title: Strain n7127 replicate 2

description:
n7127-2 .gpr
replicate 2 of 3


title: Strain n7017 replicate 1

status: Public on Apr 09 2011

type: genomic

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

description:
n7017-1 .gpr
replicate 1 of 3

hyb_protocol: The labelled DNA were mixed together with two volumes of hybridization buffer (Eurogentec, Belgium) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma.

molecule: genomic DNA

organism: Neisseria meningitidis

source_name: DNA from Strain_n7017

label_protocol: 4 µg of chromosomal DNA and 4  µg of the pooled common reference were labelled with Cy3 dCTP and Cy5 dCTP using Klenow enzyme and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were cultivated on blood agar plates at 37°C

extract_protocol: Chromosomal DNA from the meningococcal strains were isolated using Genomic Tip 20/G (Qiagen, Germany).

tag: strain

source_name: Common Reference

tag: sample type

value: Pool of DNA from all strains in this dataset


title: Strain n6894 replicate 3

description:
n6894-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_n6894


title: Strain n6904 replicate 1

description:
n6904-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_n6904


title: Strain n6904 replicate 2

description:
n6904-2 .gpr
replicate 2 of 3


title: Strain n7017 replicate 3

description:
n7017-3 .gpr
replicate 3 of 3


title: Strain n6894 replicate 2

description:
n6894-2 .gpr
replicate 2 of 3


title: Strain a95 replicate 3

description:
a95-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a95


title: Strain n6894 replicate 1

description:
n6894-1 .gpr
replicate 1 of 3


title: Strain n6904 replicate 3

description:
n6904-3 .gpr
replicate 3 of 3


title: Strain n7127 replicate 1

description:
n7127-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_n7127


title: Strain a710 replicate 1

description:
a710-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_a710


title: Strain a710 replicate 2

description:
a710-2 .gpr
replicate 2 of 3


title: Strain a707 replicate 3

description:
a707-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a707


title: Strain a78 replicate 2

description:
a78-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_a78


title: Strain a710 replicate 3

description:
a710-3 .gpr
replicate 3 of 3


title: Strain a78 replicate 3

description:
a78-3 .gpr
replicate 3 of 3


title: Strain a78 replicate 1

description:
a78-1 .gpr
replicate 1 of 3


title: Strain a95 replicate 2

description:
a95-2 .gpr
replicate 2 of 3


title: Strain a707 replicate 1

description:
a707-1 .gpr
replicate 1 of 3


title: Strain n7865 replicate 2

description:
n7865-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_n7865


title: Strain a707 replicate 2

description:
a707-2 .gpr
replicate 2 of 3


title: Strain a547 replicate 2

description:
a547-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_a547


title: Strain a95 replicate 1

description:
a95-1 .gpr
replicate 1 of 3


title: Strain a704 replicate 1

description:
a704-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_a704


title: Strain a547 replicate 3

description:
a547-3 .gpr
replicate 3 of 3


title: Strain a704 replicate 3

description:
a704-3 .gpr
replicate 3 of 3


title: Strain a533 replicate 2

description:
a533-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_a533


title: Strain a547 replicate 1

description:
a547-1 .gpr
replicate 1 of 3


title: Strain a533 replicate 3

description:
a533-3 .gpr
replicate 3 of 3


title: Strain a522 replicate 3

description:
a522-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a522


title: Strain a522 replicate 2

description:
a522-2 .gpr
replicate 2 of 3


title: Strain a522 replicate 1

description:
a522-1 .gpr
replicate 1 of 3


title: Strain a533 replicate 1

description:
a533-1 .gpr
replicate 1 of 3


title: Strain a490 replicate 3

description:
a490-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a490


title: Strain a704 replicate 2

description:
a704-2 .gpr
replicate 2 of 3


title: Strain a490 replicate 2

description:
a490-2 .gpr
replicate 2 of 3


title: Strain a4 replicate 3

description:
a4-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a4


title: Strain a490 replicate 1

description:
a490-1 .gpr
replicate 1 of 3


title: Strain a3 replicate 2

description:
a3-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_a3


title: Strain a4 replicate 2

description:
a4-2 .gpr
replicate 2 of 3


title: Strain a3 replicate 3

description:
a3-3 .gpr
replicate 3 of 3


title: Strain a31 replicate 3

description:
a31-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a31


title: Strain a31 replicate 1

description:
a31-1 .gpr
replicate 1 of 3

source_name: Common Reference


title: Strain a4 replicate 1

description:
a4-1 .gpr
replicate 1 of 3


title: Strain a3 replicate 1

description:
a3-1 .gpr
replicate 1 of 3


title: Strain a275 replicate 3

description:
a275-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a275


title: Athlete3_wbc_t3

type: RNA

city: Moscow

first: Evgeniy

last: Riabenko

address: Elizavetinskiy per., 10

country: Russia

institute: VNIIFK

description: Gene expression after MT - T3

hyb_protocol: Fragmented target DNA was hybridized on GeneChip Human Gene 1.0 ST Arrays (Affymetrix, USA) in a Hybridization Oven 640 (Affymetrix, USA) at 45ºC for 16h. Arrays were washed free of nonspecifically bound fragments and stained on Fluidics Station 450 (Affymetrix, USA) using the FS450_0007 protocol.

scan_protocol: Scanning was done on the GeneChip Scanner 3000 7G system (Affymetrix, USA) using GSOC v1.4 software.

data_processing: The data were analyzed with the RMA algorithm realized in the xps R package using default parameter values. Normalization was perfomed separately for the RTE and MT data.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: White blood cells, MT

label_protocol: Briefly, double-strand cDNA was synthesized with random hexamers tagged with a T7 promoter sequence from 2µg of total RNA. The cDNA was subsequently used as a template and amplified by T7 RNA polymerase, producing many copies of antisense cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The resulting sense strand DNA was fragmented to an average strand length of 100 bases and labeled with biotin.

extract_protocol: Blood for total RNA extraction was drawn in PAXgene blood RNA tubes (Qiagen, Germany). Total RNA was extracted as recommended by the manufacturer. RNA quality was checked using the Agilent Bioanalyzer 2100 System. For all samples, RIN was greater than 8.2.

tag: tissue

value: blood

tag: cell type

value: white blood cells

tag: age

tag: gender

value: male

tag: treatment

value: moderate treadmill test (MT)

tag: treatment time

tag: athlete identifier


title: Athlete3_wbc_t2

description: Gene expression before MT - T2

source_name: White blood cells, baseline for MT


title: Athlete7_wbc_t3

description: Gene expression after MT - T3


title: Athlete5_wbc_t3

description: Gene expression after MT - T3


title: Athlete6_wbc_t3

description: Gene expression after MT - T3


title: Athlete1_wbc_t2

description: Gene expression before MT - T2


title: Athlete4_wbc_t3

description: Gene expression after MT - T3


title: Athlete5_wbc_t2

description: Gene expression before MT - T2


title: Strain a275 replicate 2

description:
a275-2 .gpr
replicate 2 of 3


title: Athlete6_wbc_t2

description: Gene expression before MT - T2


title: Athlete1_wbc_t3

description: Gene expression after MT - T3


title: Athlete7_wbc_t2

description: Gene expression before MT - T2


title: Athlete4_wbc_t2

description: Gene expression before MT - T2


title: Strain a31 replicate 2

description:
a31-2 .gpr
replicate 2 of 3


title: Athlete2_wbc_t3

description: Gene expression after MT - T3


title: Strain a267 replicate 3

description:
a267-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a267


title: Strain a267 replicate 2

description:
a267-2 .gpr
replicate 2 of 3


title: Strain a275 replicate 1

description:
a275-1 .gpr
replicate 1 of 3


title: Athlete2_wbc_t2

description: Gene expression before MT - T2


title: Athlete19_wbc_t1

description: Gene expression after RTE - T1

source_name: White blood cells, RTE

value: ramp test to exhaustion (RTE)


title: Athlete19_wbc_t0

description: Gene expression before RTE - T0

source_name: White blood cells, baseline for RTE


title: Strain a267 replicate 1

description:
a267-1 .gpr
replicate 1 of 3


title: Strain a153 replicate 3

description:
a153-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_a153


title: Strain a153 replicate 2

description:
a153-2 .gpr
replicate 2 of 3


title: Strain a153 replicate 1

description:
a153-1 .gpr
replicate 1 of 3


title: Strain a14 replicate 1

description:
a14-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_a14


title: Athlete18_wbc_t0

description: Gene expression before RTE - T0


title: Strain 2594 replicate 2

description:
2594-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_2594


title: Athlete18_wbc_t1

description: Gene expression after RTE - T1


title: Strain 2594 replicate 3

description:
2594-3 .gpr
replicate 3 of 3


title: Athlete17_wbc_t1

description: Gene expression after RTE - T1


title: Athlete17_wbc_t0

description: Gene expression before RTE - T0


title: Strain 2137 replicate 3

description:
2137-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_2137


title: Strain 2137 replicate 2

description:
2137-2 .gpr
replicate 2 of 3


title: Strain 2807 replicate 1

description:
2807-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_2807


title: Strain 2594 replicate 1

description:
2594-1 .gpr
replicate 1 of 3


title: Strain 2807 replicate 3

description:
2807-3 .gpr
replicate 3 of 3


title: Strain a14 replicate 2

description:
a14-2 .gpr
replicate 2 of 3


title: Athlete14_wbc_t1

description: Gene expression after RTE - T1


title: Athlete15_wbc_t1

description: Gene expression after RTE - T1


title: Strain 2137 replicate 1

description:
2137-1 .gpr
replicate 1 of 3


title: Strain a14 replicate 3

description:
a14-3 .gpr
replicate 3 of 3


title: Athlete14_wbc_t0

description: Gene expression before RTE - T0


title: Athlete12_wbc_t1

description: Gene expression after RTE - T1


title: Athlete16_wbc_t0

description: Gene expression before RTE - T0


title: Athlete11_wbc_t0

description: Gene expression before RTE - T0


title: Athlete12_wbc_t0

description: Gene expression before RTE - T0


title: Athlete13_wbc_t1

description: Gene expression after RTE - T1


title: Athlete10_wbc_t1

description: Gene expression after RTE - T1


title: Athlete13_wbc_t0

description: Gene expression before RTE - T0


title: Athlete11_wbc_t1

description: Gene expression after RTE - T1


title: Athlete16_wbc_t1

description: Gene expression after RTE - T1


title: Athlete15_wbc_t0

description: Gene expression before RTE - T0


title: Strain 2807 replicate 2

description:
2807-2 .gpr
replicate 2 of 3


title: Strain 2135 replicate 2

description:
2135-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_2135


title: Strain 2135 replicate 1

description:
2135-1 .gpr
replicate 1 of 3


title: Strain 2121 replicate 3

description:
2121-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_2121


title: Strain 2121 replicate 1

description:
2121-1 .gpr
replicate 1 of 3


title: Athlete10_wbc_t0

description: Gene expression before RTE - T0


title: Strain 2121 replicate 2

description:
2121-2 .gpr
replicate 2 of 3


title: Strain 2135 replicate 3

description:
2135-3 .gpr
replicate 3 of 3


title: Strain 2120 replicate 3

description:
2120-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_2120


title: Strain 2120 replicate 1

description:
2120-1 .gpr
replicate 1 of 3


title: Strain 2120 replicate 2

description:
2120-2 .gpr
replicate 2 of 3


title: Athlete8_wbc_t0

description: Gene expression before RTE - T0


title: Athlete9_wbc_t0

description: Gene expression before RTE - T0


title: Athlete9_wbc_t1

description: Gene expression after RTE - T1


title: Athlete7_wbc_t1

description: Gene expression after RTE - T1


title: Athlete6_wbc_t0

description: Gene expression before RTE - T0


title: Athlete5_wbc_t1

description: Gene expression after RTE - T1


title: Athlete6_wbc_t1

description: Gene expression after RTE - T1


title: Athlete5_wbc_t0

description: Gene expression before RTE - T0


title: Athlete8_wbc_t1

description: Gene expression after RTE - T1


title: lin-54(n3423) dissected germline 3

city: Worcester

first: Kirsten

last: Hagstrom

state: MA

address: 377 Plantation street

department: Molecular Medicine

country: USA

institute: University of Massachusetts, Medical School

hyb_protocol: cDNA probes of three replicates were hybridized to GeneChip C. elegans genome arrays (Affymetrix). Probe-preparation, hybridization, and scanning for DNA microarray were performed at the Genomics Core facility at University of Massachusetts Medical School.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Statistical analyses were performed using R, a system for statistical computation and graphics ( http://www.r-project.org). The rma method in the affy package from Bioconductor was used in R to summarize probe level data and to normalize the dataset to remove across array variation. Log transformed data were used in subsequent analysis and plotting. WormBase version WS190 was used. To determine differentially expressed genes between wild-type and mutants, moderated T Statistics in limma was used with p-value ≤0.01, fold change ≥1.5.

label: biotin

organism: Caenorhabditis elegans

source_name: lin-54(n3423) mutant germline

label_protocol: Fluorescence-labeled cDNA probes were prepared using the One-Cycle kit (Affymetrix) and the Enzo HighYield RNA Transcript Labeling Kit (Enzo) for embryo, and the 3' IVT Express Kit (Affymetrix) for germline

growth_protocol: Strains for embryo or germline were cultured at 25o or 20oC, respectively, using standard methods.

extract_protocol: 200 µL of embryo pellet was suspended in 1 mL of Tri reagent (Molecular Research Center, Inc. TR118), flash-frozen, and dounced. Total RNA was purified with RNAeasy mini kits (Qiagen), treated with DNase, and integrity examined on agarose gel. Germline RNA was isolated as described in Chi and Reinke (2006), and linearly amplified once using MessageAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: Embryos from young adults were harvested by the bleach-alkaline method, and filtered through 100 micron mesh. Germlines were dissected in 1X egg buffer to excise the germline including mitotic tip through meiotic late pachytene 24 hours after L4 stage.

value: germline

tag: genotype

tag: genetic background


title: Athlete4_wbc_t1

description: Gene expression after RTE - T1


title: wild-type N2 dissected germline 1

source_name: wild type germline

value: wild-type


title: wild-type N2 dissected germline 2


title: Athlete7_wbc_t0

description: Gene expression before RTE - T0


title: lin-54(n2990) embryo 3

source_name: lin-54(n2990) mutant embryos

value: embryos


title: lin-54(n3423) dissected germline 2


title: wild-type N2 dissected germline 3


title: lin-54(n3423) dissected germline 1


title: Athlete4_wbc_t0

description: Gene expression before RTE - T0


title: Athlete3_wbc_t0

description: Gene expression before RTE - T0


title: Athlete3_wbc_t1

description: Gene expression after RTE - T1


title: Adrenocortical adenoma with wild-type CTNNB1-3

city: Montreal

first: julien

last: durand

state: QC

address: 3840 Rue Saint-Urbain

department: Biomedicale Science

country: Canada

institute: CRCHUM

description: Gene expression profile of an adrenocortical adenoma  with wild-type CTNNB1 gene

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Human Genome U133 Plus 2.0 GeneCHIP.

scan_protocol: GeneChips were scanned using the Genechip scanner 3000 workstation (Affymetrix)

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.

source_name: WT AA 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

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

value: Adrenocortical adenoma

tag: tumor secretion profile

value: Cortisol

value: WT CTNNB1


title: Adrenocortical adenoma with wild-type CTNNB1-1

source_name: WT AA 1


title: Adrenocortical adenoma with wild-type CTNNB1-2

source_name: WT AA 2


title: lin-54(n2990) embryo 1


title: Athlete2_wbc_t0

description: Gene expression before RTE - T0


title: Syngeneic_03

city: Nantes

first: Romain

last: Vuillefroy de Silly

address: 30 Bvd Jean Monnet

country: France

institute: INSERM UMR643

description: Syngeneic

hyb_protocol: Array hybridization was performed for 16 h at 55°C. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.

scan_protocol: Chemiluminescence detection, image acquisition, and analysis were performed using the Applied Biosystems chemiluminescence detection kit (part no. 436875D), analyzer (part no. 4338036) and version 1.1 analyzer software (part no. 4336391) according to the manufacturer’s protocol.

data_processing: Microarray raw data were analyzed by the R language and environment for statistical computing and graphics. Genes were identified using the Panther Protein Classification System Probe ID database.

label: Digoxigenin-UTP

organism: Rattus norvegicus

source_name: Syngeneic

label_protocol: The Applied Biosystems rat genome survey microarray (part no. 4337467) contained 26,857 60-mer oligonucleotide probes representing 27,088 individual rat genes. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.  Digoxigenin-UTP labeled cRNA was generated and amplified from 0.5 µg of total RNA from each sample using an Applied Biosystems NanoAmp chemiluminescent reverse transcriptase-in vitro transcription (RT-IVT) labeling kit (part no. 4365715).

growth_protocol: Rats were maintained in an SPF-free animal facility according to the institutional guidelines of the “Institut National de la Santé et de la Recherche Médicale” (INSERM).

extract_protocol: Organs were harvested at day 100 post transplantation. Sections of the kidney transplant were snap frozen in liquid nitrogen for RNA extraction. Total RNA from rat kidney transplants was prepared using the TRIzol (Invitrogen Life Technologies) extraction method. Ten micrograms of total RNA was cleaned up using RNeasy columns (Qiagen). RNA quantity and quality were determined using a NanoDrop spectrophotometer and an Agilent 2100 bioanalyzer. A rRNA 28S/18S ratio of 1.0 ± 0.1 was considered as acceptable for RNA amplification.

treatment_protocol: Lewis 1W (LEW.1W, haplotype RT1u) and Lewis 1A (LEW.1A, haplotype RT1a) rats (Centre d’Elevage Janvier, Le Genest-Saint-Isle, France) share the same genetic background but are MHC I and II mismatched. Heterotopic transplantations of 8 to 12 weeks old LEW.1W kidneys on LEW.1A animals were carried out according to the technique described by Ono & Lindsey. For syngeneic transplantations LEW.1A kidneys on LEW.1A recipients were achieved. Live-sustaining allotransplantations were performed aseptically and a binephrectomy was performed 7 days after transplantation as previously described. Blood urea and creatinine and urine protein/creatinine ratios were measured throughout the posttransplant period. Blood urea < 8 mM and blood creatinine < 40 mM were considered as normal. Transplant tolerance induction was obtained by treating rats with anti-donor anti-class II antibodies.

value: Kidney transplant

tag: transplantation

value: Syngeneic

tag: day post transplantation


title: Adrenocortical adenoma with wild-type CTNNB1-4

source_name: WT AA 4

value: Aldosterone


title: Athlete2_wbc_t1

description: Gene expression after RTE - T1

source_name: White blood cells, RTE


title: lin-54(n2990) embryo 2


title: Syngeneic_02

description: Syngeneic


title: Adrenocortical adenoma with CTNNB1 mutation (T41A)

description: Gene expression profile of  an adrenocortical adenoma  with a  S37C  CTNNB1 mutation

source_name: M AA T41A

value: CTNNB1 mutation (T41A)


title: Adrenocortical adenoma with CTNNB1 mutation_(S37C)

description: Gene expression profile of an adrenocortical adenoma  with a T41A CTNNB1 mutation

source_name: M AA S37C

value: CTNNB1 mutation (S37C)


title: Syngeneic_01

description: Syngeneic


title: Athlete1_wbc_t1

description: Gene expression after RTE - T1


title: wild-type N2 embryo 3

source_name: wild type embryos


title: Tolerant_ClassII_02

description: Tolerant state

value: Allogeneic


title: Tolerant_ClassII_01

description: Tolerant state


title: Athlete1_wbc_t0

description: Gene expression before RTE - T0

source_name: White blood cells, baseline for RTE

value: blood


title: Tolerant_ClassII_03

description: Tolerant state


title: Pool of 62 normal adrenal glands

description: Pool of total RNA from adrenal glands of 62 caucasian subjects aged 15 to 61 years old

value: Normal adrenal glands


title: wild-type N2 embryo 2


title: Adrenocortical adenoma with CTNNB1 mutation (S45P)

description: Gene expression profile of an adrenocortical adenoma  with a S45P  CTNNB1 mutation

source_name: M AA S45P

value: CTNNB1 mutation (S45P)


title: 14028sLPM20hr_vs_3121LPM20hr1_14212078_MDS.mev.refIsIB.out

status: Public on Apr 08 2011

city: Rockville

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

institute: JCVI

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

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

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

organism: Salmonella enterica

source_name: Salmonella enterica strain 14028 / LPM20/Stationary

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

growth_protocol: Strains were grown in LPM and collected 20 hours(Stationary phase) after inoculation.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer.

tag: media

tag: growth phase

value: Stationary

tag: channel

value: IB

label: Fred Heffron at Oregon Health and Science University

source_name: Salmonella enterica strain 14028 with STM3121 mutation/ LPM20/Stationary

value: 14028 with STM3121 mutation

value: IA


title: crpLPM20hr3vs14028sLPM20hr_14155609_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM crp mutation/ LPM20/Early Stationary

tag: strain

value: 14028 with crp mutation

source_name: Salmonella enterica strain 14028 / LPM20/Early Stationary


title: 14028sLPM20hr_vs_2912LPM20hr1_14212076_MDS.mev.refIsIB.out

source_name: Salmonella enterica strain 14028/ LPM20/Stationary

source_name: Salmonella enterica strain 14028 with STM2912 mutation/ LPM20/Stationary

value: 14028 with STM2912 mutation


title: wild-type N2 embryo 1

value: embryos

value: wild-type


title: csrALPM4hr2vs14028sLPM4hr_14152558_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with csrA mutation/LPM4 / Mid log

growth_protocol: Strains were grown in LPM and collected 4 hours(Mid log phase) after inoculation.

value: 14028 with csrA mutation

value: Mid log

source_name: Salmonella enterica strain 14028 /LPM4 / Mid log


title: csrALPM20hr2vs14028sLPM20hr_14155594_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with csrA mutation/ LPM20/Stationary


title: GCB LRF F/F mb1-Cre+ #1

city: Duarte

first: Takahiro

last: Maeda

state: CA

address: 1500E Duarte Rd

department: Hematopoietic Stem Cell and Leukemia Research

institute: Beckman Research Institute of the City of Hope

description:
10 wks old mice. 7 days after immunization.
Gene expression data from FACS-sorted germinal center B cells (B220+CD19+CD38-Fas+)

hyb_protocol: The resulting cRNA was used as the template for another round of amplification using the sense target labelling assay kit. Hybridization cocktails containing 5.5 μg of fragmented, end-labelled cDNA were prepared and applied to GeneChip Mouse Gene 1.0 ST arrays (GPL6246, Affymetrix). Hybridization was performed for 16 h, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script

scan_protocol: Arrays were scanned at 5 μm resolution using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to generate CEL intensity files.

data_processing: The raw data is normalized by Robust Multi-array Average(RMA) using Affymetrix Expression Console

organism: Mus musculus

source_name: Germinal center B cells of LRF knockout mouse

label_protocol: Synthesis and labelling of cDNA targets, hybridization and scanning of GeneChips were carried out by the Microarray Core Facility at City of Hope. Due to limited starting material, we used a modified two-cycle amplification protocol. Briefly, cRNA was generated using 10 ng total RNA, according to the manufacturer's protocol, by using Affymetrix's GeneChip Whole Transcript Sense Target Labelling Assay in the first cycle of amplification. The cRNA was subjected to the RiboMinus kit (Invitrogen) to remove rRNA.

extract_protocol: RNA samples were prepared using the Absolutely RNA Microprep kit (Stratagene).

treatment_protocol: LRF knockout (LRF Flox/Flox mb-1 Cre+) and control (LRF Flox/+ mb-1 Cre+) mice (4 each) were immunized with sheep red blood cells (SRBCs), and GCB cells were FACS-sorted 7 d later.

value: mixed including C57BL/6 and Zbtb7a-neo/+N1

value: LRF Flox/Flox mb1-Cre+ (LRF homozygous knockout)

value: 10 wk


title: GCB LRF F/F mb1-Cre+ #3

value: FACS-sorted germinal center B cells (B220+CD19+CD38-Fas+)


title: GCB LRF F/+ mb1-Cre+ #3

source_name: Germinal center B cells of control mouse

value: LRF Flox/+ mb1-Cre+ (LRF heterozygous)


title: GCB LRF F/F mb1-Cre+ #4


title: GCB LRF F/+ mb1-Cre+ #2


title: 14028sLPM20hr_vs_1547LPM20hr1_14212072_MDS.mev.refIsIB.out

source_name: Salmonella enterica strain 14028 with STM1547 mutation/ LPM20/Stationary

value: 14028 with STM1547 mutation


title: GCB LRF F/+ mb1-Cre+ #5


title: crpLPM4hr3vs14028sLPM4hr_14152564_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with crp mutation/LPM4 / Mid log

source_name: Salmonella enterica strain 14028/LPM4 / Mid log

growth_protocol: Strains were grown in LPM and collected 4 hours(Mid log phase) after inoculation


title: csrALBlog1vs14028sLBlog_14152568_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with csrA mutation/ LB / log

growth_protocol: Strains were grown in LB and collected at log phase.

value: LB

value: log

source_name: Salmonella enterica strain 14028/ LB / log


title: GCB LRF F/+ mb1-Cre+ #1


title: GCB LRF F/F mb1-Cre+ #2


title: crpLPM20hr1vs14028sLPM20hr_14087655_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with crp mutation/ LPM20/Early Stationary

value: Stationary

value: IB

source_name: Salmonella enterica strain 14028/ LPM20/Early Stationary


title: 14028sLPM20hr_vs_2575LPM20hr1_14212066_MDS.mev.refIsIB.out

source_name: Salmonella enterica strain 14028/ LPM20/ Stationary

source_name: Salmonella enterica strain 14028 with STM2575 mutation/ LPM20/ Stationary

value: 14028 with STM2575 mutation

value: IA


title: csrALPM20hr1vs14028sLPM20hr_14155614_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with csrA mutation/ LPM20/ Stationary


title: crpLPM4hr1vs14028sLPM4hr_14152552_MDS.mev.refIsIA.out

value: 14028 with crp mutation


title: csrALBlog2vs14028sLBlog_14152589_MDS.mev.refIsIA.out


title: crpLBlog3vs14028sLBlog_14152593_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with crp mutation/ LB / log

growth_protocol: Strains were grown in LB and collected at Log phase.


title: csrALPM4hr1vs14028sLPM4hr_14152536_MDS.mev.refIsIA.out


title: 3121LPM4hr2_vs_14028sLPM4hr_14212321_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM3121 mutation/LPM4 / Mid log

value: 14028 with STM3121 mutation


title: 2912LPM4hr2_vs_14028sLPM4hr_14212057_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2912 mutation/LPM4 / Mid log

value: 14028 with STM2912 mutation


title: 3121LBlog1vs14028sLBlog_14087679_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM3121 mutation/ LB / log


title: 3121LPM4hr1_vs_14028sLPM4hr_14212309_MDS.mev.refIsIA.out


title: 2912LPM4hr1_vs_14028sLPM4hr_14212307_MDS.mev.refIsIA.out


title: crpLBlog1vs14028sLBlog_14152575_MDS.mev.refIsIA.out


title: 3121LBlog3vs14028sLBlog_14212336_MDS.mev.refIsIA.out


title: 2912LBlog1vs14028sLBlog_14087671_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2912 mutation/ LB /  log

source_name: Salmonella enterica strain 14028/ LB /  log


title: 2912LBlog3vs14028sLBlog_14212335_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2912 mutation/ LB / log


title: 2575LBlog3vs14028sLBlog_14212323_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2575 mutation/ LB / log


title: 1547LPM4hr2_vs_14028sLPM4hr_14212062_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM1547 mutation/LPM4 / Mid log


title: 2575LBlog1vs14028sLBlog_14087672_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2275 mutation/ LB  / log

value: 14028 with STM2275 mutation


title: 2575LPM4hr1_vs_14028sLPM4hr_14212299_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2575 mutation/LPM4 / Mid log

value: Mid log

source_name: Salmonella enterica strain 14028/ LPM4 / Mid log


title: 14028sLPM4hr_vs_hilDLPM4hrpool_14212034_MDS.mev.refIsIB.out

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

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

source_name: Total RNA extracted at mid log  phase

growth_protocol: The cells were grown in LPM media to mid log phase

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

value: 14028 with hilD mutation


title: 1547LPM4hr1_vs_14028sLPM4hr_14212302_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM1547 mutation/ LPM4 / Mid log

source_name: Salmonella enterica strain 14028/LPM4 / Mid log


title: 2575LPM20hr3_vs_14028sLPM20hr_14212067_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain 14028 with STM2575 mutation/ LPM20/ Stationary

source_name: Salmonella enterica strain 14028/ LPM20/ Stationary


title: hilDLPM4hrpool_vs_14028sLPM4hr_14212051_MDS.mev.refIsIA.out


title: 1547LPM20hr3_vs_14028sLPM20hr_14212081_MDS.mev.refIsIA.out

source_name: Salmonella enterica strain with STM1547 mutation/ LPM20/Stationary

source_name: Salmonella enterica strain 14028/ LPM20/Stationary


title: 14028sLBlog_vs_hilDLBlogpool_14212033_MDS.mev.refIsIB.out

source_name: Total RNA extracted at log phase

growth_protocol: The cells were grown in LB media to log phase


title: 14028sLPM4hr_vs_fisLPM4hrpool_14212037_MDS.mev.refIsIB.out

growth_protocol: The cells were grown in LB media to mid log  phase

value: 14028 with fis mutation


title: 14028sLBlog_vs_fisLBlogpool_14212048_MDS.mev.refIsIB.out

growth_protocol: The cells were grown in LB media to log  phase


title: fisLPM20hrpool_vs_14028sLPM20hr_14212276_MDS.mev.refIsIA.out

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

source_name: Total RNA extracted at early stationary phase, mutant

growth_protocol: The cells were grown in LPM media to early stationary phase

source_name: Total RNA extracted at early stationary phase, wildtype


title: hilDLPM20hrpool_vs_14028sLPM20hr_14212274_MDS.mev.refIsIA.out

source_name: Total RNA extracted at early stationary phase


title: 14028sLPM20hr_vs_hilDLPM20hrpool_14212041_MDS.mev.refIsIB.out


title: 14028sLPM20hr_vs_fisLPM20hrpool_14212043_MDS.mev.refIsIB.out

growth_protocol: The cells were grown in LB media to early stationary phase


title: 14028sLBlog_vs_STM3096LBlogpool_14212046_MDS.mev.refIsIB.out

value: 14028 with STM3096 mutation


title: 14028sLPM4hr_vs_STM3096LPM4hrpool_14212036_MDS.mev.refIsIB.out

growth_protocol: The cells were grown in LPM media to mid log  phase


title: 14028sLPM20hr_vs_STM3096LPM20hrpool_14212042_MDS.mev.refIsIB.out


title: STM3096LPM4hrpool_vs_14028sLPM4hr_14212053_MDS.mev.refIsIA.out


title: STM3096LPM20hrpool_vs_14028sLPM20hr_14212275_MDS.mev.refIsIA.out


title: ssrABLPM4hrpool_vs_14028sLPM4hr_14212050_MDS.mev.refIsIA.out

value: 14028 with ssrAB mutation


title: 14028sLPM20hr_vs_ssrABLPM20hrpool_14212040_MDS.mev.refIsIB.out


title: ssrABLPM20hrpool_vs_14028sLPM20hr_14212273_MDS.mev.refIsIA.out


title: 2575LPM4hr2_vs_14028sLPM4hr_14212065_MDS.mev.refIsIA.out


title: 14028sLPM4hr_vs_ssrABLPM4hrpool_14212056_MDS.mev.refIsIB.out


title: ssrABLBlogpool_vs_14028sLBlog_14212086_MDS.mev.refIsIA.out


title: 14028sLBlog_vs_ssrABLBlogpool_14212032_MDS.mev.refIsIB.out


title: hilDLBlogpool_vs_14028sLBlog_14212087_MDS.mev.refIsIA.out


title: STM3096LBlogpool_vs_14028sLBlog_14212027_MDS.mev.refIsIA.out


title: phoPQLPM4hrpool_vs_14028sLPM4hr_14212055_MDS.mev.refIsIA.out

value: 14028 with PhoPQ mutation


title: phoPQLBlogpool_vs_14028sLBlog_14212082_MDS.mev.refIsIA.out


title: fisLPM4hrpool_vs_14028sLPM4hr_14212054_MDS.mev.refIsIA.out

source_name: Total RNA extracted at mid log phase

growth_protocol: The cells were grown in LPM media to mid log phase.


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.C1.0mM.VAN.120min.Cy5_14181915_MDS.mev.refIsIA.out

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

Strain PA = reference.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus strain PA/ early stationary phase (120 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 120min
after inoculation. Experiments were conducted in 3 technical replicates.

value: PA

tag: agent

tag: time

value: early stationary phase (120min)

source_name: Staphylococcus aureus strain C1/ early stationary phase (120 min)


title: 14028sLPM20hr_vs_phoPQLPM20hrpool_14212039_MDS.mev.refIsIB.out


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.C1.0mM.VAN.120min.Cy5_14181926_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media. Samples were collected at 120min after inoculation. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.T8.0mM.VAN.120min.Cy5_14192985_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/early stationary phase (120 min)

source_name: Staphylococcus aureus strain T8/early stationary phase (120 min)


title: 14028sLPM4hr_vs_phoPQLPM4hrpool_14212049_MDS.mev.refIsIB.out


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.C1.0mM.VAN.120min.Cy5_14181927_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain C1/early stationary phase (120 min)


title: 14028sLBlog_vs_phoPQLBlogpool_14212030_MDS.mev.refIsIB.out


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.T8.0mM.VAN.120min.Cy5_14192981_MDS.mev.refIsIA.out


title: phoPQLPM20hrpool_14028sLPM20hr_14212045_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.T8.0mM.VAN.60min.Cy5_14196394_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ mid log phase (60 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60 min
after inoculation. Experiments were conducted in 3 technical replicates.

value: mid log phase (60min)

source_name: Staphylococcus aureus strain T8/ mid log phase (60 min)


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.C1.0mM.VAN.90min.Cy5_14181920_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA / late log phase (90 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90min
after inoculation. Experiments were conducted in 3 technical replicates.

value: late log phase (90min)

source_name: Staphylococcus aureus strain C1 / late log phase (90 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 min after inoculation. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.C1.0mM.VAN.90min.Cy5_14181919_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ late log phase (90 min)

source_name: Staphylococcus aureus strain C1/ late log phase (90 min)


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.T8.0mM.VAN.60min.Cy5_14196390_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media. Samples were collected at 60 min after inoculation. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.C1.0mM.VAN.60min.Cy5_14196395_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA / mid log phase (60 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60min
after inoculation. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain C1 / mid log phase (60 min)


title: 9QSA04222010A.PA0mM.VAN.120min.Cy3.T8.0mM.VAN.120min.Cy5_14192978_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.T8.0mM.VAN.90min.Cy5_14192983_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ late log  phase(90 min)

source_name: Staphylococcus aureus strain T8/ late log  phase(90 min)


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.T8.0mM.VAN.60min.Cy5_14196393_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.T8.0mM.VAN.90min.Cy5_14192984_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain T8/ late log phase (90 min)


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.T8.0mM.VAN.90min.Cy5_14192982_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.90min.Cy3.C1.0mM.VAN.90min.Cy5_14181921_MDS.mev.refIsIA.out


title: fisLBlogpool_vs_14028sLBlog_14212028_MDS.mev.refIsIA.out

source_name: Total RNA extracted at log phase

growth_protocol: The cells were grown in LB media to log phase.

value: 14028 fis mutant


title: SA.7210.30min.Cy5_SA.378.30min.Cy3.14192523_MDS.mev.refIsIA.out

first: Wei

last: Liang

address: 9704 Medical Center Drive

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).
strain 378 = reference.

source_name: Staphylococcus aureus strain 378/30min/early log phase

growth_protocol: Strains were grown in TSA media and were collected at 30 min after inoculation.

treatment_protocol: Linezolid Treated

value: Linezolid

value: early log phase (30 min)

source_name: Staphylococcus aureus strain 7210/30min/early log phase


title: SA.5612.30min.Cy5_SA.378.30min.Cy3.14192518_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 5612/30min/early log phase


title: SA.3577.30min.Cy5_SA.378.30min.Cy3.14192524_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 3577/30min/early log phase


title: SA.7210.60min.Cy5_SA.378.60min.Cy3.14192514_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 378/60min/mid log phase

growth_protocol: Strains were grown in TSA media and were collected at 60 min after inoculation.

value: mid log phase (60 min)

source_name: Staphylococcus aureus strain 7210/60min/mid log phase


title: SA.3577.60min.Cy5_SA.378.60min.Cy3.14192521_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 3577/60min/mid log phase


title: SA.6939.30min.Cy5_SA.378.30min.Cy3.14192510_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 6939/30min/early log phase


title: SA.5612.60min.Cy5_SA.378.60min.Cy3.14192517_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 5612/60min/mid log phase


title: SA.6939.60min.Cy5_SA.378.60min.Cy3.14192509_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 6939/60min/mid log phase


title: SA.5612.90min.Cy5_SA.378.90min.Cy3.14192512_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 378/90min/late log phase

growth_protocol: Strains were grown in TSA media and were collected at 90 min after inoculation.

value: late log phase (90 min)

source_name: Staphylococcus aureus strain 5612/90min/late log phase


title: SA.3577.90min.Cy5_SA.378.90min.Cy3.14192520_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 3577/90min/late log phase


title: SA.7210.90min.Cy5_SA.378.90min.Cy3.14192522_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 7210/90min/late log phase


title: SA.7210.120min.Cy3_SA.378.120min.Cy5.14192502_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/120min/early stationary phase

growth_protocol: Strains were grown in TSA media and were collected at 120 min after inoculation.

value: early stationary phase (120 min)

source_name: Staphylococcus aureus strain 7210/120min/early stationary phase


title: SA.6939.120min.Cy5_SA.378.120min.Cy3.14192515_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 6939/120min/early stationary phase


title: SA.7210.120min.Cy5_SA.378.120min.Cy3.14192513_MDS.mev.refIsIA.out


title: SA.3577.120min.Cy5_SA.378.120min.Cy3.14192519_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 3577/120min/early stationary phase


title: SA.6939.120min.Cy3_SA.378.120min.Cy5.14192491_MDS.mev.refIsIB.out

growth_protocol: Strains were grown in TSA media and were collected at 120min after inoculation.


title: SA.5612.120min.Cy5_SA.378.120min.Cy3.14192511_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 5612/120min/early stationary phase


title: SA.7210.90min.Cy3_SA.378.90min.Cy5.14192499_MDS.mev.refIsIB.out


title: SA.5612.120min.Cy3_SA.378.120min.Cy5.14192504_MDS.mev.refIsIB.out


title: 9QSA_378_90m_Cy5_3577_90m_Cy3_14194574_MDS.mev.refIsIB.out


title: SA.3577.90min.Cy3_SA.378.90min.Cy5.14192497_MDS.mev.refIsIB.out


title: 9QSA_378_90m_Cy5_6939_90m_Cy3_14194638_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 6939/90min/late log phase


title: SA.3577.120minCy3_SA.378.120minCy5.14192496_MDS.mev.refIsIB.out


title: 9QSA_378_90m_Cy5_5612_90m_Cy3_14194641_MDS.mev.refIsIB.out


title: 9QSA_378_90m_Cy5_7210_90m_Cy3_14194645_MDS.mev.refIsIB.out


title: SA.3577.30min.Cy3_SA.378.30min.Cy5.14192503_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/30min/early log phase

source_name: Staphylococcus aureus strain 3577/30min/early log phase


title: SA.5612.30minCy3_SA.378.30minCy5.14192495_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 5612/30min/early log phase


title: SA.6939.30min.Cy3_SA.378.30min.Cy5.14192494_MDS.mev.refIsIB.out


title: SA.3577.60min.Cy3_SA.378.60min.Cy5.14192498_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/60min/mid log phase

source_name: Staphylococcus aureus strain 3577/60min/mid log phase


title: SA.5612.60min.Cy3_SA.378.60min.Cy5.14192508_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 5612/60min/mid log phase


title: SA.7210.60min.Cy3_SA.378.60min.Cy5.14192500_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 7210/60min/mid log phase


title: SA.6939.60min.Cy3_SA.378.60min.Cy5.14192493_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 6939/60min/mid log phase


title: SA.7210.30min.Cy3_SA.378.30min.Cy5.14192501_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 7210/30min/early log phase


title: SA.5612.90min.Cy3_SA.378.90min.Cy5.14192506_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/90min/late log phase

source_name: Staphylococcus aureus strain 5612/90min/late log phase


title: SA.6939.90min.Cy3_SA.378.90min.Cy5.14192492_MDS.mev.refIsIB.out


title: 9QSA_378_30m_Cy5_5612_30m_Cy3_14194589_MDS.mev.refIsIB.out


title: 9QSA_378_30m_Cy5_6939_30m_Cy3_14194654_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 6939/30min/early log phase


title: 9QSA_378_60m_Cy5_3577_60m_Cy3_14194580_MDS.mev.refIsIB.out


title: 9QSA_378_120m_Cy5_7210_120m_Cy3_14194643_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/120min/early stationary phase

source_name: Staphylococcus aureus strain 7210/120min/early stationary phase


title: 9QSA_378_60m_Cy5_5612_60m_Cy3_14194588_MDS.mev.refIsIB.out


title: 9QSA_378_120m_Cy5_6939_120m_Cy3_14194639_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 6939/120min/early stationary phase


title: 9QSA_378_120m_Cy5_5612_120m_Cy3_14194642_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 5612/120min/early stationary phase


title: 9QSA_378_120m_Cy5_3577_120m_Cy3_14194578_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 3577/120min/early stationary phase


title: 9QSA_378_120m_Cy3_6939_120m_Cy5_14194652_MDS.mev.refIsIA.out


title: 9QSA_378_120m_Cy3_7210_120m_Cy5_14194644_MDS.mev.refIsIA.out


title: 9QSA_378_60m_Cy5_7210_60m_Cy3_14194572_MDS.mev.refIsIB.out


title: 9QSA_378_30m_Cy5_7210_30m_Cy3_14194571_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 378/30min/early log phase


title: 9QSA_378_60m_Cy5_6939_60m_Cy3_14194655_MDS.mev.refIsIB.out


title: 9QSA_378_30m_Cy5_3577_30m_Cy3_14194584_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus strain 3577/30min/early log phase


title: 9QSA_378_120m_Cy3_5612_120m_Cy5_14194649_MDS.mev.refIsIA.out


title: 9QSA_378_30m_Cy3_3577_30m_Cy5_14194564_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media and  were collected at 30 min after inoculation.


title: 9QSA_378_90m_Cy3_7210_90m_Cy5_14194646_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 7210/90min/late log phase


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.T8.0mM.VAN.30min.Cy5_14181938_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA /early log phase(30 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 30 min
after inoculation. Experiments were conducted in 3 technical replicates.

value: early log phase (30min)

source_name: Staphylococcus aureus strain T8 /early log phase(30 min)


title: 9QSA_378_120m_Cy3_3577_120m_Cy5_14194577_MDS.mev.refIsIA.out


title: 9QSA_378_30m_Cy3_7210_30m_Cy5_14194570_MDS.mev.refIsIA.out


title: 9QSA_378_30m_Cy3_6939_30m_Cy5_14194585_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.C1.0mM.VAN.60min.Cy5_14196391_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA /mid log phase (60 min)

source_name: Staphylococcus aureus strain C1/mid log phase (60 min)


title: 9QSA04222010A.PA0mM.VAN.60min.Cy3.C1.0mM.VAN.60min.Cy5_14181914_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/mid log phase (60 min)


title: 9QSA_378_90m_Cy3_5612_90m_Cy5_14194651_MDS.mev.refIsIA.out


title: 9QSA_378_30m_Cy3_5612_30m_Cy5_14194647_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 5612/30min/early log phase


title: 9QSA_378_90m_Cy3_3577_90m_Cy5_14194576_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 378/90min/late log phase

source_name: Staphylococcus aureus strain 3577/90min/late log phase


title: 9QSA_378_60m_Cy3_7210_60m_Cy5_14194573_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 378/60min/mid log phase

source_name: Staphylococcus aureus strain 7210/60min/mid log phase


title: 9QSA_378_60m_Cy3_3577_60m_Cy5_14194579_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 3577/60min/mid log phase


title: 2275_90m_Cy3_2276_90m_Cy5_14192939_MDS.mev.refIsIA.out

first: PFGRC

last: JCVI

institute: J. Craig Venter Institute

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).
2275 = reference.

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/late log  phase (90 min)

growth_protocol: Cells were grown in TSA media containing no vancomycin. Samples were collected 90 min after inoculation.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer

value: late log phase

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 2275_60m_Cy3_2277_60m_Cy5_14192941_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/mid log  phase (60 min)

growth_protocol: Cells were grown in TSA media containing no vancomycin. Samples were collected 60 min after inoculation.

value: mid log phase

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.T8.0mM.VAN.30min.Cy5_14181937_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ early log phase(30 min)

source_name: Staphylococcus aureus strain T8/ early log phase(30 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 30 min after inoculation. Experiments were conducted in 3 technical replicates.


title: 9QSA_378_60m_Cy3_5612_60m_Cy5_14194648_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 5612/60min/mid log phase


title: 9QSA_378_90m_Cy3_6939_90m_Cy5_14194587_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 6939/90min/late log phase


title: 9QSA_378_60m_Cy3_6939_60m_Cy5_14194586_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 6939/60min/mid log phase


title: 2275_90m_Cy3_2277_90m_Cy5_14194805_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.T8.0mM.VAN.30min.Cy5_14181931_MDS.mev.refIsIA.out


title: 2275_120m_Cy3_2277_120m_Cy5_14194810_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early stationary phase (120 min)

growth_protocol: Cells were grown in TSA media containing no vancomycin. Samples were collected 120 min after inoculation.

value: early stationary phase

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)

treatment_protocol: None.

value: none .


title: 2275_60m_Cy3_2277_60m_Cy5_14192940_MDS.mev.refIsIA.out


title: 2275_90m_Cy3_2276_90m_Cy5_14192938_MDS.mev.refIsIA.out


title: 2275_120m_Cy3_2277_120m_Cy5_14194806_MDS.mev.refIsIA.out


title: 2275_60m_Cy3_2276_60m_Cy5_14193010_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 2275_60m_Cy3_2276_60m_Cy5_14193012_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.C1.0mM.VAN.30min.Cy5_14181936_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain C1/ early log phase(30 min)


title: 2275_120m_Cy3_2276_120m_Cy5_14192937_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 2275_90m_Cy3_2277_90m_Cy5_14193013_MDS.mev.refIsIA.out


title: 2275_30m_Cy3_2277_30m_Cy5_14181933_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early log phase (30 min)

growth_protocol: Cells were grown in TSA media containing no vancomycin. Samples were collected 30 min after inoculation.

value: early log phase

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.C1.0mM.VAN.30min.Cy5_14181935_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA /early log phase(30 min)

source_name: Staphylococcus aureus strain C1 /early log phase(30 min)


title: 9QSA04222010A.PA0mM.VAN.30min.Cy3.C1.0mM.VAN.30min.Cy5_14181934_MDS.mev.refIsIA.out


title: 9QSA03242010A_Q2275.120MIN.MOCK.Cy3_Q2283.120MIN.MOCK.Cy5_14194359_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 9QSA03192010A_Q2275.60MIN.MOCK.Cy3_Q2278.60MIN.MOCK.Cy5_14189459_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early log phase (60 min)

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (60 min)


title: 9QSA03192010A_Q2275.90MIN.MOCK.Cy3_Q2276.90MIN.MOCK.Cy5_14189513_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/late log phase (90 min)

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/late log phase (90 min)


title: 9QSA03192010A_Q2275.90MIN.MOCK.Cy3_Q2277.90MIN.MOCK.Cy5_14189517_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/late log phase (90 min)


title: 9QSA03242010A_Q2275.30MIN.MOCK.Cy3_Q2283.30MIN.MOCK.Cy5_14194356_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 2275_120m_Cy3_2276_120m_Cy5_14192936_MDS.mev.refIsIA.out


title: 2275_30m_Cy3_2276_30m_Cy5_14193009_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA03242010A_Q2275.60MIN.MOCK.Cy3_Q2279.60MIN.MOCK.Cy5_14194351_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/mid log phase (60 min)

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/mid log phase (60 min)


title: 9QSA03242010A_Q2275.30MIN.MOCK.Cy3_Q2279.30MIN.MOCK.Cy5_14194348_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA03192010A_Q2275.120MIN.MOCK.Cy3_Q2276.120MIN.MOCK.Cy5_14189514_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early stationary phase (120 min)


title: 9QSA03192010A_Q2275.90MIN.MOCK.Cy3_Q2278.90MIN.MOCK.Cy5_14189460_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/late log phase (90 min)


title: 9QSA03192010A_Q2275.30MIN.MOCK.Cy3_Q2277.30MIN.MOCK.Cy5_14189515_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early log phase (30 min)


title: 9QSA03192010A_Q2275.120MIN.MOCK.Cy3_Q2278.120MIN.MOCK.Cy5_14189461_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 2275_30m_Cy3_2276_30m_Cy5_14193008_MDS.mev.refIsIA.out


title: 9QSA03192010A_Q2275.30MIN.MOCK.Cy3_Q2276.30MIN.MOCK.Cy5_14189511_MDS.mev.refIsIA.out


title: 9QSA03242010A_Q2275.60MIN.MOCK.Cy3_Q2283.60MIN.MOCK.Cy5_14194357_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/mid log phase (60 min)


title: 9QSA03192010A_Q2275.120MIN.MOCK.Cy3_Q2277.120MIN.MOCK.Cy5_14189519_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 9QSA03242010A_Q2275.90MIN.MOCK.Cy3_Q2283.90MIN.MOCK.Cy5_14194358_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/late log phase (90 min)


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.T8.32mM.VAN.90min.Cy5_14192956_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ late log phase (90 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90 min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

treatment_protocol: Vancomycin 4mM

value: Vancomycin

tag: dose

source_name: Staphylococcus aureus strain T8/ late log phase (90 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90 min
after inoculation. Staphylococcus aureus  T8 was treated with 32mM Vancomycin. Experiments were conducted in 3 technical replicates

treatment_protocol: Vancomycin 32mM


title: 9QSA03192010A_Q2275.30MIN.MOCK.Cy3_Q2278.30MIN.MOCK.Cy5_14189458_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.T8.32mM.VAN.90min.Cy5_14192950_MDS.mev.refIsIA.out

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

Strain PA = reference.

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

value: PA

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90min
after inoculation. Staphylococcus aureus T8 was treated with 32mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 2275_30m_Cy3_2277_30m_Cy5_14192943_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA03192010A_Q2275.60MIN.MOCK.Cy3_Q2276.60MIN.MOCK.Cy5_14189512_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/mid log phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.T8.32mM.VAN.90min.Cy5_14192949_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA4mM.VAN.60min.Cy3.T8.32mM.VAN.60min.Cy5_14192952_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/mid log phase (60 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strainT8/mid log phase (60 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60min
after inoculation. Staphylococcus aureus T8 was treated with 32mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA03192010A_Q2275.60MIN.MOCK.Cy3_Q2277.60MIN.MOCK.Cy5_14189516_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early log phase (60 min)

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.60min.Cy3.T8.32mM.VAN.60min.Cy5_14192948_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain T8/ mid log phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.30min.Cy3.T8.32mM.VAN.30min.Cy5_14192947_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ early log phase(30 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 30min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain T8/ early log phase(30 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 30min
after inoculation. Staphylococcus aureus T8 was treated with 32mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA4mM.VAN.30min.Cy3.T8.32mM.VAN.30min.Cy5_14192944_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/early log phase(30 min)

source_name: Staphylococcus aureus strain T8/early log phase(30 min)


title: 9QSA04222010A.PA4mM.VAN.60min.Cy3.T8.32mM.VAN.60min.Cy5_14192951_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ mid log phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.T8.32mM.VAN.120min.Cy5_14192953_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/early stationary phase (120 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 120min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

value: early stationary phase (120min)

source_name: Staphylococcus aureus strain T8/early stationary phase (120 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 120min
after inoculation. Staphylococcus aureus T8 was treated with 32mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA4mM.VAN.30min.Cy3.T8.32mM.VAN.30min.Cy5_14192945_MDS.mev.refIsIA.out


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.T8.32mM.VAN.120min.Cy5_14192954_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ early stationary phase (120 min)

source_name: Staphylococcus aureus strain T8/ early stationary phase (120 min)


title: 120MIN_Q2275.Cy3_Q2276.Cy5_14211473_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early stationary  phase (120 min)

growth_protocol: Strains were grown in TSA media containing vancomycin. Samples were collected 120 min after inoculation.

treatment_protocol: Vancomycin Treated

value: vancomycin

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 120MIN_Q2275.Cy3_Q2277.Cy5_14211477__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early stationary phase (120 min)

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 120MIN_Q2275.Cy3_Q2278.Cy5_14211484__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 90MIN_Q2275.Cy3_Q2279.Cy5_14211488__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/late log  phase (90 min)

growth_protocol: Strains were grown in TSA media containing vancomycin. Samples were collected 90 min after inoculation.

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 90MIN_Q2275.Cy3_Q2276.Cy5_14211471_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 90MIN_Q2275.Cy3_Q2283.Cy5_14211495__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 60MIN_Q2275.Cy3_Q2278.Cy5_14211482__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/mid log  phase (60 min)

growth_protocol: Strains were grown in TSA media containing vancomycin. Samples were collected 60 min after inoculation.

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.C1.16mM.VAN.90min.Cy5_14192979_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ late log phase (90 min)

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

treatment_protocol: Vancomycin 4 mM

value: late log phase (90min)

source_name: Staphylococcus aureus strain C1/ late log phase (90 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90 min
after inoculation. Staphylococcus aureus C1 was treated with 16mM Vancomycin. Experiments were conducted in 3 technical replicates.

treatment_protocol: Vancomycin 16mM


title: 60MIN_Q2275.Cy3_Q2283.Cy5_14211491__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 30MIN_Q2275.Cy3_Q2279.Cy5_14211486__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early log phase (30 min)

growth_protocol: Strains were grown in TSA media containing vancomycin. Samples were collected 30 min after inoculation.

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 120MIN_Q2275.Cy3_Q2283.Cy5_14211496__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 60MIN_Q2275.Cy3_Q2277.Cy5_14211475_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 120MIN_Q2275.Cy3_Q2279.Cy5_14211489__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 60MIN_Q2275.Cy3_Q2276.Cy5_14211470_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 30MIN_Q2275.Cy3_Q2283.Cy5_14211490__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2283 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.C1.16mM.VAN.120min.Cy5_14192986_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/early stationary phase (120 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 120 min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain C1/early stationary phase (120 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 120 min
after inoculation. Staphylococcus aureus C1 was treated with 16mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.C1.16mM.VAN.90min.Cy5_14181917_MDS.mev.refIsIA.out

growth_protocol:
Strains were grown in TSA media. Samples were collected at 90 min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain C1/ late log phase(90 min)


title: 60MIN_Q2275.Cy3_Q2279.Cy5_14211487__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2279 (clinical isolate with Vancomycin resistance) as the query strain/mid log  phase (60 min)


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.T8.32mM.VAN.120min.Cy5_14192955_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/ early stationary phase (120 min)

source_name: Staphylococcus aureus strain T8/ early stationary phase (120 min)


title: 9QSA04222010A.PA4mM.VAN.90min.Cy3.C1.16mM.VAN.90min.Cy5_14181918_MDS.mev.refIsIA.out


title: 30MIN_Q2275.Cy3_Q2277.Cy5_14211474_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 30MIN_Q2275.Cy3_Q2278.Cy5_14211480__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2278 (clinical isolate with Vancomycin resistance) as the query strain/early log phase (30 min)


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.C1.16mM.VAN.120min.Cy5_14181916_MDS.mev.refIsIA.out

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60 min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

growth_protocol:
Strains were grown in TSA media. Samples were collected at 60 min
after inoculation. Staphylococcus aureus C1 was treated with 16mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA4mM.VAN.120min.Cy3.C1.16mM.VAN.120min.Cy5_14192980_MDS.mev.refIsIA.out


title: 90MIN_Q2275.Cy3_Q2277.Cy5_14211476__MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/late log  phase (90 min)

source_name: Staphylococcus aureus strain 2277 (clinical isolate with Vancomycin resistance) as the query strain/late log  phase (90 min)


title: 30MIN_Q2275.Cy3_Q2276.Cy5_14211469_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 2275 (sensitive) as the reference strain/early stationary phase (120 min)

source_name: Staphylococcus aureus strain 2276 (clinical isolate with Vancomycin resistance) as the query strain/early stationary phase (120 min)


title: 9QSA04222010A.PA.4mM.VAN.60min.Cy3.C1.16mM.VAN.60min.Cy5_14181930_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/mid log phase (60 min)

value: mid log phase (60min)

source_name: Staphylococcus aureus strain C1/mid log phase (60 min)


title: 9QSA04222010A.PA.4mM.VAN.60min.Cy3.C1.16mM.VAN.60min.Cy5_14181929_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189552_1422_90min_Cy3_vs_Q2798_90min_Cy5_MDS.mev.refIsIA.out

first: Chun-Hua

last: Wan

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

source_name: Staphylococcus aureus 1422/late log phase (90 min)

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 90 min after inoculation.

value: 1422; growth phase:late log phase

source_name: Staphylococcus aureus 2798/late log phase (90 min)

value: 2798; growth phase:late log phase


title: 9QSA04222010A.PA.4mM.VAN.30min.Cy3.C1.16mM.VAN.30min.Cy5_14181925_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus PA/ early log phase(30 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 30 min
after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin. Experiments were conducted in 3 technical replicates.

treatment_protocol: Vancomycin

source_name: Staphylococcus aureus C1/early log phase(30 min)

growth_protocol:
Strains were grown in TSA media. Samples were collected at 30 min
after inoculation. Staphylococcus aureus C1 was treated with 16mM Vancomycin. Experiments were conducted in 3 technical replicates.


title: 9QSA04222010A.PA.4mM.VAN.60min.Cy3.C1.16mM.VAN.60min.Cy5_14181928_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189551_1422_120min_Cy3_vs_Q2798_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/early stationary phase (120 min)

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 120 min after inoculation.

value: 1422; growth phase:early stationary phase

source_name: Staphylococcus aureus 2798/early stationary phase (120 min)

value: 2798; growth phase:early stationary phase


title: 9QSA03192010A_14189482_1422_30min_Cy3_vs_Q2798_30min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/early log phase(30 min)

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 30 min after inoculation.

value: 1422; growth phase:early log phase

source_name: Staphylococcus aureus 2798/early log phase(30 min)

value: 2798; growth phase:early log phase


title: 9QSA03192010A_14189480_1422_90min_Cy3_vs_Q2798_90min_Cy5_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189456_923_60min_Cy3_vs_923agr_60min_Cy5_MDS.mev.refIsIA.out

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

source_name: Staphylococcus aureus USA300/ mid log phase (60 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 60 min after inoculation.

tag: genotype/variation

value: wild type

source_name: Staphylococcus aureus USA300 "agr knockout"/ mid log phase (60 min)

value: agr knockout


title: 9QSA03192010A_14189450_923_60min_Cy3_vs_923agr_60min_Cy5_MDS.mev.refIsIA.out

value: mid log phase


title: 9QSA03192010A_14189478_1422_30min_Cy3_vs_Q2798_30min_Cy5_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189481_1422_60min_Cy3_vs_Q2798_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/mid log phase (60 min)

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 60 min after inoculation.

value: 1422; growth phase:mid log phase

source_name: Staphylococcus aureus 2798/mid log phase (60 min)

value: 2798; growth phase:mid log phase


title: 9QSA03192010A_14189556_1422_30min_Cy3_vs_Q2798_30min_Cy5_MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_160min_250ng.ml_Daptomycin_14192975.mev

first: Brian

last: Bishop

state: Maryland

institute: Bishop, Brian

source_name: Staphylococcus aureus strain 2818 / 160 min / 250ng.ml Daptomycin / early stationary phase

growth_protocol: Strains were grown in TSA media and were collected at 160 min after inoculation in the presence (250 ng.ml) of Daptomycin.

treatment_protocol: Daptomycin 250 ng.ml

source_name: Staphylococcus aureus strain 2819 / 160 min / 250ng.ml Daptomycin / early stationary phase


title: 9QSA03192010A_14189504_923_30min_Cy3_vs_923agr_30min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus USA300/ early log phase (30 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 30 min after inoculation.

value: early log phase

source_name: Staphylococcus aureus USA300 "agr knockout"/ early log phase (30 min)


title: 9QSA03192010A_14189554_1422_60min_Cy3_vs_Q2798_60min_Cy5_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189479_1422_120min_Cy3_vs_Q2798_120min_Cy5_MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_60min_2ug.ml_Daptomycin_14192957.mev

source_name: Staphylococcus aureus strain 2818 / 60 min / 2ug.ml Daptomycin / log phase

growth_protocol: Strains were grown in TSA media and were collected at 60 min after inoculation in the presence (2 ug.ml) of Daptomycin.

treatment_protocol: Daptomycin 2 ug.ml

source_name: Staphylococcus aureus strain 2819 / 60 min / 2ug.ml Daptomycin / log phase


title: 9QSA03192010A_14189477_1422_60min_Cy3_vs_Q2798_60min_Cy5_MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_60min_4ug.ml_Daptomycin_14192958.mev

source_name: Staphylococcus aureus strain 2818 / 60 min / 4ug.ml Daptomycin / log phase

growth_protocol: Strains were grown in TSA media and were collected at 60 min after inoculation in the presence (4 ug.ml) of Daptomycin.

treatment_protocol: Daptomycin 4 ug.ml

source_name: Staphylococcus aureus strain 2819 / 60 min / 4ug.ml Daptomycin / log phase


title: 9QSA03192010A_14189452_923_30min_Cy3_vs_923agr_30min_Cy5_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189527_923_60min_Cy3_vs_923agr_60min_Cy5_MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_60min_250ng.ml_Daptomycin_14192932.mev

source_name: Staphylococcus aureus strain 2818 / 60 min / 250ng.ml Daptomycin / log phase

growth_protocol: Strains were grown in TSA media and were collected at 60 min after inoculation in the presence (250 ng.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 60 min / 250ng.ml Daptomycin / log phase


title: 2818.Cy3_vs_2819.Cy5_14192976_160min_2ug.ml.mev

source_name: Staphylococcus aureus strain 2818 / 160 min / 2ug.ml Daptomycin / early stationary phase

growth_protocol: Strains were grown in TSA media and were collected at 160 min after inoculation in the presence (2 ug.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 160 min / 2ug.ml Daptomycin / early stationary phase


title: 9QSA03192010A_14189457_923_30min_Cy3_vs_923agr_30min_Cy5__MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_14192977_160min_4ug.ml.mev

source_name: Staphylococcus aureus strain 2818 / 160 min / 4ug.ml Daptomycin / early stationary phase

growth_protocol: Strains were grown in TSA media and were collected at 160 min after inoculation in the presence (4 ug.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 160 min / 4ug.ml Daptomycin / early stationary phase


title: 9QSA_923_120m_cy3_sae_120m_cy5_14194661_MDS.mev.refIsIA.out

first: Vasily

middle: A

last: Sharov

source_name: Staphylococcus aureus strain 923/ early stationary phase(120 min) (Reference)

growth_protocol: Staphylococcus aureus strain 923; early stationary phase (120 min)

value: wild-type

tag: time course

value: early stationary phase

source_name: Staphylococcus aureus USA300 "sae knockout"/ early stationary phase(120 min) (Query)

value: sae knockout


title: 2818.Cy3_vs_2819.Cy5_120min_4ug.ml_Daptomycin_14192974v.mev

source_name: Staphylococcus aureus strain 2818 / 120 min / 4ug.ml Daptomycin  / late log phase

growth_protocol: Strains were grown in TSA media and were collected 120 min after inoculation in the presence (4 ug.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 120 min / 4ug.ml Daptomycin / late log phase


title: 9QSA_923_120m_cy3_sae_120m_cy5_14194662_MDS.mev.refIsIA.out

growth_protocol: Staphylococcus aureus USA300 "sae knockout"


title: 9QSA_923_120m_cy3_sae_120m_cy5_14194656_MDS.mev.refIsIA.out


title: 2818.Cy3_vs_2819.Cy5_120min_250ng.ml_Daptomycin_14192972.mev

source_name: Staphylococcus aureus strain 2818 / 120 min / 250ng.ml Daptomycin / late log phase

growth_protocol: Strains were grown in TSA media and were collected 120 min after inoculation in the presence (250 ng.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 120 min / 250ng.ml Daptomycin / late log phase


title: 9QSA_923_90m_cy3_sae_90m_cy5_14211502_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/ late log phase(90 min) (Reference)

growth_protocol: Staphylococcus aureus strain 923; late log phase (90 min)

value: late log phase

source_name: Staphylococcus aureus USA300 "sae knockout"/ late log phase(90 min) (Query)


title: 9QSA_923_60m_cy3_sae_60m_cy5_14211499_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/ mid log phase(60 min) (Reference)

growth_protocol: Staphylococcus aureus strain 923; mid log phase (60 min)

source_name: Staphylococcus aureus USA300 "sae knockout"/ mid log phase(60 min) (Query)


title: 9QSA03192010A_14189526_923_90min_Cy3_vs_923agr_90min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus USA300/ late log phase (90 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 min after inoculation.

source_name: Staphylococcus aureus USA300 "agr knockout"/ late log phase (90 min)


title: 2818.Cy3_vs_2819.Cy5_120min_2ug.ml_Daptomycin_14192973.mev

source_name: Staphylococcus aureus strain 2818 / 120 min / 2ug.ml Daptomycin / late log phase

growth_protocol: Strains were grown in TSA media and were collected 120 min after inoculation in the presence (2 ug.ml) of Daptomycin.

source_name: Staphylococcus aureus strain 2819 / 120 min / 2ug.ml Daptomycin / late log phase


title: 9QSA04222010A.PA.4mM.VAN.30min.Cy3.C1.16mM.VAN.30min.Cy5_14181923_MDS.mev.refIsIA.out

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

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

Strain PA = reference.

source_name: Staphylococcus aureus strain PA / early log phase(30 min)

growth_protocol: Strains were grown in TSA media. Samples were collected 30 min after inoculation. Staphylococcus aureus PA was treated with 4mM Vancomycin.Experiments were conducted in 3 technical replicates.

value: PA

value: Vancomycin

value: early log phase (30min)

source_name: Staphylococcus aureus strain C1 / early log phase(30 min)

growth_protocol: Strains were grown in TSA media. Samples were collected 30 min after inoculation. Staphylococcus aureus C1 was treated with 16mM Vancomycin.Experiments were conducted in 3 technical replicates.


title: 9QSA_923_90m_cy3_sae_90m_cy5_14211500_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189455_923_90min_Cy3_vs_923agr_90min_Cy5_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189453_923_120min_Cy3_vs_923agr_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus USA300/ early stationary phase (120 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 120 min after inoculation.

source_name: Staphylococcus aureus USA300 "agr knockout"/ early stationary phase (120 min)


title: 9QSA04222010A.PA.4mM.VAN.30min.Cy3.C1.16mM.VAN.30min.Cy5_14181922_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain PA/early log phase(30 min)

source_name: Staphylococcus aureus strain C1 /early log phase(30 min)


title: 9QSA03192010A_14189525_923_120min_Cy3_vs_923agr_120min_Cy5_MDS.mev.refIsIA.out


title: 9QSA_923_60m_cy3_sae_60m_cy5_14211498_MDS.mev.refIsIA.out


title: 9QSA_923_60m_cy3_sae_60m_cy5_14211497_MDS.mev.refIsIA.out


title: normal_lung_fibroblast_cell_line089

city: Toronto

first: Ming-Sound

last: Tsao

institute: Ontario Cancer Institute/ Princess Margaret Hospital

description:
Whole-transcript expression profiling
NF089

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Raw data was pre-processed and normalized using RMA implemented in Affymetrix Expression console v1.1, expression values were summarized at the gene-core level based on NetAffx NA28 annotation library integrated in Affymetrix Expression console v1.1.

source_name: Normal lung

label_protocol: standard Affymetrix procedures

extract_protocol: Total RNA was isolated from fresh cells using Qiagen Rneasy mini kit

tag: age

tag: Sex

value: M

tag: disease state

value: Normal lung

tag: histology

value: Normal lung parenchyma

tag: Stage


title: 9QSA_923_90m_cy3_sae_90m_cy5_14211501_MDS.mev.refIsIA.out


title: normal_lung_fibroblast_cell_line690

description:
Whole-transcript expression profiling
NF690

value: F


title: normal_lung_fibroblast_cell_line094

description:
Whole-transcript expression profiling
NF094


title: normal_lung_fibroblast_cell_line927

description:
Whole-transcript expression profiling
NF927


title: normal_lung_fibroblast_cell_line549

description:
Whole-transcript expression profiling
NF549


title: normal_lung_fibroblast_cell_line727

description:
Whole-transcript expression profiling
NF727


title: 9QSA_923_30m_cy3_sae_30m_cy5_14194660_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/ early log phase(30 min) (Reference)

source_name: Staphylococcus aureus USA300 "sae knockout"/ early log phase(30 min) (Query)

growth_protocol: Strains were grown in TSA media. Samples were collected at 30min after inoculation.


title: 9QSA03192010A_14190267_923_90min_Cy3_vs_649_90min_Cy5_MDS.mev.refIsIA.out

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)
USA300 = reference and USA400 = query.

source_name: Staphylococcus aureus strain 923/late log phase (90 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 min after inoculation. Experiments were conducted in 3 technical replicates.

tag: pulsotype

source_name: Staphylococcus aureus strain 649/late log phase (90 min)

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer


title: 9QSA03192010A_14190266_923_60min_Cy3_vs_649_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/mid log phase (60 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 60 min after inoculation. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain 649/mid log phase (60 min)


title: normal_lung_fibroblast_cell_line954

description:
Whole-transcript expression profiling
NF954


title: normal_lung_fibroblast_cell_line935

description:
Whole-transcript expression profiling
NF935


title: normal_lung_fibroblast_cell_line006

description:
Whole-transcript expression profiling
NF006


title: normal_lung_fibroblast_cell_line971

description:
Whole-transcript expression profiling
NF971


title: 9QSA03192010A_14190265_923_30min_Cy3_vs_649_30min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/early log phase (30 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 30 min after inoculation. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain 649/early log phase (30 min)


title: normal_lung_fibroblast_cell_line746

description:
Whole-transcript expression profiling
NF746


title: normal_lung_fibroblast_cell_line192

description:
Whole-transcript expression profiling
NF192


title: normal_lung_fibroblast_cell_line471

description:
Whole-transcript expression profiling
NF471


title: 9QSA03192010A_14189522_923_120min_Cy3_vs_649_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/early stationary phase (120 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 120 min after inoculation. Experiments were conducted in 3 technical replicates.

source_name: Staphylococcus aureus strain 649/early stationary phase (120 min)


title: normal_lung_fibroblast_cell_line520

description:
Whole-transcript expression profiling
NF520


title: 9QSA_923_30m_cy3_sae_30m_cy5_14194659_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media. Samples were collected at 30min


title: primary_NSCLC_fibroblast_cell_line954

description:
Whole-transcript expression profiling
CAF954

source_name: primary lung cancer

value: primary lung cancer

value: Squamous cell carcinoma

value: I


title: 9QSA03192010A_14189472_923_120min_Cy3_vs_649_120min_Cy5_MDS.mev.refIsIA.out


title: primary_NSCLC_fibroblast_cell_line549

description:
Whole-transcript expression profiling
CAF549

value: Adenocarcinoma

value: III


title: primary_NSCLC_fibroblast_cell_line094

description:
Whole-transcript expression profiling
CAF094


title: primary_NSCLC_fibroblast_cell_line192

description:
Whole-transcript expression profiling
CAF192

value: Mixed large neuro- endocrine carcinoma and adenocarcinoma


title: primary_NSCLC_fibroblast_cell_line089

description:
Whole-transcript expression profiling
CAF089

value: II


title: primary_NSCLC_fibroblast_cell_line727

description:
Whole-transcript expression profiling
CAF727


title: primary_NSCLC_fibroblast_cell_line927

description:
Whole-transcript expression profiling
CAF927


title: primary_NSCLC_fibroblast_cell_line471

description:
Whole-transcript expression profiling
CAF471


title: normal_lung_fibroblast_cell_line491

description:
Whole-transcript expression profiling
NF491


title: primary_NSCLC_fibroblast_cell_line491

description:
Whole-transcript expression profiling
CAF491


title: primary_NSCLC_fibroblast_cell_line935

description:
Whole-transcript expression profiling
CAF935

value: Combined small and large cell carcinoma and adenocarcinoma


title: primary_NSCLC_fibroblast_cell_line690

description:
Whole-transcript expression profiling
CAF690


title: 9QSA_923_30m_cy3_sae_30m_cy5_14194658_MDS.mev.refIsIA.out

value: wild-type

value: early log phase

value: sae knockout


title: primary_NSCLC_fibroblast_cell_line971

description:
Whole-transcript expression profiling
CAF971


title: 9QSA03192010A_14189469_923_90min_Cy3_vs_649_90min_Cy5_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 after inoculation. Experiments were conducted in 3 technical replicates.

value: late log phase


title: 9QSA03192010A_14189470_923_60min_Cy3_vs_649_60min_Cy5_MDS.mev.refIsIA.out

value: mid log phase


title: 9QSA03192010A_14189471_923_30min_Cy3_vs_649_30min_Cy5_MDS.mev.refIsIA.out

growth_protocol:
Strains were grown in TSA media. Samples were collected at four time points in separate series of experiments
30 min, 60 min, 90 min, 120 min after inoculation. Experiments were conducted in 3 technical replicates.


title: primary_NSCLC_fibroblast_cell_line746

description:
Whole-transcript expression profiling
CAF746

value: M


title: 6QSA10082008A_923.MOCK.Cy5_V3.MOCK.Cy3_13941722_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus USA300/Mock (Reference)

source_name: Staphylococcus aureus V3/Mock (Query)

growth_protocol: Strains were grown in TSA media containing no oxacilin.


title: 9QSA03192010A_14189467_923_120min_Cy3_vs_649_120min_Cy5_MDS.mev.refIsIA.out

value: early stationary phase


title: 6QSA10082008A_923.OXA.Cy5_V3.OXA.Cy3_13941720_MDS.mev.refIsIB.out

source_name: Staphylococcus aureus USA300/Oxacilin (Reference)

treatment_protocol: Oxacilin

source_name: Staphylococcus aureus V3/Oxacilin (Query)

growth_protocol: Strains were grown in TSA media containing oxacilin.


title: 9QSA03192010A_14189466_923_30min_Cy3_vs_649_30min_Cy5_MDS.mev.refIsIA.out


title: primary_NSCLC_fibroblast_cell_line006

description:
Whole-transcript expression profiling
CAF006


title: 6QSA10082008A_923.OXA.Cy3_V3.OXA.Cy5_13941719_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media containing oxacilin


title: primary_NSCLC_fibroblast_cell_line520

description:
Whole-transcript expression profiling
CAF520


title: 6QSA10082008A_923.MOCK.Cy3_V3.MOCK.Cy5_13920105_MDS.mev.refIsIA.out

growth_protocol: Strains were grown in TSA media containing no oxacilin


title: 6QSA10082008A_923.MOCK.Cy3_V3.MOCK.Cy5_13941721_MDS.mev.refIsIA.out


title: normal_lung_fibroblast_cell_line746

description:
NF746
Genome wide DNA Methylation profiling

hyb_protocol: Standard Illumina protocol 48C, 17.5 Hours

scan_protocol: Standard Illumina protocol on iScan (Illumina)

data_processing: Standard Illumina protocol for Human Methylation 27K Beadchip quantificatin and processing in GenomeStudio v2010.2

label_protocol: Standard Illumina protocol; Illumina Infinium II methylation kit

extract_protocol: Genomic DNA was extracted using DNeasy blood and tissue kit (Qiagen, cat# 69504) following DNeasy 96 protocol.

tag: cell line

value: normal lung fibroblast cell line (NF)

value: Normal lung parenchyma


title: normal_lung_fibroblast_cell_line927

description:
NF927
Genome wide DNA Methylation profiling

value: F


title: 6QSA10082008A_923.OXA.Cy3_V3.OXA.Cy5_13920106_MDS.mev.refIsIA.out


title: 9QSA03192010A_14189448_923_120min_Cy3_vs_923agr_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus USA300/ early stationary phase (120 min)

value: wild type

source_name: Staphylococcus aureus USA300 "agr knockout"/ early stationary phase (120 min)

value: agr knockout


title: normal_lung_fibroblast_cell_line727

description:
NF727
Genome wide DNA Methylation profiling

source_name: Normal lung


title: 6QSA09032008A_V3.MOCK.CY3_V3.OXA.CY5_13917792_MDS.mev.refIsIA.out

description: This is a self-self hybridization (query/reference does not apply).

source_name: Staphylococcus aureus V3/Mock (Reference)


title: 9QSA03192010A_14189465_923_60min_Cy3_vs_649_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus strain 923/late log phase (60 min)

source_name: Staphylococcus aureus strain 649/late log phase (60 min)


title: normal_lung_fibroblast_cell_line549

description:
NF549
Genome wide DNA Methylation profiling


title: primary_NSCLC_fibroblast_cell_line927

description:
CAF927
Genome wide DNA Methylation profiling

value: primary NSCLC fibroblast cell line (CAF)

value: Adenocarcinoma

value: I


title: primary_NSCLC_fibroblast_cell_line971

description:
CAF971
Genome wide DNA Methylation profiling

value: II


title: 6QSA09032008A_923.OXA.CY3_V3.OXA.CY5_13917788_MDS.mev.refIsIA.out