title: MAS98.06_52VSd10con_Ref2

description:
MAS98.06_52VSd10con
raw data file: 050509_251485044288_S01_GE1-v5_10_Apr08_1_3.txt


title: BAPHK_cDNA1 transcriptome profile

status: Public on Dec 09 2010

type: RNA

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

country: USA

institute: The Forsyth Institute

hyb_protocol: Microarray hybridization was carried out with the customer service provided by NimbleGen.

scan_protocol: After washing and drying, the microarray slides were immediately scanned in a GenePix 4000B Scanner (Axon Instruments, Union City, CA, USA) using the provided GenePix Pro 6.1 software. NimbleScan v2.5 software was then used for spot features extraction from the scanned images.

data_processing: Two types of normalizations were performed – normalization by DNA reference array and between-array normalization. For DNA reference array normalization, intensities of cDNA signals were normalized with signals from DNA reference arrays (raw array data provided additionally) that were hybridized with fragmented genomic DNA labeled with biotin. Both normalizations were done using the Bioconductor R package “tilingArray”.

label: Biotin

molecule: total RNA

organism: Porphyromonas gingivalis

source_name: Laboratory culture on BAPHK blood plate

label_protocol: Synthesis of cDNA and biotin end-labeling were performed according to NimbleGen’s protocol (Prokaryotic Biotin-Label Procedure). First-strand cDNA was synthesized from 10 μg total RNA. The RNA together with 3 μg random hexamer primers (Invitrogen, Carlsbad, CA, USA) in a 12-μl volume was denatured at 70°C for 10 min. The solution was then cooled to 25°C and mixed to a final concentration of 0.5 mM dNTP, 20 mM DTT, 1X first strand buffer and 0.75 U/μl RNaseOUT (Invitrogen) followed by heating to 42°C. A total of 1200 U SuperScript II reverse transcriptase (Invitrogen) was added to a final volume of 54 μl and the reaction incubated overnight at 42°C. The cDNA product was treated with 0.02 U/μl RNase H (Invitrogen) and 0.01 μg/μl RNase A (Epicentre) in a 100-μl reaction to eliminate RNA contaminants. The cDNA was then purified with standard procedures for phenol: chloroform extraction using Phase-Lock Gel Light tubes (Eppendorf) followed by ethanol precipitation. Purified cDNA was fragmented to 50-200 nucleotides in size with DNase I (Applied Biosystems/Ambion), and labeled at the 3’end in a 100-μl reaction containing 0.5 U/μl Terminal Deoxynucleotidyl Transferase (Promega, Madison, WI, USA) and 0.025 mM Biotin-N6-ddATP (Enzo Life Sciences Inc., Farmingdale, NY, USA). The labeling reaction was incubated for 2 hours at 37°C. The biotin-labeled cDNA was then concentrated using Microcon YM-10 filters (Millipore, Billerica, MA, USA).

growth_protocol: P. gingivalis strain W83 was cultured anaerobically on trypticase soy agar (TSA) containing sheep blood, hemin and vitamin K (BAPHK) for 48 hours at 37°C. Upon harvest, a solution containing 2:1 (v:v) ratio of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA, USA) and 1X PBS was poured onto the plates with colonies and incubated anaerobically for 5 min. The cells were mixed and suspended in this solution, centrifuged down in a microcentrifuge tube at 5,000×g, 4°C for 10 min, and then subjected to either RNA or DNA extraction.

extract_protocol: Lysis of bacterial cells was performed according to the protocol provided with the MasterPure RNA Purification Kit (Epicentre, Madison, WI, USA). The lysate was treated with Proteinase K at 65°C for 15 min and then placed on ice. To increase the recovery rate of small RNA 0.1 volume of 5 M NaCl was added to the lysate. Acid-phenol: chloroform (5:1) (v:v) extraction was then done using Phase-Lock Gel Heavy tubes (Eppendorf, Hauppauge, NY, USA). Total RNA in the upper aqueous phase was purified with a solid-phase extraction filter supplied in the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the recommended protocol. The filter-trapped RNA was then washed and eluted with the provided wash solutions and elution buffer. To completely remove genomic DNA, the RNA extract was treated twice with Turbo DNase (Applied Biosystems/Ambion) at 37°C for 30 min, and purified again with the mirVana miRNA Isolation Kit.

tag: strain

tag: media

value: BAPHK

tag: labeled molecule

value: cDNA


title: MAS98.06_30HSd3con_Ref2

status: Public on Dec 08 2010

city: Oslo

first: Eldrid

last: Borgan

address: Ullernchausseen 70

department: Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

description:
MAS98.06_30HSd3con
raw data file: 060509_251485044291_S01_GE1-v5_10_Apr08_1_4.txt

hyb_protocol: 1.65 μg cRNA was hybridized to 4 × 44 k Agilent Whole Human Genome Oligo Microarrays at 60°C and 10 rpm for 17 hours, according to Agilent's protocol (February 2007).

scan_protocol: The arrays were scanned using an Agilent G2565A DNA microarray scanner

data_processing:
The data were extracted using Feature Extraction (v 10.1.1.1, Agilent), The microarray data was normalized and analysed using R (v 2.9.0) and the LIMMA Bioconductor package. The microarray data was normalized seperately for the reference 1 and 2, because slightly different samples were included (See SAMPLES overview). The raw signals were corrected for multiplicative detrending effects and the arrays were quantile normalized and log2 transformed. Control probes, probes which were flagged as outliers by the Feature Extraction software, and probes that were present in less than 30% of the samples were removed. The signal intensities were averaged between duplicate probes, and the data matrices were imputed using k nearest neighbour imputing (impute package, Bioconductor).
The two sets of normalized data (Ref1 and Ref2) are included as separate SAMPLES. To avoid duplication, the raw data (Agilent Feature Extraction) files are provided in the RAW_AFE.tar archive on the Series record. Please see 'description' above for raw data file name. The 105 transcripts representing choline metabolism (used in reference 1) and 38 transcripts representing glucose metabolism (used in reference 2) are also provided as supplementary files on the Series record.

organism: Homo sapiens

source_name: Breast tumor tissue from establlished orthotopic xenograft mouse model MAS98.06

label_protocol: Total RNA (700 ng) was amplified and labelled with Cy3 with Low RNA input linear amplification kit PLUS and RNA spike-in kit, according to Agilent's protocol (February 2007).

growth_protocol: The animals were fed RM1 diet (Scanbur BK, Norway) and distilled tap water ad libitum. The drinking water was supplemented with 17-β-estradiol at a concentration of 4 μg/ml in order to ensure stimulation of the estrogen receptors and promote tumor growth in the MAS98.06 xenografts. To provide equal experimental conditions, the MAS98.12 xenografts also received estradiol supplement.

extract_protocol: Trizol reagent (Invitrogen) was used to extract total RNA from fresh frozen tumor material according to the manufacturers protocol. Nanodrop and 2100 Bioanalyzer (Agilent) was used to assess the quantity and quality of RNA.

treatment_protocol: Established orthotopic xenograft models were sacrificed by cervical dislocation, tumor tissue was harvested from for 6 animals from each model for gene expression microarray analyses, at tumor diameters of approximately 13-15 mm. Samples were put in cryogenic vials and immersed in liquid nitrogen immediately after dissection and stored under cryogenic conditions until RNA extraction.

tag: tissue

value: Breast tumor tissue

tag: xenograft model

tag: intrinsic subtype

value: LuminalLike

tag: biological replicate

tag: used in reference


title: Asynchronous_Hela_exp2

type: genomic

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

description: Hela Replication Origins

hyb_protocol: The fragmented and labeled DNA was  hybridized to ENCODE01-Forward tiling arrays (P/N 900543)  All the array hybridizations were done at 45°C for 16 hours at 60rpm using an Affymetrix hybridization oven

scan_protocol: Each microarray was scanned and analyzed for signal intensities using the ChIP® Scanner 3000 and GeneChIP Operating Software (GCOS) from Affymetrix.

data_processing:
Data was quantile normalized and analyzed using the Affymetrix Tiling Array Software (TAS) or Tilecore.  Log2(Bubble Trap/Ctrl DNA) fold changes were generated in separate BAR files using a two-sample Wilcoxon test over a sliding window with a bandwidth of 500bp (Note: window size = 2*Bandwidth + 1).
results file descriptions: *.bar were generated by the TAS software. *.bar files for the Bubble Trap assay in HeLa and GM06990 cells contain log2(Bubble Trap/Ctrl DNA) fold changes for each probe.  The data is the center probe within a sliding window (500bp bandwidth) and the corresponding Hodges-Lehmann estimator calculated using all the probes within the sliding window.  *.sgr are text file versions of the binary *.bar files.

label: biotin

molecule: genomic DNA

source_name: Asynchronous Hela cellular DNA

label_protocol: Bubble trap and genomic DNA from HeLa cells were fragmented to 50-100bp size using DNaseI. The fragmented DNA was labeled either with biotin-dATP using random priming (rp) or biotin-ddATP (tt) using terminal tranferase.

growth_protocol: HeLa cells (earlytrap and bubbletrap data sets) were obtained from the American Type Culture Collection and were maintained as monolayer cultures in 5% CO2 on Minimal Essential Medium supplemented with 10% Fetal Clone II (Hyclone), 1% Glutamax and 0.1% Gentamicin (both from Invitrogen) .  GM06990 cells (gmtrap data set) were obtained from Coriell Institute for Medical Research and were maintained as suspension cultures in 5%CO2 in flasks in RPMI 1640 media supplemented with 15% Fetal Clone II, 1% Glutamax and 0.1% Gentamicin.

extract_protocol: GM06990 cells were harvested when the culture reached a cell density of  ~5X10(5) cells per ml (~10(10) cells per library) by centrifugation at 500Xg for 8m.  Hela log-phase or synchronized cell populations (~5X10(9) cells for each library) were scraped from plates, and replication intermediates (RIs; from both cell types) were partially purified by preparing nuclear matrix/DNA halo structures exactly as described in (Mesner et al.(2009b), Methods Mol. Biol. 521, 121-137) and digesting the DNA with EcoRI.  The matrix-affixed DNA was isolated and RIs further purified by adsorption to BND-cellulose and subsequent elution with caffeine.  Bubble-containing EcoRI fragments were isolated exactly as described in (Mesner and Hamlin(2009), Methods Mol. Biol. 521, 315-328 and Mesner et al (2006), Mol. Cell 21, 719-726).  Briefly, RI preparations were mixed with low-melting agarose, the molten mixture was drawn up into a 1ml syringe, without the needle, and allowed to congeal.  The resulting cylindrical plug was extruded into an electrophoresis tank after excising the syringe tip.  After exhaustive electrophoresis to get rid of linear, single-forked, and X-shaped fragments, the trapped bubble-containing fragments were isolated by agarase digestion and purified twice by ethanol precipitation.  Twenty percent of the sample was used for 2D-analysis and the remainder cloned into the EcoRI site of pGem7 (Promega).  After transformation into E.coli strain DH10B,  library clones were obtained after less than one cell division in liquid medium to avoid the propagation of sibs, and were spread onto LB-agarose plates and allowed ~10h until colonies appeared as pin pricks to the unaided eye.  They were then scraped, pooled, aliquoted, and frozen at –80oC.  Approximately 10(6) individual clones were obtained for each of the 4 libraries in which >95% contained vector inserts.

treatment_protocol: The earlytrap data set was generated from HeLa cells that were synchronized by treating with 2 mM thymidine for 14 hr to collect the population in S-phase or at the G1/S boundary, and then were released into drug-free medium for 9 hr to allow the culture to clear S-phase.  Mimosine (200 uM) was added for 13 hr to collect the population at or near the G1/S border, followed by a wash with serum free media and transfer into drug-free medium.  Eighty min later, cells were harvested and replication intermediates prepared.

tag: gender

value: female

tag: tissue type

value: cervix, epithelial, adenocarcinoma

tag: cell line

value: Hela

tag: genomic dna

value: Replication Initiating genomic DNA

source_name: control DNA

tag: control

value: control DNA


title: MAS98.12_56HSd3con_Ref1

description:
MAS98.12_56HSd3con
raw data file: 050509_251485044290_S01_GE1-v5_10_Apr08_1_3.txt

source_name: Breast tumor tissue from establlished orthotopic xenograft mouse model MAS98.12

value: BasalLike


title: MAS98.12_36HSd10con_Ref1

description:
MAS98.12_36HSd10con
raw data file: 130509_251485044310_S01_GE1-v5_10_Apr08_1_4.txt


title: MAS98.12_31HSd10con_Ref2

description:
MAS98.12_31HSd10con
raw data file: 060509_251485044291_S01_GE1-v5_10_Apr08_1_1.txt


title: MAS98.06_2VSd3con_Ref2

description:
MAS98.06_2VSd3con
raw data file: 050509_251485044289_S01_GE1-v5_10_Apr08_1_4.txt


title: Asynchronous_Hela_exp1

description: Hela Replication Origins


title: MAS98.06_16VSd10con_Ref2

description:
MAS98.06_16VSd10con
raw data file: 130509_251485044308_S02_GE1-v5_10_Apr08_1_2.txt


title: Early_S-phase_Hela_exp1_hyb2

description: Hela Early S-phase Replication Origins

source_name: Early S-phase Hela cellular DNA


title: MAS98.12_53HSd3con_Ref1

description:
MAS98.12_53HSd3con
raw data file: 130509_251485044309_S02_GE1-v5_10_Apr08_1_4.txt


title: MAS98.12_31HSd10con_Ref1


title: MAS98.06_2HSd3con_Ref1

description:
MAS98.06_2HSd3con
raw data file: 120509_251485044294_S01_GE1-v5_10_Apr08_1_3.txt


title: MAS98.06_2VSd3con_Ref1


title: MAS98.12_60HSd3con_Ref1

description:
MAS98.12_60HSd3con
raw data file: 120509_251485044294_S01_GE1-v5_10_Apr08_1_1.txt


title: MAS98.06_52VSd10con_Ref1


title: sensitive cells

city: Bronx

first: Susan

middle: K

last: Chao

state: NY

address: 1300 Morris Park Ave

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

hyb_protocol: Samples were hybridized according to the standard Affymetrix protocol

scan_protocol: Gene ST 1.0 chips were scanned using Affymetrix 7G

data_processing: Data were analyzed using Affymetrix GenChip operating software 1.4 and the quality tested using the Affymetrix Expression Console

source_name: sensitive

label_protocol: Samples were labeled according to the standard Affymetrix protocol

growth_protocol: Cell lines were grown in RPMI conatining 10%FBS at 37C with 7% CO2

extract_protocol: Total RNA was purified according to manufacturrer's instructions using Qiagen Rnesway kit

treatment_protocol: A549 were treated with .01%DMSO or 32nM discodermolide, AD32 were grown in 32nM discodermolide, AD32 4EBP1 were treated with .01%DMSO

tag: cell type

value: human lung cell line

tag: discodermolide resistance status

value: sensitive

value: AD32 4E-BP1


title: MAS98.06_30HSd3con_Ref1


title: MAS98.06_16VSd10con_Ref1


title: Early_S-phase_Hela_exp1_hyb1_2

description: Hela Early S-phase Replication Origins


title: Asynchronous_GM06990_exp1

description: GM06990 Replication Origins

source_name: Asynchronous GM06990 cellular DNA

value: blood, B-lymphocyte


title: Asynchronous_Hela_exp1_2

description: Hela Replication Origins


title: senescent cells, biological replicate 2

source_name: senescent

value: senescent

value: A549 disco


title: Early_S-phase_Hela_cells_exp1_hyb1

description: Hela Early S-phase Replication Origins


title: MAS98.12_33VSd10con_Ref1

description:
MAS98.12_33VSd10con
raw data file: 200509_251485044331_S01_GE1-v5_10_Apr08_1_3.txt


title: senescent cells, biological replicate 1


title: sensitive cells, biological replicate 3


title: WT PEG 6hr, biological rep2

city: Thuwal

first: zhenyu

last: wang

address: PSGC

country: Saudi Arabia

institute: KAUST

description: Gene expression data from WT seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the AffymetrixFluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: 16 day seedling treated with PEG 6hr

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

growth_protocol: Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates were routinely grown under continuous white  light (~75 μmol m-2 s -1) at 23±1℃.

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

treatment_protocol: 16 day old seedlings were transfer to plate contained 40% PEG solution for 6hr

value: seedlings

tag: ecotype

tag: genotype/variation

value: wild type


title: 13912533 - WT LD+2 salk vs WT SD salk

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: The impact of the TOR pathway on growth and stress responses.

hyb_protocol: WT SD salk Cy5 / WT LD+2 salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

source_name: WT SD salk

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

growth_protocol: aerial - Media= hygrometry=75% Temperature=25  Light=50uE

extract_protocol: WT SD salk:15ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: no treatment

value: Columbia

tag: genotype

value: wildtype

value: aerial

tag: developmental stage

value: boyes 3.50 (Boyes et al. Plant Cell 2001)

tag: condition

value: short day

source_name: WT LD+2 salk

extract_protocol: WT LD+2 salk:15ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Long Day - environmental treatment - light,long day:time 2day . Mutant and WT plants grew in short day conditions and some of them were transfered 2 days in long day conditions.

value: long day


title: 13912536 - lst8 SD salk vs lst8 LD+2 salk

hyb_protocol: lst8 LD+2 salk Cy5 / lst8 SD salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lst8 LD+2 salk

extract_protocol: lst8 LD+2 salk:15ug. (Extraction_ARN_au_Trizol.doc)

value: lst8 mutant

tag: tissue

source_name: lst8 SD salk

extract_protocol: lst8 SD salk:15ug. (Extraction_ARN_au_Trizol.doc)


title: 13912538 - WT SD sail vs WT LD+2 sail

hyb_protocol: WT LD+2 sail Cy5 / WT SD sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT LD+2 sail

extract_protocol: WT LD+2 sail:15ug. (Extraction_ARN_au_Trizol.doc)

source_name: WT SD sail

extract_protocol: WT SD sail:15ug. (Extraction_ARN_au_Trizol.doc)


title: 13912532 - WT SD salk vs WT LD+2 salk

hyb_protocol: WT LD+2 salk Cy5 / WT SD salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13912540 - lst8 SD sail vs lst8 LD+2 sail

hyb_protocol: lst8 LD+2 sail Cy5 / lst8 SD sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lst8 LD+2 sail

extract_protocol: lst8 LD+2 sail:15ug. (Extraction_ARN_au_Trizol.doc)

source_name: lst8 SD sail

extract_protocol: lst8 SD sail:15ug. (Extraction_ARN_au_Trizol.doc)


title: 13912537 - lst8 LD+2 salk vs lst8 SD salk

hyb_protocol: lst8 SD salk Cy5 / lst8 LD+2 salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: sensitive cells, biological replicate 2


title: 13912541 - lst8 LD+2 sail vs lst8 SD sail

hyb_protocol: lst8 SD sail Cy5 / lst8 LD+2 sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13912539 - WT LD+2 sail vs WT SD sail

hyb_protocol: WT SD sail Cy5 / WT LD+2 sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MAS98.06_2HSd3conRep_Ref2

description:
MAS98.06_2HSd3conRep
raw data file: 040609_251485044341_S01_GE1-v5_10_Apr08_1_1.txt

source_name: Breast tumor tissue from establlished orthotopic xenograft mouse model MAS98.06

value: Breast tumor tissue

tag: xenograft model

value: LuminalLike


title: ced1 PEG 6hr, biological rep2

description: Gene expression data from ced1 seedlings


title: ced1 PEG 6hr, biological rep1


title: sensitive cells, biological replicate 4

value: human lung cell line


title: WT PEG 6hr, biological rep1

description: Gene expression data from WT seedlings


title: 13912531 - lst8 LD+2 salk vs WT LD+2 salk

hyb_protocol: WT LD+2 salk Cy5 / lst8 LD+2 salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: sensitive cells, biological replicate 1

value: sensitive


title: resistant cells, biological replicate 2

source_name: resistant

value: resistant


title: 13912530 - WT LD+2 salk vs lst8 LD+2 salk

hyb_protocol: lst8 LD+2 salk Cy5 / WT LD+2 salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: resistant cells, biological replicate 3


title: at T21, biological rep4

city: PITTSBURGH

first: Dongwan

middle: Don

last: Kang

state: PA

address: 130 DeSoto Street

institute: University of Pittsburgh

description: Gene expression data from infected lung at T21

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

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

data_processing: The data were analyzed with GC-RMA

organism: Mus musculus

source_name: M.tuberculosis-infected at T21

growth_protocol: Mice were infected with 100 CFU M.tuberculosis H37Rv  and on different time points post infections, RNA was extracted from lungs

extract_protocol: RNA was extracted using RNEasy kit (Qiagen) according to manufacturer's instrcutions

treatment_protocol: On D12, 15 and D21 RNA was extracted and proceesed

tag: time

value: Day 21

tag: infection

value: lung


title: 13912529 - lst8 SD salk vs WT SD salk

hyb_protocol: WT SD salk Cy5 / lst8 SD salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13912528 - WT SD salk vs lst8 SD salk

hyb_protocol: lst8 SD salk Cy5 / WT SD salk Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: at T21, biological rep5


title: 13912527 - lst8 LD+2 sail vs WT LD+2 sail

hyb_protocol: WT LD+2 sail Cy5 / lst8 LD+2 sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control_vs_13 C_Flag leaf of Stejaree45_2nd

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

description: This experiment was performed with three independent biological replicates. The whole genome microarray consisting of a total of ~60,000 oligonucleotides was printed on two separate slides (Slides A and B).

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 50% formamide, 5X SSC, 0.1% SDS, and 10 mM DTT. Hybridization was performed by applying the labeled mixture of control and cold-treated samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified thermal hybridization blocks (SciGene Hybex Microarray Incubation System). Hybridization was performed at 42C from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

scan_protocol: Microarrays were scanned at 635nm and 532nm using the Axon 4000A scanner. Scan image was acquired and processed by the GenePix Pro 5.1.

data_processing: Noncorrelation of signal and background intensities were confirmed by plotting base 2 log background intensity in x axis and base 2 log intensity subtracted with background intensity in y axis. Prior to normalization, normal distribution of Cy3 and Cy5 intensities were tested by qqplot function in R statistical language. The spatial effects on the chip during the hybridization process were checked with spatial func in sma package. The variance difference between Cy3 and Cy5 intensities within microarray was tested by the Student's t-test under the assumptions firstly uniform and then nonuniform variances.

organism: Oryza sativa

source_name: Flag leaf of rice at ambient temperature

label_protocol: The purified mRNA was converted to cDNA and labeled with Cy3 using CyScribe Post-Labelling kit (Amersham Biosciences, UK).

extract_protocol: Total RNA was prepared from flag leaf of the cold-resistant variety, Stejaree45, which were grown at ambient temperature, and the mRNA was purified from total RNAs using a Qiagen oligotex column (Qiagen, Valencia, CA).

tag: treatment

value: control water

tag: variety

value: flag leaf

value: Booting stage

source_name: Flag leaf of rice at cold (13 ℃) water irrigation

label_protocol: The purified mRNA was converted to cDNA and labeled with Cy5 using CyScribe Post-Labelling kit (Amersham Biosciences, UK).

extract_protocol: Total RNA was prepared from flag leaf of the cold-resistant variety, Stejaree45, which were grown at ambient temperature and treated by cold (13 ℃) water irrigation at booting stage during 3 days, and the mRNA was purified from total RNAs using a Qiagen oligotex column (Qiagen, Valencia, CA).

value: cold water for 3 days


title: at T21, biological rep3


title: Control_vs_13 C_Flag leaf of Stejaree45_1st


title: myo1 replicate #3

city: San Juan

first: José

middle: R

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

hyb_protocol: Hybridization of Cy5 and Cy3 labeled cRNAs were performed using Yeast Oligo Microarrays slides and hybridization kit from Agilent technologies  (Sheldon manufacturing, Cornelius, Oregon).To each fluorescent cRNA sample,  2.2 µL  of 25X fragmentation buffer was added, then incubated at 60°C for 30 minutes. After the incubation, 55 µL of 2X GEx hybridization buffer were added to the sample. Samples were placed into the array slides. The array slides were placed in the hybridization chambers and incubated at 60°C for 17 hours. Array slides were washed in  gene expression wash buffer 1 and 2 and finally acetonitrile as stabilization and drying solution.

scan_protocol: Arrays were scanned with a VersArray Chip Reader system (Bio-Rad, Hercules, CA) at a resolution of 5μm with detector sensitivity values set between 704-800 and laser power at 85%. Scanned images were transferred to the Imagene 3.0 software program (Biodiscovery, El Segundo, CA) for further analysis to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 TIFF files (raw data).

data_processing: The microarrays raw data generated with Imagene 3 were analyzed using Limma software (Bioconductor Package 1.7).  The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array.  After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated.  The fold change in gene expression was calculated by 2(M), where M is the log2-fold change after background correction and normalization.  An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed [36]. Genes with a p-value ≤ 0.018 was established as a cutoff for differential expression. In addition, a false discovery rate (FDR) [37] was performed with Limma software.

organism: Saccharomyces cerevisiae

source_name: Cy3_YJR13 (myo1 delta mutant)

label_protocol: 1.0µg of RNA extracted from ribosomal pellets was amplified using the Low RNA input Fluorescent Linear Amplification kit (Agilent Technologies, Palo Alto, A). Briefly RNA was mixed with 1.2 µL of T7 promoter primer and nuclease free water. The reaction mix was incubated at  65°C for 10 minutes and then  reactions  was placed on ice for 5 minutes. 8.5 µL of cDNA master mix was added to each reaction and incubated at 40°C for two hours. Then the reaction was incubated at 65°C for 15 minutes. 57.6 µL of transcription master mix including the Cyanine 3-CTP (10mM)  was added and then incubated at 40°C for 2 hours, to produce the cRNA. The cRNA was purified using the RNeasy mini spin column from Qiagen and dye incorporation was monitored on an Agilent Bioanalyzer.

growth_protocol: The microarrays experiments of three biological and one technical replicates were performed in YJR12 (wt) and YJR13 (myo1∆) strains. YJR12 (wild type) and YJR13 (myo1∆) strains were obtained as haploid segregants from a cross between YJR6 (myo1::HIS5 strain) and BY4741 (obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) with continuous shaking at 200 rpm.

extract_protocol: Cells were harvesting by centrifugation (1,341g for 5min at 4ºC ). Pelleted yeast cells were washed with ice-cold lysis buffer (50mM Tris-HCl, pH 7.5, 100mM NaCl, 7mM MgCl2, 1mM DTT, 1mM PMSF and 50µg/ml cicloheximide) and then resuspended in 1.5ml of lysis buffer together with a quarter volume of acid-washed 0.5mm glass beads.  Cells were disrupted by vortex mixing for 20s with 30s intervals on ice (10 times). Unbroken cells and large debris were removed by a low speed spin (800g  for 10min).  The supernatant was centrifuged at 10,000g for 30 min at 4ºC, yielding supernatant (S10) and pellet (P10). Supernatant S10 was collected and centrifuged at 100,000g in 50% sucrose solution for 60min at 4ºC (Beckman 80 Ti rotor ) thereby yielding supernatant S100 and ribosomal pellet P100. Ribosomal pellets contained in P100 fractions was resuspended in a guanidine thiocyanate buffer containing 10% mercaptoethanol  (RLT buffer, RNeasy Mini Kit, Qiagen ). RNA was extracted using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Valencia, CA) following the manufacturer’s instructions. RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE).  The purity and integrity of the RNA was monitored by electrophoresis using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: strain

value: YJR13 (myo1∆)

source_name: Cy5_YJR12 (wild type)

label_protocol: 1.0µg of RNA extracted from ribosomal pellets was amplified using the Low RNA input Fluorescent Linear Amplification kit (Agilent Technologies, Palo Alto, A). Briefly RNA was mixed with 1.2 µL of T7 promoter primer and nuclease free water. The reaction mix was incubated at  65°C for 10 minutes and then  reactions  was placed on ice for 5 minutes. 8.5 µL of cDNA master mix was added to each reaction and incubated at 40°C for two hours. Then the reaction was incubated at 65°C for 15 minutes. 57.6 µL of transcription master mix including the Cyanine 5-CTP (10mM)  was added and then incubated at 40°C for 2 hours, to produce the cRNA. The cRNA was purified using the RNeasy mini spin column from Qiagen and dye incorporation was monitored on an Agilent Bioanalyzer.

value: YJR12 (wild type)


title: Control_vs_13 C_Glumous flower of Stejaree45_3rd

source_name: Glumous flower of rice at ambient temperature

extract_protocol: Total RNA was prepared from glumous flower of the cold-resistant variety, Stejaree45, which were grown at ambient temperature, and the mRNA was purified from total RNAs using a Qiagen oligotex column (Qiagen, Valencia, CA).

value: glumous flower

source_name: Glumous flower of rice at cold (13 ℃) water irrigation

extract_protocol: Total RNA was prepared from glumous flower of the cold-resistant variety, Stejaree45, which were grown at ambient temperature and treated by cold (13 ℃) water irrigation at booting stage during 3 days, and the mRNA was purified from total RNAs using a Qiagen oligotex column (Qiagen, Valencia, CA).


title: myo1 replicate #2

source_name: Cy3_YJR12 (wild type)

source_name: Cy5_YJR13(myo1 delta mutant)


title: myo1 replicate #1


title: resistant cells, biological replicate 1

hyb_protocol: Samples were hybridized according to the standard Affymetrix protocol

tag: cell line


title: 252978410003_B7A_CY5_ETP05_017_CY3.mev.refIsIB.out

status: Public on Dec 07 2010

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Escherichia coli

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in LB overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: 13912526 - WT LD+2 sail vs lst8 LD+2 sail

hyb_protocol: lst8 LD+2 sail Cy5 / WT LD+2 sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: aerial

value: boyes 3.50 (Boyes et al. Plant Cell 2001)

value: wildtype


title: 13912523 - WT SD sail vs lst8 SD sail

hyb_protocol: lst8 SD sail Cy5 / WT SD sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: lst8 mutant

value: short day


title: Control_vs_13 C_Glumous flower of Stejaree45_2nd


title: myo1 replicate #4


title: Control_vs_13 C_Flag leaf of Stejaree45_3rd


title: Control_vs_13 C_Glumous flower of Stejaree45_1st


title: 13912525 - lst8 SD sail vs WT SD sail

hyb_protocol: WT SD sail Cy5 / lst8 SD sail Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 252978410078_B7A_CY5_WS2741_A1_CY3.mev.refIsIB.out

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.


title: 252978410077_B7A_CY5_ETP05_002_CY3.mev.refIsIB.out


title: 252978410077_B7A_CY5_C34666_CY3.mev.refIsIB.out


title: 252978410078_B7A_CY5_2_1_CY3.mev.refIsIB.out


title: 252978410078_B7A_CY5_WS5874_A1_CY3.mev.refIsIB.out


title: 252978410078_B7A_CY5_WS4264_A1_CY3.mev.refIsIB.out


title: 252978410077_B7A_CY5_ETP05_003_CY3.mev.refIsIB.out


title: 252978410076_B7A_CY5_ETP98109_CY3.mev.refIsIB.out


title: 252978410076_B7A_CY5_C35605_CY3.mev.refIsIB.out


title: 252978410076_B7A_CY5_C35213_CY3.mev.refIsIB.out


title: 252978410077_B7A_CY5_174900_CY3.mev.refIsIB.out


title: 252978410076_B7A_CY5_178200_CY3.mev.refIsIB.out


title: 252978410075_B7A_CY5_sPRH445_CY3.mev.refIsIB.out


title: 252978410075_B7A_CY5_O78_h11_CY3.mev.refIsIB.out


title: 252978410075_B7A_CY5_ETP05_011_CY3.mev.refIsIB.out


title: 252978410064_B7A_CY5_HS_CY3.mev.refIsIB.out

value: HS


title: 252978410064_B7A_CY5_E1790_CY3.mev.refIsIB.out


title: 252978410064_B7A_CY5_E1789_CY3.mev.refIsIB.out


title: 252978410063_B7A_CY5_TW3452_CY3.mev.refIsIB.out


title: 252978410063_B7A_CY5_sPRH372_CY3.mev.refIsIB.out


title: 252978410064_B7A_CY5_sPRH609_CY3.mev.refIsIB.out


title: 252978410063_B7A_CY5_COSIN07_14_CY3.mev.refIsIB.out

value: cosin 07-14


title: 252978410069_B7A_CY5_sPRH421_CY3.mev.refIsIB.out


title: DU145 control (non-specific siRNA) 1

city: Washington

first: Olga

middle: A

last: Timofeeva

state: DC

address: 3900 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

description: scrambled siRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Matrix table was generated using BRB-ArrayTools Version: 4.1.0 - Beta_3 Release (October 2010) using GC-RMA as normalization method.

source_name: DU145 treated with scrambled siRNA for 48 hr

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

growth_protocol: DU145 prostate cancer cell line was obtained from American Type Culture Collection. Cells were maintained in RPMI 1640 supplemented with 10% heat-inactivated FBS. Cell cultures were maintained at 37°C under a humidified atmosphere of 5% CO2 in an incubator.

extract_protocol: Extraction of total RNA was performed according to the Qiagen RNeasy manufacturer's instructions.

treatment_protocol: Cells were treated with STAT3 siRNA or scrabled (non-specific) siRNA for 48 hr. Western blot with STAT3 antibody confirmed decrease in STAT3 levels.

value: DU145 prostate cancer cell line

value: control


title: 252978410070_B7A_CY5_sPRH20_CY3.mev.refIsIB.out


title: 252978410070_B7A_CY5_ICDDR_B_p7_CY3.mev.refIsIB.out


title: 252978410075_B7A_CY5_ETP05_035_CY3.mev.refIsIB.out


title: 252978410070_B7A_CY5_NR_12_CY3.mev.refIsIB.out


title: 252978410069_B7A_CY5_sPRH610_CY3.mev.refIsIB.out


title: DU145 STAT3 siRNA-1

description: STAT3 siRNA

source_name: DU145 treated with STAT3 siRNA for 48 hr

value: STAT3 knockdown


title: 252978410063_B7A_CY5_B7A_CY3.mev.refIsIB.out


title: DU145 STAT3 siRNA-2

description: STAT3 siRNA


title: 252978410069_B7A_CY5_sPRH25_CY3.mev.refIsIB.out


title: DU145 ST3-Hel2A-2-1

description: Gene expression data from DU145 treated with ST3-Hel2A-2

source_name: DU145 treated with ST3-Hel2A-2 for 3hr

treatment_protocol: Cells were treated with ST3-Hel2A-2 or DMSO for 3 hr

tag: agent


title: DU145 control-3

description: Gene expression data from DU145 treated with DMSO

source_name: DU145 treated with DMSO for 3hr


title: DU145 control-2


title: DU145 control (non-specific siRNA) 2

description: scrambled siRNA


title: 252978410070_B7A_CY5_sPRH612_CY3.mev.refIsIB.out


title: 252978410069_B7A_CY5_278485_1_CY3.mev.refIsIB.out


title: 252978410068_B7A_CY5_WS3294A_CY3.mev.refIsIB.out


title: DU145 control-1


title: DU145 ST3-Hel2A-2-3


title: DU145 ST3-Hel2A-2-2


title: 252978410068_B7A_CY5_M408C1_CY3.mev.refIsIB.out


title: 252978410068_B7A_CY5_ICDDR_B_p_10_CY3.mev.refIsIB.out


title: brain_sham_6h_rep1

city: Chuo

first: Hideki

last: Shojo

state: Yamanashi

address: 1110 shimokato

department: Graduate School of Medical Science

country: Japan

institute: University of Yamanashi

description:
non-injured control
6-sham(M-21)

hyb_protocol: cRNA were hybridized on GeneChip rat genome 230 2.0 using the Hybridization Oven 640 110V. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix 00-0074).

data_processing: Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v11.0.2 software (Agilent). Compared data from experimental conditions are normalized versus array's base line median considered for each case.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: lateral cortex, non-injured control

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 0.4 ug PolyA RNA (One-cycle Target Labeling: GeneChip Expression Analysis Technical Manual, 701021 Rev. 5).

growth_protocol: Rats were performed craniectomy of diameter 4.8 mm over the right parietal cortex under general anesthesia. A cranial Leur adapter of inner diameter 2.5 mm was placed on the craniectomy site and mounted to the skull by using dental acrylic resin. The animals were housed for 48 h, and they were then re-anesthetized. The cranial Leur adapter was filled with saline and attached to the fluid percussion device. Animals were subjected to sham or moderate (3.3 ± 0.3 atm) fluid percussions.

extract_protocol: Polyadenylated RNA was isolated using the Quickprep micro mRNA purification kit (Amersham, USA) according to the manufacturer’s protocol.

treatment_protocol: Rats were transcardially perfused with physiological saline under general anesthesia at 3, 6, 12 and 48 h after moderate fluid percussion or the sham operation. The brains were quickly removed and cut coronally into 2-mm-thick sections.  The cortices that corresponded to the contusion areas were removed. They were then placed in RNAlaterTM (Takara, Japan) overnight at 4°C and stored at –20 °C until use.

value: Wistar

tag: gender

value: male

tag: age

value: 8 weeks old

value: brain, lateral cortex

tag: stress

value: non-injured control


title: brain_sham_3h_rep1

description:
non-injured control
3-sham(M-28)


title: brain_at 12h after trauma_rep3

description:
impacted region
12(M-26)

source_name: lateral cortex, traumatic brain injury

value: moderate fluid percussion injury


title: 252978410062_B7A_CY5_WS7179_A2_CY3.mev.refIsIB.out


title: brain_at 48h after trauma_rep3

description:
impacted region
48(M-24)


title: 252978410032_B7A_CY5_BCE066_DS5_CY3.mev.refIsIB.out

value: BCE066, DS5


title: brain_sham_12h_rep1

description:
non-injured control
12-sham(M-27)


title: 252978410032_B7A_CY5_BCE049_DS3_CY3.mev.refIsIB.out

value: BCE049, DS3


title: 252978410031_B7A_CY5_ETP05_015_CY3.mev.refIsIB.out


title: brain_at 6h after trauma_rep1

description:
impacted region
6(M-9)


title: 252978410067_B7A_CY5_F5656_C1_CY3.mev.refIsIB.out


title: brain_sham_48h_rep1

description:
non-injured control
48-sham(M-25)


title: 252978410031_B7A_CY5_BCE068_MS10_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteri


title: 252978410032_B7A_CY5_BCE011_DS3_CY3.mev.refIsIB.out

value: BCE011, DS3


title: brain_at 3h after trauma_rep3

description:
impacted region
3(M-20)


title: brain_at 48h after trauma_rep2

description:
impacted region
48(M-23)


title: 252978410031_B7A_CY5_BCE068_MS23.mev.refIsIB.out


title: 252978410032_B7A_CY5_BCE062_MS24_CY3.mev.refIsIB.out


title: 252978410067_B7A_CY5_WS7162_A1_CY3.mev.refIsIB.out


title: brain_at 6h after trauma_rep2

description:
impacted region
6(M-12)


title: 252978410066_B7A_CY5_WS1933D_CY3.mev.refIsIB.out


title: 252978410066_B7A_CY5_WS6582_A1_CY3.mev.refIsIB.out


title: brain_at 48h after trauma_rep1

description:
impacted region
48(M-3)


title: brain_at 6h aftert rauma_rep3

description:
impacted region
6(M-18)


title: 252978410067_B7A_CY5_ETEC_8_11_CY3.mev.refIsIB.out

value: ETEC 8/11


title: brain_at 12h after trauma_rep2

description:
impacted region
12(M-14)


title: 252978410067_B7A_CY5_B2C_CY3.mev.refIsIB.out


title: brain_at 3h after trauma_rep2

description:
impacted region
3(M-17)


title: 252978410068_B7A_CY5_CFT073_CY3.mev.refIsIB.out


title: brain_at 3h after trauma_rep1

description:
impacted region
3(M-5)


title: Rat treated with live Yp-wild type and Yp-pYV variant 36hr, rep 5

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
Gene expression data from rat treated with live Yp-wild type and Yp-pYV variant 36hr rep 5.
1589_JEC_5_rat_30_30-R301-pYV-+LiveWT_01_1601

hyb_protocol: Five μg of the cRNA was fragmented and hybridized to a Rat 230 2.0 Affymetrix GeneChip (one chip per sample; 5-10 biological replicates per sample type). All samples were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to manufacturer protocols (Affymetrix; Santa Clara CA).

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Yp genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: lymph node, live Yp-wild type and Yp-pYV variant, 36hr

label_protocol: One μg of total RNA was amplified and biotin-ddUTP-labeled using the Enzo BioArray™ Single-Round RNA Amplification and Biotin Labeling System (ENZO Life Sciences Inc; Farmingdale, NY).

growth_protocol: The fully virulent Y. pestis 195/P wild-type strain, originally isolated from a patient with pneumonic plague in India, and a pYV– variant of this strain were used in this study. Starter cultures were grown overnight in heart infusion broth (HIB) at 28°C. The bacteria were then subcultured in Luria broth (LB) for 18h at 21°C to mimic the temperature during passage though the flea. Bacteria were quantified by Petroff-Hausser direct count, and inocula were prepared that contained 5 x10^4 WT bacteria/ml or 5 x 10^9 pYV– bacteria/ml in sterile PBS, pH 7.4.

extract_protocol: Isolated right inguinal lymph nodes from groups of five to 10 rats were pressed through a 70 μm cell strainer into 10 ml of RNAprotect (Qiagen; Valencia, CA). One ml of each sample was removed for bacterial load analysis by quantitative RT- PCR. The remaining sample was centrifuged at 4000 x g for 10 min, the RNAprotect decanted, and the resulting pellet stored at -80º C. The RNA was prepared for microarray analysis. Briefly, the samples were homogenized using QIAshredder columns and total RNA was isolated using the RNeasy 96 kit (Qiagen). The RNA quality and quantity were measured on a Bioanalyzer 2100 using RNA LabChips (Agilent Technologies; Santa Clara, CA) and spectrophotometry.

treatment_protocol: Six- to eight-week-old female Brown Norway rats (Rattus norvegicus) were injected intradermally in the right lower lumbar region with 50 ul of PBS containing 10^3 CFU of WT or 10^8 CFU of pYV– Y. pestis 195/P. Additional groups of rats were injected with 50 ul of sterile PBS, 10^8 paraformaldehyde-killed WT Y. pestis 195/P, or co-infected with 10^3 CFU of WT and 10^8 CFU of the pYV– variant. At 36 or 60h after infection, the rats were euthanized and the right inguinal lymph node were collected.

value: Brown Norway

value: female

value: 6-8 weeks

value: lymph node

value: Yersinia pestis 195/P wild type and pYV–variant


title: Rat treated with live Yp-wild type and Yp-pYV variant 36hr, rep 3

description:
Gene expression data from rat treated with live Yp-wild type and Yp-pYV variant 36hr rep 3.
1587_JEC_5_rat_28_28-R299-pYV-+LiveWT_01_1604


title: 252978410031_B7A_CY5_BCE054_DS4_CY3.mev.refIsIB.out

value: BCE054, DS4


title: 252978410066_B7A_CY5_ICDDR_P_2_CY3.mev.refIsIB.out


title: 252978410030_B7A_ETP98066_CY3.mev.refIsIB.out


title: 252978410065_B7A_CY5_E8775_CY3.mev.refIsIB.out


title: Rat treated with live Yp-wild type and Yp-pYV variant 36hr, rep 2

description:
Gene expression data from rat treated with live Yp-wild type and Yp-pYV variant 36hr rep 2.
1586_JEC_5_rat_27_27-R298-pYV-+LiveWT_01_2599


title: 252978410062_B7A_CY5_WS4087_A1_CY3.mev.refIsIB.out


title: brain_at 12h after trauma_rep1

description:
impacted region
12(M-13)


title: Rat treated with killed Yp-wild type 36hr, rep 5

description:
Gene expression data from rat treated with killed Yp-wild type 36hr rep 5.
1569_JEC_5_rat_10_10-R281-KilledWT_01_2588

source_name: lymph node, killed Yp-wild type, 36hr

value: killed Yersinia pestis 195/P wild type


title: 252978410066_B7A_CY5_2230_CY3.mev.refIsIB.out


title: Rat treated with killed Yp-wild type 36hr, rep 3

description:
Gene expression data from rat treated with killed Yp-wild type 36hr rep 3.
1567_JEC_5_rat_08_8-R279-KilledWT_01_2676


title: 252978410030_B7A_CY5_ETP98105_CY3.mev.refIsIB.out


title: 252978410062_B7A_CY5_DS168_1_CY3.mev.refIsIB.out


title: Rat treated with Yp-wild type septicemic, rep 9

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 9
961_JEC_4_rat_39_Yp195P60h_01_1690

source_name: lymph node, Yp-wild type, septicemic, 60hr

value: Yersinia pestis 195/P wild type


title: 252978410030_B7A_CY5_ETP05_008_CY3.mev.refIsIB.out


title: 252978410065_B7A_CY5_E2528_C1_CY3.mev.refIsIB.out


title: Rat treated with Yp-wild type septicemic, rep 10

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 1.0
962_JEC_4_rat_40_Yp195P60h_01_1676


title: Rat treated with killed Yp-wild type 36hr, rep 4

description:
Gene expression data from rat treated with killed Yp-wild type 36hr rep 4.
1568_JEC_5_rat_09_9-R280-KilledWT_01_1539


title: Rat treated with killed Yp-wild type 36hr, rep 1

description:
Gene expression data from rat treated with killed Yp-wild type 36hr rep 1.
1565_JEC_5_rat_06_6-R277-KilledWT_01_2694


title: 252978410062_B7A_CY5_PE360_CY3.mev.refIsIB.out


title: 252978410030_B7A_CY5_C36255_CY3.mev.refIsIB.out


title: Rat treated with Yp-wild type septicemic, rep 8

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 8
960_JEC_4_rat_38_Yp195P60h_01_1541


title: 252978410065_B7A_CY5_M424_C1_CY3.mev.refIsIB.out


title: 252978410029_B7A_CY5_sPRH_604_CY3.mev.refIsIB.out


title: Rat treated with live Yp-wild type and Yp-pYV variant 36hr, rep 4

description:
Gene expression data from rat treated with live Yp-wild type and Yp-pYV variant 36hr rep 4.
1588_JEC_5_rat_29_29-R300-pYV-+LiveWT_01_1618


title: Rat treated with Yp-wild type septicemic, rep 7

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 7
959_JEC_4_rat_37_Yp195P60h_01_1687


title: Rat treated with killed Yp-wild type 36hr, rep 2

description:
Gene expression data from rat treated with killed Yp-wild type 36hr rep 2.
1566_JEC_5_rat_07_7-R278-KilledWT_01_6339


title: 252978410061_B7A_CY5_COSIN07_92_CY3.mev.refIsIB.out

value: cosin 07-92


title: Rat treated with live Yp-wild type and Yp-pYV variant 36hr, rep 1

description:
Gene expression data from rat treated with live Yp-wild type and Yp-pYV variant 36hr rep 1.
1585_JEC_5_rat_26_26-R297-pYV-+LiveWT_01_1555


title: Rat treated with Yp-wild type septicemic, rep 6

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 6.
958_JEC_4_rat_36_Yp195P60h_01_1557


title: Rat treated with Yp-wild type septicemic, rep 3

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 3.
955_JEC_4_rat_33_Yp195P60h_01_1720


title: 252978410029_B7A_CY5_sPRH_443_CY3.mev.refIsIB.out


title: 252978410029_B7A_CY5_sPRH_403_CY3.mev.refIsIB.out


title: 252978410061_B7A_CY5_COSIN07_88_CY3.mev.refIsIB.out

value: cosin 07-88


title: 252978410029_B7A_CY5_sPRH_606_CY3.mev.refIsIB.out


title: 252978410073_B7A_CY5_WS2173A_CY3.mev.refIsIB.out


title: Rat treated with Yp-wild type septicemic, rep 5

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 5.
957_JEC_4_rat_35_Yp195P60h_01_1542


title: Rat treated with Yp-wild type septicemic, rep 4

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 4.
956_JEC_4_rat_34_Yp195P60h_01_1667


title: Rat treated with Yp-wild type bubonic, rep 6

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 6.
952_JEC_4_rat_30_Yp195P36h_01_1525

source_name: lymph node, Yp-wild type, bubonic, 36hr


title: 1h iron 1

city: Marburg

first: Julia

last: Gödeke

address: Karl-von-Frisch-Strasse 10

department: Ecophysiology

country: Germany

institute: Max Planck Istitute for terrestrial Microbiology

hyb_protocol: Samples were loaded onto the arrays and hybridization was done over night (16 hours) at 45°C, using argon pressure to move the samples within the arrays.

scan_protocol: After the hybridization the chip is washed with the “febit GT-standard (external incubation)” hybridization profile and a standard detection using the appropriate filter set in  the Geniom® One Instrument.

data_processing: To assess the reproducibility of the biological replicates, the Pearson Correlation Coefficients were calculated. Quantile normalized signal intensity generated by the Febit company using R.

organism: Shewanella oneidensis MR-1

source_name: total bacterial cells

label_protocol: febit uses the MICROBExpressTM kit from Ambion to remove 16S and 23S rRNA from RNA samples. For each array 3 μg of total RNA were purified according to the manufacturer’s instructions. Following, the MessageAmpTMII-Bacteria kit from Ambion was applied for labelling the mRNA. The kit provides a transcription of RNA in cDNA, following a transcription in cRNA while enrichment of all nucleic acid molecules is included. After labelling samples were dried in a speed-vac and fragmented with a fragmentation buffer. Finally, febit’s proprietary standard Longmer Hybridization Buffer (15 μl per array) was added.

growth_protocol: Cells were grown on beads in a hydrodynamic cell harvesting sytem consisting of syringe columns filled with glass or oxidized iron beads (5 mm diameter), providing a large surface without creating void space. Medium flow is maintained by a peristaltic pump at a medium turnover rate of 6-8 min. This system was shown to maintain aerobic conditions (> 5 mg O2/ml) for longer than 4 h.

extract_protocol: Total RNA was extracted from S. oneidensis MR-1 cells using the hot phenol method. Residual chromosomal DNA was removed using Turbo DNA-freeTM (Applied Biosystems) following the manufacturer’s instructions.

tag: surface

value: oxidized iron beads

tag: time period of attachment


title: Rat treated with Yp-wild type septicemic, rep 1

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 1.
953_JEC_4_rat_31_Yp195P60h_01_1544


title: Rat treated with Yp-wild type septicemic, rep 2

description:
Gene expression data from rat treated with Yp-wild type septicemic rep 2.
954_JEC_4_rat_32_Yp195P60h_01_1661


title: Rat treated with Yp-wild type bubonic, rep 5

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 5.
951_JEC_4_rat_29_Yp195P36h_01_1532


title: 252978410028_B7A_CY5_WS3080A_CY3.mev.refIsIB.out


title: 1h iron 2


title: 1h glass 2

value: glass beads

value: 1 h


title: 252978410061_B7A_CY5_COCAR07_40_CY3.mev.refIsIB.out

value: cocar 07-40


title: 252978410073_B7A_CY5_WS1896_A1_CY3.mev.refIsIB.out


title: 1h glass 1


title: Rat treated with Yp-wild type bubonic, rep 2

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 2.
948_JEC_4_rat_26_Yp195P36h_01_1692


title: 252978410073_B7A_CY5_E7476A_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Young_MA82

city: Paris

first: Sophie

last: Nadaud

address: 91 Bd de l'hopital

institute: INSERM

description: The array was first analyzed using Illumina's BeadScan software. The array was then checked for background and hybridisation intensities and homogeneity.

hyb_protocol: 750 ng of amplified and Cy3-labelled RNA were used directly hybridized on the Beadchips for 16 hours at 58°C following Illumina’s instructions. Beadchips were then washed following Illumina's protocol.

scan_protocol: Beadchips were scanned on the Illumina BeadXpress® platform available on the site of hospital La Pitié-Salpêtrière (http://www.p3s.chups.jussieu.fr/) according to the manufacturer’s protocol.

data_processing: Raw data were normalized with the Quantiles-method using IlluminaGUI R-package (Schultze and Eggle, Bioinformatics 2007 23(11):1431-1433). Present/Absent call was determined with the detection p-values using IlluminaGUI. Analysis (comparisons between patients under 60 named young and patients over 75 named old) was then performed on the 13792 probes which are called Present in at least half of the samples of one of the 2 groups (young or old).

source_name: Media from human mammary artery, patient under 60 (young)

label_protocol: 250 ng of total RNA was amplified using TotalPrep RNA Amplification kit (Ambion, Applied Biosystems, Courtaboeuf, France) and biotin-16-UTP were incorporated. Amplified RNA concentration and quality were determined using Nanodrop and Agilent 2100 Bioanalyzer (RNA nano LabChip). 750 ng of amplified RNA were used for DirectHyb Assay where RNA is labelled with Streptavidin-Cy3 following illumina's protocol.

treatment_protocol:
The mammary artery segments was kept in physiological solution at 4°C and, the same day,was dissected by mechanically dissociating the media from the adventitia and immediately freezing it in liquid nitrogen.
Frozen medias (usually 50-150 mg) were crushed in ice in 6 volumes of Lysis Binding Buffer from mirVana miRNA isolation kit (Ambion, Applied Biosystems, Courtaboeuf, France) and total RNA were prepared according to the manufacturer’s instructions. 5-20 µg total RNA were obtained.
To avoid any genomic contamination, each RNA was treated with rDNase I using DNA-freeTM DNase treatment and removal reagents from Ambion (Applied Biosystems, Courtaboeuf, France).
RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France). RNA quality was assayed using RNA nano LabChip ® and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). Only patients with a RNA Integrity number greater than 7 (determined by the Bioanalyzer) and a 28S/18S value greater than 1 were selected for the following studies.

value: male

value: Mammary artery

tag: surgical procedure

value: coronary bypass surgery (surgical waste)


title: Rat treated with Yp-wild type bubonic, rep 3

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 3.
949_JEC_4_rat_27_Yp195P36h_01_1566

value: Brown Norway


title: Rat treated with Yp-wild type bubonic, rep 1

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 1.
947_JEC_4_rat_25_Yp195P36h_01_1548

value: female


title: 252978410060_B7A_CY5_WS3596_A4_CY3.mev.refIsIB.out


title: 252978410028_B7A_CY5_TW3576_CY3.mev.refIsIB.out


title: 0.25h glass 2


title: Hum_Mammary_media_Old_M123

source_name: Media from human mammary artery, patient over 75 (old)

extract_protocol:
Frozen medias (usually 50-150 mg) were crushed in ice in 6 volumes of Lysis Binding Buffer from mirVana miRNA isolation kit (Ambion, Applied Biosystems, Courtaboeuf, France) and total RNA were prepared according to the manufacturer’s instructions. 5-20 µg total RNA were obtained.
To avoid any genomic contamination, each RNA was treated with rDNase I using DNA-freeTM DNase treatment and removal reagents from Ambion (Applied Biosystems, Courtaboeuf, France).
RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France). RNA quality was assayed using RNA nano LabChip ® and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). Only patients with a RNA Integrity number greater than 7 (determined by the Bioanalyzer) and a 28S/18S value greater than 1 were selected for the following studies.


title: 252978410073_B7A_CY5_214_4_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Young_M113


title: 252978410028_B7A_CY5_TW3439_CY3.mev.refIsIB.out


title: Rat treated with Yp-pYV variant 60hr, rep 6

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 6.
946_JEC_4_rat_24_Yp195PpYV-60h_01_1602

source_name: lymph node, Yp-pYV variant, 60hr

value: 6-8 weeks

value: Yersinia pestis pYV–variant


title: Rat treated with Yp-wild type bubonic, rep 4

description:
Gene expression data from rat treated with Yp-wild type bubonic rep 4.
950_JEC_4_rat_28_Yp195P36h_01_1700

value: lymph node


title: planktonic 1

value: logarithmic aerobic growing cells


title: 0.25h glass 1


title: Hum_Mammary_media_Young_MA83


title: 252978410028_B7A_CY5_ETP98073_CY3.mev.refIsIB.out


title: Rat treated with Yp-pYV variant 60hr, rep 4

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 4.
944_JEC_4_rat_22_Yp195PpYV-60h_01_1622


title: Hum_Mammary_media_Old_M104


title: Rat treated with Yp-pYV variant 60hr, rep 5

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 5.
945_JEC_4_rat_23_Yp195PpYV-60h_01_1675


title: 252978410011_B7A_CY5_NN_34_1_3_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Young_M116


title: Rat treated with Yp-pYV variant 60hr, rep 3

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 3.
943_JEC_4_rat_21_Yp195PpYV-60h_01_1552


title: 252978410060_B7A_CY5_E1791_CY3.mev.refIsIB.out


title: 252978410072_B7A_CY5_sPRH605_CY3.mev.refIsIB.out


title: Rat treated with Yp-pYV variant 60hr, rep 2

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 2.
942_JEC_4_rat_20_Yp195PpYV-60h_01_1634


title: Rat treated with Yp-pYV variant 60hr, rep 1

description:
Gene expression data from rat treated with Yp-pYV variant 60hr rep 1.
941_JEC_4_rat_19_Yp195PpYV-60h_01_1644


title: Hum_Mammary_media_Old_M100


title: planktonic 2


title: ge3bl_2 with array type maize from Affymetrix

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription.

hyb_protocol: labelled extract quantity: 10ug

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

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

organism: Zea mays

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

growth_protocol: stem - Planting date: 21/04/2009 Pool de 5 plantes/ lignée/repetition conditions météo en Juillet pendant les prélèvements (station météo des Verrines) RG: Rayonnement global horaire (Joules/cm2) 202     T: Température instantanée horaraire (degrés Celsuis)20.27     U: humidité instantanée horaire (poucentage) 53

tag: harvest date

value: stem

tag: genotype

value: F98902 line, coming from "Iodent" genotype

tag: phenotype

value: Dent type grain


title: ge4bl_2 with array type maize from Affymetrix

tag: tissue

value: F2 line, coming from "lacaune" genotype

value: Flint type grain


title: 252978410072_B7A_CY5_O63_nm_CY3.mev.refIsIB.out


title: 252978410011_B7A_CY5_E9034A_CY3.mev.refIsIB.out


title: ge2bl_2 with array type maize from Affymetrix

value: F7033 line, coming from "(LorenaXF252)XF252" genotype

value: yellow grain , Flint-Dent type


title: Hum_Mammary_media_Young_M103


title: ge5bl_2 with array type maize from Affymetrix

value: Cm484 line, coming from "200-2-1" genotype

value: Flint-Dent grain type


title: 252978410072_B7A_CY5_ICDDR_B_p6_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Young_M92

value: male

value: Mammary artery


title: 252978410011_B7A_CY5_E1777_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Old_M95

value: coronary bypass surgery (surgical waste)


title: 252978410011_B7A_CY5_DS26_1_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Young_M54

description: The array was first analyzed using Illumina's BeadScan software. The array wasthen checked for background and hybridisation intensities and homogeneity.


title: Rat treated with Yp-pYV variant 36hr, rep 3

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 3.
937_JEC_4_rat_15_Yp195PpYV-36h_01_1606

source_name: lymph node, Yp-pYV variant, 36hr

value: Brown Norway

value: female

tag: time


title: ge1bl_2 with array type maize from Affymetrix

value: F7025 line, coming from "IodentXF113bm3" genotype

value: yellow grain, Flint-Dent type


title: ge5bl_1 with array type maize from Affymetrix


title: Hum_Mammary_media_Old_M75


title: Rat treated with Yp-pYV variant 36hr, rep 5

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 5.
939_JEC_4_rat_17_Yp195PpYV-36h_01_1620

value: 6-8 weeks

value: lymph node

value: Yersinia pestis pYV–variant


title: Rat treated with Yp-pYV variant 36hr, rep 4

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 4.
938_JEC_4_rat_16_Yp195PpYV-36h_01_1588


title: ge4bl_1 with array type maize from Affymetrix

value: stem


title: Hum_Mammary_media_Old_M91


title: Rat treated with Yp-pYV variant 36hr, rep 2

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 2.
936_JEC_4_rat_14_Yp195PpYV-36h_01_1695


title: 252978410010_B7A_CY5_ICDDR_B_p13_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: ge3bl_1 with array type maize from Affymetrix

value: F98902 line, coming from "Iodent" genotype

value: Dent type grain


title: 252978410065_B7A_CY5_350C1A_CY3.mev.refIsIB.out


title: Hum_Mammary_media_Old_M50


title: Rat treated with Yp-pYV variant 36hr, rep 1

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 1.
935_JEC_4_rat_13_Yp195PpYV-36h_01_1598


title: Hum_Mammary_media_Young_M49


title: 252978410027_B7A_ETEC20_10_CY3.mev.refIsIB.out


title: ge1bl_1 with array type maize from Affymetrix


title: Rat treated with Yp-pYV variant 36hr, rep 6

description:
Gene expression data from rat treated with Yp-pYV variant 36hr rep 6.
940_JEC_4_rat_18_Yp195PpYV-36h_01_1609


title: 252978410010_B7A_CY5_ICDDR_B_p4_CY3.mev.refIsIB.out


title: Rat treated with PBS 60hr, rep 5

description:
Gene expression data from rat treated with PBS 60hr rep 5.
933_JEC_4_rat_11_PBS60h_01_1621

source_name: lymph node, PBS, 60hr

value: PBS


title: 252978410072_B7A_CY5_COSIN07_36_CY3.mev.refIsIB.out

value: cosin 07-36


title: Rat treated with PBS 60hr, rep 4

description:
Gene expression data from rat treated with PBS 60hr rep 4.
932_JEC_4_rat_10_PBS60h_01_1632


title: 252978410060_B7A_CY5_C35134_CY3.mev.refIsIB.out


title: Rat treated with PBS 60hr, rep 1

description:
Gene expression data from rat treated with PBS 60hr rep 1.
929_JEC_4_rat_07_PBS60h_01_1633


title: HRG_AFB1_0.05µM_n3_replicate 1

city: Rennes

first: rozenn

last: jossé

address: 2 av Prof Léon Bernard

institute: INSERM U991

description: Gene expression after 24h-treatment with 0.05µM AFB1 in HepaRG cells

hyb_protocol: 1650 ng of Cy3-RNAs were hybridized using the Hybridisation Kit Plus (Agilent) onto 4×44K Whole Human Genome Microarrays (G4112F, Agilent). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HRG_AFB1_0.05µM_n3_replicate 1

label_protocol: Five hundred ng of total RNA from each cell culture were reverse-transcribed into double-strand cDNAs and amplified for 2 h at 40°C using the Quick Amp Labeling Kit (Agilent). cDNAs were transcribed into antisense cRNA and labeled with CTP-Cy3 fluorescent dye for 2 h at 40°C following the manufacturer's protocol. Cyanine-labeled cRNAs were purified using RNeasy minikit (Qiagen, Inc., Valencia, CA).

growth_protocol: HepaRG cells were seeded at a density of 2.6x104 cells/cm2 in Williams’ E medium supplemented with 10% FCS, 100 units/mL penicillin, 100 μg/mL streptomycin, 5 μg/mL insulin, 2 mM glutamine and 5x10−5 M hydrocortisone hemisuccinate. After two weeks they were shifted to the same culture medium supplemented with 2% DMSO for two more weeks. At that time HepaRG cells were well differentiated and used for treatments by chemicals. Human hepatocytes undergoing resection for primary and secondary tumors were obtained by collagenase perfusion of histologically normal liver fragments and used for the preparation of RNA samples and primary cultures. Hepatocyte cultures were obtained by seeding 170,000 cells/cm² in 6-well plates in a Williams’ E medium supplemented with 10% FCS, 100 units/µl penicillin, 100 µg/ml streptomycin, 1 µg/ml insulin, 2 mM glutamine, and 1 µg/ml bovine serum albumin. The medium was discarded 12 h after seeding, and cells were thereafter maintained in serum-free medium supplemented with 5 x 10-5 M hydrocortisone hemisuccinate. HH were used 24 h after seeding.

extract_protocol: Cells were harvested in lysis buffer (RLT buffer and β-mercaptoethanol). Total RNA was isolated using the RNeasy mini kit (Qiagen). RNA quantity and purity were assessed with a Nanodrop ND-1000 spectrophotometer (Nyxor Biotech, Paris, France) and RNA integrity was checked with a Bioanalyzer 2100 (Agilent Technologies, Massy, France).

treatment_protocol: AFB1 was dissolved in DMSO and treatments were performed in a FCS-free medium. All control and treated cultures received 0.1% DMSO as the vehicle final concentration.

value: HepaRG

value: 0.05µM aflatoxin B1 (AFB1)


title: HRG_Control_n3_replicate 2

description: Gene expression after 24h-treatment with 0.1% DMSO in HepaRG cells

source_name: HRG_Control_n3_replicate 2

value: untreated


title: Rat treated with PBS 60hr, rep 6

description:
Gene expression data from rat treated with PBS 60hr rep 6.
934_JEC_4_rat_12_PBS60h_01_1597


title: 252978410060_B7A_CY5_ARG2_CY3.mev.refIsIB.out


title: 252978410027_B7A_CY5_sPRH_420_CY3.mev.refIsIB.out


title: Rat treated with PBS 60hr, rep 2

description:
Gene expression data from rat treated with PBS 60hr rep 2.
930_JEC_4_rat_08_PBS60h_01_1591


title: 252978410010_B7A_CY5_ICDDR_B_p1_CY3.mev.refIsIB.out


title: HRG_Control_n3_replicate 1

source_name: HRG_Control_n3_replicate 1


title: Rat treated with PBS 36hr, rep 5

description:
Gene expression data from rat treated with PBS 36hr rep 5.
927_JEC_4_rat_05_PBS36h_01_1641

source_name: lymph node, PBS, 36hr


title: Rat treated with PBS 60hr, rep 3

description:
Gene expression data from rat treated with PBS 60hr rep 3.
931_JEC_4_rat_09_PBS60h_01_1613


title: Rat treated with PBS 36hr, rep 6

description:
Gene expression data from rat treated with PBS 36hr rep 6.
928_JEC_4_rat_06_PBS36h_01_1605


title: 252978410071_B7A_CY5_O157_h7_CY3.mev.refIsIB.out


title: HRG_AFB1_0.25µM_n3_replicate 1

description: Gene expression after 24h-treatment with 0.25µM AFB1 in HepaRG cells

source_name: HRG_AFB1_0.25µM_n3_replicate 1

value: 0.25µM aflatoxin B1 (AFB1)


title: Rat treated with PBS 36hr, rep 4

description:
Gene expression data from rat treated with PBS 36hr rep 4.
926_JEC_4_rat_04_PBS36h_01_1636


title: Rat treated with PBS 36hr, rep 3

description:
Gene expression data from rat treated with PBS 36hr rep 3.
925_JEC_4_rat_03_PBS36h_01_1528


title: 252978410027_B7A_CY5_sPRH_414_CY3.mev.refIsIB.out


title: HRG_AFB1_0.25µM_n2_replicate 1

source_name: HRG_AFB1_0.25µM_n2_replicate 1


title: RR2_wtdctDAAA_2_Cy3_ch1_rpoNdctDAAA_2_7DE1158

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri Mar 28 07:37:35 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

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 Typhimurium

source_name: Transcription_profile from wt grown in presence of dctDAAA, replicate 2

label_protocol: Standard labeling using Cy3-dCTP with reverse transcriptase and random hexamers

extract_protocol: RNEasy kit (Qiagen)

tag: genotype/variation

value: wt

tag: growth phase

value: late log

value: dctDAAA

source_name: Transcription_profile from rpoN mutant grown in presence of dctDAAA, replicate 2

label_protocol: Standard labeling using Cy5-dCTP with reverse transcriptase and random hexamers

value: rpoN mutant


title: HRG_Control_n2_replicate 2

source_name: HRG_Control_n2_replicate 2

tag: treatment


title: ge2bl_1 with array type maize from Affymetrix

description: Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription.

value: F7033 line, coming from "(LorenaXF252)XF252" genotype

value: yellow grain , Flint-Dent type


title: 252978410010_B7A_CY5_229_1_CY3.mev.refIsIB.out

tag: strain


title: RR2_wtdctDAAA_3_Cy3_ch1_rpoNdctDAAA_3_7DE1159

description: biological replicate, Date of Scan Fri Mar 28 07:43:16 2008

source_name: Transcription_profile from wt grown in presence of dctDAAA, replicate 3

source_name: Transcription_profile from rpoN mutant grown in presence of dctDAAA, replicate 3


title: 252978410022_B7A_CY5_ETP98042_CY3.mev.refIsIB.out


title: Rat treated with PBS 36hr, rep 1

description:
Gene expression data from rat treated with PBS 36hr rep 1.
923_JEC_4_rat_01_PBS36h_01_1615

value: Brown Norway

value: female

value: 6-8 weeks

value: lymph node


title: 252978410071_B7A_CY5_COSIN07_61_CY3.mev.refIsIB.out

value: cosin 07-61


title: 252978410027_B7A_CY5_LSN03_016011_A_CY3.mev.refIsIB.out


title: HRG_AFB1_0.25µM_n1_replicate 1

source_name: HRG_AFB1_0.25µM_n1_replicate 1

tag: cell line


title: HRG_Control_n2_replicate 1

source_name: HRG_Control_n2_replicate 1


title: 252978410071_B7A_CY5_COCAR07_043_CY3.mev.refIsIB.out


title: HRG_AFB1_0.05µM_n1_replicate 2

source_name: HRG_AFB1_0.05µM_n1_replicate 2


title: HRG_AFB1_0.25µM_n1_replicate 2

source_name: HRG_AFB1_0.25µM_n1_replicate 2