL


title: cultured for day 11, biological rep3


title: cre 0

description: replicate 1

value: 0 hour


title: MEF p2 8hr

description: replicate 1


title: cre 12h BMP Adr

description: replicate 1


title: pbabe 12h BMP Adr

description: replicate 1


title: pbabe 12h Adr (0.3um)

description: replicate 1


title: cre 12h bmp (100ng/ml)

description: replicate 1


title: RW1 1XSSC_55 degree C

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Water 14 genomic DNA control

hyb_protocol: For hybridization, slides (CodeLink« Activated Slides, SurModics) were inserted into the hybridization chamber (SlideBooster SB401/800, Advalytics) and covered by coverslips (ImplenGmbH). After 10 min of incubation samples were added by diffusion. Buffer AM101 (100ul per well) and AS100 (100 ul) (both from Advalytix) were used for humidity stabilizing and temperature diffusion control respectively. Hybridization was tested at temperatures between 42 and 60 degree C with increments of 2 degree C. Optimal hybridization conditions were 55 degree C for 18 h. Slides were washed subsequently in 1X SSC 0.3% SDS (5 min, 40 degree C), twice in 1X SSC (1 min each, 20  degree C), in 0.5X SSC (1min, 20  degree C), in 0.1 SSC 0.3% SDS (1 min, 40  degree C), and twice in 0.1X SSC (1min, 20  degree C).Slides were centrifuged (ArrayIt« Microarray High-Speed Centrifuge, Arrayit Corporation) and scanned using genomic DNA Microarray Scanner (Agilent Technologies) at conditions recommended by the manufacturer.

scan_protocol: Microarrays were scanned using Agilent Scanner System (G2565CA G3 upgrade, Agilent Technology) with 5 ?m resolution

data_processing: The data were analyzed with Imagene 5.0 (BioDiscovery) using default analysis settings

organism: Rhizorhabdus wittichii RW1

source_name: Pure culture

label_protocol: genomic DNA was  labeled using terminal transferase (Roche) and Cy5-dUTP (GE Healthcare) following the procedure provided by the companies but incubating 4 h at 37 degree C

growth_protocol: Stationary phase from mineral medium with dibenzofurane

extract_protocol: Genomic DNA from pure cultures or environmental samples (10 ml pure culture or 50 ml of aquifer water) was extracted essentially as described previously (AEM vol 67. No.5 p 2354-2359). Briefly, pelleted cells were resuspended in 1 ml Tris/HCl (100 mM pH 8.0), supplemented with 100 mM EDTA, 100 mM NaCl, 1% (wt/vol) polyvinylpyrrolidone and 2% (wt/vol) sodium dodecyl sulfate and transfered to a 2 ml Lysing Matrix E tube (Qbiogene). Cells were lyzed in a Fast Prep  -24 instrument (40 sec, intensity 5.5). Samples were centrifuged at 14.000 X g for 1 min at 4  C and the supernatant washed with 1 volume phenol/chloroform (1:1), centrifuged and the aqueous phase washed with 1 volume chloroform. After centrifugation, nucleic acids (aqueous phase) were precipitated with 1 volume of ice-cold isopropanol and 1:10 volume of 3M sodium acetate and purified using a Sepharose 4B spin column. Typically, two-three such column purification steps were necessary to reach a transparent solution, out of which DNA was precipitated with 3 volumes of ethanol and 1:10 volume of 3M sodium acetate. After centrifugation and washing with 80% ethanol the pellet was resuspended in 50  l of milliQ water. Quality and quantity of DNA was analyzed on 1% agarose gels and spectrophotometrically by determination of the A260/A280 ratio.

tag: sample type

value: Sphingomonas wittichii RW1

tag: treatment

value: 1XSSC_55 degree C


title: RW1 2XSSC_55 degree C

description: Water 14 genomic DNA control

value: 2XSSC_55 degree C


title: pbabe 12h bmp (100ng/ml)

description: replicate 1

tag: time


title: RW1 0.1XSSC_55 degree C

description: Water 14 genomic DNA control

value: 0.1XSSC_55 degree C


title: LB400 3XSSC_50 degree C

description: Water 14 genomic DNA control

organism: Paraburkholderia xenovorans LB400

growth_protocol: Stationary phase from mineral medium with biphenyl

value: Burkholderia xenovorans LB400

value: 3XSSC_50 degree C


title: Water 16 RNA  naphthalene

description: Water 14 genomic DNA control

organism: unidentified microorganism

source_name: Environment

growth_protocol: Four days incubation at 20 degree C and 50 rpm

extract_protocol: Environmental samples (50 ml aquifer water) were centrifuged at 4  C and 4000 rpm for 30 min and the pellet resuspended in 1 ml of RNAprotect Bacterial Reagent (Qiagen) and incubated for 10 min on ice. The pellet obtained after centrifugation (5 min, 13000 rpm) was resuspended in 1 ml of RNAproTM Solution (MP Biomedicals), placed into Lyzing Matrix B tubes (MP Biomedicals) and lyzed in a Fast Prep  -24 instrument (40 sec, intensity 6.0). The supernatant obtained after centrifugation was washed twice with equal volumes of chloroform followed by addition of three volumes of ethanol (-20  C). The aqueous phase was transferred to an RNeasy Mini Kit column (Qiagen), washed with RW1 and RPE buffers (according to the manufacturer) and eluted in 50   l RNase free water. DNA was digested by incubation with turbo DNase (Ambion) essentially following the instruction of the manufacturer, however incubating for 2 hours. RNA was purified by the RNeasy Mini Kit (Qiagen). Quality and quantity of RNA was analyzed by denaturated agarose gel electrophoresis and spectrophotometrically by determination of the A260/A280 ratio.

value: water

value: naphthalene


title: JMP134 1XSSC_55 degree C

description: Water 14 genomic DNA control

organism: Cupriavidus pinatubonensis JMP134

growth_protocol: Stationary phase from mineral medium with 2,4-dichloro-phenoxy acetate

value: Cupriavidus necator JMP134


title: JMP134 0.1XSSC_55 degree C

description: Water 14 genomic DNA control


title: F1 2XSSC_55 degree C

description: Water 14 genomic DNA control

organism: Pseudomonas putida F1

growth_protocol: Stationary phase from mineral medium with toluene

value: Pseudomonas putida F1


title: F1 3XSSC_50 degree C

description: Water 14 genomic DNA control


title: LB400 1XSSC_55 degree C

description: Water 14 genomic DNA control


title: JMP134 3XSSC_50 degree C

description: Water 14 genomic DNA control


title: F1 1XSSC_55 degree C

description: Water 14 genomic DNA control


title: LB400 2XSSC_55 degree C

description: Water 14 genomic DNA control


title: LB400 0.1XSSC_55 degree C

description: Water 14 genomic DNA control


title: Water 16 genomic DNA  naphthalene

description: Water 14 genomic DNA control


title: F1 0.1XSSC_55 degree C

description: Water 14 genomic DNA control


title: Water 14 RNA control

description: Water 14 genomic DNA control


title: Water 14 RNA naphthalene

description: Water 14 genomic DNA control


title: pbabe 0

description: replicate 1

value: MEF


title: Water 16 genomic DNA control

description: Water 14 genomic DNA control


title: Water 16 RNA control

description: Water 14 genomic DNA control


title: JMP134 2XSSC_55 degree C

description: Water 14 genomic DNA control


title: W24D_rep3

city: Taipei

first: Ting-Fang

last: Wang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.(NimbleGen Arrays User’s Guide  Gene Expression Arrays,V6.0  )

scan_protocol: The protocol for scanning one-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0. (NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.0)

data_processing: NimbleScan software (V2.6) was used to obtain raw data(.pair) and converte to gene expression value (.calls). Quantile normalization algorithm was used for normalization methods.

organism: Trichoderma reesei

source_name: Hypocrea jecorina CBS999.97 wild-type

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NimbleGen Arrays User’s Guide  Gene Expression Arrays  ,V6.0)

growth_protocol: Hypocrea jecorina CBS999.97(MAT1-2)  wild-type and Hypocrea jecorina CBS999.97 (MAT1-2) env1 delet strain were inculated in the center of the cellophane-covered malt extract agar (MEA) plate and incubated in a plant growth chamber at 25℃ for 7.25 days.

extract_protocol: Total RNAs were extracted using TRI reagent® soln (Ambion), and  purified using the RNeasy® plant  Mini Kit (QIAGEN).

treatment_protocol: The Mycelia were freeze-dried and ground in liquid nitrogen using a mortar and pestle.

value: Wildtype

tag: condition


title: W24D_rep1


title: W24D_rep2


title: Water 14 genomic DNA naphthalene

description: Water 14 genomic DNA control


title: W24L_rep2


title: colorectal_parental_61

city: Seoul

first: Ye-Ah

last: Kim

address: Yongon-dong Jongno-gu

department: Seoul National University College of Medicine

country: South Korea

institute: Cancer Research Institute

hyb_protocol: Hybridization to Affymetrix Gene 1.0 ST array according to the manufacturer's protocol to perform gene expression profiling experiments (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: After 16 hours of hybridization at 45 °C and rotating at 60 rpm, arrays were washed and stained on a GeneChip Fluidics Station (Affymetrix, Inc.) and scanned using the Gene Chip Scanner 3000 (Affymetrix, Inc.).

data_processing: The CEL intensity data extracted by GCOS (Gene Chip Operating Software) was used for data analysis. Raw data was processed using Affymetrix® Expression Console software using default RMA parameters.

label_protocol: High quality RNA (RNA integrity number > 9.0) was used for expression microarray analysis in which 100 ng of the total RNA was processed for biotin labeled target preparation.

growth_protocol: The cell lines were incubated with RPMI1640 or DMEM media with 10% FBS and 1.1% of penicillin.

extract_protocol: Total RNA was extracted from induced radio-resistant and parental cell lines using TRIzol and purified using an Rneasy Mini Kit.

treatment_protocol: They were exposed to a total 80 Gy of Cesium-137 before they were extracted.

tag: disease

value: Rectal cancer

tag: irradiation

value: 0 Gy


title: W24L_rep3


title: W12D12L_rep3


title: colorectal_radiation_503

value: 80 Gy


title: colorectal_radiation_283


title: Water 14 genomic DNA control

description: Water 14 genomic DNA control


title: colorectal_parental_503


title: W12L12D_rep1


title: E24L_rep1

source_name: Hypocrea jecorina CBS999.97 delta-env1


title: E24L_rep2


title: E24D_rep1


title: colorectal_parental_283


title: W12L12D_rep2


title: E24D_rep2


title: W12D12L_rep1


title: W24L_rep1


title: E12L12D_rep1


title: E24L_rep3


title: E12D12L_rep3


title: W12L12D_rep3


title: W12D12L_rep2


title: E24D_rep3


title: E12L12D_rep2


title: colorectal_radiation_61


title: E12L12D_rep3


title: E12D12L_rep2


title: Blood_Ctr_51_probe2_rep1

city: Trieste

first: alberto

last: Pallavicini

address: via Giorgierei 5

department: Life Sciences

country: Italy

institute: University of Trieste

hyb_protocol: Hybridizations were performed according to the standard protocol supplied with CustomArrayTM 90K (CombiMatrix Irvine, CA, USA).  Probes were designed from 12194 UniGenes (NCBI - Build #13) by mean of OligoWiz 2.0 software (Wernersson and Nielsen, 2005). For each Unigene, 2 nonredundant 35-40mer probes were spotted in triplicate on the chip. Bacterial and plant probes were also spotted on the slide as negative control.

scan_protocol: The microarray was scanned using a Perkin Elmer laser scanner and data were extracted from the image using CombiMatrix Microarray Imager Software (CombiMatrix Irvine, CA, USA).

data_processing: A quantile normalization algorithm was applied as described in Bolstad (2003). This method is a generalization of standard median normalization techniques which match only the 50% quantile of each sample’s signal distribution. Afterwards an in-slide replicates analysis from Midas was used to reduce data redundancy.  To evaluate the significant over and under expressed genes between experimental groups, the ratios of T3 to T0 and of T51 to T0 were first calculated for each gene within replicates and data were log(2) transformed to ensure variance homogeneity. Finally, a tab delimited file was imported to MeV software (v 4.6- http://www.tm4.org/mev/; Saeed et al., 2003) and used to perform one-way ANOVA with group as fixed factor. P-values were based on permutation test, with 1000 permutations, and Bonferroni correction was applied setting alpha (critical p-value) at 0.001.

organism: Ovis aries

source_name: blood

label_protocol: One-hundred ng of each pool were submitted to double round of amplification using Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Inc.). At the end of amplification protocol aRNA was labeled with Cy5 dye

extract_protocol: The extraction of RNA from blood samples was performed with PAXgeneTM blood RNA kit (PreAnalitiX GmbH, Hombrechtikon, Switzerland) following the manufacturer’s instructions.

tag: breed

value: Sarda sheep

tag: fed

value: basal diet


title: biofilm, hyb. at 55ºC

city: Girona

first: Chloé

last: Bonnineau

address: Campus Montilivi, s/n

country: Spain

institute: Institute of Aquatic Ecology, University of Girona

description: Fluvial biofilms cultured in laboratory from an inoculum of the stream Parthe (Leipzig, Germany)

hyb_protocol: For C. reinhardtii, S. vacuolatus and biofilm, three hybridisation temperatures were tested (55ºC, 60ºC and 65ºC). 1.65 μg of labelled RNA was used for hybridisation according to manufacturer indications. After 17h of hybridisation, arrays were washed with stabilization and drying solution (Quick Amp Labelling kit, Agilent Technologies®).

scan_protocol: Microarrays were scanned at 5 μm resolution using GenePix ® 4400A Scanner (MDS Analytical Technologies GmbH, Ismaning, Germany) at 532 nm. PMTs (Photo Multiplier Value) were auto-adjusted for each slide to a saturation tolerance of 0.01 %, PMT (427, 438 and 457 for slides hybridized at 65ºC, 60º C and 55ºC, respectively). Spot identification was performed utilizing the circular feature alignment of GenePix Pro 7 software (Axon) and Agilent GAL files.

data_processing:
Data analyses were performed using Knime 2.1.2 with R extension for data organization and normalization. F532 medians were first log2 transformed and then normalized by quantile normalization. Flag value given by GenePix Pro 7 software and SNR:signal to noise ratio.
Only 'functional genes probes' (not Scenedesmus vacuolatus or Chlamydomons reinhardtii probes) were used in this study. FGP were further filtered for detection (FLAGs) and by Signal to noise ratio (SNR).

organism: environmental samples

source_name: Mature biofilms collected after 5-weeks growth in laboratory

label_protocol: 300 ng of RNA extracted from C. reinhardtii and 900 ng from S. vacuolatus and biofilms were used for labelling with Cyanine 3 using the Quick Amp Labelling kit (Agilent Technologies®, Böblingen, Germany). For S. vacuolatus and biofilms samples, transcription time was extended by 30 min to 2 h 30 min. Purification of labelled RNA was performed using RNeasy Mini Plant Kit (Qiagen®) as described above.

extract_protocol: Trizol extraction was performed according to manufacturer's instructions for C. reinhardtii and S. vacuolatus samples. A modified protocol was used for RNA extraction from biofilm communities using 1 mL of Trizol for cells disruption and a similar amount of supernatant and chloroform. RNA precipitation was done by adding 2 volumes of polyethylene glycol (PEG) solution (30% PEG, 1.6 M NaCl) to 1 volume of supernatant. After 2 hours of incubation at room temperature and 10 min. centrifugation at maximal speed and 4ºC, the RNA pellet was washed twice with 200 μL of cold ethanol, air dried at room temperature and reconstituted in 50 μL of DEPC water (5 min. incubation at 55ºC).

tag: hybridisation temperature


title: chlamydomonas, hyb. at 60ºC

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii


title: chlamydomonas, hyb. at 55ºC


title: scenedesmus, hyb. at 65ºC

organism: Scenedesmus vacuolatus

source_name: Scenedesmus vacuolatus

tag: subspecies

value: Shih. Et Krauss strain 211-15


title: scenedesmus, hyb. at 60ºC


title: E12D12L_rep1


title: biofilm, hyb. at 65ºC


title: Blood_Ctr_51_probe1_rep2


title: scenedesmus, hyb. at 55ºC


title: RB1035 replicate #1

city: Koeln

first: Roman-Ulrich

last: Mueller

address: Kerpener Str. 62

institute: University Hospital Cologne

data_processing: marray package version 1.22.0 (Bioconductor)

organism: Caenorhabditis elegans

source_name: pre-reproductive adults

label_protocol: Agilent Low Input Quick Amp Labeling Kit according to manufacturer's instructions

growth_protocol: worms were grown on NGM agar plates seeded with OP50

extract_protocol: bead-based homogenization and RNA extraction using the Qiagen miRNEasy kit

treatment_protocol: worms were synchronized using egg prep and young pre-reproductive adults were picked for RNA prep

tag: strain

value: flcn-1 mutant

tag: age

value: pre-reproductive adults


title: Blood_Larch_51_probe2_rep2

value: injected with ACTH

value: Larix decidua sawdust


title: RB1035 replicate #3

hyb_protocol: according to manufacturer's instructions


title: Blood_Ctr_51_probe2_rep2


title: Blood_Larch_51_probe2_rep1


title: WTN2 replicate #1

scan_protocol: according to manufacturer's instructions

value: wild type


title: chlamydomonas, hyb. at 65ºC


title: Blood_Poli_51_probe1_rep1

value: Echinacea angustifolia roots


title: Blood_Poli_51_probe2_rep1


title: Blood_Poli_51_probe1_rep2


title: WTN2 replicate #2


title: Blood_Ctr_51_probe1_rep1


title: Blood_Echi_51_probe2_rep2

value: Echinacea angustifolia flowers


title: Blood_Echi_51_probe1_rep1


title: Blood_Andro_51_probe2_rep1

value: Andrographis paniculata


title: WTN2 replicate #3


title: RR_DH_P150_Cy5_ch1_B150_Cy3_ch2_7DE1415

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: time course, Date of Scan Thu Jun 19 11:13:21 2008

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817.pro

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

label_protocol: incorporation of Cy5-dUTP with Reverse Transcriptase

growth_protocol: ATCC4931 parental strain at midlog phase, grown in TSB, 150min after addition of 50ppm DTAC

extract_protocol: RNEasy Midi Kit (Qiagen) after immediate protection of RNA integrity during harvest of cells in RNAProtect reagent

label_protocol: incorporation of Cy3-dUTP with Reverse Transcriptase

growth_protocol: ATCC4931 SRS strain with elevated resistance to DTAC, at midlog phase, grown in TSB, 150min after addition of 330ppm DTAC

value: SRS DTAC resistant strain B


title: Blood_Andro_51_probe2_rep2


title: RB1035 replicate #2


title: Blood_Larch_51_probe1_rep1


title: Blood_Echi_51_probe1_rep2


title: Blood_Ctr_3_probe2_rep2


title: Blood_ACTH_51_probe2_rep1


title: Blood_Poli_51_probe2_rep2


title: Blood_Andro_51_probe1_rep2


title: Blood_Echi_51_probe2_rep1


title: Blood_Larch_51_probe1_rep2


title: Blood_ACTH_51_probe1_rep1


title: Blood_Ctr_3_probe2_rep1


title: Blood_Poli_3_probe2_rep2


title: Blood_ACTH_51_probe1_rep2


title: Blood_Ctr_3_probe1_rep1


title: Blood_Poli_3_probe2_rep1


title: Blood_Ctr_3_probe1_rep2


title: RR_DH_P30_Cy5_ch1_B30_Cy3_ch2_7DE1414

description: time course, Date of Scan Thu Jun 19 11:07:30 2008

growth_protocol: ATCC4931 parental strain at midlog phase, grown in TSB, 30min after addition of 50ppm DTAC

growth_protocol: ATCC4931 SRS strain with elevated resistance to DTAC, at midlog phase, grown in TSB, 30min after addition of 330ppm DTAC


title: RR_DH_P0_Cy5_ch1_B0_Cy3_ch2_7DE1412

description: time course, Date of Scan Thu Jun 19 10:52:35 2008

growth_protocol: ATCC4931 parental strain at midlog phase, grown in TSB, time zero

growth_protocol: ATCC4931 SRS strain with elevated resistance to DTAC, at midlog phase, grown in TSB, time zero


title: RR_DH_P10_Cy5_ch1_B10_Cy3_ch2_7DE1413

description: time course, Date of Scan Thu Jun 19 10:59:41 2008

growth_protocol: ATCC4931 parental strain at midlog phase, grown in TSB, 10min after addition of 50ppm DTAC

growth_protocol: ATCC4931 SRS strain with elevated resistance to DTAC, at midlog phase, grown in TSB, 10min after addition of 330ppm DTAC


title: Blood_Andro_51_probe1_rep1


title: Blood_Poli_3_probe1_rep1


title: Blood_Poli_3_probe1_rep2


title: Blood_Larch_3_probe2_rep1


title: Blood_Larch_3_probe1_rep1


title: Blood_Echi_3_probe2_rep1


title: Blood_Andro_3_probe1_rep1


title: Blood_Ctr_0_probe1_rep2


title: Blood_ACTH_3_probe1_rep2


title: Blood_Larch_3_probe2_rep2


title: Blood_Echi_3_probe2_rep2


title: Blood_ACTH_3_probe2_rep1


title: Blood_Andro_3_probe1_rep2


title: Blood_ACTH_3_probe2_rep2


title: Blood_Larch_3_probe1_rep2


title: Blood_Ctr_0_probe1_rep1


title: Blood_ACTH_3_probe1_rep1


title: Blood_Echi_3_probe1_rep2


title: Blood_Ctr_0_probe2_rep1


title: Blood_Ctr_0_probe2_rep2


title: Blood_Andro_3_probe2_rep1


title: Blood_Poli_0_probe2_rep2


title: Blood_Poli_0_probe2_rep1


title: Blood_Larch_0_probe1_rep2


title: Blood_Larch_0_probe2_rep1


title: Blood_Echi_3_probe1_rep1


title: Blood_Poli_0_probe1_rep2


title: Blood_Larch_0_probe2_rep2


title: Blood_Poli_0_probe1_rep1


title: Blood_Andro_3_probe2_rep2


title: biofilm, hyb. at 60ºC


title: Blood_Larch_0_probe1_rep1


title: Blood_Echi_0_probe2_rep2


title: Blood_Andro_0_probe1_rep1


title: Blood_Echi_0_probe2_rep1


title: Blood_ACTH_0_probe2_rep2


title: Blood_Andro_0_probe1_rep2


title: Blood_Echi_0_probe1_rep1


title: Blood_Andro_0_probe2_rep2


title: Blood_Echi_0_probe1_rep2


title: Blood_ACTH_51_probe2_rep2


title: Blood_ACTH_0_probe1_rep2


title: Blood_ACTH_0_probe2_rep1


title: Blood_ACTH_0_probe1_rep1


title: Blood_Andro_0_probe2_rep1


title: rpoS_nutrient_broth_rep5

city: Corvallis

first: Joyce

last: Loper

state: OR

address: 3420 NW Orchard Ave

department: Horticultural Crops Research Laboratory

institute: USDA-ARS

description: Technical replicate 1 of biological replicate 3

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each. The sequences are: At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGrpoSA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG).  Dry using a speed vac.  Make pre-hybridization buffer by combining:  0.5 g BSA;  37 mL DEPC water;  12.5 mL 20X SSC;  0.5 mL 10% SDS.  Incubate pre-hybridization buffer for 20 minutes at 42 degrees C.  Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar.  Incubate for 20 minutes at 42 degrees C.  Make hybridization buffer by combining:  500 microliters fomamide;  250 microliters 20X SSC;  10 microliters 10% SDS;  240 microliters DEPC water.  Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter.  Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer.  Add 60 microliters hybridization buffer to speed vac-dried probes.  Put slide into pre-hybridization buffer in coplin jar.  Incubate for 45 minutes at 42 degrees C.  Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand.  Dry slide by spinning.  Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature.  Dip in 100% EtOH and dry with a Chem Wipe.  Heat probes for 15 minutes at 95 degrees C with occassional flicking to resuspend probes.  Remove probes from heat block and centrifuge for 2 minutes at 15,000g.  Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip.  Hybridize overnight at 42 degrees C.  Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C.  Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature.  Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature.  Dry slide by spinning.

scan_protocol: Slides were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15, and applying the default quality control filter options. The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software). Channel 'A' = Cy3. Channel 'B' = Cy5.

organism: Pseudomonas protegens

source_name: rpoS mutant of P. protegens Pf-5

label_protocol: Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:  5.2 microliters 20.3 ng/microliter cab RNA;  12.5 microliters 16.839 ng/microliter ltp4 RNA;  18.6 microliters 22.634 ng/microliter rca RNA;  41.8 microliters 15.068 ng/microliter rbcL RNA;  4.7 microliters 13.279 ng/microliter ltp6 RNA;  11.8 microliters 21.313 ng/microliter rcp1 RNA;  40.7 microliters 23.23 ng/microliter nac RNA;  4.6 microliters 18.177 ng/microliter xcp2 RNA;  14.7 microliters 11.436 ng/microliter prk RNA;  18.9 microliters 11.084 ng/microliter tim RNA;  826.5 microliters water.  And for Cy3 pool:  5.2 microliters 20.3 ng/microliter cab RNA;  12.5 microliters 16.839 ng/microliter ltp4 RNA;  18.6 microliters 22.634 ng/microliter rca RNA;  41.8 microliters 15.068 ng/microliter rbcL RNA;  1.6 microliters 13.279 ng/microliter ltp6 RNA;  3.9 microliters 21.313 ng/microliter rcp1 RNA;  13.6 microliters 23.23 ng/microliter nac RNA;  13.9 microliters 18.177 ng/microliter xcp2 RNA;  44.1 microliters 11.436 ng/microliter prk RNA;  56.8 microliters 11.084 ng/microliter tim RNA;  788.1 microliters water.  To label RNA sample combine:  4 micrograms RNA;  2 microliters 3 mg/mL random hexamers (Invitrogen);  2 microliters arabidopsis spike-in control RNA;  DEPC water to a final volume to 17.5 microliters.  Mix and incubated at 70 degrees C for 10 minutes.  Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.  Add:  6 microliters 5X Superscript II buffer (Invitrogen);  3 microliters 0.1 M dithiothreitol;  1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;  2 microliters SuperScript II (Invitrogen).  Mix and incubated overnight at 42 degrees C.  Add:  10 microliters 1 M NaOH;  10 microliters 0.5 M EDTA.  Incubate for 15 minutes at 65 degrees C.  Add:  25 microliters 1 M Tris pH 7.4;  400 microliters PB buffer (Qiagen).  Apply sample to QIAquick column (Qiagen).  Centrifuge for 1 minute at 15,000g.  Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).  Centrifuge for 1 minute at 15,000g.  Repeat wash.  Empty collection tube and centrifuge for 1 minute at 15,000g.  Transfer column to fresh tube.  Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).  Incubate for 1 minute.  Centrifuge for 1 minute at 15,000g.  Repeat elution for a final volume of 60 microliters.  Dry sample using a speed vac.  Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).  Allow the sample to resuspend for 15 minutes at room temperature.  Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.  Incubate for 1 hour at room temperature in the dark.  Add 4.5 microliters 4 M hydroxylamine.  Incubate for 15 minutes at room temperature in the dark.  Add:  35 microliters 100 mM NaOAc pH 5.2;  500 microliters PB buffer.  Apply to Qiaquick column.  Centrifuge for 1 minute at 15,000g.  Wash with 750 microliters PE buffer (Qiagen).  Centrifuge for 1 minute at 15,000g.  Repeat wash.  Empty collection tube and centrifuge for 1 minute at 15,000g.  Transfer column to fresh tube.  Add 30 microliters EB buffer (Qiagen).  Incubate for 1 minute.  Centrifuge for 1 minute at 15,000g.  Repeat elution for a final volume of 60 microliters.  Check quality of probes spectrophotometrically from 200nm to 700nm.  Store at -80 degrees C.  Use this protocol to label 12 ug RNA and combine products for one hyb.

growth_protocol: Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC. This plate was used to  inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC. Inoculum was washed in  sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05. Three replicate cultures were  grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 2.0-2.4. For each replicate culture, RNA was pretreated with RNAProtect  (Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.

extract_protocol: Extractions were done using the RNA/DNA Midi Kit (Qiagen, Valencia, CA) followed by an on-column DNAse treatment (RNeasy Mini Kit with DNAse I; Qiagen, Valencia, CA). PCR was performed on the RNA to determine that detectable DNA had been removed and RNA samples were analyzed for quality using the BioAnalyzer 2100 (Agilent, Palo Alto, CA).

value: rpoS mutant

source_name: P. protegens Pf-5 wild-type

value: wild-type


title: rpoS_nutrient_broth_rep4

description: Technical replicate 2 of biological replicate 2


title: rpoS_nutrient_broth_rep2

description: Technical replicate 2 of biological replicate 1