title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_60mg/kg_3days_exp2720_rep3_12869

description:
HybID: 12869
treated sample for experiment (RepID) 2720
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM220247: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_60mg/kg_3days_exp2720_rep2_12868
Replicate experimental sample: GSM220246: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_60mg/kg_3days_exp2720_rep1_13758
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: 3 days


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_7days_exp2676_rep2_12862

status: Public on Mar 28 2008

type: RNA

city: Mountain View

first: Jeremy

last: Gollub

state: CA

address: 325 E. Middlefield Rd.

country: USA

institute: Iconix Biosciences

description:
HybID: 12862
treated sample for experiment (RepID) 2676
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM220239: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_7days_exp2676_rep3_12863
Replicate experimental sample: GSM220237: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_7days_exp2676_rep1_13755
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

label: biotin

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LIVER, 1-NAPHTHYL ISOTHIOCYANATE, 30mg/kg, 7 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

value: male

tag: tissue

value: LIVER

tag: treatment compound

value: 1-NAPHTHYL ISOTHIOCYANATE

tag: dose

value: 30 mg/kg

tag: solvent

value: CORN OIL

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 7 days

tag: experiment date


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep3_15099

description:
HybID: 15099
treated sample for experiment (RepID) 2675
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM220235: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep2_12860
Replicate experimental sample: GSM220234: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep1_12861
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, 1-NAPHTHYL ISOTHIOCYANATE, 30mg/kg, 3 days


title: WT 0.8 with CcpA 0.8 (164538)

city: Wageningen

first: Menno

middle: van der

last: Voort

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

hyb_protocol: One microgram target was denatured by boiling for 3 min and immediate cooling on ice prior to hybridization. The target was mixed at 68 °C with Ambion slidehyb #1 hybridization buffer (Ambion Europe Ltd., Huntingdon, UK). Hybridization buffer with the target was applied to the slide by use of a Lifterslip. The slide and Lifterslip were incubated for 16 h at 49°C, after which it was washed at 20°C for 5 min with low stringency buffer (2x SSC and 0.5% SDS) and 5 min with high stringengy buffer (1x SSC and 0.25% SDS. The slide was dried by centrifugation at 1500 rpm for 1 min, prior to scanning.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 100% laser intensity, and 10 micron scan resolution.

data_processing: Loewess-normalisation, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite. The VALUE column reports normalized, log10 (CcpA/wildtype) ratios.

molecule: total RNA

organism: Bacillus cereus ATCC 14579

source_name: Wildtype OD600 0.8

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total B. cereus RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007, PMID: 17416654, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=17416654

tag: wildtype strain harvested from BHI at mid-exponential growth (OD600 of 0.8)

source_name: CcpA OD600 0.8

tag: ccpA delelion strain harvested from BHI at mid-exponential growth (OD600 of 0.8)


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep1_12861

description:
HybID: 12861
treated sample for experiment (RepID) 2675
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM220235: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep2_12860
Replicate experimental sample: GSM220236: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_3days_exp2675_rep3_15099
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: WT 0.2 with CcpA 0.2 (164601)

source_name: wildtype OD600 0.2

tag: wildtype strain harvested from BHI at early exponential growth (OD600 of 0.2)

source_name: ccpA OD600 0.2

tag: ccpA deletion strain harvested from BHI at early exponential growth (OD600 of 0.2)


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep1_12857

description:
HybID: 12857
treated sample for experiment (RepID) 2680
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM220233: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep3_12858
Replicate experimental sample: GSM220232: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep2_12859
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, 1-NAPHTHYL ISOTHIOCYANATE, 30mg/kg, 1 days

value: 1 days


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep2_12859

description:
HybID: 12859
treated sample for experiment (RepID) 2680
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM220231: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep1_12857
Replicate experimental sample: GSM220233: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep3_12858
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep3_12858

description:
HybID: 12858
treated sample for experiment (RepID) 2680
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM220231: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep1_12857
Replicate experimental sample: GSM220232: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_1days_exp2680_rep2_12859
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: ccpA 8 with wildtype 8 (164480)

source_name: ccpA OD600 8

tag: ccpA deletion strain harvested from BHI at stationary growth phase (OD600 of 8)

source_name: wildtype OD600 8

tag: wildtype strain harvested from BHI at stationary growth phase (OD600 of 8)


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep2_12856

description:
HybID: 12856
treated sample for experiment (RepID) 2714
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM220230: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep3_12854
Replicate experimental sample: GSM220228: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep1_12855
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, 1-NAPHTHYL ISOTHIOCYANATE, 30mg/kg, .25 days

tag: Sprague-Dawley

value: .25 days


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep1_12855

description:
HybID: 12855
treated sample for experiment (RepID) 2714
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM220230: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep3_12854
Replicate experimental sample: GSM220229: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep2_12856
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

tag: age


title: ccpA 4 with wildtype 4 (164533)

source_name: ccpA OD600 4

tag: ccpA deletion strain harvested from BHI at transition growth phase (OD600 of 4)

source_name: wildtype OD600 4

tag: wildtype strain harvested from BHI at transition growth phase (OD600 of 4)


title: wildtype 8 with CcpA 8 (164479)


title: S48 G_SigE

status: Public on Mar 27 2008

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

description: Human THP1 Macrophages infected with SigE (Mtb mutant) vs. uninfected THP1 (biological replicate G)

hyb_protocol: For each microarray two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacturer's specifications.  Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG  Human 19K array and incubated overnight at 55 °C in a hybridization chamber (GeneMachines, San Carlos, CA).  In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and treated cells, respectively.  The second hybridization was carried out for 3 h at 65 °C in the hybridization chambers.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software.

data_processing: The images were processed using GenePix 5.1 and resulting text files were exported to Microsoft Excel and TMEV for further analysis

organism: Homo sapiens

source_name: uninfected THP1 cells (biological replicate G)

label_protocol: cDNAs were generated from 5 µg of total RNA per sample by reverse transcription (RT) for 2 h at42°C using the 3DNA SubmicroTM Oligo Expression Array detection kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA).

growth_protocol: The THP-1 human monocytic cell line was obtained from the ATCC.   Cells were grown in RPMI 1640 supplemented with 10% fetal calf serum (FCS), 0.45% glucose, 0.15% sodium pyruvate and 4mM L-glutamine.  Cultures were maintained at a density of 106cells/ml.  Ten 175cm2 flasks were seeded with 100 ml of 106THP-1 cells/ml.  THP-1 cells were differentiated with 40nM PMA (phorbol myristate acetate) overnight at 37°C, 5%CO2 and 95% humidity.

extract_protocol: After 24h of infection monolayer were disrupted with 1 ml of TRI reagent.  Samples were incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quagen).  The purified RNA was kept at -80°C until further use.

treatment_protocol: No infection was performed

tag: THP1 Macrophage

tag: infected with SigE (Mtb mutant)

source_name: THP1 Macrophages infected with with SigE (Mtb mutant) (biological replicate G)

extract_protocol: After 24h, the monolayer were disrupted with 1 ml of TRI reagent.  Samples were incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quagen).  The purified RNA was kept at -80°C until further use.

treatment_protocol: Mtb cultures were grown exponentially in the 7H9 liquid media to an OD of 0.2 (2x107 CFU/ml) for the infection.  An appropriate volume of this culture was suspended in RPMI with 20% FCS to obtain a bacterial suspension of 2x106 cfu/ml. 100ml of bacterial suspension were add to each flask  at multiplicity of infection (MOI) of 2.  Macrophages and bacteria were incubated for 2 h.  After incubation macrophages were washed with warm PBS (2 X, 50ml) and 100ml of RPMI +20% FCS were added to each flask.

tag: uninfected


title: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep3_12854

description:
HybID: 12854
treated sample for experiment (RepID) 2714
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM220228: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep1_12855
Replicate experimental sample: GSM220229: LIVER_1-NAPHTHYL_ISOTHIOCYANATE_30mg/kg_.25days_exp2714_rep2_12856
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

tag: sex

tag: tissue

tag: treatment compound

tag: dose

tag: solvent

tag: administration route


title: CcpA 0.8 with WT 0.8 (164602)

tag: ccpA deletion strain harvested from BHI at mid-exponential growth (OD600 of 0.8)

source_name: wildtype OD600 0.8

tag: wildtype strain harvested from BHI at mid-exponential growth (OD600 of 0.8)


title: CcpA 0.2 with WT 0.2 (164600)

source_name: CcpA OD600 0.2

tag: ccpA deletion strain harvested from BHI at early exponential growth (OD600 of 0.2)

tag: wildtype strain harvested from BHI at early exponential growth (OD600 of 0.2)


title: S45 F_Rv

description: Human THP1 Macrophages infected with Mtb H37Rv vs. uninfected THP1 (biological replicate F)

source_name: uninfected THP1 cells (biological replicate F)

tag: infected with Mtb H37Rv strain

source_name: THP1 Macrophages infected with H37Rv (biological replicate F)


title: WT 4 with ccpA 4 (164603)


title: S50 F_SigE

description: Human THP1 Macrophages infected with SigE (Mtb mutant) vs. uninfected THP1 (biological replicate F)

source_name: THP1 Macrophages infected with with SigE (Mtb mutant) (biological replicate F)


title: S24 E_SigE

description: Human THP1 Macrophages infected with SigE (Mtb mutant) vs. uninfected THP1 (biological replicate E)

source_name: uninfected THP1 cells (biological replicate E)

source_name: THP1 Macrophages infected with with SigE (Mtb mutant) (biological replicate E)


title: S27 B_Rv

description: Human THP1 Macrophages infected with Mtb H37Rv vs. uninfected THP1 (biological replicate B)

source_name: uninfected THP1 cells (biological replicate B)

source_name: THP1 Macrophages infected with H37Rv (biological replicate B)


title: S21 E_Rv

description: Human THP1 Macrophages infected with Mtb H37Rv vs. uninfected THP1 (biological replicate E)

source_name: THP1 Macrophages infected with H37Rv (biological replicate E)


title: sigE 24hrs after infection in macrophage rep 10S  vs. sigE grown in 7H9 media rep 10S

hyb_protocol: Slides were blocked prior to hybridization using BSA The purified DNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).  The probes were covered by a flat 22x22mm coverslip (Corning) and hybridized in sealed hybridization chambers (Genemachines) for sixteen hours in a 50°C water bath.

scan_protocol: The slides were scanned using an Axon 4000B scanner

data_processing: The images were processed using GenePix 5.1 and resulting text files were exported to Microsoft Excel

organism: Mycobacterium tuberculosis

source_name: sigE grown in 7H9 media

label_protocol: Total RNA was reversed transcribed into DNA using Superscript II RT in the presence of Cyanine-3 or Cyanine-5 dUTP (PerkinElmer) by a modification of the procedure described by Voskuil et. al. (Voskuil et. al, 2003).  This was accomplished using a reaction mix with a final concentration of 0.17ug/ul random hexamers (IDT), 0.96x first strand buffer (Invitrogen), 9.6mM DTT (Invitrogen), 0.44mM dATP, dCTP and dGTP (Invitrogen), 0.02mM dTTP (Invitrogen), 0.06mM Cyanine 3 or 5 dUTP (PerkinElmer) and 9.4units Superscript II (Invitrogen).  The combination of reaction mix and total RNA was incubated for ten minutes at 25°C followed by ninety minutes at 42°C.  The labeled DNA probes were then purified and concentrated using a Microcon YM10 filter (Millipore) and TE buffer pH 8.0 (Ambion).  Slides were blocked prior to hybridization using BSA The purified DNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).

growth_protocol: Bacterial stocks were maintained at -80?C in 7H9ADCTW (Middlebrook 7H9 (Difco) supplemented with 1x ADC [0•5% bovine serum albumin, fraction V (Boehringer Manheim), 0•2% glucose and 0•085% NULLCl], 0•2% glycerol and 0•1% Tween 80).   Aliquots of bacteria were thawed and cultured in solid media 7H10 ADCTW.   For preparation of liquid cultures bacteria growing in 7H10 agar plates were resuspended in 7H9ADCTW media at an OD: 0.05.  Liquid cultures were grown in plastic roller bottles in a roller apparatus until OD 0.2.

extract_protocol: Mtb RNA from in vitro cultures:  Bacterial cell pellets were resuspended in 1 ml TRI reagent  (Molecular Research Center,OH) and immediately transferred to a 2ml screw cap microcentrifuge tube with o-rings containing 0.5ml zirconia beads (0.1mm diameter, Biospec Products, Inc., OH).  Samples were disrupted by two 1-min pulses in a BeadBeater, keeping the samples on ice for 2 minutes in between the pulses.  The liquid was removed from the beads, incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quiagen).  The eluted RNA was kept at -80°C until further use.

tag: Mutant strain sigE

tag: Time

value: Control exponentially growing sigE in 7H9 media

source_name: sigE  24hrs after infection in macrophage (THP1)

extract_protocol: Macrophages infected with Mtb were lysed with 20 ml per 175 cm2 flask of guanidinium thiocyanate -based buffer (25 mM sodium citrate/4 M guanidine thiocyanate/0.5% N-lauryl sarcosine/0.125 M mercaptoethanol, 0.5% Tween 80, pH 7.0) and eukaryotic DNA was sheared by homogenization of the samples for 5 min with a Vertis homogenizer  (Vertis).  Samples were spin down for 30 min at 4,000xg and bacterial pellets were washed with 10 ml of guanidinium thiocyanate -based buffer and spin down for 15 min at 4,000xg.  Bacterial cell pellets were resuspended in 1 ml TRI reagent  (Molecular Research Center,OH) and immediately transferred to a 2ml screw cap microcentrifuge tube with o-rings containing 0.5ml zirconia beads (0.1mm diameter, Biospec Products, Inc., OH).  Samples were disrupted by two 1-min pulses in a BeadBeater, keeping the samples on ice for 2 minutes in between the pulses.  The liquid was removed from the beads, incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quiagen).  The eluted RNA was kept at -80°C until further use.

treatment_protocol: Ten 175cm2 flasks were seeded with 100 ml of 106 THP-1 cells/ml.  THP-1 cells were differentiated with 40 nMolar PMA (phorbol myristate acetate) overnight at 37°C, 5%CO2 and 95% humidity.  Mtb cultures were grown exponentially in the usual 7H9ADCTW to an OD of 0.2 for the infection.  An appropriate volume of this culture was resuspended in RPMI with 20% FCS to obtain a bacterial suspension of 2x106 cfu/ml.  One hundred milliliters of bacterial suspension were added to each flask (MOI: 2). Macrophages and bacteria were incubated for 2 h.  After incubation macrophages were washed with warm PBS and 100ml of RPMI +20% FCS were added to each flask.   Infections were followed for 24 hours and cells from five flasks were processed  for bacterial RNA extraction.

value: 24hrs after infection


title: S49 G_Rv

description: Human THP1 Macrophages infected with Mtb H37Rv vs. uninfected THP1 (biological replicate G)

source_name: THP1 Macrophages infected with H37Rv (biological replicate G)


title: S34 D_SigE

description: Human THP1 Macrophages infected with SigE (Mtb mutant) vs. uninfected THP1 (biological replicate D)

source_name: uninfected THP1 cells (biological replicate D)

source_name: THP1 Macrophages infected with with SigE (Mtb mutant) (biological replicate D)


title: S35 D_Rv

description: Human THP1 Macrophages infected with Mtb H37Rv vs. uninfected THP1 (biological replicate D)

source_name: THP1 Macrophages infected with H37Rv (biological replicate D)


title: sigE 24hrs after infection in macrophage rep 11S vs.H37Rv 24hrs after infection in macrophage  rep 11R

source_name: H37Rv 24hrs after infection in macrophage (THP1)

tag: Wild type strain H37Rv

source_name: sigE 24hrs after infection in macrophage (THP1)


title: sigE 24hrs after infection in macrophage rep 1S vs.H37Rv 24hrs after infection in macrophage  rep 1R


title: sigE 24hrs after infection in macrophage rep 2S  vs. sigE grown in 7H9 media rep 2S


title: sigE 24hrs after infection in macrophage rep 9S vs.H37Rv 24hrs after infection in macrophage  rep 9R


title: sigE 24hrs after infection in macrophage rep 8S  vs. sigE grown in 7H9 media rep 8S


title: sigE 24hrs after infection in macrophage rep 8S vs.H37Rv 24hrs after infection in macrophage  rep 8R


title: sigE 24hrs after infection in macrophage rep 11S  vs. sigE grown in 7H9 media rep 11S


title: sigE 24hrs after infection in macrophage rep 9S  vs. sigE grown in 7H9 media rep 9S


title: sigE maintained 2hs in RPMI media rep 2S vs. H37Rv maintained 2hs in RPMI media rep 2R

source_name: sigE maintained 2hs in RPMI

value: sigE maintained 2hs in RPMI

source_name: H37Rv maintained 2hs in RPMI

value: H37Rv maintained 2hs in RPMI


title: S32 B_SigE

description: Human THP1 Macrophages infected with SigE (Mtb mutant) vs. uninfected THP1 (biological replicate B)

tag: THP1 Macrophage

source_name: THP1 Macrophages infected with with SigE (Mtb mutant) (biological replicate B)


title: S66 H_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate H)

hyb_protocol: For each microarray two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacturer's specifications.  Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG  Mouse 22k array and incubated overnight at 55 °C in a hybridization chamber (GeneMachines, San Carlos, CA).  In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and treated cells, respectively.  The second hybridization was carried out for 3 h at 65 °C in the hybridization chambers.

organism: Mus musculus

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate H)

growth_protocol: Bone marrow cells were extracted from the femurs and tibiae of mice.  Red cells were removed with lysis solution (0.15M NH4Cl, 1mM KHCO3, 0.1mM EDTA). For BMMO, bone marrow cells were cultured in DMEM medium supplemented with 20% fetal bovine serum (FBS) and 25% supernatant derived from confluent L929 cell cultures. At day 7, immature macrophages were collected. This procedure yields a pure population of M-CSF-dependent, adherent macrophage.

treatment_protocol: 4x10^ 06 mouse BMM were seeded in 75 cm2 flasks. Cultures were infected with Mtb SigE mutant strains at a multiplicity of infection of 5.

tag: Bone Marrow Macrophage

tag: infected with SigE (Mtb mutant)

tag: No pre-treatment with IFN-gamma

source_name: BMMO treated with INF gamma and uninfected (biological replicate H)


title: S71 K_Rv

description: Mouse Bone Marrow Macrophages infected with Mtb H37Rv vs. uninfected BMMO (biological replicate K)

source_name: Mouse Bone Marrow Macrophages infected with Mtb H37Rv  (biological replicate K)

treatment_protocol: 4x10^ 06 mouse BMM were seeded in 75 cm2 flasks. Cultures were infected with Mtb H37Rv at a multiplicity of infection of 5.

tag: infected with Mtb H37Rv

tag: uninfected


title: sigE maintained 2hs in RPMI media rep 11S vs. H37Rv maintained 2hs in RPMI media rep 11R


title: sigE 24hrs after infection in macrophage rep 2S vs.H37Rv 24hrs after infection in macrophage  rep 2R


title: sigE 24hrs after infection in macrophage rep 10S vs.H37Rv 24hrs after infection in macrophage  rep 6R


title: sigE maintained 2hs in RPMI media rep 8S vs. H37Rv maintained 2hs in RPMI media rep 8R


title: S70 J_SigE

description: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate J)

source_name: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) (biological replicate J)


title: S67 I_Rv

description: Mouse Bone Marrow Macrophages infected with Mtb H37Rv vs. uninfected BMMO (biological replicate I)

source_name: Mouse Bone Marrow Macrophages infected with Mtb H37Rv  (biological replicate I)


title: sigE maintained 2hs in RPMI media rep 10S vs. H37Rv maintained 2hs in RPMI media rep 6R

description: sigE maintained 2hs in RPMI media rep 1 0S vs. H37Rv maintained 2hs in RPMI media rep 6R


title: sigE grown in 7H9 media rep 1S vs. H37Rv grown in 7H9 media rep 1R

source_name: H37Rv grown in 7H9 media

value: Control exponentially growing H37Rv in 7H9 media

value: Control exponentially growing sigE mutant in 7H9 media


title: S63 G_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate G)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate G)

tag: 48 h before infection cells  were treated with 100 U/ml IFN-gamma.

source_name: BMMO treated with INF gamma and uninfected  (biological replicate G)


title: sigE maintained 2hs in RPMI media rep 1S vs. H37Rv maintained 2hs in RPMI media rep 1R


title: sigE grown in 7H9 media rep 11S vs. H37Rv grown in 7H9 media rep 11R

source_name: sigE grown in 7H9 media


title: sigE maintained 2hs in RPMI media rep 9S vs. H37Rv maintained 2hs in RPMI media rep 9R


title: S68 I_SigE

description: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate I)

source_name: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) (biological replicate I)


title: Control 120 days sample 3

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from murine motor neurons

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430A GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: G93A non transgenic littermate 805

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
10 um lumbar spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each animal 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: Male mouse 120 day old


title: sigE grown in 7H9 media rep 10S vs. H37Rv grown in 7H9 media rep 6R


title: S64 G_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate G)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate G)

source_name: BMMO treated with INF gamma and uninfected (biological replicate G)


title: G93A 120 days sample 3

source_name: G93A mouse 802

tag: Transgenic male mouse 120 day old


title: S62 F_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate F)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate F)

source_name: BMMO treated with INF gamma and uninfected (biological replicate F)


title: sigE grown in 7H9 media rep 9S vs. H37Rv grown in 7H9 media rep 9R

source_name: H37Rv grown in 7H9 media rep 9R

source_name: sigE grown in 7H9 media rep 9S


title: S59 E_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate E)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate E)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate E)


title: G93A 120 days sample 2

source_name: G93A mouse 801


title: Control 120 days sample 2

source_name: G93A non transgenic littermate 803


title: S61 F_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate F)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate F)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate F)


title: S69 J_Rv

description: Mouse Bone Marrow Macrophages infected with Mtb H37Rv vs. uninfected BMMO (biological replicate J)

source_name: Mouse Bone Marrow Macrophages infected with Mtb H37Rv  (biological replicate J)


title: Control 120 days sample 1

source_name: G93A non transgenic littermate 800


title: sigE grown in 7H9 media rep 8S vs. H37Rv grown in 7H9 media rep 8R

source_name: sigE grown in 7H9 media rep 8S

source_name: H37Rv grown in 7H9 media rep 8R


title: Control 90 days sample 3

source_name: G93A non transgenic littermate 1424

tag: Male mouse 90 day old


title: S60 E_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate E)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate E)

source_name: BMMO treated with INF gamma and uninfected (biological replicate E)


title: S58 D_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate D)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate D)

source_name: BMMO treated with INF gamma and uninfected (biological replicate D)


title: S65 H_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate H)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate H)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate H)


title: S57 D_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate D)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate D)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate D)


title: G93A 120 days sample 1

source_name: G93A mouse 799


title: sigE grown in 7H9 media rep 2S vs. H37Rv grown in 7H9 media rep 2R

source_name: sigE grown in 7H9 media rep 2S

source_name: H37Rv grown in 7H9 media rep 2R


title: S56 C_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate C)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate C)

source_name: BMMO treated with INF gamma and uninfected (biological replicate C)


title: H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 4 (D 24hrs)

hyb_protocol: Slides were blocked prior to hybridization using BSA The purified cDNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).  The probes were covered by a flat 22x22mm coverslip (Corning) and hybridized in sealed hybridization chambers (Genemachines) for sixteen hours in a 50°C water bath.

source_name: H37Rv 24hrs after infection in macrophage (THP1)

label_protocol: Total RNA was reversed transcribed into cDNA using Superscript II RT in the presence of Cyanine-3 or Cyanine-5 dUTP (PerkinElmer) by a modification of the procedure described by Voskuil et. al. (Voskuil et. al, 2003).  This was accomplished using a reaction mix with a final concentration of 0.17ug/ul random hexamers (IDT), 0.96x first strand buffer (Invitrogen), 9.6mM DTT (Invitrogen), 0.44mM dATP, dCTP and dGTP (Invitrogen), 0.02mM dTTP (Invitrogen), 0.06mM Cyanine 3 or 5 dUTP (PerkinElmer) and 9.4units Superscript II (Invitrogen).  The combination of reaction mix and total RNA was incubated for ten minutes at 25°C followed by ninety minutes at 42°C.  The labeled cDNA probes were then purified and concentrated using a Microcon YM10 filter (Millipore) and TE buffer pH 8.0 (Ambion).  Slides were blocked prior to hybridization using BSA The purified cDNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).

growth_protocol: The Mtb strains H37Rv was used for all the experiments.  Bacterial stocks were maintained at -80?C in 7H9ADCTW (Middlebrook 7H9 (Difco) supplemented with 1x ADC [0•5% bovine serum albumin, fraction V (Boehringer Manheim), 0•2% glucose and 0•085% NaCl], 0•2% glycerol and 0•1% Tween 80).   Aliquots of bacteria were thawed and cultured in solid media 7H10 ADCTW.   For preparation of liquid cultures bacteria growing in 7H10 agar plates were resuspended in 7H9ADCTW media at an OD: 0.05.  Liquid cultures were grown in plastic roller bottles in a roller apparatus until OD 0.2.

tag: strain H37Rv

source_name: H37Rv grown in 7H9 media


title: Control 90 days sample 2

source_name: G93A non transgenic littermate 1644


title: H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 3 (C 24hrs)


title: H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 5 (E 24hrs)


title: S24 B_H37Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate B)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate B)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate B)


title: S25 B_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate B)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate B)

source_name: BMMO treated with INF gamma and uninfected (biological replicate B)


title: S55 C_Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate C)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate C)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate C)


title: S26 A_SigE

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate A)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with SigE (Mtb mutant) (biological replicate A)

source_name: BMMO treated with INF gamma and uninfected (biological replicate A)


title: H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 2 (B 24hrs)


title: Control 90 days sample 1

source_name: G93A non transgenic littermate 1642


title: Control 60 days sample 2

source_name: G93A non transgenic littermate 1264

tag: Male mouse 60 day old


title: G93A 90 days sample 1

source_name: G93A mouse 1645

tag: Transgenic male mouse 90 day old


title: G93A 90 days sample 2

source_name: G93A mouse 1647


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 5 (E 4hrs)

source_name: H37Rv 4hrs after infection in macrophage (THP1)

treatment_protocol: Ten 175cm2 flasks were seeded with 100 ml of 106 THP-1 cells/ml.  THP-1 cells were differentiated with 40 nMolar PMA (phorbol myristate acetate) overnight at 37°C, 5%CO2 and 95% humidity.  Mtb cultures were grown exponentially in the usual 7H9ADCTW to an OD of 0.2 for the infection.  An appropriate volume of this culture was resuspended in RPMI with 20% FCS to obtain a bacterial suspension of 2x106 cfu/ml.  One hundred milliliters of bacterial suspension were added to each flask (MOI: 2). Macrophages and bacteria were incubated for 2 h.  After incubation macrophages were washed with warm PBS and 100ml of RPMI +20% FCS were added to each flask.   Infections were followed for 4 hours and cells from five flasks were processed  for bacterial RNA extraction.

value: 4hrs after infection


title: H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 1 (A 24hrs)


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 4 (D 4hrs)


title: S23 A_H37Rv

description: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv vs. uninfected BMMO (biological replicate A)

source_name: Mouse Bone Marrow Macrophages treated with INF gamma and infected with Mtb H37Rv  (biological replicate A)

source_name: BMMO treated with INF gamma and uninfected  (biological replicate A)


title: Control 60 days sample 3

source_name: G93A non transgenic littermate 1265


title: G93A 60 days sample 3

source_name: G93A mouse 1266

tag: Transgenic male mouse 60 day old


title: S74 L_SigE

description: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate L)

source_name: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) (biological replicate L)


title: Control 60 days sample 1

description: Gene expression data from murine motor neurons

source_name: G93A non transgenic littermate 1263


title: S76 M_SigE

description: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate M)

source_name: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) (biological replicate M)


title: S75 M_Rv

description: Mouse Bone Marrow Macrophages infected with Mtb H37Rv vs. uninfected BMMO (biological replicate M)

source_name: Mouse Bone Marrow Macrophages infected with Mtb H37Rv  (biological replicate M)


title: G93A 60 days sample 2

source_name: G93A mouse 1262


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 3 (C 4hrs)

source_name: H37Rv grown in 7H9 media


title: C. elegans_Cd_24h_rep15

status: Public on Mar 26 2008

city: Research Triangle Park

first: Yuxia

last: Cui

state: NC

address: 111 TW Alexander Dr.

department: ETP, DIR

institute: NIEHS

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).

data_processing: GeneSpring GX per spot and per chip: intensity dependent (Lowess) normalization, natural log ratio Treated/Control

organism: Caenorhabditis elegans

source_name: Control

extract_protocol: To isolate total RNA, frozen nematode pellets were ground into fine powder using a liquid nitrogen-chilled mortar and pestle before homogenization in TRIzol (Invitrogen).  Total RNA was subsequently purified using RNAeasy kits (Qiagen) prior to microarray experiments.

treatment_protocol: The Bristol N2 strain of C. elegans was cultured in S-medium with Escherichia coli OP50 as a food source.  Total RNA was prepared from non-treated control nematodes and those exposed to 100 uM cadmium for 24 h.

tag: Caenorhabditis elegans, N2 wild type

source_name: 24h treated


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 2 (B 4hrs)

tag: Time


title: G93A 90 days sample 3

source_name: G93A mouse 1423


title: S72 K_SigE

description: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) vs. uninfected BMMO (biological replicate K)

source_name: Mouse Bone Marrow Macrophages infected with SigE (Mtb mutant) (biological replicate K)


title: C. elegans_Cd_24h_rep16

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.


title: C. elegans_Cd_24h_rep17


title: C. elegans_Cd_24h_rep13


title: C. elegans_Cd_24h_rep18


title: C. elegans_Cd_24h_rep14


title: C. elegans_Cd_24h_rep12


title: C. elegans_Cd_24h_rep11


title: C. elegans_Cd_24h_rep8


title: C. elegans_Cd_24h_rep7


title: C. elegans_Cd_24h_rep9


title: S73 L_Rv

description: Mouse Bone Marrow Macrophages infected with Mtb H37Rv vs. uninfected BMMO (biological replicate L)

source_name: Mouse Bone Marrow Macrophages infected with Mtb H37Rv  (biological replicate L)


title: C. elegans_Cd_24h_rep10


title: C. elegans_Cd_24h_rep4


title: C. elegans_Cd_24h_rep3


title: C. elegans_Cd_4h_rep18

treatment_protocol: The Bristol N2 strain of C. elegans was cultured in S-medium with Escherichia coli OP50 as a food source.  Total RNA was prepared from non-treated control nematodes and those exposed to 100 uM cadmium for 4 h.

source_name: 4h treated


title: G93A 60 days sample 1

source_name: G93A mouse 1261


title: C. elegans_Cd_24h_rep2


title: C. elegans_Cd_24h_rep5


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 1 (A 4hrs)

source_name: H37Rv 4hrs after infection in macrophage (THP1)


title: C. elegans_Cd_24h_rep1


title: C. elegans_Cd_4h_rep17


title: C. elegans_Cd_4h_rep14


title: C. elegans_Cd_4h_rep16


title: C. elegans_Cd_24h_rep6


title: C. elegans_Cd_4h_rep15


title: C. elegans_Cd_4h_rep13


title: C. elegans_Cd_4h_rep7


title: C. elegans_Cd_4h_rep8


title: C. elegans_Cd_4h_rep12


title: C. elegans_Cd_4h_rep6


title: C. elegans_Cd_4h_rep5


title: C. elegans_Cd_4h_rep10


title: C. elegans_Cd_4h_rep4


title: C. elegans_Cd_4h_rep9


title: TG hippocampus 2 (ABI)

status: Public on Mar 25 2008

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

hyb_protocol: Applied Biosystems default hyb protocol

scan_protocol: Applied Biosystems default scan protocol

data_processing: VSN transformation and normalization

source_name: Hippocampus DLCK transgenic mice

label_protocol: Applied Biosystems default labelling kit

extract_protocol: Trizol

tag: Male C57/BL6j


title: C. elegans_Cd_4h_rep2


title: WT hippocampus 5 (ABI)

source_name: Hippocampus WT mice


title: C. elegans_Cd_4h_rep1


title: WT hippocampus 3 (ABI)


title: TG hippocampus 4 (ABI)


title: C. elegans_Cd_4h_rep11


title: C. elegans_Cd_4h_rep3


title: TG hippocampus 3 (ABI)


title: WT hippocampus 2 (ABI)


title: TG hippocampus 5 (ABI)


title: TG hippocampus 1 (ABI)


title: Patient 83224 at week 32

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

description: Gene expression data from patients with Poor outcome at week 32 time point

hyb_protocol: Follow Affymetrix's protocol

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: The data were analyzed using RMA normalization method. Probesets that are "absent" in all samples are eliminated in the laster state of analysis.

source_name: PBMC samples at week 32

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

growth_protocol: PBMC samples

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

treatment_protocol: PBMC samples from HIV seropositive patients at different time points

tag: This sample is from Poor outcome group at week 32


title: WT hippocampus 1 (ABI)


title: PC5_Xba

type: genomic

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

institute: Cancer Research UK

description: Several serial frozen tissue sections (20 µm thickness) were prepared for tissue microdissection. An additional 4-µm section was also made for detailed histological examination by hematoxylin-eosin staining. Only PDAC regions were microdissected under visualization with an inverted microscope (Nikon 66906, Tokyo, Japan) using a sterile 26-gauge needle.

hyb_protocol: Hybridization was performed at 45°C for 16h in a hybridization machine (Affymetrix).

scan_protocol: The arrays were washed and stained on the Affymetrix fluidics Station 450 and the signal intensities were measured using the Affymetrix GeneChip® Scanner 3000.

data_processing: The raw images were analyzed using the Affymetrix GCOS (Ver1.4) software. For genotyping analysis, we used the Affymetrix GTYPE (Ver4.1) software that implements an accurate genotyping algorithm, BRLMM (http://www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx).

molecule: genomic DNA

source_name: Pancreatic ductal adenocarcinoma (PDAC)

label_protocol: The experiments were performed according to the manufacturer's instructions (GeneChip® Mapping 50K HindIII or XbaI Assay Kit). Briefly, 250 ng of tumor DNA was digested by either HindIII or XbaI restriction enzyme (New England Biolabs, Boston, MA, USA). After ligation to an appropriate adaptor for each enzyme, PCR reaction was carried out using a generic primer that recognizes the adapter sequence. The PCR products from four reactions were pooled, concentrated, fragmented by DNase I and then, labeled with biotin.

extract_protocol: Microdissected tumor DNA was extracted using a SePaGene DNA extraction kit (SankoJunyaku Co., Ltd., Tokyo, Japan).

tag: Age

tag: Sex

value: Male

tag: Tissue

value: PDAC

tag: Stage

value: III

tag: Call rate


title: WT hippocampus 4 (ABI)


title: Patient 83242 at week 12

description: Gene expression data from patients with Poor outcome at week 12 time point

source_name: PBMC samples at week 12

tag: This sample is from Poor outcome group at week 12


title: Patient 83227 at week 24

description: Gene expression data from patients with Poor outcome at week 24 time point

source_name: PBMC samples at week 24

tag: This sample is from Poor outcome group at week 24


title: Patient 83242 at week 0

description: Gene expression data from patients with Poor outcome at week 0 time point

source_name: PBMC samples at week 0

tag: This sample is from Poor outcome group at week 0


title: Patient 83225 at week 0


title: Patient 83224 at week 0


title: PC5_Hind


title: Patient 72719 at week 24


title: Patient 83227 at week 0


title: PC19_Hind

value: Female

value: IVb


title: Patient 72708 at week 24


title: Patient 72710 at week 24


title: Patient 83225 at week 24


title: Patient 72719 at week 0


title: Patient 72710 at week 0


title: Patient 621409 at week 24


title: Patient 630694 at week 0


title: Patient 621409 at week 0


title: Patient 373732 at week 24


title: Patient 72708 at week 0


title: Patient 373732 at week 0


title: Patient 51270 at week 24


title: Patient 630694 at week 24


title: PC11_Hind


title: Patient 373718 at week 0


title: Patient 373707 at week 24


title: Patient 373718 at week 24


title: Patient 51270 at week 0


title: Patient 373679 at week 24


title: Patient 373700 at week 0


title: Patient 321399 at week 0


title: Patient 281266 at week 24


title: Patient 281286 at week 0


title: Patient 281286 at week 24


title: Patient 291214 at week 24


title: Patient 373679 at week 0


title: Patient 281266 at week 0


title: Patient 373700 at week 24


title: Patient 373707 at week 0


title: Patient 321399 at week 18

description: Gene expression data from patients with Poor outcome at week 18 time point

source_name: PBMC samples at week 18

tag: This sample is from Poor outcome group at week 18


title: Patient 291214 at week 0


title: Patient 141612 at week 24


title: Patient 108041 at week 0


title: Patient 108053 at week 24


title: Patient 141612 at week 0


title: Patient 220963 at week 0


title: Patient 108053 at week 0


title: Patient 220963 at week 12


title: Patient 83241 at week 24

description: Gene expression data from patients with Good outcome at week 24 time point

tag: This sample is from Good outcome group at week 24


title: Patient 83221 at week 24


title: Patient 83241 at week 0

description: Gene expression data from patients with Good outcome at week 0 time point

tag: This sample is from Good outcome group at week 0


title: Patient 83221 at week 0


title: Patient 108046 at week 0


title: Patient 72701 at week 24


title: Patient 108041 at week 24


title: Patient 72701 at week 0


title: Patient 520819 at week 24


title: Patient 108046 at week 24


title: Patient 44624 at week 24


title: Patient 70466 at week 0


title: Patient 44624 at week 0


title: Patient 70466 at week 24


title: Patient 51284 at week 0


title: Patient 520819 at week 0


title: Patient 43379 at week 0


title: Patient 43379 at week 24


title: Patient 373713 at week 24


title: Patient 321183 at week 24


title: Patient 373734 at week 24


title: Patient 272386 at week 24


title: Patient 373713 at week 0


title: Patient 321183 at week 0


title: Patient 272386 at week 0


title: Patient 272385 at week 24


title: Patient 373722 at week 0


title: Patient 373698 at week 24


title: Patient 373734 at week 0


title: Patient 272385 at week 0


title: Patient 272384 at week 24


title: Patient 272221 at week 24


title: Patient 373698 at week 0


title: Patient 373722 at week 24


title: Patient 121522 at week 24


title: Patient 121522 at week 0


title: Patient 220946 at week 0


title: Patient 220946 at week 24


title: Patient 272384 at week 0


title: Patient 108036 at week 0


title: Patient 108037 at week 0


title: Patient 272221 at week 0


title: Patient 108036 at week 24


title: Patient 108037 at week 24


title: Patient 101141 at week 0


title: Patient 101141 at week 24


title: Cancer tissue from patient 770926-1

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42C under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2X SSC at 42C for 5 min, and 0.2% SSC for 5 min at room temperature.

scan_protocol: Arrays were scanned with a LuxScanTM 10K-A laser confocal scanner and the images obtained were then analyzed using LuxScan 3.0TM software (both from CapitalBio, Beijing, China).

data_processing: After average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out when expression signal were lower than 800 in all samples.  Signal was normalized using the median center tool for genes in the Cluster 3.0 software before performing the unsupervised clustering with complete linkage and uncentered Pearson correlation to underlying the structure of the miRNA expression (Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns (Proc Natl Acad Sci U S A 1998;95:14863-8).

source_name: Cancer tissue from patient 770926-1

label_protocol: 4 ug of low-molecular-weight RNA was labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon, Lafayette, CO) with 2 units T4 RNA ligase (New England Biolabs, Ipswich, MA).  The labeling reaction was performed at 4C for 2 h.  Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol and after washing with ethanol and drying was resuspended in 15 ul of hybridization buffer containing 3X SSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Carlsbad, CA) and the low-molecular-weight RNA was isolated by using the Ambion miRNA Isolation Kit

tag: Cancer tissue from patient 770926-1


title: Adjacent normal tissue from patient 771521-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 770926-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 770926-2

tag: Cancer tissue from patient 770926-2


title: Adjacent normal tissue from patient 772387-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 771916-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 770282-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 770282-1

tag: Cancer tissue from patient 770282-1


title: Cancer tissue from patient 770282-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 770282-2

tag: Cancer tissue from patient 770282-2


title: Adjacent normal tissue from patient 770926-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 770926-2

description: the microRNA expression in the tissue


title: Patient 101774 at week 24


title: Cancer tissue from patient 769441-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 769441-1

tag: Cancer tissue from patient 769441-1


title: Cancer tissue from patient 769441-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 769441-2

tag: Cancer tissue from patient 769441-2


title: Patient 102128 at week 24


title: Patient 102128 at week 0


title: Adjacent normal tissue from patient 769441-1

description: the microRNA expression in the tissue


title: Patient 101774 at week 0


title: Patient 51284 at week 24


title: Adjacent normal tissue from patient 770282-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 190122-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190122-1

tag: Cancer tissue from patient 190122-1


title: Cancer tissue from patient 220114-1

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42C under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2X SSC at 42 C for 5 min, and 0.2% SSC for 5 min at room temperature.

source_name: Cancer tissue from patient 220114-1

tag: Cancer tissue from patient 220114-1


title: Cancer tissue from patient 190245-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190245-2

tag: Cancer tissue from patient 190245-2


title: Cancer tissue from patient 190245-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190245-1

tag: Cancer tissue from patient 190245-1


title: Cancer tissue from patient 190122-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190122-2

tag: Cancer tissue from patient 190122-2


title: Cancer tissue from patient 190519-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190519-1

tag: Cancer tissue from patient 190519-1


title: Cancer tissue from patient 190649-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190649-1

tag: Cancer tissue from patient 190649-1


title: Adjacent normal tissue from patient 770282-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 769441-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 190519-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190519-2

tag: Cancer tissue from patient 190519-2


title: Cancer tissue from patient 190649-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190649-2

tag: Cancer tissue from patient 190649-2


title: Cancer tissue from patient 193126-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193126-1

tag: Cancer tissue from patient 193126-1


title: Cancer tissue from patient 193169-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193169-2

tag: Cancer tissue from patient 193169-2


title: Cancer tissue from patient 191280-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 191280-2

tag: Cancer tissue from patient 191280-2


title: Cancer tissue from patient 190858-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190858-1

tag: Cancer tissue from patient 190858-1


title: Cancer tissue from patient 190858-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 190858-2

tag: Cancer tissue from patient 190858-2


title: Cancer tissue from patient 191280-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 191280-1

tag: Cancer tissue from patient 191280-1


title: Cancer tissue from patient 193126-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193126-2

tag: Cancer tissue from patient 193126-2


title: Cancer tissue from patient 195442-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 195442-1

tag: Cancer tissue from patient 195442-1


title: Cancer tissue from patient 195442-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 195442-2

tag: Cancer tissue from patient 195442-2


title: Cancer tissue from patient 205837-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205837-2

tag: Cancer tissue from patient 205837-2


title: Cancer tissue from patient 195519-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 195519-2

tag: Cancer tissue from patient 195519-2


title: Cancer tissue from patient 204488-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204488-2

tag: Cancer tissue from patient 204488-2


title: Cancer tissue from patient 204488-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204488-1

tag: Cancer tissue from patient 204488-1


title: Cancer tissue from patient 195519-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 195519-1

tag: Cancer tissue from patient 195519-1


title: Cancer tissue from patient 211678-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 211678-1

tag: Cancer tissue from patient 211678-1


title: Cancer tissue from patient 205837-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205837-1

tag: Cancer tissue from patient 205837-1


title: Cancer tissue from patient 205569-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205569-1

tag: Cancer tissue from patient 205569-1


title: Cancer tissue from patient 211678-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 211678-2

tag: Cancer tissue from patient 211678-2


title: Cancer tissue from patient 193169-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193169-1

tag: Cancer tissue from patient 193169-1


title: Cancer tissue from patient 212090-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 212090-2

tag: Cancer tissue from patient 212090-2


title: Cancer tissue from patient 212090-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 212090-1

tag: Cancer tissue from patient 212090-1


title: Cancer tissue from patient 220243-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 220243-1

tag: Cancer tissue from patient 220243-1


title: Cancer tissue from patient 220243-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 220243-2

tag: Cancer tissue from patient 220243-2


title: Cancer tissue from patient 220114-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 220114-2

tag: Cancer tissue from patient 220114-2


title: Cancer tissue from patient 205569-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205569-2

tag: Cancer tissue from patient 205569-2


title: Cancer tissue from patient 222428-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 222428-1

tag: Cancer tissue from patient 222428-1


title: Cancer tissue from patient 222428-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 222428-2

tag: Cancer tissue from patient 222428-2


title: Cancer tissue from patient 222634-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 222634-1

tag: Cancer tissue from patient 222634-1


title: Cancer tissue from patient 222634-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 222634-2

tag: Cancer tissue from patient 222634-2


title: Cancer tissue from patient 225107-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 225107-2

tag: Cancer tissue from patient 225107-2


title: Cancer tissue from patient 224890-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 224890-1

tag: Cancer tissue from patient 224890-1


title: Cancer tissue from patient 224890-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 224890-2

tag: Cancer tissue from patient 224890-2


title: Cancer tissue from patient 225107-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 225107-1

tag: Cancer tissue from patient 225107-1


title: Cancer tissue from patient 226927-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 226927-2

tag: Cancer tissue from patient 226927-2


title: Cancer tissue from patient 226927-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 226927-1

tag: Cancer tissue from patient 226927-1


title: Cancer tissue from patient 775415-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 775415-1

tag: Cancer tissue from patient 775415-1


title: Cancer tissue from patient 774938-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774938-1

tag: Cancer tissue from patient 774938-1


title: Adjacent normal tissue from patient 774938-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 774938-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 775415-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 775415-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 774938-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774938-2

tag: Cancer tissue from patient 774938-2


title: Cancer tissue from patient 775415-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 775415-2

tag: Cancer tissue from patient 775415-2


title: Cancer tissue from patient 775857-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 775857-1

tag: Cancer tissue from patient 775857-1


title: Adjacent normal tissue from patient 775857-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 775857-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 776743-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 776743-1

tag: Cancer tissue from patient 776743-1


title: Adjacent normal tissue from patient 776743-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 776743-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 776743-2

tag: Cancer tissue from patient 776743-2


title: Cancer tissue from patient 775857-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 775857-2

tag: Cancer tissue from patient 775857-2


title: Adjacent normal tissue from patient 776743-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 774764-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774764-2

tag: Cancer tissue from patient 774764-2


title: Cancer tissue from patient 774764-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774764-1

tag: Cancer tissue from patient 774764-1


title: Adjacent normal tissue from patient 774764-2

description: the microRNA expression in the tissue


title: 290404 C2

city: Giessen

first: Alexander

middle: Claus

last: Langheinrich

state: Hessen

address: Klinikstrasse 36

department: Radiology

country: Germany

institute: University of Giessen

description: No further description available.

hyb_protocol: The activity was measured with a liquid scintillization counter (Hidex). cDNA with 8–14x10E6 cpm was used for hybridization at 68°C overnight on nylon filters. Hybridization was carried out in Atlas ExpressHyp buffer supplied with the kit. The filters were then washed according to the kit protocol.

scan_protocol: For scanning, filters were wrapped in plastic foil and exposed for 4–7 days to imaging plates (Fuji Photo Film) in a lead sheathing. The films were read out with a phosphoimager system (FUJIX BAS 1000). The scanned images were analyzed using the AtlasImage 2.0 software.

data_processing:
Spot intensities were adjusted by a global normalization using the sum method
provided by the software. The mean global background was subtracted from the spot intensities. Spots were considered present when the spot intensity was at least twice the background intensity.

source_name: hCASMC

label_protocol:
RNA was reverse transcribed and labeled following the protocol given in the Altlas cDNA Expression Arrays User Manual (PT3140-1) using the reagents supplied by the Atlas Human Array Kit.
Briefly, 2-5 μg total RNA per sample were primed with 1.2 μl CDS primer (5’ 70°C; RT 10’) and reverse transcribed and radioactively labeled using
the master mix supplied with the kit following the kit protocol. The reverse transcriptase of the kit was substituted by 100U MMLV-RT obtained from Promega. Radioactively labeled cDNAs were purified using the purification columns provided with the kit and eluted in 100 μl elution buffer.

growth_protocol:
hCASMC were grown in supplemented growth medium containing 5%
FCS (SmGM-2; Clonetics, Verviers, Belgium). Following 24h of serum starvation (synchronization) in basal medium lacking growth factors and FSC, cells were incubated in SmGM-2 for additional 24h. Finally, cells were harvested for further microarray analysis.

extract_protocol: total RNA was extracted using the QIAgen RNA Micro Kit following the kit protocol including DNAse treatment.

tag: Control

tag: Cell cultures grown in 5% FCS in the absence of c³Ado


title: 220604 K1

description: No further description available.

growth_protocol:
hCASMC were grown in supplemented growth medium containing 5%
FCS (SmGM-2; Clonetics, Verviers, Belgium). Following 24h of serum starvation (synchronization) in basal medium lacking growth factors and FSC in the presence of c³Ado (50µM), cells were incubated in SmGM-2 for additional 24h in the presence of c³Ado (50µM). Finally, c3Ado-treated cells were harvested for further microarray analysis.

tag: Treated

tag: Cell cultures grown in 5% FCS in the presence of c³Ado


title: Adjacent normal tissue from patient 774764-1

description: the microRNA expression in the tissue