title: MKN_45_P_Lysate_rep2

city: Nagaizumi-cho

first: Keiichi

last: HATAKEYAMA

state: Sunto-gun, Shizuoka

address: 1007 Shimonagakubo

country: Japan

institute: Shizuoka Cancer Center Research Institute

description: gene expression in Cellular lysate of MKN45P

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65 Celsius in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 Celsius GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT XDR Hi is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MKN_45_P, lysate, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  cRNA yield were checked with the NanoDrop Spectrophotometer, and quality of cRNA was then confirmed using Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: The gastric cancer cell lines were grown in RPMI 1640 supplemented with 10% FBS, glutamine (0.3 mg/ml), penicillin (100 unit/ml) and streptomycin (0.1 mg/ml) in a humidified 5% CO2 incubator.

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: he cell lines were harvested using Trypsin-EDTA (Gibco, Grand Island, NY) and washed twice with PBS (pH 7.4). Briefly, after aspiration of supernatant, cellular pellets were gently washed twice with PBS.

tag: phenotype

value: highly metastatic


title: MKN_45_P_Lysate_rep1

status: Public on Jun 01 2010

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: MKN_45_P, lysate, replicate 1

tag: cell line


title: Lineage I wildtype compared to sigma B null mutant

city: Ithaca

first: Haley

middle: Franks

last: Oliver

state: NY

address: 410 Stocking

department: Food Science

country: USA

institute: Cornell University

description: Expression profiles were measured from three independent RNA extractions, resulting in 12 replicate spots per gene (array contains quadruplicate spots).

hyb_protocol: Briefly, microarray slides were blocked in a prehybridization buffer supplemented with bovine serum albumen (BSA) (Sigma-Aldrich), washed with deionized water then isopropyl alcohol. Dried Cy3- and Cy5-labeled cDNA was hydrated with hybridization buffer containing 0.6 mg/ml sheared salmon sperm DNA (Invitrogen), denatured twice at 95ºC for 5 minutes and briefly centrifuged. cDNA was hybridized to the microarray at 42ºC for 16 hours. Following hybridization, slides were washed according to the PFGRC/JCVI M008 protocol and dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.) using the following general scanning parameters: pixel size=10, focus position=20, lines to average=1, laser power=100%. The auto-PMT function was used to scan the slides with an acceptable PMT range of 400-900. Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis. The PFGRC/JCVI L. monocytogenes microarray contained multiple probes for certain loci that lacked a 70mer consensus sequence for a given locus among the four strains represented on the microarray. In instances where multiple probes were present for a single locus, the probe that best matched the sequence for a given strain used in the present study was selected as the representative probe for subsequent analyses for that strain. BLASTN was used to calculate the hybridization index (HI), the percent identity between each probe and each strain; BLASTN results were parsed to compare percent identity between each strain and the probes. EGD-e locus names were used to describe the corresponding open reading frames (ORFs) in the lineage I, IIIA, and IIIB strains as these genomes have not yet been annotated; EGD-e locus names were also used in lieu of 10403S locus names to facilitate comparisons among all strains in this study. Genes unique to F2365, F6852 and H7858 (i.e. genes with no EGD-e homologue) maintained their locus names. Genes with higher transcript levels in a wildtype strain compared to its isogenic ΔsigB mutant (fold change > 1.5) and adjusted p-values < 0.05 were considered positively differentially expressed, and thus σB-dependent.

label: Rep 1 Cy3; Rep2 Cy5; Rep3 Cy3

organism: Listeria monocytogenes

source_name: Lineage I FSL J1-194 wildtype

label_protocol: The Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (PFGRC/JCVI) L. monocytogenes microarray version 2 was used to identify mRNA transcript level differences between wildtype strains and their respective ∆sigB mutants. The PFGRC/JCVI microbial RNA aminoallyl labeling for microarray standard operating procedure M007 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to reverse transcribe and label the total RNA. Spectrophotometry was used to quantify cDNA and total picomoles of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ) incorporation. Cy3- and Cy5-labeled cDNA was combined and thoroughly dehydrated prior to hybridization. PFGRC/JCVI standard operating procedure M008 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to hybridize the Cy-dye labeled cDNA to the microarray.

extract_protocol: RNAProtect bacterial reagent (Qiagen, Valencia, CA) was added to the cultures according to manufacturer’s instructions to stabilize the mRNA; pellets were stored at -80°C prior to RNA isolation. RNA was isolated as previously described. Briefly, bacterial cells were lysed enzymatically with lysozyme (Fisher Scientific, Pittsburg, PA), and mechanically, using 6 sonication bursts (Misonix, Farmingdale, NY) at 18W on ice for 30 seconds. Total RNA was isolated and purified using the RNeasy Midi kit (Qiagen) according to the manufacturer’s protocol. RNA was eluted from the column using RNase-free water. Total RNA was incubated with RNasin (Promega, Madison, WI) to inhibit RNases, and RQ1 DNase (Promega) to remove DNA contamination. After phenol:chloroform extraction, UV spectrophotometry (Nanodrop, Wilmington, DE) was used to quantify and assess purity of the RNA. RNA integrity was assessed by agarose gel electrophoresis. Purified RNA was stored in RNase-free water at -80°C prior to reverse transcription.

tag: strain

value: FSL J1-194 wildtype

tag: phase

value: stationary

label: Rep 1 Cy5; Rep2 Cy3; Rep3 Cy5

source_name: Lineage I FSL C6-001 delete sigma B mutant

value: FSL C6-001 delete sigma B mutant


title: Stroma_treatment HPHF+_S 22

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 22

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior to scanning, the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 82 microarrays were normalized for dye and array effects (i.e., Lowess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Stromal tissue, HPHF+ diet

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as per manufacturer's instructions.

extract_protocol: Calves were killed and their mammary glands were removed. A sample of parenchyma and fat pad was dissected and snap-frozen in liquid nitrogen. Tissue was weighed (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen).

treatment_protocol: Holstein calves (1-3 days old) were fed 1 of 4 different milk replacers until the age of 65 days old.

tag: breed

value: Holstein

tag: age

value: 65 days

tag: mammary tissue

value: stroma (fat pad)

tag: diet

value: HPHF+

source_name: Reference

extract_protocol: Calves were killed, and tissue samples were dissected and snap-frozen in liquid nitrogen. Tissue was weighed (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen).

tag: tissue

value: mammary, liver, muscle, adipose, placenta


title: Lineage IIIB wildtype compared to sigma B null mutant

source_name: Lineage IIIB FSL J1-194 wildtype

value: FSL J1-208 wildtype

source_name: Lineage IIIB FSL O1-005 delete sigma B mutant

value: FSL O1-005 delete sigma B mutant


title: Lineage II wildtype compared to sigma B null mutant

source_name: Lineage II 10403S wildtype

value: 10403S wildtype

source_name: Lineage II FSL A1-254 delete sigma B mutant

value: FSL A1-254 delete sigma B mutant


title: MKN_45_Lysate_rep1

description: gene expression in Cellular lysate of MKN45

source_name: MKN_45, lysate, replicate 1


title: Stroma_treatment HPLF_S 23

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 23

source_name: Stromal tissue, HPLF diet

value: HPLF


title: MKN_45_Lysate_rep2

source_name: MKN_45, lysate, replicate 2


title: Lineage IIIA wildtype compared to sigma B null mutant

source_name: Lineage IIIA FSL J2-071 wildtype

value: FSL J2-071 wildtype

source_name: Lineage IIIA FSL O1-006 delete sigma B mutant

value: FSL O1-006 delete sigma B mutant


title: Stroma_treatment Control_S 20

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 20

source_name: Stromal tissue, control diet

value: control


title: Stroma_treatment HPHF_S 15

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 15

source_name: Stromal tissue, HPHF diet

value: HPHF


title: Stroma_treatment HPHF+_S 17

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 17


title: Stroma_treatment HPHF+_S 12

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 12


title: Stroma_treatment HPHF_S 16

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 16


title: Stroma_treatment HPLF_S 19

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 19


title: Stroma_treatment HPHF+_S 13

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 13


title: Stroma_treatment HPLF_S 8

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 8


title: Stroma_treatment HPHF+_S 5

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 5


title: Stroma_treatment HPLF_S 11

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 11


title: Stroma_treatment HPLF_S 9

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 9


title: Stroma_treatment Control_S 14

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 14


title: Stroma_treatment Control_S 10

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 10


title: Stroma_treatment Control_S 7

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 7


title: Stroma_treatment HPHF_S 24

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 24


title: MKN45P_Lysate_rep1

description: gene expression and variation of alternative splicing in Cellular lysate of MKN45P

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99°C for 5 min, then 45°C for 5 min centrifuge at max speed for 1 min • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm using Hybridization Oven 640• Fluidics washing is Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomics Suite software.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: MKN45P, lysate, replicate 1

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were then treated with the RiobMinusHuman/mouse Transcriptome Isolation kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: The cell lines were harvested using Trypsin-EDTA (Gibco, Grand Island, NY) and washed twice with PBS (pH 7.4). Briefly, after aspiration of supernatant, cellular pellets were gently washed twice with PBS.

tag: cell type

value: high-metastatic gastric cancer


title: Parenchyma_treatment HPHF_P 24

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 24

source_name: Parenchymal tissue, HPHF diet

value: parenchyma


title: Parenchyma_treatment HPLF_P 23

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 23

source_name: Parenchymal tissue, HPLF diet


title: Parenchyma_treatment HPLF_P 19

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 19


title: PR89a

city: Minneapolis

first: Anthony

middle: James

last: Smith

state: MN

address: 420 Delaware Street S.E.

department: Microbiology

institute: University of Minnesota

description: lymph node, biological replicate 1

hyb_protocol: Fifteen micrograms of fragmented cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0 array.

scan_protocol: After hybridization, chips were washed, stained with streptavidin-phycoerythrin, and scanned with GeneChip Operating Software at the Biomedical Genomics Center at the University of Minnesota.  The experiments from each RNA sample were duplicated in the preparation of each cRNA probe and microarray hybridization.

data_processing: The .cel files produced by the Affymetrix data analysis platform were uploaded into the Expressionist program (Genedata, Pro version 4.5) and the expression level for each of the ~56,000 probe sets on the arrays was quantified using the RMA algorithm.  The mean expression level from duplicate chips from the same individual’s RNA was computed and used in the subsequent analysis.  The RMA algorithm produces a summary of gene expression that is of log scale; we utilized this log scale for all analyses. To examine the relationship between gene expression and viral load, a linear regression model was fit with gene expression as the response variable and disease stage and the log of viral load as predictor variables.  We controlled for disease stage when examining the relationship between viral load and gene expression because we previously found an association between gene expression and disease stage for HIV-1 infection [9] (additionally, there is an association between disease stage and viral load for HIV-1-infected subjects naïve to HAART).  The p-values for the null hypothesis (testing no association between viral load and gene expression) were then transformed to q-values using the q-value package in the statistical software program R.  By varying the threshold for the q-values, one can obtain a set of genes that are found to be associated with viral load at a given false discovery rate. As the number of genes found to be associated with viral load increases dramatically as this threshold rises above ~7%, we used the conservative cut-off value of 7% for the false discovery rate.  To summarize the association between log of viral load and gene expression, we computed the partial correlation between these two quantities for all genes while controlling for the effect of disease stage.

source_name: Inguinal lymph node from HIV-1-infected individual

label_protocol: Double stranded cDNA and biotin-labeled cRNA probes were synthesized from 5 micrograms of total RNA with a MessageAmp II aRNA kit (Ambion). The cRNA probes were column purified and fragmented with a Fragmentation kit (Ambion).

extract_protocol: Inguinal lymph node biopsies from 22 HIV-1-infected subjects at different clinical stages were obtained for this University of Minnesota institutional review board–approved microarray study. Each lymph node biopsy was placed into a Falcon tube and snap-frozen by dropping it into liquid nitrogen. Frozen lymph nodes were homogenized with a power homogenizer (Heat Systems Ultrasonic) in TRIzol (Invitrogen) without thawing.  Total RNA was isolated following the manufacturer’s protocol and further purified with an RNeasy Mini Kit (Qiagen).

value: Inguinal lymph node

tag: gender

value: Male

tag: race

value: Caucasian

tag: peripheral blood cd4+ t cells (cells/ml)

tag: plasma hiv-1 rna levels (copies/ml)


title: Stroma_treatment HPHF_S 1

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 1

value: Holstein

value: 65 days

value: stroma (fat pad)


title: Parenchyma_treatment HPHF_P 15

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 15

value: mammary, liver, muscle, adipose, placenta


title: Parenchyma_treatment HPHF+_P 13

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 13

source_name: Parenchymal tissue, HPHF+ diet

value: HPHF+


title: Stroma_treatment HPHF+_S 3

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 3

source_name: Stromal tissue, HPHF+ diet

source_name: Reference


title: Stroma_treatment Control_S 4

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 4


title: Parenchyma_treatment HPHF_P 16

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 16


title: Stroma_treatment HPHF_S 2

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
S 2


title: Parenchyma_treatment HPLF_P 9

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 9


title: Parenchyma_treatment HPHF+_P 5

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 5


title: Parenchyma_treatment Control_P 10

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 10

source_name: Parenchymal tissue, control diet


title: MKN45_Lysate_rep1

description: gene expression and variation of alternative splicing in Cellular lysate of MKN45

source_name: MKN45, lysate, replicate 1

value: gastric cancer


title: Parenchyma_treatment HPLF_P 8

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 8


title: Parenchyma_treatment HPLF_P 11

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 11


title: Parenchyma_treatment Control_P 20

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 20


title: Parenchyma_treatment Control_P 4

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 4


title: Parenchyma_treatment HPHF+_P 3

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 3


title: Parenchyma_treatment HPHF_P 2

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 2


title: Parenchyma_treatment HPHF_P 1

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 1


title: STZ 4

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
Diabetes was induced by intraperitoneal injection of STZ.
Replicate 4 of 4.
1685398124_I

hyb_protocol: Standard Illumina hybridization protocol. Cy3-Streptavidin was incorporated during the Wash and Block protocol as a fluor for scanning.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in GenomeStudio v1.0.6.

label: biotin

organism: Rattus norvegicus

source_name: Retina, STZ

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

growth_protocol: Rats had free access to food and water, and were maintained on a 12 hour light/dark cycle.

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

treatment_protocol: Diabetes was induced in Sprague-Dawley male rats (Charles River Laboratories, Wilmington, MA) by intraperitoneal injection of 65 mg/kg streptozotocin (STZ) (Sigma-Aldrich, St. Louis, MO) in 10mM sodium citrate pH 4.5 vehicle. Control rats were injected with an equal dose of vehicle only.

value: Sprague-Dawley

value: male

value: retina

tag: treatment

value: streptozotocin (STZ)


title: Sapko1.0

city: London

first: Robert

middle: Harris

last: Nicolas

address: 44 Lincoln's Inn feilds

department: Transcription

country: United Kingdom

institute: LRI Cancer research UK

description: cDNA from Sap KO Tcell DPs mouse 1

hyb_protocol: PICR 11uM feature

scan_protocol: Genechips were scanned using the Affymetrix Genechip Scanner 3000G

data_processing: Data was analysed within Bioconductor. Probe set expression measures were calculated using Robust Multichip Average default method from the Affy package.

organism: Mus musculus

source_name: Sap KO/Untreated

label_protocol: PICR 1 cycle Taget labelling V 1, cocktail V2 (DMSO)

growth_protocol: DP Tcells were purified on the cell sorter using anti-CD4 and anti-CD8 the Cells were then rested for 2 hours  in RPMI with 10% FCS at 37°C.

extract_protocol: Total RNA was purified further with the GenElute kit (Sigma) according to the manufacturers instructions

treatment_protocol: The DPs were spun onto anti-CD3 coated or non-coated plates and incubated 30min

value: Black 6J

value: 8 weeks

value: thymus

value: double positive T cells (DPs)

tag: genotype/variation

value: Sap KO

value: Untreated


title: Parenchyma_treatment Control_P 7

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 7

value: parenchyma

value: control


title: Parenchyma_treatment HPHF+_P 12

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 12

value: Holstein

value: 65 days


title: STZ 3

description:
Diabetes was induced by intraperitoneal injection of STZ.
Replicate 3 of 4.
1685398124_F


title: Control 2

description:
Replicate 2 of 5.
1685398123_G

source_name: Retina, control

value: vehicle control


title: Control 5

description:
Replicate 5 of 5.
1685398124_H


title: STZ 2

description:
Diabetes was induced by intraperitoneal injection of STZ.
Replicate 2 of 4.
1685398124_D


title: Control 1

description:
Replicate 1 of 5.
1685398123_B


title: CAN2 Cu 12time 1st

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

hyb_protocol: Microarray Hybridization and Washing. C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110g, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by coverslide 22X22.  The Cy3/Cy5-labeled cDNA samples were applied in between coverslide and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied into the chamber hole, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed, including one-dye swap experiment.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100B scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 6.0) and gal file (http://genomeold.wustl.edu/activity/ma/cneoformans/).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity by employing LOWESS M normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans H99

source_name: CAN2 Cu 12time 1st

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Promega), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr.  For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy3 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy5.  For a dye-swap experiment, control and test RNAs were labeled oppositely.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: For total RNA isolation used in DNA microarray, the WT H99 and CTR4::CAN2 strains were cultured in 50 ml YPD medium at 30°C for 24 hr, washed with sterile PBS buffer twice, and resuspended with sterile water. Then 1ml of resuspended cells was innoculated into 100ml of fresh YNB(Obtical density at 600nm is about 0.2) and incubated for 12hr.

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT, hog1, ssk1, and skn7 mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: For zero-time samples, 50 ml out of the 100 ml culture was sampled and rapidly frozen in liquid nitrogen. Then 20ml of the resuspended culture was inoculated into a 200 ml of fresh YNB medium containing either BCS (for induction of CAN2) or CuSO4 (for repression of CAN2), and further incubated for up to 36 hr at 30°C. During incubation, 50 ml of the culture was sampled after 12 hrs.

tag: genotype/varation

tag: agent

tag: time point

value: 12 hr

source_name: pooled total RNA from all strain all time point all stress

tag: reference


title: H99 Cu 12time 1st

source_name: H99 Cu 12time 1st

value: wild type

value: pooled total RNA from all strain all time point all stress


title: H99 Cu 12time 3rd

source_name: H99 Cu 12time 3rd


title: CAN2 Cu 12time 3rd

source_name: CAN2 Cu 12time 23rd


title: H99 Cu 12time 2nd

source_name: H99 Cu 12time 2nd


title: H99 BCS 12time 3rd

source_name: H99 BCS 12time 3rd

value: BCS


title: CAN2 0time 2nd

source_name: CAN2 0time 2nd

value: 0 hr


title: CAN2 BCS 12time 2nd

source_name: CAN2 BCS 12time 2nd


title: CAN2 BCS 12time 3rd

source_name: CAN2 BCS 12time 3rd


title: CAN2 0time 3rd

source_name: CAN2 0time 3rd


title: CAN2 0time 1st

source_name: CAN2 0time 1st


title: STZ 1

description:
Diabetes was induced by intraperitoneal injection of STZ.
Replicate 1 of 4.
1685398124_C

tag: strain

value: Sprague-Dawley

value: male

value: retina

value: streptozotocin (STZ)


title: H99 BCS 12time 2nd

source_name: H99 BCS 12time 2nd


title: CAN2 BCS 12time 1st

source_name: CAN2 BCS 12time 1st


title: Control 4

description:
Replicate 4 of 5.
1685398124_E


title: H99 0time 3rd

source_name: H99 0time 3rd


title: Control 3

description:
Replicate 3 of 5.
1685398123_J


title: CAN2 Cu 12time 2nd

source_name: CAN2 Cu 12time 2nd


title: H99 BCS 12time 1st

source_name: H99 BCS 12time 1st


title: FHCE1 vs IHCE1 human epididymal cells replicate 3

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

country: Canada

institute: INRS-Institut Armand-Frappier

description: Replicate 3 of 3, IHCE1 vs FHCE1, no dye swap

hyb_protocol: 0.75 mg of cRNA were hybridized to the Agilent microarrays (Agilent Human 1A Microarray (V2) G411B) using the Agilent In Situ Hybridization Kit Plus) according to the protocol provided by the manufacturer.

scan_protocol: Following hybridization, microarrays were scanned with a ScanArray Express scanner (Perkin Elmer). Fluorescence ratios for array elements were extracted using the ScanArray Express Software (Perkin Elmer) and imported into the GeneSpring 6.1 software (Agilent Technologies) for further analysis.

data_processing: GeneSpring Software 6.1 (Agilent) was used for analysis following LOWESS normalization. A dye swap was applied to some of the samples (CT1neg-CL1neg and CT2neg-CL2neg).

label_protocol: Fluorescent cRNA were prepared from 500ng of total RNA using the Agilent Low RNA Input Linear Amplification Kit. As a last step of the extraction procedure, the cRNA was purified with the Rneasy Mini-Kit (Qiagen).

growth_protocol: Cells were grown to confluence on inserts (Corning) in a humified chamber (32°C, 5% CO2).

extract_protocol: Total cellular RNA was isolated using the Illustra RNAspin Mini kit (GE Healthcare, Buckinghamshire, Germany) according to the manufacturer’s instructions. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: epididymis

value: SV40 immortalized primary cell line

tag: fertility status

value: fertile

value: obstructive azoospermic patient


title: FHCE1 vs IHCE1 human epididymal cells replicate 2

description: Replicate 2 of 3, IHCE1 vs FHCE1, dye swap


title: Parenchyma_treatment HPHF+_P 22

description:
A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipose, and placenta) were used as reference (Cy5 in Ch1 and Cy3 in Ch2).
P 22

source_name: Parenchymal tissue, HPHF+ diet

tag: breed

tag: age

tag: mammary tissue

value: parenchyma

value: HPHF+

source_name: Reference

value: mammary, liver, muscle, adipose, placenta


title: H99 0time 2nd

source_name: H99 0time 2nd

source_name: pooled total RNA from all strain all time point all stress


title: FHCE1 vs IHCE1 human epididymal cells replicate 1

description: Replicate 1 of 3, IHCE1 vs FHCE1, dye swap

tag: tissue

tag: cell type


title: SNU77

status: Public on May 21 2010

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro, Yeongtong-gu

institute: Ajou University School of Medicine

description: Gene expression data from hepatocellular carcinoma

hyb_protocol: Hybridization and detection were performed with Affymetrix Human Genome U133A 2.0 chips according to standard protocols.

scan_protocol: GeneChips were scanned GeneChip scanner 3000 using GCOS software

data_processing: The data were analyzed with RMA normalization method.

source_name: combined hepatocellular carcinoma and cholangiocarcinoma

label_protocol: 5 ug of total RNA from the HCC tissues was used for labeling according to standard protocols recommended by Affymetrix, Inc

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


title: SNU72

value: combined hepatocellular carcinoma and cholangiocarcinoma


title: SNU78

source_name: cholangiocarcinoma

value: cholangiocarcinoma


title: SNU89


title: SNU68

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: SNU81


title: SNU82


title: SNU85


title: SNU74


title: SNU79


title: SNU90


title: SNU84


title: SNU86


title: SNU70


title: SNU76


title: SNU80


title: SNU73


title: SNU69


title: SNU71


title: SNU87


title: SNU75


title: SNU83


title: SNU65


title: SNU64


title: SNU67


title: SNU57


title: SNU66


title: SNU63


title: SNU60


title: SNU59


title: SNU62


title: SNU47


title: SNU53


title: SNU42


title: SNU44


title: SNU55


title: SNU54


title: SNU49


title: SNU43


title: SNU46


title: SNU39


title: SNU41


title: SNU61


title: SNU50


title: SNU45


title: SNU56


title: SNU48


title: SNU58


title: SNU52


title: SNU88


title: SNU51


title: SNU38


title: SNU35


title: SNU36


title: SNU30


title: SNU34


title: SNU40


title: SNU33


title: SNU31


title: SNU21


title: SNU15


title: SNU16


title: SNU29


title: SNU10


title: SNU28


title: SNU22


title: SNU26


title: SNU24


title: SNU12


title: SNU19


title: SNU13


title: SNU18


title: SNU37


title: SNU17


title: SNU20


title: SNU25


title: SNU14


title: SNU11


title: SNU32


title: SNU7


title: SNU6


title: SNU8


title: SNU4


title: SNU2


title: SNU1


title: C600

status: Public on May 20 2010

city: Duarte

first: Ravi

last: Bhatia

state: CA

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

hyb_protocol: Standard Affymetrix protocol (15 µg cRNA from each sample was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays)

scan_protocol: Standard Affymetrix protocol

data_processing:
Microarray data analyses were performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4).
Expression data were normalized using the robust multiarray average (RMA) algorithm, with background adjustment, quantile normalization and median polish summarization.
Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package.
Gene Set Enrichment Analyses (GSEA) was performed using GSEA software version 2.04 [http://www.broadinstitute.org/gsea/] to detect enrichment of predetermined gene sets using t-scores and gene sets in C2 (curated gene sets) category from the Molecular Signature Database (MsigDB).

source_name: sorted CML CD34+CD38- cells treated with the combination of IM and LBH

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA from 5000 cells was extracted using the RNeasy kit (Qiagen), amplified and labeled using GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA).

treatment_protocol: CML CD34+CD38- cells were selected using flow cytometry sorting and treated with IM, LBH and the combination of IM and LBH or cultured without exposure to drugs (controls) for 24 hours (n=3 each).

tag: subjectid

tag: imatinib

value: IM

value: LBH


title: SNU3


title: C598

source_name: sorted CML CD34+CD38- cells treated with IM

value: NoLBH


title: C599

source_name: sorted CML CD34+CD38- cells treated with LBH

value: NoIM


title: C596


title: Prednisolone-treated GRdim mouse, biological rep6

city: Nijmegen

first: Raoul

last: Frijters

address: Geert Grooteplein Zuid 26-28

department: Centre for Molecular and Biomolecular Informatics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Gene expression data from liver of prednisolone-treated mice with a dimerization-defective glucocorticoid receptor

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Processing and downstream statistical analysis of the microarray data was done using the R Statistics package. Data were normalized using the gcrma algorithm.

source_name: Liver of prednisolone-treated GRdim mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by RNeasy clean-up.

treatment_protocol: Mice were treated subcutaneously with 1 mg/kg prednisolone (5% DMSO and 5% Chremophor in manitol, 10 ml/kg) once and sacrificed 180 minutes later by cervical dislocation. All experiments were performed in the morning between 9 and 10 o'clock. The mice were exposed to a regular dark-light-cycle (lights on between 6 AM and 6 PM) and had access to water and food ad libitum at any time.

value: liver

value: Balb/c

tag: gender

value: male

tag: genotype

value: prednisolone


title: SNU9


title: C594


title: C597

source_name: sorted CML CD34+CD38- cells cultured without exposure to drugs (controls)


title: Prednisolone-treated GRdim mouse, biological rep2


title: Prednisolone-treated GRdim mouse, biological rep1


title: C595


title: C593


title: Prednisolone-treated GRdim mouse, biological rep4

value: female


title: Prednisolone-treated GRdim mouse, biological rep5


title: C591


title: C592


title: Vehicle-treated GRdim mouse, biological rep3

description: Gene expression data from liver of vehicle-treated mice with a dimerization-defective glucocorticoid receptor

source_name: Liver of vehicle-treated GRdim mice

value: vehicle


title: Vehicle-treated GRdim mouse, biological rep6


title: Prednisolone-treated GRdim mouse, biological rep3


title: Vehicle-treated GRdim mouse, biological rep4


title: Vehicle-treated GRdim mouse, biological rep5


title: Vehicle-treated GRdim mouse, biological rep2


title: C589


title: C590


title: Mouse Testes PolyA+ RNA, 2

status: Public on May 18 2010

type: mixed

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

hyb_protocol: Arrays were hybridized in a GeneChip Fluidics Station 450 using standard protocol “EukGE-WS2v5_450”.

scan_protocol: Arrays were scanned in an Affymetrix 7G scanner.

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. All samples were quantile normalized with a bandwidth of 70, using a genomic DNA hybridization as reference.

molecule: polyA RNA

source_name: Mouse testes polyA+ RNA

label_protocol: cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ｰC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with GeneChip Labeling reagent (Affymetrix) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

extract_protocol: Total or PolyA+ RNA was obtained from Clontech. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 10 ug of RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen). The cDNA was then directly used for second strand synthesis, after which the double-stranded cDNA (ds-cDNA) was purified using PCR purification columns (Qiagen) in combination with the nucleotide cleanup kit protocols.

value: testes

molecule: genomic DNA

source_name: Mouse genomic DNA

label_protocol: Genomic DNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37C until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with GeneChip Labeling reagent (Affymetrix) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

extract_protocol: Genomic DNA was obtained from Clontech.

tag: sample type

value: reference


title: Mouse Liver Total RNA, 2

source_name: Mouse liver total RNA


title: Vehicle-treated WT mouse, biological rep6

description: Gene expression data from liver of vehicle-treated wild type mice

source_name: Liver of vehicle-treated wild type mice

value: wild type glucocoricoid receptor


title: Mouse Testes Total RNA, 2

source_name: Mouse testes total RNA


title: Vehicle-treated WT mouse, biological rep4


title: Mouse Liver PolyA+ RNA, 2

source_name: Mouse liver polyA+ RNA


title: Mouse Heart Total RNA, 2

source_name: Mouse heart total RNA

value: heart


title: Prednisolone-treated WT mouse, biological rep3

description: Gene expression data from liver of prednisolone-treated wild type mice

source_name: Liver of prednisolone-treated wild type mice


title: Prednisolone-treated WT mouse, biological rep6


title: Mouse Heart PolyA+ RNA, 2

source_name: Mouse heart polyA+ RNA


title: Human Liver PolyA+ RNA, 5

source_name: Human liver polyA+ RNA

source_name: Human genomic DNA


title: Vehicle-treated WT mouse, biological rep2


title: Vehicle-treated WT mouse, biological rep3


title: Vehicle-treated WT mouse, biological rep5


title: Prednisolone-treated WT mouse, biological rep1


title: Human Testes PolyA+ RNA, 5

source_name: Human testes polyA+ RNA


title: Mouse Brain Total RNA, 2

source_name: Mouse brain total RNA

value: brain


title: Mouse Brain PolyA+ RNA, 2

source_name: Mouse brain polyA+ RNA


title: Prednisolone-treated WT mouse, biological rep4


title: Prednisolone-treated WT mouse, biological rep5


title: Prednisolone-treated WT mouse, biological rep2


title: Human Testes Total RNA, 5

source_name: Human testes total RNA


title: Human Liver Total RNA, 5

source_name: Human liver total RNA


title: Vehicle-treated WT mouse, biological rep1


title: Human Heart Total RNA, 5

source_name: Human heart total RNA


title: Human Heart PolyA+ RNA, 5

source_name: Human heart polyA+ RNA


title: Human Liver Total RNA, 7


title: Human Brain PolyA+ RNA, 5

source_name: Human brain polyA+ RNA


title: Human Testes Total RNA, 7


title: Human Liver PolyA+ RNA, 7


title: Human Heart Total RNA, 7


title: Human Testes PolyA+ RNA, 7


title: Human Brain Total RNA, 5

source_name: Human brain total RNA


title: Human Brain PolyA+ RNA, 7


title: Human Brain Total RNA, 7


title: Human Heart PolyA+ RNA, 7


title: Human Testes Total RNA, 1


title: Human Testes PolyA+ RNA, 1


title: Human Liver PolyA+ RNA, 1


title: Human Liver Total RNA, 1


title: Human Heart Total RNA, 1


title: Human Brain Total RNA, 1


title: Human Heart PolyA+ RNA, 1


title: Human Testes PolyA+ RNA, 2


title: Human Testes Total RNA, 2


title: Human Brain PolyA+ RNA, 1


title: Human Liver Total RNA, 2


title: Human Heart PolyA+ RNA, 2


title: Human Liver PolyA+ RNA, 2


title: Vehicle-treated GRdim mouse, biological rep1

source_name: Liver of vehicle-treated GRdim mice


title: Human Brain Total RNA, 2


title: SNU27

source_name: hepatocellular carcinoma


title: Human Brain PolyA+ RNA, 2


title: SNU23


title: Human Testes PolyA+ RNA, 3


title: Human Testes Total RNA, 3


title: Human Heart PolyA+ RNA, 3


title: Human Heart Total RNA, 3


title: Human Liver Total RNA, 3


title: Human Testes Total RNA, 4


title: Human Liver Total RNA, 4


title: Human Brain Total RNA, 3


title: Human Heart Total RNA, 2


title: Human Liver PolyA+ RNA, 3


title: Human Liver PolyA+ RNA, 4


title: Human Testes PolyA+ RNA, 4


title: Human Brain Total RNA, 4


title: Human Heart Total RNA, 4


title: Human Heart PolyA+ RNA, 4


title: SNU5


title: Human Brain PolyA+ RNA, 3


title: Human Brain PolyA+ RNA, 4


title: Mouse Testes PolyA+ RNA, 7

source_name: Mouse testes polyA+ RNA

source_name: Mouse genomic DNA


title: Mouse Heart Total RNA, 7

source_name: Mouse heart total RNA


title: Human Liver Total RNA, 6


title: Mouse Liver PolyA+ RNA, 7

source_name: Mouse liver polyA+ RNA


title: Mouse Heart PolyA+ RNA, 7

source_name: Mouse heart polyA+ RNA


title: Mouse Testes Total RNA, 7

source_name: Mouse testes total RNA


title: Mouse Brain PolyA+ RNA, 7


title: Mouse Liver Total RNA, 7

source_name: Mouse liver total RNA


title: Human Testes Total RNA, 6

source_name: Human genomic DNA


title: Mouse Testes Total RNA, 6


title: Human Heart Total RNA, 6


title: Human Heart PolyA+ RNA, 6


title: Mouse Brain Total RNA, 7

source_name: Mouse brain total RNA


title: Human Brain PolyA+ RNA, 6


title: Mouse Liver PolyA+ RNA, 6


title: Mouse Heart Total RNA, 6


title: Mouse Heart PolyA+ RNA, 6


title: Mouse Testes PolyA+ RNA, 1


title: Human Brain Total RNA, 6


title: Mouse Brain Total RNA, 6


title: Mouse Liver PolyA+ RNA, 1


title: Mouse Testes Total RNA, 4


title: Mouse Testes PolyA+ RNA, 4


title: Mouse Liver Total RNA, 1


title: Mouse Brain PolyA+ RNA, 6

source_name: Mouse brain polyA+ RNA


title: Mouse Liver Total RNA, 4


title: Mouse Heart Total RNA, 1


title: Mouse Liver PolyA+ RNA, 4


title: Mouse Heart PolyA+ RNA, 1


title: Mouse Brain Total RNA, 1


title: Mouse Brain PolyA+ RNA, 1


title: Mouse Heart PolyA+ RNA, 4


title: Mouse Brain Total RNA, 4


title: Human Testes PolyA+ RNA, 6

source_name: Human testes polyA+ RNA


title: Mouse Heart Total RNA, 4


title: Mouse Brain PolyA+ RNA, 4


title: Mouse Testes Total RNA, 5


title: Mouse Liver PolyA+ RNA, 5


title: Mouse Heart Total RNA, 5


title: Mouse Heart PolyA+ RNA, 5


title: Mouse Testes Total RNA, 1


title: Mouse Testes PolyA+ RNA, 5


title: Mouse Brain Total RNA, 5


title: Mouse Brain PolyA+ RNA, 5


title: Mouse Testes Total RNA, 3


title: Mouse Liver Total RNA, 3


title: Mouse Heart Total RNA, 3


title: Mouse Liver PolyA+ RNA, 3


title: Mouse Brain PolyA+ RNA, 3


title: Mouse Brain Total RNA, 3


title: Mouse Heart PolyA+ RNA, 3


title: Mouse Liver Total RNA, 5


title: DA2 24hr

status: Public on May 15 2010

city: Solna

first: Alan

last: Gillett

address: CMM L8:04

country: Sweden

institute: Karolinska Institutet

data_processing: Applied Biosystems SDS2.1

source_name: bone-marrow derived macrophages

growth_protocol: Bone-marrow derived macrophages induced with L929 media

extract_protocol: Rneasy kit (Qiagen) with Dnase I treatment, cDNA with iscript (BioRad)

treatment_protocol: 1 or 24 hour treatment with zymosan

tag: background genotype

value: parental

tag: time

value: zymosan

value: bone-marrow derived macrophages


title: DA3 24hr

tag: agent


title: DA2 1hr


title: R11-124hr

value: congenic


title: DA3 1hr


title: Mouse Testes PolyA+ RNA, 3


title: DA1 24hr


title: R11-4 1hr


title: DA1 1hr


title: DA4 1hr


title: R11-1 1hr


title: R11-2 24hr


title: R11-3 1hr


title: R11-3 24hr


title: R11-2 1hr


title: DA4 24hr


title: R11-4 24hr


title: S. rolfsii_EPSmax13_37h_rep1

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

country: Germany

institute: Technische Universität München

description: Gene expression after 37hr in Exopolysaccharid production inducing media.

hyb_protocol: Oligomers for hybridizattion were designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene. Microarray hybridization, was performes according to Agilent Gene Expression Hybridization Kit user guide (http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=34822&liid=4377).

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

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_ and Grid: 017067_D_F_20070615) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Expression data were analyzed by imaGenes GmbH using an in-house developed data analysis pipeline. After quantile normalization, genes were defined as differentially expressed if their expression levels varied at least 2 fold in EPSmax13 samples compared to EPSmin17 samples and if the difference was statistically significant (Student’s t-test, P-value cut-off of 0.05).

organism: Agroathelia rolfsii

source_name: total RNA from S. rolfsii grown in EPSmax13 for 37h, replicate 1

label_protocol: For comparative expression profiling, total RNA was isolated from S. rolfsii, cultured for 37 h in EPSmax13 and EPSmin17 media as described above. Labelling was performed with the Agilent's low RNA Input Amplifikation Kit PLUS (http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=42629), which generates fluorescent cRNA (sample input 500 ng, The method uses T7 RNA polymerase, which simultaneously amplifies target material and incooperate cynine 3-labelled CTP. The labelled RNA was purified by Quiagen's RNeasy mini spin colums and quantified by using NanoDrop ND-1000 UV-VIS spectrophotometer version 3.2.1. by ImaGenes (Berlin)

growth_protocol: S. rolfsii strain ATCC15205 was cultivated at 28°C in shake flasks containing 50 ml EPS medium (C-source, N-source, 2 g/l K2HPO4, 0.5 g/l KCl, 0.5 g/l MgSO4*7H2O, 0.05 g/l FeSO4*7H2O, 1 g/l yeast extract, 0.7 g/l citric acid 7*H2O. pH 4.5). EPSmax13 contained 40 g/l glucose and 3.0 g/l NaNO3 as C- and N-sources, whereas EPSmin17 used 40 g/l fructose and 1.9 g/l NH4Cl, respectively. 2 cm2 of S. rolfsii mycelia grown on EPSmax13 plates covered with cellophan was harvested, disintegrated with a scalpel and given into 50 ml of EPSmax13 medium or EPSmin 17 medium respectively

extract_protocol: After homogenization using a dismembrator (Braun Biotech), the pulverized homogenate was resuspended in 5 ml RNA extraction buffer (4 M guanidine isothiocyanate; 0.1 M Tris/HCl, pH 7.5; 1 % β-Mercaptoethanol, 0.5 % N-laurylsarcosine). After centrifugation (5000×g, 10 min, RT), the supernatant was subjected to ultracentrifugation using 5 M caesium chloride (30.,000×g, 19 h, RT). The resulting RNA pellet was precipitated using 2 volumes of ice-cold EtOH (96%) and 1/10 volumes of 8 M LiCl.

treatment_protocol: Due to the high amounts of EPS produced, extraction of intact total RNA from S. rolfsii cultures was only possible by using a caesium chloride-based ultracentrifugation method. In brief, 1 g of S. rolfsii mycelium was harvested by filtration and frozen in liquid nitrogen.

value: Basidiomycete

tag: condition

value: EPS inducing condition


title: S. rolfsii_EPSmin17_37h_rep3

description: Gene expression after 37hr in Exopolysaccharid production non-inducing media.

source_name: total RNA from S. rolfsii grown in EPSmin17 for 37h, replicate 3

tag: strain

value: EPS non-inducing condition


title: S. rolfsii_EPSmax13_37h_rep3

source_name: total RNA from S. rolfsii grown in EPSmax13 for 37h, replicate 3

tag: cell line


title: S. rolfsii_EPSmin17_37h_rep1

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_ and Grid: 017067_D_F_20070615) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: total RNA from S. rolfsii grown in EPSmin17 for 37h, replicate 1


title: Methylated control #2

status: Public on May 12 2010

type: genomic

city: Ann Arbor

first: Regina

last: de los Santos

state: MI

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

description: Methylated Control

hyb_protocol: Standard Illumina hybridization protocol used for Infinium assays

scan_protocol: Standard Illumina scanning protocol used for Infinium assays

data_processing: Illumina's BeadStudio Methylation Module V3.2  was used to produce average beta values for each sample. R software v2.9.0 were used to calculate statistics and create graphs. Additionally, DAVID Functional Annotation Clustering tool and SAS v9.2 was used for some statistical analyses.

label: ALEXA 555, ALEXA 647

source_name: Whole blood

label_protocol: The Infinium Methylation protocol does not require the extract to be labelled

extract_protocol: Genomic DNA was extracted using the QiaAmp DNA MiniKit from Qiagen, following the manufacturer's recommended protocol

value: Whole blood

tag: disease status

value: PTSD unaffected


title: S. rolfsii_EPSmax13_37h_rep2

source_name: total RNA from S. rolfsii grown in EPSmax13 for 37h, replicate 2


title: Unmethylated control #2

description: Unmethylated Control


title: Replicate of sample 68

description: Replicate


title: PTSD_unaffected_#72

description: sample 95


title: PTSD_unaffected_#74

description: sample 97


title: PTSD_unaffected_#69

description: sample 90


title: PTSD_affected_#22

description: sample 91

value: PTSD affected


title: Replicate of sample 67

description: Replicate


title: PTSD_affected_#23

description: sample 92


title: PTSD_unaffected_#76

description: sample 99


title: Methylated control #1

description: Methylated Control


title: Unmethylated control #1

description: Unmethylated Control


title: PTSD_unaffected_#67

description: sample 88


title: PTSD_unaffected_#75

description: sample 98


title: PTSD_unaffected_#70

description: sample 93


title: PTSD_unaffected_#65

description: sample 86


title: PTSD_unaffected_#77

description: sample 100


title: PTSD_unaffected_#71

description: sample 94


title: PTSD_unaffected_#73

description: sample 96


title: PTSD_unaffected_#66

description: sample 87


title: PTSD_unaffected_#63

description: sample 83


title: PTSD_unaffected_#68

description: sample 89


title: PTSD_affected_#17

description: sample 78


title: PTSD_affected_#20

description: sample 82


title: PTSD_unaffected_#64

description: sample 85


title: PTSD_affected_#21

description: sample 84


title: PTSD_affected_#18

description: sample 79


title: PTSD_unaffected_#62

description: sample 80


title: PTSD_affected_#19

description: sample 81


title: PTSD_affected_#16

description: sample 77


title: PTSD_unaffected_#58

description: sample 73


title: PTSD_unaffected_#52

description: sample 67


title: PTSD_unaffected_#59

description: sample 74


title: PTSD_unaffected_#56

description: sample 71


title: PTSD_unaffected_#54

description: sample 69


title: PTSD_unaffected_#49

description: sample 64


title: PTSD_unaffected_#50

description: sample 65


title: PTSD_affected_#15

description: sample 62


title: PTSD_unaffected_#55

description: sample 70


title: PTSD_unaffected_#45

description: sample 58


title: PTSD_unaffected_#46

description: sample 60


title: PTSD_affected_#11

description: sample 52


title: PTSD_unaffected_#38

description: sample 48


title: PTSD_unaffected_#51

description: sample 66


title: PTSD_affected_#12

description: sample 55


title: PTSD_unaffected_#47

description: sample 61


title: PTSD_unaffected_#43

description: sample 54


title: PTSD_unaffected_#48

description: sample 63


title: PTSD_unaffected_#57

description: sample 72


title: PTSD_unaffected_#60

description: sample 75


title: PTSD_affected_#14

description: sample 59


title: PTSD_unaffected_#39

description: sample 49


title: PTSD_unaffected_#53

description: sample 68


title: PTSD_affected_#13

description: sample 56


title: PTSD_unaffected_#42

description: sample 53


title: PTSD_unaffected_#41

description: sample 51


title: PTSD_unaffected_#36

description: sample 45


title: PTSD_unaffected_#44

description: sample 57


title: PTSD_unaffected_#40

description: sample 50


title: PTSD_affected_#10

description: sample 46


title: PTSD_unaffected_#37

description: sample 47


title: PTSD_unaffected_#33

description: sample 42


title: PTSD_unaffected_#34

description: sample 43


title: PTSD_affected_#7

description: sample 32


title: PTSD_unaffected_#31

description: sample 40


title: PTSD_unaffected_#26

description: sample 33


title: PTSD_unaffected_#29

description: sample 36


title: PTSD_affected_#9

description: sample 39


title: PTSD_unaffected_#24

description: sample 29


title: PTSD_unaffected_#35

description: sample 44


title: PTSD_affected_#8

description: sample 38


title: PTSD_unaffected_#22

description: sample 27


title: PTSD_unaffected_#32

description: sample 41


title: PTSD_unaffected_#30

description: sample 37


title: PTSD_unaffected_#25

description: sample 31


title: PTSD_unaffected_#19

description: sample 24


title: PTSD_unaffected_#17

description: sample 22


title: PTSD_unaffected_#28

description: sample 35


title: PTSD_unaffected_#16

description: sample 21


title: PTSD_unaffected_#15

description: sample 19


title: PTSD_unaffected_#18

description: sample 23


title: PTSD_unaffected_#23

description: sample 28


title: PTSD_affected_#6

description: sample 30


title: PTSD_unaffected_#20

description: sample 25


title: PTSD_unaffected_#27

description: sample 34


title: PTSD_affected_#5

description: sample 20


title: PTSD_unaffected_#21

description: sample 26


title: PTSD_unaffected_#12

description: sample 16


title: PTSD_unaffected_#13

description: sample 17


title: PTSD_unaffected_#14

description: sample 18


title: PTSD_unaffected_#11

description: sample 15


title: PTSD_unaffected_#7

description: sample 9


title: PTSD_unaffected_#8

description: sample 10


title: PTSD_unaffected_#9

description: sample 11


title: PTSD_affected_#1

description: sample 6


title: PTSD_unaffected_#10

description: sample 13


title: PTSD_affected_#2

description: sample 8


title: PTSD_affected_#3

description: sample 12


title: PTSD_unaffected_#5

description: sample 5


title: PTSD_unaffected_#6

description: sample 7


title: PTSD_unaffected_#3

description: sample 3


title: PTSD_unaffected_#1

description: sample 1


title: PTSD_affected_#4

description: sample 14


title: PTSD_unaffected_#4

description: sample 4


title: PTSD_unaffected_#2

description: sample 2


title: PTSD_unaffected_#61

description: sample 76


title: TERC-/- bone

status: Public on May 10 2010

city: odense

first: Hamid

last: Saeed

state: Fyn

address: Winslows parken 1st floor

department: Endocrinology

country: Denmark

institute: Odense University Hospital/ University of Southern Denmark

description: 3 RNA samples (tibia) mixed

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse tibia bone

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

growth_protocol: Bone samples so no growth protocols but mice were 22 weeks old (tibia were obtained from 3 mice and RNA was mixed)

extract_protocol: RNA was extracted with Trizol reagent (from 3 mice tibia and mixed), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No Treatment

tag: genetic background

value: Female

value: 22 wk

value: bone

value: TERC-/-


title: TERC+/+ bone

description: 3 RNA samples (tibia) mixed

tag: age

value: TERC+/+


title: FX-fibroblasts A

city: Ramat Gan

first: Achia

last: Urbach

address: Bar Ilan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

description: Fibroblasts from Fragile X patients obatined from Coriell cat# GM05848

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: GM05848 fibro

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: fibroblasts


title: Yswap_F_P11

status: Public on May 08 2010

city: Cambridge

first: Pan-Pan

last: Jiang

state: MA

address: 16 Divinity Ave c/o Hartl Lab

department: Organismic and Evolutionary Biology

institute: Harvard University

hyb_protocol: Genisphere 3DNA system

scan_protocol: Axon scanner and Genepix

data_processing: Ratios were taken from Limma package after Loess normalization of the raw intensities data originally obtained in Genepix

organism: Drosophila melanogaster

source_name: YI, France background

label_protocol: Genisphere 3DNA system

growth_protocol: 24hr light, humidity controlled, males 3 days old at time of RNA extraction

extract_protocol: Trizol RNA extraction

treatment_protocol: Treatment: 2 Y-lineages and 3 background-lineages in every possible pairing

tag: y-lineage

value: YI

tag: background

value: France

value: male

source_name: YF, France background

value: YF


title: WT-fibroblasts

description: Normal BJ cells

source_name: BJ-fibroblasts

tag: cell type

value: Normal BJ cells


title: WT-iPS#28

description: iPS cells clone #28 derived from normal BJ cells

value: iPS cells


title: FX-iPS-B

description: iPS cells from FX-fibroblasts B

value: iPS cells from FX-fibroblasts B


title: Yswap_F_P12


title: FX-ES

description: HESCs from human embryos determined through PGD to carry the fragile X mutation

source_name: FX-ES

value: HESCs


title: Yswap_F_P8


title: ES

description: H9 HESC line

source_name: ES (H9)

value: H9 HESC line


title: Diff.-FX-ES-iPS

description: iPS cells from the Diff.-FX-ES cells

value: iPS cells from the Diff.-FX-ES cells


title: FX-iPS-A

description: iPS cells from FX-fibroblasts A

value: iPS cells from FX-fibroblasts A


title: Yswap_F_P7


title: Yswap_I_P3

source_name: YF, India background

value: India

source_name: YI, India background


title: Yswap_4361_P16

source_name: YF, 4361 background

source_name: YI, 4361 background


title: Yswap_F_P5


title: Yswap_I_P19


title: Yswap_I_P4


title: Yswap_F_P6


title: HaCaT S-flurbiprofen vs R-flurbiprofen 1 AMC4941

status: Public on May 09 2010

city: Adelaide

first: Benjamin

last: Lewis

state: South Australia

address: Frome Road

department: Sansom Institute

country: Australia

institute: University of South Australia

description: This sample is part of a series which makes up an investigation of the gene expression changes induced by R-flurbiprofen and S-flurbiprofen utilising the HaCaT cell line.

hyb_protocol: Carried out by the Adelaide Microarray Centre Prior to hybridization each microarray is immersed in 50 ml of hot Milli-Q water (80-95C) and agitated gently for 5 min. The slide is then dried by centrifugation at 750rpm for 5min. The labeled cDNA is mixed with 0.64μL of 25mg/mL yeast tRNA, 4μL of 2mg/mL poly A and 20μL of 1mg/mL Cot-1 DNA. The mix is dried under reduced pressure then dissolved in the appropriate volume of formamide and 6.25 X SSC The mixture is heated to 100C for 3min., transferred directly to ice then 0.5μL of 10% SDS is added before the solution is applied to the centre of the cover slip. The array is lowered onto the cover slip then incubated at 42C overnight in a humidified chamber. Following incubation, the array is immersed in solution A Solution A (0.5 X SSC, 0.01% SDS) until the coverslip disengages the surface. After the coverslip is discarded the array is washed in Solution A for 5 min., Solution B (0.5 X SSC) for 5 min then Solution C (0.2 X SSC) for 3 min. The slide is dried in a centrifuge at 750 rpm for 5 min and stored in the dark prior to scanning.

data_processing:
Carried out by the Adelaide Microarray Centre.
Images analysed and data extracted using the Spot Software package (CSIRO Australia). Background correction was applied to mean spot intensities. Ratios were determined based on the spot intensities, with the ratio then normalised. Linear regression was used to identify statistical significance.

source_name: Total RNA extracted from HaCaT cells treated with S-flurbiprofen

extract_protocol:
Pelletted cells are dissolved in 500µL Trizol then 100µL of chloroform is added and the mixture is vortexed, left on ice for 15min. then centrifuged (6500 x g ) for 30min. at 4C.
The upper aqueous phase is retained, mixed with an equal volume of 70% ethanol (in DEPC H2O) then the RNA is further purified using a Qiagen RNeasy kit. Briefly, the RNA/ethanol mixture is applied to a RNeasy column then centrifuged at 6500 x g for 1min.  The eluent is re-passed through the column which is then washed with 700µL of buffer RW1. The column is washed twice with 500µL of buffer RPE then residual buffer is removed by spinning the column at 6500 x g for 1min.  The purified RNA is eluted into a clean tube with 30µL of DEPC treated water.
The RNA was then concentrated by precipitation.
Add 1/10 volume of 3M sodium acetate (pH=5.2) and 2 volumes of ethanol. The mixture is cooled to -80C for 30min then RNA is pelletted by spinning (6500 x g ) for 20min. at 4C. The pellet is washed by adding 500µL of ethanol and spinning at (6500 x g ) for 10min.  The supernatant is decanted and the pellet is left to dry for 60min. at room temperature. The RNA is dissolved in DEPC treated water and the concentration is determined.
Aliquots of 30ug in 20uL of DEPC H2O were used for labelling and hybridisation.

treatment_protocol: Confluent HaCaT cells were treated with 1mM S-flurbiprofen dissolved in RPMI-1640 media, 1x GlutaMax-1, 10% FBS for 4 hours.

value: HaCaT

tag: treatment

value: S-flurbiprofen

source_name: Total RNA extracted from HaCaT cells treated with R-flurbiprofen

label_protocol:
Carried out by the Adelaide Microarray Centre
2µL of anchored polyT(V)N (2µg/µL) is added and the RNA aliquot is incubated at 70C for 10min. The sample is then placed on ice.
The sample is mixed with 6µL of 5X Superscript II buffer, 2µL of 0.1M DTT, 2µL of Superscript II (200U/µL) and 0.6µL of aminoallyl (aa) dNTP mix (25mM dATP, 25mM dGTP, 25mM dCTP, 10mM dTTP and 15mM aa dUTP) then incubated at 42C for 2.5 hours.
The RNA is hydrolysed by adding 10µL of 0.25M NaOH, 10µL of 0.5M EDTA (pH=8) and incubating the mix at 65C for 15min.. The reaction is neutralised by adding 15µL of 0.2M acetic acid.
The cDNA is purified using a QIAquick PCR purification kit. Briefly, the cDNA is mixed with 300µL of buffer PB then applied to the Qiagen column and centrifuged at 6500 x g for 1min.. The eluent is re-passed through the column. The column is washed twice with 600µL of buffer PE then residual buffer is removed by spinning the column at 6500 x g for 1min.. The sample is eluted into a clean tube with 90µL of Milli Q water.
The purified cDNA is dried under reduced pressure then dissolved in 9µL of 0.1M NaHCO3 (pH 9.0). The mixture is added to a Cy dye aliquot*, mixed then left to incubate at room temperature for 60min. in the dark.
The labeled cDNA is mixed with 41µL of Milli Q water then purified using a QIAquick PCR purification kit. Briefly, the cDNA is mixed with 250µL of buffer PB then applied to the Qiagen column and centrifuged at 6500 x g for 1min.. The eluent is re-passed through the column. The column is then washed twice with 600µL of buffer PE then residual buffer is removed by spinning the column at 6500 x g for 1min.. The sample is eluted into a clean tube with 90µL of Milli Q water. The purified labeled cDNA samples appear purple after being dried under reduced pressure.
*One Cy dye sachet (Amersham cat#PA23001 and PA25001) is dissolved in 73µL of anhydrous DMSO then 4.5µL aliquots are distributed into sealable tubes. Each aliquot is dried under reduced pressure, sealed then stored in a dessicator at –20C.

treatment_protocol: Confluent HaCaT cells were treated with 1mM R-flurbiprofen dissolved in RPMI-1640 media, 1x GlutaMax-1, 10% FBS for 4 hours.

value: R-flurbiprofen


title: FX-fibroblasts C

description: Fibroblasts from Fragile X patients obatined from Coriell cat# GM09497

source_name: GM09497 fibro


title: Yswap_I_P14


title: WT-iPS#29

description: iPS cells clone #29 derived from normal BJ cells


title: HaCaT Control vs R-flurbiprofen 2 AMC4943

scan_protocol: Carried out by the Adelaide Microarray Centre.

source_name: Total RNA extracted from HaCaT cells, untreated control

label_protocol:
2µL of anchored polyT(V)N (2µg/µL) is added and the RNA aliquot is incubated at 70C for 10min. The sample is then placed on ice.
The sample is mixed with 6µL of 5X Superscript II buffer, 2µL of 0.1M DTT, 2µL of Superscript II (200U/µL) and 0.6µL of aminoallyl (aa) dNTP mix (25mM dATP, 25mM dGTP, 25mM dCTP, 10mM dTTP and 15mM aa dUTP) then incubated at 42C for 2.5 hours.
The RNA is hydrolysed by adding 10µL of 0.25M NaOH, 10µL of 0.5M EDTA (pH=8) and incubating the mix at 65C for 15min.. The reaction is neutralised by adding 15µL of 0.2M acetic acid.
The cDNA is purified using a QIAquick PCR purification kit. Briefly, the cDNA is mixed with 300µL of buffer PB then applied to the Qiagen column and centrifuged at 6500 x g for 1min.. The eluent is re-passed through the column. The column is washed twice with 600µL of buffer PE then residual buffer is removed by spinning the column at 6500 x g for 1min.. The sample is eluted into a clean tube with 90µL of Milli Q water.
The purified cDNA is dried under reduced pressure then dissolved in 9µL of 0.1M NaHCO3 (pH 9.0). The mixture is added to a Cy dye aliquot*, mixed then left to incubate at room temperature for 60min. in the dark.
The labeled cDNA is mixed with 41µL of Milli Q water then purified using a QIAquick PCR purification kit. Briefly, the cDNA is mixed with 250µL of buffer PB then applied to the Qiagen column and centrifuged at 6500 x g for 1min.. The eluent is re-passed through the column. The column is then washed twice with 600µL of buffer PE then residual buffer is removed by spinning the column at 6500 x g for 1min.. The sample is eluted into a clean tube with 90µL of Milli Q water. The purified labeled cDNA samples appear purple after being dried under reduced pressure.
*One Cy dye sachet (Amersham cat#PA23001 and PA25001) is dissolved in 73µL of anhydrous DMSO then 4.5µL aliquots are distributed into sealable tubes. Each aliquot is dried under reduced pressure, sealed then stored in a dessicator at –20C.

treatment_protocol: Untreated control

value: untreated control


title: HaCaT S-flurbiprofen vs Control 2 AMC4946


title: HaCaT Control vs S-flurbiprofen 1 AMC4942


title: HaCaT Control vs R-flurbiprofen 3 AMC4945


title: FX-fibroblasts B

description: Fibroblasts from Fragile X patients obatined from Coriell cat# GM07072

source_name: GM07072 fibro

value: fibroblasts


title: HaCaT R-flurbiprofen vs Control 1 AMC4940

treatment_protocol: Untreated control cells


title: HaCaT R-flurbiprofen vs S-flurbiprofen 2 AMC4944


title: Yswap_4361_P17

value: YI


title: Yswap_4361_P13


title: Yswap_4361_P20


title: Yswap_4361_P18


title: MG1655 rimO biological rep2

status: Public on May 07 2010

city: Laurel

first: Isha

middle: R

last: Patel

state: MD

address: 8301 Muirkirk Rd,

department: Division of Molecular Biology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on E.coli GeneChip 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were normalized using Robust Multi-Array Averaging (RMA) in Affymetrix Power Tools. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Escherichia coli

source_name: rimO mutant cells harvested at mid log growth phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bacterial cells were grown in LB broth till mid-log growth phase in a shaking incubator at 37 degrees

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

treatment_protocol: Cells were harvested in acidic phenol


title: MG1655 ycaO biological rep2

source_name: ycaO mutant cells harvested at mid log growth phase


title: MG1655 biological rep1

source_name: wild type bacterial cells harvested at mid log growth phase


title: MG1655 rimO Tet biological rep1

description: The rimO-tet is a deletion of the rimO gene with a tet cassette.


title: MG1655 rimO biological rep1


title: MG1655 rimO Tet biological rep2


title: MG1655 ycaO biological rep1


title: Yswap_4361_P15


title: MG1655 biological rep2


title: Patient 10 DIN

status: Public on May 05 2010

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Array CGH analysis of a female patient with flat epithelial atypia (DIN1a).

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).

scan_protocol: Slides were scanned at 10 µm resolution using an Agilent scanner. PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not subtracted. Signal intensities were normalized by subgrid LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.

label: Alexa Fluor 3

source_name: DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection was performed at multiple sites using Veritas Arcturus. Cells were digested in 10 µl TE, pH 9, and 0.5 µl proteinase K (20 mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10 min, the digest was stored at -20°C. Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

treatment_protocol: Whole genome amplification by GenomePlex (Sigma).

value: female

tag: tissue

value: flat epithelial atypia (DIN1a)

label: Alexa Fluor 5

source_name: DNA pool isolated from laser captured microdissected formalin-fixed, paraffin-embedded healthy tissue.

value: mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens


title: Patient 11 DIN

tag: gender


title: Patient 5 DIN

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.


title: Patient 9 DIN


title: Patient 6 LIN

description: Array CGH analysis of a female patient with classic lobular intraepithelial neoplasia (LIN).

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10µl TE, pH 9, and 0.5µl proteinase K (20mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10min, the digest was stored at -20°C.  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

value: lobular intraepithelial neoplasia


title: Patient 3 DIN


title: Patient 8 DIN


title: Patient 6 DIN


title: Patient 2 DIN


title: Patient 9 LIN


title: Patient 12 DIN


title: Patient 11 LIN


title: Patient 4 DIN


title: Patient 8 LIN


title: Patient 10 LIN


title: Patient 3 LIN


title: Patient 2 LIN


title: Patient 5 LIN


title: Patient 7 LIN


title: 13969307 - irx12 2 vs wt 2

status: Public on May 01 2010

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

hyb_protocol: wt 2 Cy5 / irx12 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: wt 2

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

growth_protocol: stem - media: in soil hydrometry: 40% temperature: 22°C light: 13h

treatment_protocol: no treatment

value: columbia

tag: genotype variation

value: wild type

tag: harvest date

source_name: irx12 2

growth_protocol: stem - Media: in soil  hydrometry: 40% temperature: 22°C light: 13h


title: Patient 4 LIN


title: UH328

city: Honolulu

middle: Francis

last: Garcia

state: Hawaii

address: 651 Ilalo Street

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: John A Burns School of Medicine

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). Fold change data is available as a supplementary file on the Series record.

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes (blood)

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Streptococcus pyogenes 328 was grown to late-log/early-stationary phase (O.D. 600nm 0.8) aerobically (5% CO2) at 37°C in Todd Hewitt Broth with 0.1% Yeast Extract

extract_protocol: Total RNA was extracted according to Froeliger and Fives-Taylor (Froeliger, 1998) with some modifications using acid-washed glass beads (Sigma Aldrich, St. Louis, MO) and phenol/chloroform/isoamyl alcohol (125:24:1 Fisher Biotech, Lawn, NJ) and treated with DNase (Ambion, Austin,TX). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Greenwood Molecular Biology Facility (University of Hawaii, Honolulu, HI USA).

tag: isolate

value: blood

value: emm 81

tag: gene

value: CovS 11-bp insertion

tag: phenotype

value: no cysteine protease activity


title: Patient 1 LIN


title: 13969306 - wt 2 vs irx12 2

hyb_protocol: irx12 2 Cy5 / wt 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969304 - wt 2 vs kim 2

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

source_name: kim 2

value: kim


title: 13969308 - wt 2 vs lac17 2

hyb_protocol: lac17 2 Cy5 / wt 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac17 2


title: 13969319 - lac17 2 vs wt 2

hyb_protocol: wt 2 Cy5 / lac17 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: UH322

source_name: Streptococcus pyogenes (pharyngeal)

growth_protocol: Streptococcus pyogenes 322 was grown to late-log/early-stationary phase (O.D. 600nm 1.1) aerobically (5% CO2) at 37°C in Todd Hewitt Broth with 0.1% Yeast Extract

value: pharyngeal

value: wild-type

value: cysteine protease activity


title: 13969154 - wt 1 vs lac17 1

hyb_protocol: lac17 1 Cy5 / wt 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac17 1

source_name: wt 1