title: C. acetobutylicum Lactose Replicate 3

status: Public on May 15 2010

city: Adelphi

first: Christian

last: Sund

state: MD

address: 2800 Powder Mill Road

institute: US Army Research Laboratory

description: This data is the third of three replicates

hyb_protocol: Two ug of Cy3 labeled ds-cDNAs were transferred to new tubes, dried in a SpeedVac (Eppendorf), and rehydrated in 3.3 ul Sample Tracking Control solution (Roche NimbleGen). Then 8.7 ul hybridization solution containing 6 ul 2X Hybridization Buffer (Roche NimbleGen), 2.4 ul Hybridization Component A (Roche NimbleGen), and 0.3 ul Alignmet Oligo (Roche NimbleGen) was added to each tube. Eight ul of each Cy3 labeled ds-cDNA was transferred to a separate port of a 4-plex Mixer (Roche NimbleGen) which was previously adhered to a 4-plex gene expression array (Roche NimbleGen) designed for C. acetobutylicum. Each quadrant of the array contained 2 replicates of 9 probes approximately 60 bp in length for each of the 3,842 open reading frames annotated in the C. acetobutylicum genome. The arrays were hybridized at 42 °C for 16 h in a NimbleGen Hybridization System 4 (Roche NimbleGen) using mix mode B. Following removal of the hybridization chambers the microarray slides were washed using a NimbleGen Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: The arrays were imaged with an Agilent Microarray Scanner (Agilent) at 532 nm, 2 µm resolution.

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 (Roche NimbleGen, Inc.).

organism: Clostridium acetobutylicum ATCC 824

source_name: Lactose Replicate 3

label_protocol: Synthesis of Cy3 labeled cDNA and hybridization to DNA microarrays was performed essentially as described by the NimbleGen Arrays User’s Guide for Gene Expression Analysis (Roche NimbleGen). Double stranded cDNA (ds-cDNA) was synthesized from 10 ug random hexamer primed total RNA using a Superscript Double-Stranded cDNA Synthesis kit (Invitrogen). RNA was then removed by incubating samples with 2 ng/ul (final concentration) of RNase A (Promega) at 37 C for 10 min. The ds-cDNA was purified using a phenol:cholorform extraction followed by ethanol precipitation. The resulting ds-cDNA pellet was dissolved in 20 ul water and the quality of ds-cDNA was determined by analysis in an Agilent Bioanalyzer (Agilent Technologies). Samples were only used if they had a concentration greater than 100 ng/ul, an A260/A280 ratio greater than 1.8, and a median size greater than 400 bp. For each sample, 1 µg of ds-cDNA, 40 ul Cy3-labeled nonamers (TriLink Biotechnologies) (diluted to a concentration of 20 ug/42 ul of 125 mM Tris pH 7.4, 12.5 mM MgCl2, 1.75 ul/ml β-mercaptoethanol), and sufficient water to bring the reaction volume to 80 ul was incubated at 98 C for 10 minutes and then cooled in an ice water bath for 10 min. Ten ul dNTPs (Invitrogen) (10 mM dATP, 10 mM dGTP, 10 mM dTTP, 10 mM dCTP in 1 M Tris HCl pH 7.4, 0.01 M EDTA), 2 ul 50 U/ul Klenow Fragment (New England Biolabs), and 8 ul water were added to each reaction. The reactions were incubated at 37 uC in the dark for 2 h. The reactions were stopped by addition of 10 ul 0.5 M EDTA.

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g lactose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)

extract_protocol: The cultures were treated with rifampicin, chloramphenicol, and phenylmethanesulfonyl fluoride (PMSF) at final concentrations of 30 µg/ml, 50 µg/ml, and 0.5 mM, respectively. Cultures were immediately placed in an ice water bath for 15 minutes after which 7.5 mls were centrifuged in sealed tubes for 10 minutes, 5,000 ×g at 4 °C. The supernatant was decanted and the cell-containing pellets were suspended in 750 µl of a solution containing a 1:1 ratio of RNA protect (Qiagen) and phosphate buffered saline. After a 5 min incubation period at room temperature the cell suspensions were pelleted by centrifugation and stored at -80 °C. The cell pellets were thawed on ice and the cells were suspended in 1.5 ml RLT buffer (Invitrogen) supplemented with 150 µl β-mercaptoethanol and homogenized with 0.1 mm Zirconia/Silica beads (BioSpec) in a Mini-Beadbeater-16 (BioSpec) for 4 min. Total RNA was extracted from homogenized cells using an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. The quantity and integrity of the RNA was determined using an Agilent Bioanalyzer.

treatment_protocol: Cells were grown to and OD of 0.2 then samples were taken.

tag: strain

value: Clostridium acetobutylicum ATCC 824


title: Medium 4h (Lactate HUVEC Chip4)

status: Public on May 16 2010

type: RNA

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description: Slides were scanned in a microarray scanner (Genetix Limited, Hampshire, UK). Photomultiplier tube voltage was set to 100% for both red and green channels. The two resulting green and red images were overlaid using ImaGene 5 (BioDiscovery, Inc., CA, USA).

hyb_protocol: Pre-hybridization Note: Do not allow the slides to dry during the pre-hybridization and washing procedure. 1. Pre-warm an appropriate volume of Nexterion 70mer Oligo Pre-Hyb to 48°C for 10 minutes until the precipitate is completely dissolved. 2. Incubate slides in Nexterion 70mer Oligo Pre-Hyb for 45 min at 48°C. Use a large enough volume of buffer to ensure that all slides are completely covered with Nexterion Pre-Hyb. 3. During the pre-hybridization step, prepare Wash Solution 1 by diluting Nexterion 70mer Oligo Wash B 1:40 with diH2O. Prepare 50 ml per slide (i.e. 1.25 ml Nexterion 70mer Oligo Wash B, add diH2O to 50 ml). 4. Wash 5 min in Wash Solution 1 at 20 to 25°C. 5. Rinse with diH2O for 30 sec. 6. Dry the Nexterion Slide E with nitrogen. Hybridization Prewarm Hybsolution 15 minutes before hybridization at 68°C. Clean coverslips with dH20 and 100% Ethanol and dry the coverslips with nitrogen. 1. Pipette 40µl of hybridization to the solution. Denature the fragmented target in the hyb-buffer by heating at 95°C for 3 min. Then let the probe cool down for 1 min at RT. Afterwards place the target onto the array surface of a prehybridized slide under the coverslip 3. Hybridize the slide at 48°C for 16 hours. Post-hybridization washing Note: Do not allow the slides to dry during the hybridization and washing procedure. Wash Solution 2, 3 and 4 should be prepared in advance. Use at least 50 ml solution per slide. Post-hybridization washing solutions: Preparation: Wash Solution 2: 50 ml Nexterion 70mer Oligo Wash A, 25 ml Nexterion 70mer Oligo Wash B, Make up to 500 ml with diH2O Wash Solution 3: 50 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O Wash Solution 4: 5 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O 1. Place the array into a slide rack and immerse in a dish containing Wash Solution 2. Wash in the above solution 1 x 10 min at 20 to 25°C. 2. Wash 1 x 10 min in Wash Solution 3 at 20 to 25°C. 3. Wash 1 x 10 min in Wash Solution 4 at 20 to 25°C. 4. Dry the array with nitrogen. 5. Protect the array from light, dust and abrasion of the array surface, until ready for scanning.

scan_protocol: not further discription needed

data_processing: The data was normalized using median normalization on the normexp-background corrected expression values, followed by a  in-between-array quantile normalization. Both the median and quantile normalization methods were used as provided in the limma package.

molecule: total RNA

organism: Homo sapiens

source_name: Reference

label_protocol: Amino Allyl MessageAmp II aRNA Amplification Kit performed according to the provided manual

extract_protocol: Universal Human Reference RNA, Stratagene

tag: sample type

value: global Reference

source_name: Medium 4h

extract_protocol: Machery & Nagel RNA extraction kit performed according to the provided manual

tag: agent

value: Medium

tag: cell type

value: HUVECS

tag: time point


title: C. acetobutylicum Lactose Replicate 1

country: USA

description: This data is the first of three replicates

source_name: Lactose Replicate 1


title: C. acetobutylicum Lactose Replicate 2

description: This data is the second of three replicates

source_name: Lactose Replicate 2


title: C. acetobutylicum Xylose Replicate 1

source_name: Xylose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g xylose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Xylose Replicate 3

source_name: Xylose Replicate 3


title: C. acetobutylicum Xylose Replicate 2

source_name: Xylose Replicate 2


title: C. acetobutylicum Fructose Replicate 1

source_name: Fructose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g fructose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Fructose Replicate 3

description: This data is the Third of three replicates

source_name: Fructose Replicate 3


title: Proband 8 12h (Clock Genes Chip31)

status: Public on May 17 2010

source_name: Proband 8 12h

tag: tissue

value: oral mucosa

tag: individual

value: proband 8


title: C. acetobutylicum Fructose Replicate 2

source_name: Fructose Replicate 2


title: C. acetobutylicum Maltose Replicate 1

source_name: Maltose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g maltose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Maltose Replicate 2

source_name: Maltose Replicate 2


title: C. acetobutylicum Maltose Replicate 3

source_name: Maltose Replicate 3


title: P98 UK prostate cancer

type: genomic

city: London

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: Hybridized to human SNP 6.0 array

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

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

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

label: Biotin

molecule: genomic DNA

source_name: UK prostate cancer

label_protocol: As per manufacturer (Affymetrix)

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

value: Prostate cancer


title: P9 UK normal prostate

description: Hybridized to human SNP 6.0 array

source_name: UK normal prostate

value: Normal prostate


title: P55 UK prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH40 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array

source_name: Chinese prostate cancer


title: SH32 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: P55 UK normal prostate

description: Hybridized to human SNP 6.0 array


title: SH20 Chinese normal prostate

description: Hybridized to human SNP 6.0 array

source_name: Chinese normal prostate


title: C. acetobutylicum Mannose Replicate 3

source_name: Mannose Replicate 3

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g mannose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: SH15 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: P9 UK prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Arabinose Replicate 1

source_name: Arabinose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g arabinose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Mannose Replicate 2

source_name: Mannose Replicate 2


title: SH16 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH20 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH18 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Mannose Replicate 1

source_name: Mannose Replicate 1


title: SH21 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Arabinose Replicate 2

source_name: Arabinose Replicate 2


title: P130 UK normal prostate

description: Hybridized to human SNP 6.0 array


title: SH22 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: P68 UK prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH16 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH21 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH19 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH17 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH19 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Sucrose Replicate 1

source_name: Sucrose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g Sucrose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: SH18 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Sucrose Replicate 2

source_name: Sucrose Replicate 2


title: P130 UK prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Starch Replicate 1

source_name: Starch Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g Starch. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Sucrose Replicate 3

source_name: Sucrose Replicate 3


title: C. acetobutylicum Arabinose replicate 3

source_name: Arabinose replicate 3


title: SH17 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Starch Replicate 2

source_name: Starch Replicate 2


title: SH15 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH14 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Galactose Replicate 1

source_name: Galactose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g galactose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: SH40 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: C. acetobutylicum Starch Replicate 3

source_name: Starch Replicate 3


title: C. acetobutylicum Cellobiose Replicate 1

source_name: Cellobiose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g cellobiose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Galactose Replicate 3

source_name: Galactose Replicate 3


title: C. acetobutylicum Galactose Replicate 2

source_name: Galactose Replicate 2


title: SH14 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array

source_name: Chinese prostate cancer


title: C. acetobutylicum Cellobiose Replicate 2

source_name: Cellobiose Replicate 2

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g cellobise. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: C. acetobutylicum Cellobiose Replicate 3

source_name: Cellobiose Replicate 3


title: C. acetobutylicum Glucose Replicate 1

source_name: Glucose Replicate 1

growth_protocol: Cells were grown to an OD of 0.2 in clostridia growth media containing the following per liter of distilled water: KH2PO4, 0.75 g; K2HPO4, 0.75 g; MgSO4 · H2O, 0.4 g; MnSO4 · H2O, 0.01 g; FeSO4 · 7 H2O, 0.01 g; NaCl, 1.0 g; asparagine, 2.0 g; yeast extract, 5.0 g; (NH4)2SO4, 2.0 g; carbohydrate, 5 g glucose. (Wiesenborn, D. P., et al. Appl Environ Microbiol 54:2717-2722.)


title: DHF-RA-169

status: Public on May 01 2010

city: Baltimore

first: Andreas

middle: Sebastian

last: Barth

address: 720 Rutland Ave.

department: Medicine, Division of Cardiology

institute: Johns Hopkins University

description: Gene expression in failing right atrial myocardium

hyb_protocol: 0.825 ug of each Cy3-labeled sample was used for hybridization on Agilent 44K whole canine genome microarray at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol using stabilization and drying solution.

scan_protocol: Microarrays were scanned using an Agilent G2565AA Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: gMedianSignal (raw values) after quantile normalization, without pos. and neg. control probes. Differentially expressed transcripts were identified with Significance Analysis of Microarrays (SAM).

organism: Canis lupus familiaris

source_name: Myocardium, right atrium, failing

label_protocol: 0.4 ug total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: After sacrificing the animal, myocardial tissue was transported to the lab in ice-cold saline, snap-frozen in liquid nitrogen and stored at -80 degrees Celsius. RNA was isolated from frozen tissue.

extract_protocol: Total RNA was isolated with TRIzol reagent from the subendocardium of the anterior and lateral LV walls in the distribution of the LAD and left circumflex artery, respectively. RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.

treatment_protocol: Dyssynchronous heart failure (DHF): One week after ablation of the left bundle branch, animals were paced at 200 beats per minute for 6 weeks from the right atrium (via epicardial pacing leads).

tag: disease state

value: dyssynchronous heart failure (DHF)

tag: developmental stage

value: Adult

tag: gender

value: male


title: DHF-A-424


title: C. acetobutylicum Glucose Replicate 2

source_name: Glucose Replicate 2


title: DHF-RA-151


title: RetliCFN42_WT_vs_NifA_11dpi_rep2

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: Transcriptional profiling in symbiosis 11 days post-inoculation was compared between wild type strain and nifA mutant.

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 45 ul of hybridization buffer UniHyb (TeleChem International INC). The mixture was hybridized at 42 C for 14 to 16 h. Hybridized arrays were washed with 2X SSC, 0.1% SDS at 42 C for 2 min, and, subsequently, with 0.1X SSC at room temperature for 2 min, and twice with 0.1X SSC at room temperature for 2 min.

scan_protocol: The array was scanned using a pixel size of 10 um with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA).

data_processing: Spot detection, mean signals, mean local background intensities, image segmentation, and signal quantification were determined for the microarray images using the Array-Pro Analyzer 4.0 software (Media Cybernetics, L.P). Microarray data analysis was performed with genArise software, developed in the Computing Unit of the Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico (http://www.ifc.unam.mx/genarise/). The Lowess normalization was applied using the genArise software. This software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point and defines a z-score where z measures the number of standard deviations that a data point is from the mean: zi = [Ri•mean(R)]/sd(R), where zi is the z-score for each element; mean (R) is the mean log ratio; Ri is the log ratio for each element; and sd(R) is the standard deviation of the log ratio.

organism: Rhizobium etli CFN 42

source_name: Nodules of eleven days post-inoculation, nifA mutant

label_protocol: 10 ug of RNA was labeled with Cy3-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

extract_protocol: Approximately 3 g of nodules were immersed in liquid nitrogen and macerated. Total RNA was isolated by acid hot-phenol extraction as described previously by de Vries et al.

tag: growth conditions

value: Symbiosis with bean 11 days post-inoculation

tag: genotype/variation

value: nifA mutant

source_name: Nodules of eleven days post-inoculation, wild type

label_protocol: 10 ug of RNA was labeled with Cy5-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

value: wild type


title: RetliCFN42_WT_vs_NifA_11dpi_rep1


title: RetliCFN42_WT_vs_NifA_11ddi_rep3


title: NF-RA-07-017

description: Gene expression in non-failing right atrial myocardium

source_name: Myocardium, right atrium, non-failing

treatment_protocol: Non-failing control

value: control (NF)


title: DHF-RA-32


title: DHF-RA-136


title: C. acetobutylicum Glucose Replicate 3

source_name: Glucose Replicate 3


title: NF-RA-105


title: NF-RA-12


title: NF-RA-125


title: NF-RA-07-034


title: NF-RA-273


title: NF-RA-269


title: NF-RA-289


title: NF-RA-281

growth_protocol: After sacrificing the animal, myocardial tissue was transported to the lab in ice-cold cardioplegic solution, snap-frozen in liquid nitrogen and stored at -80 degrees Celsius. RNA was isolated from frozen tissue.

treatment_protocol: non-failing control


title: NF-RA-283


title: Oryzias latipes_7day_30ng/L_rep3

city: Tsukuba

first: Katsuyuki

last: Kadota

address: Tokodai 5-13-11

department: Research

country: Japan

institute: Japan Pulp and Paper Research Institute, Inc.

description: Gene expression after 7 day in 30 ng/L E2 treated whole medaka

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Medaka Genome Oligo Microarrays (G2514F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryzias latipes

source_name: Oryzias latipes, 7 day, 30 ng/L, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The experiment was performed in a climate chamber at 24±1oC and with 16 h light-8 h dark photoperiod. Each aquarium contained 90 medaka.

extract_protocol: Each frozen medaka samples were ground with a mortar and pestle in liquid nitrogen. Total RNA was isolated from each powder samples using the Quagen RNwasy Lipid Tissue Midi Kit (Quagen) following procedures recommended by the manufacture. The RNA quantity and purity were determined by NanoDrop ND1000 spectrophometer at 260/280 nm and 260/230 nm (Nano Drop Technologies Wilmington, Delaware) and Agilent Bioanalyzer 2100 and and RNA 6000 Nano LabChip Kit (Agilent Technologies). Only RNA samples with RIN values of 9, or higher, were used for the analysis.

treatment_protocol: Larval fishes were exposed to E2 at concentrations of 0, 3, 30 and 100 ng/L in 3 L glass beakers containing 2L dechlorinated tap water for 7 days after birth, respectively. Thirty fish each were collected (for n=3 experiments), flash-frozen in liquid nitrogen, and stored at -80oC until RNA extraction.

value: whole blood

tag: dose

value: 30 ng/L


title: DHF-RA-152


title: Oryzias latipes_7day_30ng/L_rep2

source_name: Oryzias latipes, 7 day, 30 ng/L, replicate 2


title: Oryzias latipes_7day_3ng/L_rep3

description: Gene expression after 7 day in 3 ng/L E2 treated whole medaka

source_name: Oryzias latipes, 7 day, 3 ng/L, replicate 3

value: 3 ng/L


title: Oryzias latipes_7day_100ng/L_rep1

description: Gene expression after 7 day in 100 ng/L E2 treated whole medaka

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 1


title: Oryzias latipes_7day_3ng/L_rep2

source_name: Oryzias latipes, 7 day, 3 ng/L, replicate 2


title: Oryzias latipes_7day_0ng/L_rep3

description: Gene expression after 7 day in 0 ng/L E2 treated whole medaka

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 3

value: 0 ng/L


title: Oryzias latipes_7day_3ng/L_rep1

source_name: Oryzias latipes, 7 day, 3 ng/L, replicate 1


title: SH6 Chinese normal prostate

description: Hybridized to human SNP 6.0 array

source_name: Chinese normal prostate


title: SH5 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: Oryzias latipes_7day_0ng/L_rep1

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 1


title: Oryzias latipes_7day_0ng/L_rep2

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 2


title: SH1 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH5 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array

source_name: Chinese prostate cancer


title: SH4 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH7 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH2 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH3 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: PAH-6-PBMC-STY

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

data_processing:
Genotype calls were made using the BRLMM (GPL3718, GPL3720) and Birdseed v2(GPL6801) algorithms as implemented in Affymetrix power tools.
Locus-specific copy number estimates were generated in Partek Genomics Suite using default parameters and 270 hapmap samples as diploid controls.

source_name: peripheral blood mononuclear cells cultured from subject PAH-6

label_protocol: standard Affymetrix

growth_protocol: as reported in Xu, W., Koeck, T., Lara, A. R., Neumann, D., DiFilippo, F. P., Koo, M., Janocha, A. J., Masri, F. A., Arroliga, A. C., Jennings, C. et al. (2007) Proc. Natl. Acad. Sci. U. S. A 104, 1342-1347.

extract_protocol: Qiagen DNA mini

tag: disease status

value: Pulmonary Arterial Hypertension

value: peripheral blood mononuclear cells


title: PAH-6-PAEC-STY

source_name: pulmonary artery epithelial cells cultured from subject PAH-6

value: pulmonary artery epithelial cells


title: SH6 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: DHF-RA-76

source_name: Myocardium, right atrium, failing


title: Oryzias latipes_7day_30ng/L_rep1

source_name: Oryzias latipes, 7 day, 30 ng/L, replicate 1


title: Oryzias latipes_7day_100ng/L_rep2

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 2


title: SH3 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: PAH-1-PAEC-STY

source_name: pulmonary artery epithelial cells cultured from subject PAH-1


title: PAH-1-PMEC-STY

source_name: pulmonary microvascular endothelial cells cultured from subject PAH-1


title: Oryzias latipes_7day_100ng/L_rep3

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 3


title: PAH-1-PBMC-STY

source_name: peripheral blood mononuclear cells cultured from subject PAH-1


title: PAH-1-BSMC-STY

source_name: bronchial smooth muscle cells cultured from subject PAH-1

value: bronchial smooth muscle cells


title: SH4 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array

value: Prostate cancer


title: PAH-1-AEC-STY

source_name: airway endothelial cells cultured from subject PAH-1

value: airway endothelial cells


title: NF-RA-07-097

source_name: Myocardium, right atrium, non-failing


title: SH2 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH1 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: PAH-1-PASMC-STY

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-1


title: COPD-2-PAEC

source_name: pulmonary artery epithelial cells cultured from subject COPD-2

value: Chronic Obstructive Pulmonary Disease


title: CF-2-PAEC

source_name: pulmonary artery epithelial cells cultured from subject CF-2

value: Cystic Fibrosis


title: COPD-3-PAEC

source_name: pulmonary artery epithelial cells cultured from subject COPD-3


title: COPD-1-PASMC

source_name: pulmonary artery smooth muscle cells cultured from subject COPD-1


title: COPD-2-PASMC

source_name: pulmonary artery smooth muscle cells cultured from subject COPD-2


title: CF-1-PAEC

source_name: pulmonary artery epithelial cells cultured from subject CF-1


title: PAH-8-PAEC

hyb_protocol: standard Illumina

scan_protocol: standard Illumina

data_processing: standard Illumina

label: C-Bio and A-DNP

source_name: airway endothelial cells cultured from subject PAH-8

label_protocol: standard Illumina

value: airway endothelial cell


title: control-7-PAEC

source_name: airway endothelial cells cultured from subject control-7

value: Control (non-diseased subject)


title: PAH-1-PBMC

source_name: peripheral blood mononuclear cells collected from subject PAH-1

value: peripheral blood mononuclear cell


title: control-8-PAEC

source_name: airway endothelial cells cultured from subject control-8


title: PAH-8-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-8


title: PAH-7-PASMC-B

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-7, culture B

value: pulmonary artery smooth muscle cell


title: PAH-7-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-7


title: control-6-PAEC

source_name: airway endothelial cells cultured from subject control-6


title: PAH-9-PAEC

source_name: airway endothelial cells cultured from subject PAH-9


title: control-5-PAEC

source_name: airway endothelial cells cultured from subject control-5


title: PAH-1-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-1


title: PAH-7-PBMC

source_name: peripheral blood mononuclear cells collected from subject PAH-7


title: PAH-4-BSMC

source_name: bronchial smooth muscle cells cultured from subject PAH-4


title: PAH-5-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-5


title: PAH-3-BSMC

source_name: bronchial smooth muscle cells cultured from subject PAH-3


title: PAH-4-PASMC

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-4


title: PAH-5-PASMC

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-5


title: COPD-1-PAEC

source_name: pulmonary artery epithelial cells cultured from subject COPD-1


title: PAH-7-PASMC-A

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-7, culture A


title: PAH-3-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-3


title: PAH-4-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-4


title: PAH-2-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-2


title: PAH-9-PAEC

source_name: pulmonary artery epithelial cells cultured from subject PAH-9


title: PAH-1-PAEC

source_name: airway endothelial cells cultured from subject PAH-1


title: PAH-3-PASMC

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-3


title: PAH-6-PBMC-NSP

source_name: peripheral blood mononuclear cells cultured from subject PAH-6


title: Lung_AJ_PBS_28day_rep4

status: Public on Apr 30 2010

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

description: replicate 4: 1855537036_E

hyb_protocol: 20 hour hybridization period at 58°C

scan_protocol: Illumina BeadStation 500G - BeadArray Reader standard

data_processing: Force positive background correction, variance stabilizing transformation, robust spline normalization

label: biotin

organism: Mus musculus

source_name: lung

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791)

extract_protocol: RNA was isolated from whole lung homogenates using the TRIzol (Invitrogen, Carlsbad, CA) method and then cleaned according to the manufacturer’s instructions using a RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Phosphate buffered saline, gas metal arc stainless steel, or gas metal arc mild steel welding fume was instilled in mice 4 times over a 10 day perios and allowed to recover for 28 days or 16 weeks prior to sacrifice and collection of lung tissue

value: A/J

tag: treatment

value: Phosphate Buffered Saline

tag: recovery time

value: 28 days


title: PAH-1-PBMC

source_name: peripheral blood mononuclear cells cultured from subject PAH-1


title: Lung_AJ_GMS_28day_rep4

description: replicate 4: 1855537036_G

value: Gas Metal Arc-Mild Steel


title: PAH-6-PAEC-NSP

source_name: pulmonary artery epithelial cells cultured from subject PAH-6


title: PAH-1-BSMC-NSP

source_name: bronchial smooth muscle cells cultured from subject PAH-1


title: PAH-1-PBMC-NSP


title: PAH-5-PBMC

source_name: peripheral blood mononuclear cells collected from subject PAH-5


title: Lung_C57_GMS_28day_rep4

description: replicate 4: 1855537036_C


title: PAH-1-PAEC-NSP

source_name: pulmonary artery epithelial cells cultured from subject PAH-1


title: Lung_AJ_GMS_28day_rep3

description: replicate 3: 1855537004_G


title: Lung_C57_PBS_28day_rep4

description: replicate 4: 1855537036_A


title: PAH-1-PASMC-NSP

source_name: pulmonary artery smooth muscle cells cultured from subject PAH-1


title: Lung_C57_GSS_28day_rep4

description: replicate 4: 1855537036_B

value: Gas Metal Arc-Stainless Steel


title: PAH-3-PASMC

value: Pulmonary Arterial Hypertension


title: Lung_C57_GMS_28day_rep3

description: replicate 3: 1855537004_C


title: PAH-7-PAEC-A

source_name: airway endothelial cells cultured from subject PAH-7, culture A


title: PAH-5-PAEC

source_name: airway endothelial cells cultured from subject PAH-5


title: Lung_AJ_GSS_28day_rep4

description: replicate 4: 1855537036_F


title: Lung_AJ_GMS_28day_rep2

description: replicate 2: 1842779039_G


title: Lung_AJ_GSS_28day_rep3

description: replicate 3: 1855537004_F


title: Lung_C57_PBS_28day_rep3

description: replicate 3: 1855537004_A


title: Lung_AJ_PBS_28day_rep2

description: replicate 2: 1842779039_E


title: PAH-4-PAEC

source_name: airway endothelial cells cultured from subject PAH-4


title: PAH-1-PMEC-NSP

source_name: pulmonary microvascular endothelial cells cultured from subject PAH-1


title: Lung_C57_GMS_28day_rep2

description: replicate 2: 1842779039_C


title: control-3-PAEC

source_name: airway endothelial cells cultured from subject control-3


title: Lung_AJ_GSS_28day_rep2

description: replicate 2: 1842779039_F


title: control-4-PAEC

source_name: airway endothelial cells cultured from subject control-4


title: Lung_AJ_GSS_28day_rep1

description: replicate 1: 1842779033_F


title: Lung_C57_GSS_28day_rep3

description: replicate 3: 1855537004_B


title: control-1-PAEC

source_name: airway endothelial cells cultured from subject control-1


title: PAH-2-PBMC

source_name: peripheral blood mononuclear cells collected from subject PAH-2


title: PAH-2-PAEC

source_name: airway endothelial cells cultured from subject PAH-2


title: PAH-1-AEC-NSP

source_name: airway endothelial cells cultured from subject PAH-1


title: Lung_AJ_PBS_28day_rep1

description: replicate 1: 1842779033_E

source_name: lung


title: Lung_AJ_GMS_28day_rep1

description: replicate 1: 1842779033_G


title: PAH-3-PAEC

source_name: airway endothelial cells cultured from subject PAH-3


title: Lung_C57_PBS_28day_rep2

description: replicate 2: 1842779039_A


title: Lung_AJ_GMS_16wk_rep3

description: replicate 3: 4068838032_G

value: 16 weeks


title: Lung_C57_GMS_16wk_rep4

description: replicate 4: 4068838033_C


title: Lung_C57_GSS_16wk_rep4

description: replicate 4: 4068838033_B


title: Lung_C57_PBS_16wk_rep4

description: replicate 4: 4068838033_A


title: PAH-7-PAEC-B

source_name: airway endothelial cells cultured from subject PAH-7, culture B


title: Lung_AJ_PBS_16wk_rep3

description: replicate 3: 4068838032_E


title: Lung_AJ_GMS_16wk_rep4

description: replicate 4: 4068838033_G


title: Lung_C57_PBS_28day_rep1

description: replicate 1: 1842779033_A


title: Lung_AJ_PBS_28day_rep3

description: replicate 3: 1855537004_E


title: Lung_ AJ_PBS_16wk_rep4

description: replicate 4: 4068838033_E


title: Lung_C57_GSS_28day_rep1

description: replicate 1: 1842779033_B


title: Lung_AJ_GSS_16wk_rep4

description: replicate 4: 4068838033_F


title: control-2-PAEC

source_name: airway endothelial cells cultured from subject control-2


title: Lung_C57_GMS_28day_rep1

description: replicate 1: 1842779033_C


title: Lung_C57_GSS_28day_rep2

description: replicate 2: 1842779039_B


title: Lung_C57_GMS_16wk_rep3

description: replicate 3: 4068838032_C


title: Lung_AJ_GSS_16wk_rep3

description: replicate 3: 4068838032_F


title: Lung_C57_GMS_16wk_rep2

description: replicate 2: 4068838012_C


title: Lung_C57_PBS_16wk_rep3

description: replicate 3: 4068838032_A


title: Lung_C57_GSS_16wk_rep3

description: replicate 3: 4068838032_B


title: Lung_C57_GSS_16wk_rep2

description: replicate 2: 4068838012_B


title: Lung_AJ_GMS_16wk_rep1

description: replicate 1: 4068838011_G


title: D.rerio_SC_MO_vs control_28hpf_embryos_3rd

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM SC (Standard Control) morpholino
SC_MO_3rd

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) according to Agilent protocol G4140-90050 v.5.7 (www.Agilent.com) for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: Microarray data were processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies).

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of sequences. The significance cut-off for ratios of SC_MO injected embryos versus 1xPhenol Red/ Danieu injected embryos was set at P ≤ 10-2 and absolute fold change equal or larger than 1.2.

organism: Danio rerio

source_name: D.rerio_1xPhenol Red/ Danieu injected 28hpf embryos_3

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye(GE Healthcare) and column purified.

growth_protocol: Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean see salts).

extract_protocol: Embryos were directly homogenized in TRIZOL® Reagent. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RIN value of 9 and a minimum RIN value of 8.

treatment_protocol: Embryos were injected with 1xPhenol Red (dye)/ Danieu buffer and then grown till 28 hours post fertilization (hpf) as confirmed by morphological critera (Kimmel et al.)

value: reference

value: 28hpf embryos

value: 1x Phenol Red (dye)/ Danieu buffer

source_name: D.rerio_1mM SC morpholino injected 28hpf embryos_3

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye(GE Healthcare) and column purified.

treatment_protocol: Embryos were injected with 1mM SC (Standard Control) morpholino and then grown till 28 hours post fertilization (hpf) as confirmed by morphological critera (Kimmel et al.)

value: test

value: 1mM SC (Standard Control) morpholino


title: Lung_AJ_GMS_16wk_rep2

description: replicate 2: 4068838012_G


title: D.rerio_SC_MO_vs control_28hpf_embryos_2nd

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM SC (Standard Control) morpholino
SC_MO_2nd

source_name: D.rerio_1xPhenol Red/ Danieu injected 28hpf embryos_2

source_name: D.rerio_1mM SC morpholino injected 28hpf embryos_2


title: Lung_AJ_GSS_16wk_rep2

description: replicate 2: 4068838012_F


title: Lung_AJ_GSS_16wk_rep1

description: replicate 1: 4068838011_F


title: Lung_C57_PBS_16wk_rep2

description: replicate 2: 4068838012_A


title: Lung_AJ_PBS_16wk_rep2

description: replicate 2: 4068838012_E


title: D.rerio_SC_MO_vs control_28hpf_embryos_1st

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM SC (Standard Control) morpholino
SC_MO_1st

source_name: D.rerio_1xPhenol Red/ Danieu injected 28hpf embryos_1

source_name: D.rerio_1mM SC morpholino injected 28hpf embryos_1


title: Lung_AJ_PBS_16wk_rep1

description: replicate 1: 4068838011_E


title: D.rerio_PU1_MO_vs control_28hpf_embryos_2nd

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM PU.1 morpholino
PU.1_MO_2nd

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of sequences. The significance cut-off for ratios of PU1_MO injected embryos versus 1xPhenol Red/ Danieu injected embryos was set at P ≤ 10-2 and absolute fold change equal or larger than 1.2.

source_name: D.rerio_1mM PU.1 morpholino injected 28hpf embryos_2

treatment_protocol: Embryos were injected with 1mM PU.1 morpholino and then grown till 28 hours post fertilization (hpf) as confirmed by morphological critera (Kimmel et al.)

value: 1mM PU.1 morpholino


title: Lung_C57_GMS_16wk_rep1

description: replicate 1: 4068838011_C


title: D.rerio_GFP+ myeloid cells vs GFP- cells from 28hpf spi1-gfp embryos_2nd

description:
CH1: GFP- cell fraction from FACS sorting of 28hpf spi1-gfp embryos
CH2: GFP+ myeloid cell fraction from FACS sorting of 28hpf spi1-gfp embryos
GFP- vs GFP+_2nd

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of sequences. The significance cut-off for ratios of GFP+ versus GFP- cells was set at P ≤ 10-2 and absolute fold change equal or larger than 1.2.

source_name: D.rerio_GFP- cells from 28hpf spi1-GFP_2

extract_protocol: total RNA was extracted from 200000-400000 cells using RNAqueous Micro Kit

treatment_protocol: Embryos were staged at 28 hours post fertilization (hpf) by morphological critera (Kimmel et al.) and then enzymatically dissociated into single cell suspension, which was next subjected to FACS sorting into GFP+ myeloid cell fraction and GFP- cell fraction

tag: cell fraction

value: GFP- cell fraction

tag: protocol

value: FACS sorting

tag: cell line

value: spi1-gfp transgenic line

source_name: D.rerio_GFP+ myeloid cells from 28hpf spi1-GFP_2

tag: GFP+ myeloid cell fraction


title: D.rerio_PU1_MO_vs control_28hpf_embryos_3rd

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM PU.1 morpholino
PU.1_MO_3rd

tag: agent

source_name: D.rerio_1mM PU.1 morpholino injected 28hpf embryos_3


title: Lung_C57_GSS_16wk_rep1

description: replicate 1: 4068838011_B

tag: strain


title: D.rerio_PU1_MO_vs control_28hpf_embryos_1st

description:
CH1: 28hpf embryos injected with 1x Phenol Red (dye)/ Danieu buffer
CH2: 28hpf embryos injected with 1mM PU.1 morpholino
PU.1_MO_1st

source_name: D.rerio_1mM PU.1 morpholino injected 28hpf embryos_1


title: Lung_C57_PBS_16wk_rep1

description: replicate 1: 4068838011_A


title: rhesus hippocampal DG, 23.25 years old, replicate 3

status: Public on Apr 15 2010

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Standard Affymetrix

organism: Macaca mulatta

source_name: Rhesus hippocampus DG

label_protocol: Standard Affymetrix

extract_protocol: Standard Affymetrix

tag: Female


title: rhesus hippocampal DG, 25.00 years old, replicate 2


title: rhesus hippocampal DG, 20.25 years old, replicate 7


title: D.rerio_GFP+ myeloid cells vs GFP- cells from 28hpf spi1-gfp embryos_1

description:
CH1: GFP- cell fraction from FACS sorting of 28hpf spi1-gfp embryos
CH2: GFP+ myeloid cell fraction from FACS sorting of 28hpf spi1-gfp embryos
GFP- vs GFP+_1st

source_name: D.rerio_GFP-cells from 28hpf spi1-GFP_1

source_name: D.rerio_GFP+ myeloid cells from 28hpf spi1-GFP_1


title: rhesus hippocampal DG, 24.75 years old, replicate 10


title: rhesus hippocampal DG, 23.25 years old, replicate 11


title: rhesus hippocampal DG, 6.50 years old, replicate 9


title: rhesus hippocampal DG, 6.50 years old, replicate 8


title: rhesus hippocampal DG, 6.50 years old, replicate 4


title: rhesus hippocampal CA1, 6.50 years old, replicate 1

source_name: Rhesus hippocampus CA1


title: rhesus hippocampal CA1, 23.25 years old, replicate 11


title: rhesus hippocampal CA1, 7.25 years old, replicate 12


title: rhesus hippocampal CA1, 6.50 years old, replicate 4


title: rhesus hippocampal CA1, 7.75 years old, replicate 5


title: rhesus hippocampal DG, 7.75 years old, replicate 1


title: mature endodermis, biologlcal rep2

city: Ithaca

first: Ji-Young

last: Lee

state: NY

address: Tower Rd.

institute: Boyce Thompson Institute

description: Gene expression data from mature endodermis of Arabidopsis seedling roots

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: Arabidopsis roots of 6 day old seedlings

label_protocol: Biotinylated cRNA was prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seedlings were grown vertically for 6 days at 22 degree under 16 hours of day and 8 hours of night.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH)

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh in two rows. About 1cm long root tips were harvested and placed in the protoplast solution as described in Birnbaum et al. (2005) Nat. Methods. GFP expressing protoplasts  were isolated from Fluorescence Activated Cell Sorter to collect total RNA.

tag: tissue

value: endodermis

tag: genotype

value: wild type columbia

tag: age

value: 6 day old seedlings


title: mature endodermis, biologlcal rep1

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: rhesus hippocampal CA1, 20.25 years old, replicate 7


title: rhesus hippocampal CA1, 24.75 years old, replicate 10


title: rhesus hippocampal CA1, 23.25 years old, replicate 3


title: rhesus hippocampal CA1, 6.50 years old, replicate 9


title: rhesus hippocampal CA1, 25.00 years old, replicate 2


title: rhesus hippocampal CA1, 24.25 years old, replicate 6


title: AdeLacZ treated-rep3

city: Cleveland

first: Pallavi

last: Bhattaram

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Beadstudio 2.1

source_name: AdeLacZ treated

label_protocol: cRNA labeled with Biotin was synthesized according to direct hybridization assay protocol from Illumina

growth_protocol: Primary limb bud cells were isolated from E11.5 mouse embryos and cultured for 6h before treatment

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: Primary limb bud cells  were left untreated, or  were treated with LacZ or Cre expressing adenovirus for 24h

tag: source tissue

value: Forelimb and hindlimb buds

tag: cell type

value: Primary limb bud cells

tag: developmental stage

value: embyonic day 11.5

value: AdeLacZ treated control


title: AdeLacZ treated-rep1


title: AdeCre treated-rep3

source_name: AdeCre treated

value: AdeCre treated mutant


title: Untreated-rep2

source_name: Untreated

value: Wild type


title: rhesus hippocampal DG, 7.75 years old, replicate 5


title: AdeCre treated-rep2


title: Untreated-rep1


title: mature endodermis, biologlcal rep3


title: AdeLacZ treated-rep2


title: AdeCre treated-rep1


title: Virgin, luminal, replicate 3

status: Public on Apr 10 2010

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Virgin, luminal, replicate 3

hyb_protocol: Complementary RNA (1.5 µg) was hybridised to Illumina MouseWG-6 V2 BeadChips.

scan_protocol: After washing, chips were with Cy3 and scanned in an Illumina BeadArray Reader.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normalized using the neqc function (which does normexp background correction and quantile normalisation using control probes) with offset 50.

source_name: FACS sorted mammary cell subpopulation

label_protocol: Up to 250 ng of RNA was labelled with the standard Total Prep RNA amplification kit (Ambion)

extract_protocol: Total RNA was isolated from the MaSC-enriched population (CD29hiCD24+) and luminal cells population (CD29loCD24+) sorted at > 90% purity using the miRNeasy Mini kit (Qiagen) and the DNA-free Kit (Ambion). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

tag: gender

value: female

tag: cell subpopulation

value: luminal

tag: pregnancy status

value: Virgin

tag: beadchip barcode

tag: beadchip section

value: C


title: 12.5 dP, luminal, replicate 3

description: 12.5 dP, luminal, replicate 3

value: Pregnant

value: B


title: Virgin, MaSC-enriched, replicate 3

description: Virgin, MaSC-enriched, replicate 3

value: MaSc-enriched


title: 12.5 dP, luminal, replicate 4

description: 12.5 dP, luminal, replicate 4

value: E


title: 12.5 dP, MaSC-enriched, replicate 2

description: 12.5 dP, MaSC-enriched, replicate 2


title: 12.5 dP, MaSC-enriched, replicate 1

description: 12.5 dP, MaSC-enriched, replicate 1


title: Virgin, MaSC-enriched, replicate 2

description: Virgin, MaSC-enriched, replicate 2


title: Virgin, luminal, replicate 2

description: Virgin, luminal, replicate 2

value: A


title: 12.5 dP, luminal, replicate 2

description: 12.5 dP, luminal, replicate 2


title: Virgin, MaSC-enriched, replicate 1

description: Virgin, MaSC-enriched, replicate 1


title: 12.5 dP, luminal, replicate 1

description: 12.5 dP, luminal, replicate 1

value: D


title: 12.5 dP, MaSC-enriched, replicate 4

description: 12.5 dP, MaSC-enriched, replicate 4

value: F


title: 12.5 dP, MaSC-enriched, replicate 3

description: 12.5 dP, MaSC-enriched, replicate 3


title: Control, Luminal, technical replicate of replicate 1

value: Luminal

tag: mouse type

value: control

tag: mouse pool (biological replicate)


title: Virgin, luminal, replicate 1

description: Virgin, luminal, replicate 1


title: Ovx, Luminal, techinical replicate of replicate 1

value: OVX


title: Ovx, Luminal, replicate 2

description: Ovx, Luminal, replicate 2


title: Ovx, MaSC-enriched, replicate 2

description: Ovx, MaSC-enriched, replicate 2

value: MaSC-enriched


title: Control, MaSC-enriched, replicate 2

description: Control, MaSC-enriched, replicate 2


title: Control, Luminal, replicate 2

description: Control, Luminal, replicate 2


title: Control, MaSC-enriched, technical replicate of replicate 2


title: Control, MaSC-enriched, replicate 1

description: Control, MaSC-enriched, replicate 1


title: Ovx, Luminal, replicate 1

description: Ovx, Luminal, replicate 1


title: rhesus hippocampal DG, 7.25 years old, replicate 12


title: Control, Luminal, replicate 1

description: Control, Luminal, replicate 1


title: rhesus hippocampal CA1, 6.50 years old, replicate 8


title: interstitial stromal cells (PC-D10)

city: kent

first: Gail

middle: C

last: Fraizer

address: 251 Cunningham Hall

department: Biological Sciences

institute: Kent State University

description: Gene Expression data from LCM captured prostate cancer interstitial stormal cells (PC-D10), same tumor as  A14

hyb_protocol: Following fragmentation, 10 ug of biotin labeled cRNA was  hybridized for 16 hr at 45C to Affymetrix Human Genome U133A 2.0 chips (HG_U133A 2.0)  according to the Affymetrix GeneChip Expression Analysis Technical Manual (2004).  The hybridized arrays were washed and stained in the Affymetrix Fluidics Station 400 using the Midi_euk2v3 labeling kit for detection by scanning.

scan_protocol: The U133A 2.0 chips were scanned using an Affymetrix® GeneChip® scanner 3000. The signal intensities were normalized to the spike-controls located on the array chip. Platform used was GPL571.

data_processing: The data were analyzed with GeneChip Operating System 1.1 using the MAS 5.0 algorithm, with  Affymetrix default analysis settings and global scaling as normalization method, and using the default normalization target setting of 500.

source_name: interstitial stormal cells,captured by LCM

label_protocol: The total amplified cDNA was biotin labeled as recommended by the Affymetrix GeneChip Expression Analysis Technical Manual (2004).

extract_protocol: The cells captured by the LCM were lysed and RNA extracted as per manufacturer’s recommendations for Pico Pure RNA isolation kit (Arcturus Bioscience, Molecular Devices). After treatment with DNase, the RNA quantity and quality were checked using the Agilent RNA Pico-Chip on the Bioanalyzer 2100 (Agilent Bioscience, Mt View, CA).  RNA quality was measured by 18s/28s ratio and degraded RNA samples were omitted. 1 ng of RNA was amplified using the RiboAmp HS kit (Arcturus Bioscience, Molecular Devices) in two-rounds of linear amplification of RNA.

treatment_protocol: Frozen sections were stained and dehydrated as recommended by manufacturer of the HistoGene LCM staining kit (Arcturus Bioscience, Molecular Devices). The slide was dehydrated through increasing concentrations of Ethanol and Xylene then placed in the Laser Capture Microscope (Arcturus Auto Pix). Areas of the slide with the most abundant glandular epithelial cells were identified and a Cap-Sure HS LCM cap (Molecular Devices) was aligned over the tissue.  Microscopy was performed to verify cells were removed from sections and retained on the cap. After isolating the epithelial cells then the same marked slide was aligned for additional collection of interstitial stromal cells . Cell capture and lysis was completed within 2 hours to maintain quality RNA

value: interstitial stromal cells

tag: disease state

value: Prostatic adenocarcinoma

tag: gleason score

value: Gleason (3+4)

tag: age(yrs)

tag: other

value: same tumor as A14


title: interstitial stromal cells (PC-B10)

description: Gene Expression data from LCM captured prostate cancer interstitial stormal cells (PC-B10), same tumor as  A6.

tag: tissue

value: Gleason (3+3)

value: same tumor as A6


title: epithelial cells (PC-A14)

description: Gene Expression data from LCM captured prostate cancer epithelial cells (PC-A14), same tumor as  D10

source_name: Epithelial cells, captured by LCM

value: epithelial cells

value: same tumor as D10


title: epithelial cells (PC-A6)

description: Gene Expression data from LCM captured prostate cancer epithelial cells (PC-A6), same tumor as  B10.

value: same tumor as B10


title: interstitial stromal cells (PC-D9)

description: Gene Expression data from LCM captured prostate cancer interstitial stormal cells (PC-D9), same tumor as  A5

value: same tumor as A5


title: 30 minute acclimation response - replicate 2

status: Public on Apr 09 2010

city: Durham

first: John

middle: G

last: Rowland

address: South Road

department: Biological & Biomedical Sciences

institute: Durham University

description: Biological replicate 2 of 4.

hyb_protocol: cDNA in hybridisation buffer was put onto the microarray slide, sealed with a coverslip and placed in a hybridisation chamber containing 75ul of 2x SSC. Hybridisation was performed at 65C for 16hours. Following hybridisation, microarray slides were washed briefly in 2x SSC to remove the coverslip. Microarrays were then washed in 2x SSC for 10 minutes at 60C followed by washing in 0.2x SSC with 0.2% SDS. This was followed by washing twice in 0.2x SSC for 5 minutes at room temperature, rinsed briefly in high-purity water and dried using compressed air. Dried microarrays were stored in the dark prior to imaging.

scan_protocol: Images were acquired with a GMS418 array scanner (Affymetrix, www.affymetrix.com) and quantified using ImaGene V. 5.5 software (BioDiscovery, www.biodiscovery.com)

data_processing:
ImaGene Version 5.5 (www.biodiscovery.com) was used for data processing. Spot signal intensity was determined after local background subtraction and normalised based on total signal intensity of all genes on the array except for genes encoding rRNAs.
Normalization method: Total intensity normalization
Additional data processing/filtering: Average ratios generated for replicated spots. Data from biological replicates averaged to give average fold-change in expression. Differential expression defined as a greater than 2-fold change (ratios of >=2.0 for up-regulation and <=0.5 for down-regulation).

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep2

label_protocol: CyeDye-labelled cDNA was synthesised, samples combined and purified using a MMLV RNA fluorescent labelling kit (TaKaRa Bio). cDNA was dried before being resuspended in 25ul of Hybridisation Buffer (6x SSC, 5x Denhardt's solution, 0.2% SDS, 0.1mg/ml salmon sperm DNA). Samples were incubated at 95C for 2 minutes, cooled briefly on ice and centrifuged at 16,000g for 10 minutes to remove particulates.

growth_protocol: Grown at 25C, BG-11 medium, continuous illumination, bubbled with 1% CO2 in air.

extract_protocol: For each sample, a 50ml aliquot of culture was mixed with an equal volume of ice-cold 5% phenol in ethanol to prevent cellular metabolic processes. Cells were centrifuged at 4,000g for 5 min at 4°C and resuspended in an additional volume of fresh ice-cold 5% phenol in ethanol. After further centrifugation the pellets were immediately frozen and stored at -80°C prior to RNA extraction. Cell pellets were resuspended in 500ul of resuspension buffer (50mM Tris-HCl, 5mM EDTA, 0.5% SDS in Nuclease-free water). Acid phenol (500ul phenol, pH8.0 and 50ul 3M Sodium Acetate, pH4.0) was added and the mixture incubated at 65°C for 10-20 minutes with vortexing at 2-minute intervals. Samples were centrifuged at 16,000g for 5 minutes and the aqueous phase recovered. This was then extracted twice in an equal volume of phenol:chloroform:isoamylalcohol (25:24:1), followed by chloroform:isoamylalcohol (24:1) extraction and recovery of the aqueous phase. Nucleic acid was precipitated by the addition of a one-tenth volume of 3M Sodium Acetate, pH 4.0 and 2.5 volumes of ice-cold ethanol, incubated at -20C for 30 minutes. Nucleic acids were then pelleted by centrifugation at 16,000g for 10 minutes at -20C and the supernatant discarded. Nucleic acids were then resuspended in 200ul of DNaseI reaction buffer and 10 units of DNaseI added. Samples were incubated at 37C for 30 minutes, after which 80ul of 0.5mg/ml Protease K in 0.5% SDS was added and incubated at 37C for 30 minutes. RNA was extracted by phenol:chloroform:isoamylalcohol extraction and precipitated as before. RNA pellets were air-dried and resuspended in 50 - 100 ul nuclease-free water.

treatment_protocol: Transfer of culture to growth at 38C. Sampled over time.

tag: strain

value: Wild-type

source_name: Synechocystis WT, Thermal Acclimation Series, 30 mins - Rep2


title: 30 minute acclimation response - replicate 3

description: Biological replicate 3 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep3

source_name: Synechocystis WT, Thermal Acclimation Series, 30 mins - Rep3


title: 30 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep4

source_name: Synechocystis WT, Thermal Acclimation Series, 30 mins - Rep4


title: 60 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 60 mins - Rep4


title: epithelial cells (PC-A5)

description: Gene Expression data from LCM captured prostate cancer epithelial cells (PC-A5), same tumor as  D9.

value: same tumor as D9


title: 10 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 10 mins - Rep4


title: 30 minute acclimation response - replicate 1

description: Biological replicate 1 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep1

source_name: Synechocystis WT, Thermal Acclimation Series, 30 mins - Rep1


title: 20 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 20 mins - Rep4


title: 60 minute acclimation response - replicate 3

description: Biological replicate 3 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 60 mins - Rep3


title: HeLa_Pol3ChIParray_rep1 Slide 4

status: Public on Apr 14 2010

city: Bethesda

first: Andrew

middle: J

last: Oler

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 4 of 10

hyb_protocol: ChIP array hybridization and wash were carried out according the Agilent Technologies Mammalian ChIP-on-chip protocol version 10.0 (www.Agilent.com).

scan_protocol: Arrays were scanned with Agilent Technologies’ Scanner C (Cat. G2505C).

data_processing: Feature Extraction was performed with Agilent Technologies FE version 10.1.1.22 using the default ChIP settings.  Arrays were analyzed using DNA Analytics’ ChIP-chip analysis module (Agilent) and bound regions for all ten arrays were determined using the default analysis settings.  Briefly, default Feature Extraction (FE) output was used for normalization and the FE Error Model was used for Error Modeling.  Enriched regions were determined using the Whitehead Per Array Neighbourhood Model.  A probe is considered bound based on the average intensity of itself and 2 of its neighbors.  In this model, the average must pass a p-value cutoff of 0.0001 and either the central probe and a neighbor must pass p-value cutoffs of  0.0001 and 0.01, respectively, or a single neighbor has to pass a p-value cutoff of 0.005.

source_name: HeLa S3

label_protocol: ChIP, amplification and labeling were carried out according the Agilent Technologies Mammalian ChIP-on-chip protocol version 10.0 (www.Agilent.com).

growth_protocol: HeLa S3 cells were cultured and harvested by Biovest International according to standard protocols.  Briefly, cells were grown in Joklik's modified MEM in suspension flasks with 5% newborn calf serum and harvested at mid log phase (about 0.5-0.65 x 10^6/ml).

extract_protocol: Crosslinked Hela cells (Biovest International), were used to perform Chromatin Immunoprecipitation for RPC32 (Santa Cruz Biotechnology cat # SC-21754).

value: HeLa S3, ATCC CCL-2.2

tag: cell line

tag: chip antibody

value: RPC32 (Pol III), sc-21754


title: 60 minute acclimation response - replicate 1

description: Biological replicate 1 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 60 mins - Rep1


title: HeLa_Pol3ChIParray_rep1 Slide 2

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 2 of 10


title: 120 minute acclimation response - replicate 3

description: Biological replicate 3 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 120 mins - Rep3


title: Ovx, MaSC-enriched, technical replicate of replicate 2

source_name: FACS sorted mammary cell subpopulation

value: female

value: B


title: 120 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 120 mins - Rep4


title: 120 minute acclimation response - replicate 1

description: Biological replicate 1 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 120 mins - Rep1


title: 120 minute acclimation response - replicate 2

description: Biological replicate 2 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep2

source_name: Synechocystis WT, Thermal Acclimation Series, 120 mins - Rep2


title: HeLa_Pol3ChIParray_rep1 Slide 8

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 8 of 10


title: HeLa_Pol3ChIParray_rep1 Slide 9

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 9 of 10


title: 240 minute acclimation response - replicate 1

description: Biological replicate 1 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 240 mins - Rep1


title: 240 minute acclimation response - replicate 2

description: Biological replicate 2 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 240 mins - Rep2


title: 240 minute acclimation response - replicate 3

description: Biological replicate 3 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep3

source_name: Synechocystis WT, Thermal Acclimation Series, 240 mins - Rep3


title: 480 minute acclimation response - replicate 2

description: Biological replicate 2 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 480 mins - Rep2


title: 480 minute acclimation response - replicate 3

description: Biological replicate 3 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 480 mins - Rep3


title: 480 minute acclimation response - replicate 1

description: Biological replicate 1 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep1

source_name: Synechocystis WT, Thermal Acclimation Series, 480 mins - Rep1


title: 480 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep4

source_name: Synechocystis WT, Thermal Acclimation Series, 480 mins - Rep4


title: HeLa_Pol3ChIParray_rep1 Slide 1

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 1 of 10

source_name: HeLa S3


title: HeLa_Pol3ChIParray_rep1 Slide 5

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 5 of 10


title: HeLa_Pol3ChIParray_rep1 Slide 7

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 7 of 10


title: HeLa_Pol3ChIParray_rep1 Slide 3

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 3 of 10


title: HeLa_Pol3ChIParray_rep1 Slide 6

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 6 of 10


title: Control siRNA/c-myc null Rat-1 (15.19)-4

status: Public on Apr 07 2010

city: New York

first: Kevin

last: O'Donovan

address: 1230 York Avenue

institute: Rockefeller Univeristy

description: Gene expresion data from Control siRNA-treated Rat-1 (15.19) cells 3 hours following release from mitotic (nocodazole) block

hyb_protocol: The biotinylated cRNA targets are were cleaned up, fragmented, and hybridized to GeneChip expression arrays according to standard Affymetrix protocols

scan_protocol: Gene chips were scanned using the GeneArray® Scanner from Affymetrix

data_processing: The data were normalized using MAS5.0 and analyzed using GenespringGX 4.0

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion protocol from 6 ug total RNA (MessageAmp RNA Amplification Kits)

growth_protocol: Cells were grown in DMEM/10% FBS/Pen-Strep

extract_protocol: Rat-1 cells were washed twice with PBS and RNA was harvested directly using the RLT buffer from the Rneasy kit from Qiagen

treatment_protocol: Cells were treated with cdr2 or control siRNAs 48 hours prior to synchronization in mitosis. Cells were synchronized by incubating in 2mM thymidine for 18 hours followed by washout for 3 hours then addition of 0.8uM nocodazole for 12 hours. RNA was harvested 3 hours after release from a mitotic block.

value: Rat-1 fibroblast cell line 15.19

tag: genotype/variation

value: c-myc null

tag: protocol

value: control


title: cdr2 siRNA/c-myc null Rat-1 (15.19)-1

description: Gene expresion data from cdr2 siRNA siRNA-treated Rat-1 (15.19) cells 3 hours following release from mitotic (nocodazole) block

value: siRNA-mediated cdr2 knockdown


title: cdr2 siRNA/c-myc null Rat-1 (15.19)-3

source_name: cdr2 siRNA siRNA-treated Rat-1 (15.19) cells 3 hours following release from mitotic (nocodazole) block


title: cdr2 siRNA/c-myc null Rat-1 (15.19)-4


title: Control siRNA/c-myc null Rat-1 (15.19)-2

source_name: Control siRNA-treated Rat-1 (15.19) cells 3 hours following release from mitotic (nocodazole) block


title: Ovx, MaSC-enriched, replicate 1

description: Ovx, MaSC-enriched, replicate 1

source_name: FACS sorted mammary cell subpopulation

tag: gender

value: MaSC-enriched

value: OVX

value: D


title: cdr2 siRNA/c-myc null Rat-1 (15.19)-2


title: Control siRNA/c-myc null Rat-1 (15.19)-3


title: cdr2 siRNA/WT Rat-1 (TGR)-2

description: Gene expresion data from cdr2 siRNA siRNA-treated Rat-1 (TGR) cells 3 hours following release from mitotic (nocodazole) block

value: Rat-1 fibroblast cell line TGR

value: c-myc wild type


title: cdr2 siRNA/WT Rat-1 (TGR)-3

source_name: cdr2 siRNA siRNA-treated Rat-1 (TGR) cells 3 hours following release from mitotic (nocodazole) block


title: Control siRNA/c-myc null Rat-1 (15.19)-1


title: cdr2 siRNA/WT Rat-1 (TGR)-4


title: Control siRNA/WT Rat-1 (TGR)-4

description: Gene expresion data from Control siRNA-treated Rat-1 (TGR) cells 3 hours following release from mitotic (nocodazole) block


title: cdr2 siRNA/WT Rat-1 (TGR)-1


title: Control siRNA/WT Rat-1 (TGR)-3

source_name: Control siRNA-treated Rat-1 (TGR) cells 3 hours following release from mitotic (nocodazole) block


title: FB-bCat-prom1-replicate1

status: Public on Apr 01 2010

city: Bronx

first: Herb

last: Lachman

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

hyb_protocol: Hybridize protocol according to Nimblegen manufacturer protocol.

scan_protocol: Arrays were scanned on the Agilent Scanner according to manufacturer protocol.

data_processing: Nimblescan 2.4 software was used for peak finding ('peaks_mapToFeatures.txt' supplementary files) and data processing was based on standard protocols. Values represent scaled log2 ratio, which is the ratio of the input signals for the experimental (IP) and control (input) samples co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Centering is performed by subtracting the bi-weight mean for the log-ratio values for all features on the array from each log-ratio value.

source_name: b-Catenin ChIP DNA from human fetal brain tissue

label_protocol: Label protocol according Nimblegen manufacturer protocol.

extract_protocol: Fetal brain tissue was chopped on a cold clean suface into small pieces and added to 10mls of Dulbecco's Eagle Medium. Formaldehyde was added at a final of 1%. Sample was rotated at room temperature for 15 minutes. Crosslinking stopped with glycine at a final concentration of 0.125M and rotated at room temperature for 5 minutes. Samples were centrifuged at 1,200rpm for 5 minutes and washes twice with cold 1X PBS. Tissues was disaggegrated with a dounce homogenizer and lysed with three different lysis buffers. Lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes and centrifuged. Lysis buffer 2 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl pH8, 200mM NaCl; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes, rotated for 5 minutes, and centrifuged. Lysis buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl; fresh protease inhibitor cocktail mix 1:100) vortexed and pipetted sample. Crosslinked sample was sheared at average size of 500bp for 9 1/2 minutes, 30 second pulse on and 15 second pulse off at a 40% amplitude using a Sonicator. Lysate was centrifuged.

value: Brain

value: Female

value: Anti-b-Catenin (Upstate cell signaling solutions, Catalog #06-734, Lot# 32480)

source_name: Input DNA from human fetal brain tissue


title: FB-bCat-prom1-replicate2


title: Cdr2 siRNA-HeLa-1

description: Gene expresion data from cdr2 siRNA siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block

source_name: cdr2 siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block

extract_protocol: HeLa cells were washed twice with PBS and RNA was harvested directly using the RLT buffer from the Rneasy kit from Qiagen

value: HeLa cell-cervical carcinoma


title: Control siRNA/WT Rat-1 (TGR)-2


title: Control siRNA-HeLa-3

description: Gene expresion data from Control siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block


title: Control siRNA/WT Rat-1 (TGR)-1


title: E10.5 Magoh mutant cortex, biological rep 4

status: Public on Apr 04 2010

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

hyb_protocol: Labelled and fragmented cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST chips overnight. The chips were washed and stained by the Affymetrix Fluidics Station.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were caluculated using Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software. RMA normalziation was performed to generate the CHP files. Genesifter software and Pairwise comparisons were perfomed with Benjamini and Hochberg correction.

source_name: Magoh-Mos2 heterozygous E10.5 cortices

label_protocol: Per RNA labeling, 300 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chip

growth_protocol: E10.5 embyros were harvested from pregnant females and cortices (pair per embyro) were carefully dissected and placed on ice

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

treatment_protocol: Lysates were gently homogenized in cold PBS and then Trizol and frozen at -80C

value: embryonic brain cortex

tag: genotype

value: Magoh

tag: genetic background

tag: age


title: E10.5 Magoh mutant cortex, biological rep 1


title: Cdr2 siRNA-HeLa-2


title: E10.5 wild-type cortex, biological rep 2

source_name: C57BL/6 E10.5 cortices

value: wild type


title: E10.5 Magoh mutant cortex, biological rep 3


title: E10.5 wild-type cortex, biological rep 3


title: Control siRNA-HeLa-1

source_name: Control siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block


title: Control siRNA-HeLa-2


title: E10.5 wild-type cortex, biological rep 5


title: E10.5 wild-type cortex, biological rep 4


title: E10.5 Magoh mutant cortex, biological rep 5


title: E10.5 wild-type cortex, biological rep 1


title: mp53 + IR, biological replicate 2

city: New Haven

first: Tanya

last: Bondar

state: CT

address: 300 Cedar str TAC S660

institute: Yale University

description: mp53 + IR, biological replicate 2

hyb_protocol: 1.5 ug of cRNA were hybridized to Illumina Mouse-6 Expression BeadChip v1.1 by standard Illumina protocol

scan_protocol: standard Illumina protocol

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

source_name: mp53 + IR

label_protocol: biotin label was incorporated by in vitro transcription during the second round of RNA amplification

extract_protocol: Total RNA was isolated from 200 sorted cells by standard Trizol protocol (Invitrogen) with addition of glycogen, then amplified using RiboAmpHS kit (from Arcturus)

tag: cell type

value: R26-mp53 (fully recombined)

tag: competitive status

value: no competition

tag: treatment

value: irradiated


title: mp53 (mosaic) + IR, biological replicate 2

source_name: mp53 (mosaic) + IR

value: R26-mp53 (mosaic)

value: winner


title: mp53 (mosaic), biological replicate 2

description: mp53 (mosaic), biological replicate 2

source_name: mp53 (mosaic)


title: WT (mosaic) + IR, biological replicate 2

source_name: WT (mosaic) + IR

value: WT (mosaic)

value: loser


title: WT + IR, biological replicate 2

description: WT + IR, biological replicate 2

source_name: WT + IR

value: WT


title: mp53 (mosaic) + IR, biological replicate 1


title: WT (mosaic), biological replicate 2

description: WT (mosaic), biological replicate 2

source_name: WT (mosaic)


title: Ppu_Soil_3CBminus

first: yong

last: wang

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

institute: National Institute for Agro-Environmental Sciences

description: This sample is the soil culture of Pseudomonas putida KT2440/pSL1 in the absence of 3-chlorobenzoate.

hyb_protocol: Hybridization was performed by Roche Inc., Tokyo, Japan, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche Inc., Tokyo, Japan, 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.).

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida KT2440/pSL1 at the absence of 3CB

label_protocol: Labeling was performed by Roche Inc., Tokyo, Japan, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Pseudomonas putida KT2440/pSL1 was inoculated from a glycerol stock to a LB agar plate with kanamycin (50 µg/ml), and incubated at 30°C overnight. Then this strain was subcultured overnight in LB medium with kanamycin (50 µg/ml) at 28°C. One ml of this liquid culture (OD600 = 1.0) was centrifuged to collect cells. After washing twice with 10 mM Na2HPO4/NaH2PO4 buffer (pH 6.8), cells were resuspended and diluted 10-fold. For RNA extraction, 0.2 ml of the diluted bacteria suspension were mixed with 1.8 g sterilized soil in 15-ml tubes, to which 3-chlorobenzoate (3CB) was added at a final concentration of 250 ppm in the case of 3CB+ samples. To ensure a homogeneous distribution of 3CB in the soil, 3CB was first mixed with Celite® powder (Wako, Osaka, Japan) as previously described (Morimoto et al. Microbes Environ. 20(3): 151-159.). The soil culture of the bacteria was incubated at 30ºC for 24 h (3CB- samples) or 48 h (3CB+ samples).

extract_protocol: Firstly, total RNA was extracted from soil using a RNA PowerSoil Total RNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instruction with a modification, in which a centrifugation (2,500 g for 10 min at room temperature) was conducted between the cell lysis and the phenol extraction to separate cell lysate from soil. Then, purification using a MicroSpin S-400 HR spin column (GE Healthcare, Little Chalfont, UK), DNase digestion using a TURBO DNA-free DNase (Ambion, Austin, TX) and concentration using a RNeasy Mini Kit column (Qiagen, Valencia, CA) were conducted as described previously (Wang et al. J Appl Microbiol 107:1168-1177). Finally, the RNA fractions were further concentrated by ethanol precipitation to reach a high concentration (1 μg/μl) for microarray analysis. The concentration of RNA was determined using a Nanodrop system (Nanodrop, Wilmington, DE). The integrity of RNA was assessed by agarose gel electrophoresis, and by the 23S/16S ratio on an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA) conducted at Roche Inc., Tokyo, Japan.

value: KT2440 strain containing an introduced plasmid, pSL1

tag: phenotype

value: Degrade 3CB completely

tag: accession


title: Control

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: untreated Y79 cells (control)

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45 mL sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 1 min at RT to dry the slides completely.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software. Recommended Percentile Shift Normalization and samples normalized with respect to control samples. Significant miRNA’S up and down regulated showing one fold and above among the groups was identified. Differentially regulated miRNA were clustered using hierarchical clustering to identify significant expression patterns. Using GeneSpring software miRNA targets was identified.

source_name: untreated Y79 cells (control)

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vaccum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Total RNA extracted using using mirVana miRNA Isolation kit (Ambion, AM1560) following manufacturer's instructions

treatment_protocol: Y79 cells were treated with 20uM curcumin for 48hrs.

value: Y79 retinoblastoma cells


title: mp53 + IR, biological replicate 1

description: mp53 + IR, biological replicate 1


title: mp53 (mosaic), biological replicate 1

description: mp53 (mosaic), biological replicate 1


title: WT + IR, biological replicate 1

description: WT + IR, biological replicate 1


title: WT (mosaic) + IR, biological replicate 1


title: Ppu_Soil_3CBplus

description: This sample is the soil culture of Pseudomonas putida KT2440/pSL1 in the presence of 3-chlorobenzoate.

source_name: Pseudomonas putida KT2440/pSL1 at the presence of 3CB


title: Treated 1

description: curcumin treated Y79 cells

source_name: curcumin treated Y79 cells


title: RORalpha1delDE, 2

city: St Lucia

first: Michael

middle: Andrew

last: Pearen

state: Queensland

address: The University of Queensland

institute: Institute for Molecular Bioscience

description:
Transgenic mice contained a truncated version of human RORalpha1 (RORalpha1delDE) where the entire E region and part of the hinge/D region have been removed. This transgene is driven by a skeletal muscle specific human skeletal alpha-actin (HSA) promoter.
4068846001_E

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned with Illumina BeadStation Scanner.

data_processing: Data was compiled using BeadStudio v2.3.41 (Illumina). Normalized data was produced using GeneSpring GX version 11 via normalization to control genes, where control genes were represented by all genes with an Illumina detection score equal to one in at least three out of the six samples (7730 control genes in total).

source_name: quadriceps femoris

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Mice (backcrossed C57Bl/6J background) were housed in QBP vivarium (University of Queensland, St. Lucia, Queensland, Australia) with 12h light–dark cycle and fed a standard diet containing 4.6% total fat (from Specialty Feeds, Glen Forrest, Western Australia) and water provided ad libitum.

extract_protocol: Mice were overnight fasted and then sacrificed at 9:00AM in the morning. RNA was extracted from snap frozen quadriceps femoris with tri-reagent (Sigma), followed by treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100.

tag: replicate


title: Treated 2

description: curcumin treated Y79 cells


title: WT (mosaic), biological replicate 1

description: WT (mosaic), biological replicate 1


title: RORalpha1delDE, 1

description:
Transgenic mice contained a truncated version of human RORalpha1 (RORalpha1delDE) where the entire E region and part of the hinge/D region have been removed. This transgene is driven by a skeletal muscle specific human skeletal alpha-actin (HSA) promoter.
4068846001_D


title: RORalpha1delDE, 3

description:
Transgenic mice contained a truncated version of human RORalpha1 (RORalpha1delDE) where the entire E region and part of the hinge/D region have been removed. This transgene is driven by a skeletal muscle specific human skeletal alpha-actin (HSA) promoter.
4068846001_F


title: Wild Type, 2

value: Wild Type


title: Wild Type, 3


title: Wild Type, 1


title: UAMS-1 (agr codY) stationary rep 2

city: Omaha

first: Paul

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

hyb_protocol: 1.5 micrograms (ug) of labeled total RNA was applied to an S. aureus Affymetrix GeneChip hybridized @ 45 degrees Celsius (C) for 16 hr in an Affymetrix hybridization oven.  The sample was then washed 60 times in non-stringent buffer (Wash A; 6X SSPE, 0.01% Tween-20) at 45C followed by 60 washes in stringent buffer (Wash B; 1X MES, 25 mM NaCl, 0.01% Tween-20) at 45 C in an Affymetrix Fluidics station (450).  The sample was then subjected to the following stains/wash steps: 1. 10 min of Stain 1 (1X MES, 1.2 mg BSA, 6 ug Streptavidin) at 25C, 2. 40 washes with Wash A, 3. 10 min of Stain 2 (1X MES, 1.2 mg BSA, 60 ug Goat-IgG, and 3 ug biotinylated antistreptavidin), 4. 10 min of Stain 3 (1X MES, 1.2 mg BSA, 6 ug Streptavidin-Phycoerythrin), 5. 60 washes with Wash A at 25C.

scan_protocol: The GeneChip was scanned in an Affymetrix 7G scanner, with manufacturer default settings.

data_processing: The raw signal intensity value and present/absent determinations were calculated based on Affymetrix MAS5 algorithm.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus total bacterial RNA

label_protocol: RNA was reverse transcribed, cDNA fragmented, 3’ biotinylated, mixed with exogenous labeled “spike-in” transcripts and hybridized to S. aureus GeneChips following the manufacturer’s recommendations for antisense prokaryotic arrays (Affymetrix, Santa Clara, CA).

growth_protocol: S. aureus colonies from tryptic soy agar plates were used to inoculate a 3-mL culture in tryptic soy broth (TSB). This flask and four additional 3-ml cultures with successive 100-fold dilutions of the initial inoculum were incubated overnight.  The next day, flasks were selected that contained cultures with an OD600 of 3-7, and used to inoculate fresh TSB to a starting OD600 of 0.05. After the bacteria reached an OD600 between 0.5 and 2, they were diluted again in fresh TSB to an OD600 of 0.05 to ensure that the experimental cultures were adapted to exponential growth phase. RNA was extracted from stationary phase samples (OD600 = 8-11).

extract_protocol: Twenty ml of cells were added to 20 ml ice cold acetone:ethanol (1:1) and stored at -80oC overnight. For RNA isolation, -80oC suspensions were thawed on ice and centrifuged at 5,000 X g at 4oC for 10 min.  The supernatant was removed, the cell pellet was resuspended in 1 ml ice cold TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0), and transferred to a pre-chilled lysing matrix B tube (Q-BIOgene, Irvine, CA).  Cells were lysed by shaking in an FP120 shaker (Q-BIOgene) two times at a setting of 4.5 for 20 s.  Suspensions were then centrifuged at 13,000 X g at 4oC for 10 min and the supernatant was used for RNA isolation with an RNeasy Mini column, following the manufacturer recommendations for on-the-column DNase treatment and RNA purification (Qiagen, Valencia, CA).

value: CM19 (UAMS-1 but agr- codY-)

tag: phase

value: stationary


title: UAMS-1 (agr codY) stationary rep 1


title: UAMS-1 (codY) stationary rep 2

value: MS1 (UAMS-1 but codY-)


title: UAMS-1 (agr) stationary rep 2

value: CM18 (UAMS-1 but agr-)


title: FB-bCat-prom2-replicate2

source_name: b-Catenin ChIP DNA from human fetal brain tissue

tag: tissue

value: Brain

value: Female

value: Anti-b-Catenin (Upstate cell signaling solutions, Catalog #06-734, Lot# 32480)

source_name: Input DNA from human fetal brain tissue


title: FB-bCat-prom2-replicate1


title: UAMS-1 (codY) stationary rep 1

tag: strain


title: UAMS-1 stationary rep 2


title: UAMS-1 (codY)exponential rep 2

growth_protocol: S. aureus colonies from tryptic soy agar plates were used to inoculate a 3-mL culture in tryptic soy broth (TSB). This flask and four additional 3-ml cultures with successive 100-fold dilutions of the initial inoculum were incubated overnight.  The next day, flasks were selected that contained cultures with an OD600 of 3-7, and used to inoculate fresh TSB to a starting OD600 of 0.05. After the bacteria reached an OD600 between 0.5 and 2, they were diluted again in fresh TSB to an OD600 of 0.05 to ensure that the experimental cultures were adapted to exponential growth phase. RNA was extracted from exponential phase samples (OD600 = 0.6-0.8).

value: exponential


title: UAMS-1 (agr) stationary rep 1


title: UAMS-1 stationary rep 1


title: UAMS-1 (codY) exponential rep 3


title: UAMS-1 (agr- codY-) exponential rep 2

source_name: Staphylcoccus aureus total bacterial RNA


title: UAMS-1 (agr) exponential rep 2


title: UAMS-1 (codY) exponential rep 1


title: UAMS-1 (agr- codY-) exponential rep 1


title: 240 minute acclimation response - replicate 4

description: Biological replicate 4 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep4

value: Wild-type

source_name: Synechocystis WT, Thermal Acclimation Series, 240 mins - Rep4


title: UAMS-1 (agr) exponential rep 1


title: Wild type exponential rep1


title: 60 minute acclimation response - replicate 2

description: Biological replicate 2 of 4.

source_name: Synechocystis WT, Thermal Acclimation Series, 0 mins - Rep2

source_name: Synechocystis WT, Thermal Acclimation Series, 60 mins - Rep2


title: Wild type exponential rep 2