title: Yersinia pestis_Fur regulon_37°C_rep8

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

institute: Institute of Microbiology and Epidemiology

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongsto a newly established biovar, Microtus. The fur mutant of Y. pestis was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the fur mutant was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transformed to 37 °C for 1 h prior to the addition of 40 μM FeCl3 for 30 min.

hyb_protocol: For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5×SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

scan_protocol: The slides were scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments).

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode.

label: Cy5 or Cy3

organism: Yersinia pestis

source_name: Yersinia pestis_fur mutant_iron rich_37 °C_30min_rep8

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

extract_protocol: Total RNA was extracted from two independent batches of cultures. To minimize bacterial RNA degradation and preserve gene transcription profile, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each aliquot, mixed thoroughly and placed at room temperature for 5 min. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter), exactly following the kit’s manual. Briefly, cell pellets were collected from the bacteria cultures by centrifugation. The lysis of cell samples was performed by Protease K digestion at 65°C for 15min, and protein was then removed from the lysed sample with the protein precipitation reagent provided by the kit. Isopropanol was added to precipitate nucleic acid and the residue DNA was removed with RNase-free DNase I. The RNA was then recovered with isopropanol. The RNAs from each four aliquots were pooled together. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: Yersinia pestis fur mutant was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transformed to 37 °C for 1 h prior to the addition of 40 μM FeCl3 for 30 min.

label: Cy3 or Cy5

source_name: Yersinia pestis_wild-type strain_iron rich_37 °C_30min_rep8

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Yersinia pestis wild-type strain was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transformed to 37 °C for 1 h prior to the addition of 40 μM FeCl3 for 30 min.


title: Yersinia pestis_iron starvation_37 °C_rep8

status: Public on Aug 01 2008

type: RNA

description: Y. pestis strain 201 was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transfered to 37 °C for 1 h prior to the addition of the iron chelator 2,20-dipyridyl (DP) or FeCl3.

molecule: total RNA

source_name: Yersinia pestis, iron starvation, 37 °C, 2, 2'-dipyridyl, 30min

tag: Yersinia pestis strain 201 was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transformed to 37 °C for 1 h prior to the addition of the iron chelator 2,20-dipyridyl (DP).

source_name: Yersinia pestis, iron rich, 37 °C, 40 μM FeCl3

tag: Yersinia pestis strain 201 was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. The bacteria were pre-cultivated to the middle exponential phase at 26 °C and then the cultures at 26 °C were transformed to 37 °C for 1 h prior to the addition of FeCl3.


title: Yersinia pestis_PhoP regulon_low pH_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. Y. pestis phoP mutant was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the phoP mutant were grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in acid TMH medium (pH 5.5) and grown to exponential phase (A620nm of approximately 0.8) at 26°C.

source_name: Yersinia pestis, phoP mutant, pH 5.5

tag: Yersinia pestis phoP mutant was grown to exponential phase in acid TMH medium (pH5.5) at 26°C.

source_name: Yersinia pestis, wild-type strain, pH 5.5

tag: Yersinia pestis wild-type strain 201 was grown to exponential phase in acid TMH medium at 26°C.


title: Yersinia pestis_Fur regulon_26°C_rep8

description: Y. pestis strain 201 and fur mutant was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. Cultures obtained at 26 °C were treated with 40 μM FeCl3 for 30 min.

source_name: Yersinia pestis_fur mutant_iron rich_26 °C_30min_rep8

tag: Yersinia pestis fur mutant was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. Cultures obtained at 26 °C were treated with 40 μM FeCl3 for 30 min.

source_name: Yersinia pestis_wild-type strain_iron rich_26 °C_30min_rep8

tag: Yersinia pestis wild-type strain 201 was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 μM of FeCl3 as the sole iron source. Cultures obtained at 26 °C were treated with 40 μM FeCl3 for 30 min.


title: S35 vs. pLRT - repeat 3 - mAdbID:51257

city: Bethesda

first: Kathleen

last: Kelly

state: MD

address: 37 Convent Drive

department: Cancer and Cell Biology Branch

country: USA

institute: National Institutes of Health

description: mAdb experiment ID: 51257

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.41;; 2.05;; n/a;; n/a Temperature: 38.13

data_processing:
Data Processing Protocol
Calculation Method: Signal intensities of microarray features were calculated by subtracting the median local background from the median signal intensity. Features were considered for analysis if in the range 50-300ìm with signal intensity greater than 100 in both channels that were greater than one standard deviation above background with at least a 2:1 signal to background ratio. Signal intensities for an entire microarray were normalized to the 50% percentile median value, to correct for superior cy3 or cy5 labeling of one sample versus the other, or to superior cDNA synthesis of one sample versus the other. After filtering and normalization, the cy3 and cy5 values for the pLRT control cDNA and the experimental (V12 or effector domain) cDNA were expressed as a ratio to indicate the fold up- or down-regulation relative to the pLRT control cDNA.

organism: Homo sapiens

source_name: pLRT - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: cDNA was labeled with Cy3 monofunctional reactive dye to amino allyl-modified dUTP incorporated into cDNA using the FairPlay Microarray labeling kit (Stratagene, La Jolla, CA).

extract_protocol:
Trizol Extraction
Extraction method: guanidium HCL/phenol-chloroform
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 250 ng/ml
Treatment time: 72 hours

tag: Cell line

value: HME16C human mammary epithelial cells

tag: Cell type

value: hTERT immortalized human mammary epithelial cells

tag: Other

value: These cells were infected with the control pLRT retroviral expression vector that does not express a gene product.

label_protocol:
Cy5 Labeling Protocol
Other: cDNA was labeled with Cy5 monofunctional reactive dye to amino allyl-modified dUTP incorporated into cDNA using the FairPlay Microarray labeling kit (Stratagene, La Jolla, CA).

value: These cells were infected with the pLRT-H-RasV12S35 retroviral expression vector that directs the doxycycline-inducible expression of activated RasV12S35.

tag: genotype/variation


title: Yersinia pestis_OxyR regulon_H2O2_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. Y. pestis oxyR mutant was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the oxyR mutant were grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium and grown to middle exponential phase (A620nm of approximately 0.8) at 26°C. Bacterial cells were then exposed to 1mM H2O2  for 30 min.

source_name: Yersinia pestis, oxyR mutant, H2O2, 30min

tag: Yersinia pestis oxyR mutant grown to middle exponential phase at 26 °C was then exposed to 1 mM H2O2 for 30 min.

source_name: Yersinia pestis, Wild-type strain, H2O2, 30min

tag: Yersinia pestis wild-type strain 201 grown to middle exponential phase at 26 °C was then exposed to 1 mM H2O2 for 30 min.


title: Yersinia pestis_Oxidative stress_H2O2_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium and grown to middle exponential phase (A620nm of approximately 0.8) at 26°C. Bacterial cells were then exposed to 1mM H2O2 or H2O.

source_name: Yersinia pestis, H2O2, 30min

tag: Yersinia pestis strain 201 grown to exponential phase at 26 °C was exposed to 1mM H2O2 (hydrogen peroxide) for 30min.

source_name: Yersinia pestis, H2O, 30min

tag: Yersinia pestis strain 201 grown to exponential phase at 26 °C was allowed to continue growing at 26 °C for 30 min by addition of the same amount of water.


title: Yersinia pestis_iron starvation_26 °C_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. Bacteria was grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. Bacterial cells were then exposed to iron starvation or not.

source_name: Yersinia pestis, iron starvation, 26 °C, 2, 2'-dipyridyl, 30min

tag: Yersinia pestis strain 201 were grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. The cultures obtained at 26 °C were treated with 100 mM of DP (2, 2'-dipyridyl) to elicit iron starvation.

source_name: Yersinia pestis, iron rich, 26 °C, 40 μM FeCl3

tag: Yersinia pestis strain 201 were grown at 26 °C to the middle exponential growth phase (an A620 of about 0.8) in TMH medium containing 10 mM of FeCl3 as the sole iron source. The cultures obtained at 26 °C were added with 40 μM FeCl3 to ensure iron rich conditions.


title: Yersinia pestis_Nutrition deficiency_Stationary growth phase_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium (minimal medium) or BHI (rich medium) to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium or BHI medium and grown to stationary phase (A620nm of approximately 2.0).

source_name: Yersinia pestis, Stationary growth phase, TMH

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3  monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Yersinia pestis strain 201 was grown to stationary phase in TMH (minimal) medium.

source_name: Yersinia pestis, Stationary growth phase, BHI

tag: Yersinia pestis strain 201 was grown to stationary phase in BHI (rich) medium.


title: S35 vs. pLRT - repeat 4 - mAdbID:51258

description: mAdb experiment ID: 51258

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.32;; 2.04;; n/a;; n/a Temperature: 38.23

source_name: pLRT - Cy5


title: Yersinia pestis_low Mg2+_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was pre-cultivated in the TMH media containing 20 mM MgCl2 to an OD620 of about 0.6. Bacteria were harvested, washed twice with TMH medium containing 10 μM MgCl2, and then resuspended in the 10 μM or 20 mM Mg2+ TMH media for 1 hr.

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the eight replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode.

source_name: Yersinia pestis, 10 μM Mg2+

tag: Yersinia pestis strain 201 were pre-cultivated in the TMH media containing 20 mM MgCl2 to an OD620 of about 0.6. Bacteria were harvested, washed twice with TMH medium containing 10 μM MgCl2, and then resuspended in the 10 μM Mg2+ TMH media for 1 hr.

source_name: Yersinia pestis, 20 mM Mg2+

tag: Yersinia pestis strain 201 were pre-cultivated in the TMH media containing 20 mM MgCl2 to an OD620 of about 0.6. Bacteria were harvested, washed twice with TMH medium containing 10 μM MgCl2, and then resuspended in the 20 mM Mg2+ TMH media for 1 hr.


title: G37 vs. pLRT - repeat 4 - mAdbID:49119

description: mAdb experiment ID: 49119

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.94;; 2.09;; n/a;; n/a Temperature: 39.85

value: These cells were infected with the pLRT-H-RasV12G37 retroviral expression vector that directs the doxycycline-inducible expression of activated RasV12G37.


title: S35 vs. pLRT - repeat 2 - mAdbID:51256

description: mAdb experiment ID: 51256

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.29;; 2.04;; n/a;; n/a Temperature: 37.94


title: Yersinia pestis_Nutrition deficiency_Exponential growth phase_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium (minimal medium) or BHI (rich medium) to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium or BHI medium and grown to middle exponential phase (A620nm of approximately 0.8).

source_name: Yersinia pestis, Exponential growth phase, TMH

tag: Yersinia pestis strain 201 was grown to middle exponential phase in TMH (minimal) medium.

source_name: Yersinia pestis, Exponential growth phase, BHI

tag: Yersinia pestis strain 201 was grown to middle exponential phase in BHI (rich) medium.


title: G37 vs. pLRT - repeat 2 - mAdbID:48888

description: mAdb experiment ID: 48888

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.31;; 1.76;; n/a;; n/a Temperature: 35.64


title: Yersinia pestis_Growth phase (TMH)_Exponential vs Stationary_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown to middle exponential phase (A620nm of approximately 0.8) or stationary phase  (A620nm of approximately 2.0).

source_name: Yersinia pestis, Exponential phase, TMH

tag: Yersinia pestis strain 201 grown to middle exponential phase in the chemical defined TMH medium.

source_name: Yersinia pestis, stationary phase, TMH

tag: Yersinia pestis strain 201 grown to stationary phase in the chemical defined TMH medium.


title: Yersinia pestis_PhoP regulon_low Mg2+_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. Y. pestis phoP mutant was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the phoP mutant were grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were washed and diluted 1:20 in fresh TMH medium with 10 μM MgCl2 and grown to exponential phase (A620nm of approximately 0.8) at 26°C.

source_name: Yersinia pestis, phoP mutant, 10 μM Mg2+

tag: Yersinia pestis phoP mutant was grown to middle exponential phase in TMH medium with 10 μM MgCl2 at 26°C.

source_name: Yersinia pestis, wild type strain, 10 μM Mg2+

tag: Yersinia pestis wild-type strain 201 was grown to middle exponential phase in TMH medium with 10 μM MgCl2 at 26°C.


title: G37 vs. pLRT - repeat 1 - mAdbID:48887

description: mAdb experiment ID: 48887

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.28;; 1.87;; n/a;; n/a Temperature: 35.41

source_name: pLRT - Cy3

tag: Cell line

tag: Cell type

tag: Other

tag: genotype/variation


title: V12 vs. pLRT - repeat 4 - mAdbID:50814

description: mAdb experiment ID: 50814

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.98;; 2.17;; n/a;; n/a Temperature: 38.1

value: These cells were infected with the pLRT-H-RasV12 retroviral expression vector that directs the doxycycline-inducible expression of activated RasV12.


title: Yersinia pestis_Growth phase (BHI)_Exponential vs Stationary_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a BHI medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh BHI medium, and the cells were grown to middle exponential phase (A620nm of approximately 0.8) or stationary phase  (A620nm of approximately 2.0).

source_name: Yersinia pestis, Exponential phase, BHI

tag: Yersinia pestis strain 201 grown to exponential phase in BHI medium.

source_name: Yersinia pestis, stationary phase, BHI

tag: Yersinia pestis strain 201 grown to stationary phase in BHI medium.


title: S35 vs. pLRT - repeat 1 - mAdbID:51255

description: mAdb experiment ID: 51255

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.35;; 2.03;; n/a;; n/a Temperature: 37.67


title: V12 vs. pLRT - repeat 1 - mAdbID:50811

description: mAdb experiment ID: 50811

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.93;; 2.16;; n/a;; n/a Temperature: 37.06


title: G37 vs. pLRT - repeat 3 - mAdbID:49118

description: mAdb experiment ID: 49118

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.94;; 2.26;; n/a;; n/a Temperature: 39.66


title: V12 vs. pLRT - repeat 2 - mAdbID:50812

description: mAdb experiment ID: 50812

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.96;; 2.17;; n/a;; n/a Temperature: 37.35


title: Yersinia pestis_acid stress_pH5.5_10min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to pH5.5 for 10 min.

source_name: Yersinia pestis, pH5.5, 10 min

tag: Yersinia pestis strain 201 exposed to acid medium (pH5.5) for 10 min

source_name: Yersinia pestis, pH7.2

tag: Yersinia pestis strain 201 grown in the normal condition (pH7.2)


title: V12 vs. pLRT - repeat 3 - mAdbID:50813

description: mAdb experiment ID: 50813

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 1.96;; 2.17;; n/a;; n/a Temperature: 37.75


title: Yersinia pestis_OmpR regulon (high salinity)_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. The ompR mutant of Y. pestis was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the mutant strain was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to 0.5 M NaCl for 30min.

source_name: Yersinia pestis, ompR mutant, high salinity, 30 min

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Yersinia pestis ompR mutant in response to 0.5 M NaCl for 30min (high salinity).

source_name: Yersinia pestis, wild-type strain, high salinity, 30 min

tag: Yersinia pestis wild-type strain 201 in response to 0.5 M NaCl for 30min (high salinity).


title: Yersinia pestis_tetracycline treatment_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to 80 μg/ml tetracycline for 30 min..

source_name: Yersinia pestis, tetracycline, 30min

tag: Yersinia pestis strain 201 grown to middle exponential phase was treated with 80 μg/ml tetracycline for 30 min.

source_name: Yersinia pestis, without tetracycline

tag: Yersinia pestis strain 201 without tetracycline treatment.


title: Yersinia pestis_Chloramphenicol treatment_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to 40 μg/ml chloramphenicol for 30min or not.

source_name: Yersinia pestis, Chloramphenicol treatment, 30 min

tag: Yersinia pestis strain 201 grown to middle exponential phase was treated with 40 μg/ml chloramphenicol for 30min.

source_name: Yersinia pestis_without chloramphenicol treatment

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Yersinia pestis strain 201 without treatment of chloramphenicol


title: Yersinia pestis_OmpR regulon (high osmolarity)_30min_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belongs to a newly established biovar, Microtus. The ompR mutant of Y. pestis was generated by using the one-step inactivation method based on the lambda phage recombination. Both the WT strain and the mutant strain was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to 5.0 M sorbitol for 30 min (high osmolarity).

source_name: Yersinia pestis, OmpR mutant (high osmolarity), 30 min

tag: Yersinia pestis ompR mutant in response to 5.0 M sorbitol for 30 min (high osmolarity)

source_name: Yersinia pestis, wild-type strain (high osmolarity), 30 min

tag: Yersinia pestis wild-type strain 201 in response to 0.5 M sorbitol for 30 min (high osmolarity)


title: lung_ABCG1-/-

status: Public on Jul 30 2008

city: Los Angeles

first: Angel

last: Baldan

state: CA

address: 675 Charles Young Dr.

institute: UCLA

description: Oligonucloetide probes are spotted on 128 spots. Positive and negative controls are included. SuperArray GEArray cat. num. OMM-011

hyb_protocol: following manufacturer's intructions (SuperArray)

data_processing: online analysis and data processing, at SuperArray's web

label: biotin

organism: Mus musculus

source_name: Lung, inferior left lobe

label_protocol: True-Labeling AMP (SuperArray)

extract_protocol: Total RNA extracted from lung using Trizol (Invitrogen)

treatment_protocol: mice were fed regular chow diet for 8 months

tag: pooled RNA (4 mice)

tag: AGE

value: 8 months

tag: SEX

value: male


title: lung_WT

scan_protocol: following manufacturer's intructions (SuperArray)


title: miRNA BM-MSC_donor3–P8

status: Public on Jul 29 2008

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: miRNA Donor3-P8

hyb_protocol: Labeling of total RNA for miChip v8 April 2007 (Human) hybridizations has been described in detail before (Castoldi M et al., Methods, Volume 43, Issue 2, October 2007, Pages 146-152) For each sample a microarray chamber with a microarray gasket slide (Agilent technologies, cat. G2534-60005) was prepared and labeled samples are sandwiched between the microarray gasket slide and the printed arrays. The secured holders were placed into the hybridization oven (Agilent technologies, cat. G2545A), and hybridization is carried out for at least 16 h with a rotating speed of four using a hybridization temperature of 54 °C. After hybridization, arrays were washed. Microarray chambers are removed one by one from the hybridization oven. Microarray chambers are opened and the gasket slide-array sandwiches are submerged in washing buffer 1 (W1; 2 x SSC, 0.1%SDS, at room temperature), and separated using forceps. Subsequently, hybridized arrays were stored in W1 (room temperature) until all arrays have been removed from the oven and separated from the microarray gasket slides. Successively, arrays were transferred into fresh W1 (room temperature) and washed on a rocking shaker for 10 min. Then, arrays were washed once in washing buffer 2 (W2, 0.2 x SSC, at room temperature) and washing buffer 3 (W3, 0.1 x SSC, at room temperature), each time for 10 min, and once in W3 for 5 min (all washes are performed at room temperature on a shaker). Finally, arrays are rinsed in double-distilled water (room temperature) and dried by centrifugation at 1500 rpm for 2 min at room temperature.

scan_protocol: Array images are generated by using the Genepix 4200AL laser scanner (Auto Loader, Molecular Devices). For this purpose miChip arrays are scanned in batches using the Genepix auto PMT (Photo Multiplayer) algorithm, with pixel saturation tolerance set to 0.2%.

data_processing: Tiff images generated by the Genepix 4200AL laser scanner are loaded into the Genepix 6 microarray analysis software (Molecular Devices). Artifact-associated spots are eliminated both by software- and visual-guided flags. Signal intensities are measured according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. Genepix 6 microarray analysis software saves data into a TAB delimited file using the “.GPR” file extension. GPR files are used for subsequent data analysis.

label: Cy-3 labeling

source_name: bone marrow mesenchymal stem cells of donor3 - passage 8

label_protocol:
Labeling of total RNA for miChip v8 April 2007 (Human) hybridizations has been described in detail before (Castoldi M et al., Methods, Volume 43, Issue 2, October 2007, Pages 146-152)
3 µg of total RNA was aliquoted in a volume of 10 µl of RNase free water and placed on ice. To minimize variability a labeling master mix was prepared that contains 1 x T4 RNA ligase buffer (Ambion), ATP (1.3 mM, final concentration), RNase inhibitors (20 U, final amount), RNA ligase (10 U, final amount), Cy3 labeled RNA linker (5´-p-rUrUrUrU-Cy3-3´, Biospring; 6.67 M, final concentration) and PEG (15.5%, final concentration) per reaction. 20 µl of the labeling master mix was added to the 3 µg of total RNA to yield a final volume of 30 µl. The reaction mix was then incubated for 12–16 h at 4°C. T4 RNA ligase and RNase inhibitor were heat denatured for 5 min at 95 °C and the reaction is briefly spun to collect the condensate at the bottom of the tube. Samples were stored on ice until further use. 70 µl of precipitation master mix containing sodium acetate (300 mM, final concentration) and linear acrylamide (2.5 g, final amount) per reaction was added to each sample. To precipitate the RNA, 300 µl of 100% ethanol were added to each sample and then samples are incubated for at least one hour at -80 °C. Samples are spun for 30 min at 20,000g, 4 °C. The supernatant was discarded and pellets were washed with 1 ml of 75% ethanol and centrifuged for 5 min at 13,000 rpm at room temperature. Pellets are then briefly air-dried at room temperature. Subsequently, pellets were dissolved in 440 µl of hybridization buffer [5 x SSC, 0.1% SDS, 25% formamide and 100 µg/ml of herring sperm DNA (Promega, D181B)], denatured for 5 min at 95 °C, and centrifuged for 5 min at 13,000 rpm at room temperature.

growth_protocol:
Human bone marrow (BM) samples were taken after informed consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. Mesenchymal stem cells (MSC) were isolated in the culture medium described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625).
The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548).  MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cells were harvested by trypsination after passage 8

tag: mesenchymal stem cells from human bone marrow

tag: (alternatively named mesenchymal stromal cells)

tag: Passage 8 (senescent passage)


title: miRNA BM-MSC_donor2–P7

description: miRNA Donor2-P7

source_name: bone marrow mesenchymal stem cells of donor2 - passage 7

treatment_protocol: Cells were harvested by trypsination after passage 7

tag: Passage 7 (senescent passage)


title: miRNA BM-MSC_donor3–P2

description: miRNA Donor3-P2

source_name: bone marrow mesenchymal stem cells of donor3 - passage 2

treatment_protocol: Cells were harvested by trypsination after passage 2

tag: Passage 2


title: Yersinia pestis_high osmolarity_20min_rep6

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 0.5 M sorbitol for 20 min (high osmolarity) or not.

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode.

source_name: Yersinia pestis, 0.5 M sorbitol, 20 min

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of six replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

extract_protocol: Total RNA was extracted from three independent batches of cultures. To minimize bacterial RNA degradation and preserve gene transcription profile, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each aliquot, mixed thoroughly and placed at room temperature for 5 min. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter), exactly following the kit’s manual. Briefly, cell pellets were collected from the bacteria cultures by centrifugation. The lysis of cell samples was performed by Protease K digestion at 65°C for 15min, and protein was then removed from the lysed sample with the protein precipitation reagent provided by the kit. Isopropanol was added to precipitate nucleic acid and the residue DNA was removed with RNase-free DNase I. The RNA was then recovered with isopropanol. The RNAs from each four aliquots were pooled together. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 0.5 M sorbitol for 20 min (high osmolarity).

source_name: Yersinia pestis_without high osmolarity

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of six replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.


title: miRNA BM-MSC_donor1–P10

description: miRNA Donor1-P10

source_name: bone marrow mesenchymal stem cells of donor1 - passage 10

treatment_protocol: Cells were harvested by trypsination after passage 10

tag: Passage 10


title: Yersinia pestis_growth temperature shift_rep6

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6.

source_name: Yersinia pestis, grown at 37 °C

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) was grown to middle exponential phase and transferred to 37 °C for 3 hr.

source_name: Yersinia pestis

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of six replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) was grown to middle exponential phase and continually grown at 26 °C for 3 hr.


title: Yersinia pestis_antibacterial peptide_rep8

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. Bacterial cells were then exposed to different in vitro stresses.

source_name: Yersinia pestis, polymyxin B treatmnt

tag: Yersinia pestis strain 201 treated with treatment of 80 μg/ml polymyxin B for 30 min.

source_name: Yersinia pestis_without treatment of antibacterial peptide

tag: Yersinia pestis strain 201 without treatment of 80 μg/ml polymyxin B for 30 min.


title: Yersinia pestis_heat shock_10min_rep6

description: Y. pestis strain 201 was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.8. The cultures were transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 45 °C or 37 °C for 10 min.

hyb_protocol: For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry to scan.

source_name: Yersinia pestis, 45 degree,10min

label_protocol: 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark.The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

extract_protocol: total RNA was extracted from three independent batches of cultures. To minimize bacterial RNA degradation and preserve gene transcription profile, double-volume of RNAprotect Bacteria Reagent (Qiagen) was immediately added, mixed thoroughly and placed at room temperature for 5 min. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter), exactly following the kit’s manual. Briefly, cell pellets were collected from the bacteria cultures by centrifugation. The lysis of cell samples was performed by Protease K digestion at 65°C for 15min, and protein was then removed from the lysed sample with the protein precipitation reagent provided by the kit. Isopropanol was added to precipitate nucleic acid and the residue DNA was removed with RNase-free DNase I. The RNA was then recovered with isopropanol. The RNAs from each four aliquots were pooled together. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: Yersinia pestis strain 201 (F1+,VW+, Pgm+, and Pst+), avirulent to humans, belonging to a newly established biovar, Microtus, was grown to exponential phase at 26 °C and transfered to 37 °C for 1 hr, then exposed to 45 °C for 10 min.

source_name: Yersinia pestis, 37 degree,10min

label_protocol: 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark.The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Yersinia pestis strain 201 (F1+,VW+, Pgm+, and Pst+), avirulent to humans, belonging to a newly established biovar, Microtus, was grown to exponential phase at 26 °C and transfered to 37 °C for 1 hr.


title: miRNA BM-MSC_donor2–P2

description: miRNA Donor2-P2

source_name: bone marrow mesenchymal stem cells of donor2 - passage 2


title: Yersinia pestis_cold shock_1hr_rep6

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to cold shock (10 °C ) for 1 hr or not.

hyb_protocol: For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

source_name: Yersinia pestis, 10 °C, 1 hr

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of six replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42°C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50°C, and was stored at -20°C until use.

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown to middle exponential phase at 26 °C. Overnight culture of strain 201 was used to inoculate the fresh TMH medium, and it was allowed to grow at 26 °C to the exponential growth phase (A620 = 0.6). Bacteria were then transferred to grow at 37 °C for 1 h. Samples were collected 1 h after shock at 10 °C.

source_name: Yersinia pestis, before cold shock


title: miRNA BM-MSC_donor1–P9

description: miRNA Donor1-P9

source_name: bone marrow mesenchymal stem cells of donor1 - passage 9

treatment_protocol: Cells were harvested by trypsination after passage 9

tag: Passage 9


title: LNCaP_3a-diol-6h-After-Tmt

city: Oklahoma City

first: Hsueh-Kung

last: Lin

state: OK

address: Room 462, 800 Research Parkway

department: Urology

institute: University of Oklahoma Health Sciences Center

description: Details can be found in Nunlist EH, Dozmorov I, Tang Y, Cowan R, Centola M, Lin HK. Partitioning of 5a-dihydrotestosterone and 5a-androstane-3a, 17b-diol activated pathways for stimulating human prostate cancer LNCaP cell proliferation  J Steroid Biochem Mol Biol 2004;91(3):157-170.; Zimmerman RA, Dozmorov I, Nunlist EH, Tang Y, Li X, Cowan R, Centola M, Frank MB, Culkin DJ, Lin HK. 5a-Androstane-3a,17b-diol activates pathway that resembles the epidermal growth factor responsive pathways in stimulating human prostate cancer LNCaP cell proliferation. Prostate Cancer Prostatic Dis 2004;7(4):364-374.

hyb_protocol: The array membranes were first prehybridized with 5 ml ExpressHybTM solution (Clontech) in the presence of 0.5 mg denatured sheared salmon sperm DNA (Invitrogen) at 68 °C for 30 min.  The Atlas Array membranes were hybridized with a mixture of denatured [α-32P]-dATP-labeled probes (20 x 106 cpm) and 5 µg Cot-1 DNA at 68 oC for 16-18 hours.  Membranes were then washed 4 times for 30 min each at 68°C in 2X SSC plus 1% SDS, followed by one 30 min wash at 68 °C in 0.1X SSC plus 0.5% SSC and one final 5 min wash in 2X SSC at room temperature

scan_protocol: Washed membranes were exposed to phosphor-imaging screens (Packard BioScience; Meriden, CT); and images were captured using a Cyclone storage phosphorimager system (Packard BioScience).  Results from the phosphor-imaging screen were presented as digital light units (DLU) and interpreted using OptiQuant image analysis software (Packard BioScience)

data_processing:
The background of the array membranes was determined by the average and standard deviation (SD) of all 276 background spots for each array consisting of spots between probes areas and spots on the rims indicated in the array membranes.  Total system noise around the true zero point was normally distributed with right-tail positively skewed.  Points exceeding 3 SD above the mean were eliminated until the true normal distribution was successively observed; usually this procedure involved the removal of no more than 5-10 points.  The mean of the remaining background measurements was subtracted from all expression measurements.  Genes whose expression levels exceeded above 2 SD of the background levels were considered to be regulated genes

Three raw data files are associated with each Sample:
Raw data in columnar format
Raw data with overlaid mapping template
Raw data from microarray slide

label: 35 µCi [a-32P]-dATP

source_name: LNCaP prostate cancer cell line

label_protocol: Radio-labeled probes were prepared from reverse transcription using 5 µg of the pooled total RNA from each time point in the presence of gene specific primers (CDS specific primers; Clontech), 35 µCi [a-32P]-dATP, 200 units Superscript II reverse transcriptase (Invitrogen), and dNTPs in a total of 10 µl.  Reactions were performed at 42 oC for 1 hour.  The radio-labeled cDNAs were purified; and radioactivity was determined with LS 6000IC scintillation counter (Beckman Coulter)

growth_protocol: Passaged every 3-5 days or whenever cells reach 70-80% confluence

extract_protocol: Total RNA was extracted from LNCaP cells treated with 10-11 M 3α-diol at 0, 1, 3, 6, 12, 24, and 48 hours after stimulation using Trizol (Invitrogen)

treatment_protocol: Maintained in the complete medium consisting of RPMI 1640 supplemented with 10% FBS, 5 units/ml penicillin, and 5 µg/ml streptomycin at 37 C and 5% CO2

tag: LNCaP cells


title: LNCaP_3a-diol-0h-No-Tmt

description:
Details can be found in
Nunlist EH, Dozmorov I, Tang Y, Cowan R, Centola M, Lin HK. Partitioning of 5a-dihydrotestosterone and 5a-androstane-3a, 17b-diol activated pathways for stimulating human prostate cancer LNCaP cell proliferation  J Steroid Biochem Mol Biol 2004;91(3):157-170.
Zimmerman RA, Dozmorov I, Nunlist EH, Tang Y, Li X, Cowan R, Centola M, Frank MB, Culkin DJ, Lin HK. 5a-Androstane-3a,17b-diol activates pathway that resembles the epidermal growth factor responsive pathways in stimulating human prostate cancer LNCaP cell proliferation. Prostate Cancer Prostatic Dis 2004;7(4):364-374.

tag: LNCaP cell line


title: LNCaP_3a-diol-1h-After-Tmt


title: LNCaP_3a-diol-3h-After-Tmt


title: miRNA BM-MSC_donor1–P8

description: miRNA Donor1-P8

source_name: bone marrow mesenchymal stem cells of donor1 - passage 8

tag: mesenchymal stem cells from human bone marrow

tag: Passage 8


title: miRNA BM-MSC_donor1–P4

description: miRNA Donor1-P4

source_name: bone marrow mesenchymal stem cells of donor1 - passage 4

treatment_protocol: Cells were harvested by trypsination after passage 3

tag: (alternatively named mesenchymal stromal cells)

tag: Passage 4


title: Yersinia pestis_high salinity_20min_rep6

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 0.5 M NaCl or 0.9% NaCl for 20 min.

source_name: Yersinia pestis, high salinity, 20 min

growth_protocol:
Overnight culture of strain 201 was used to inoculate the fresh TMH medium, and it was allowed to grow at 26 °C to the exponential growth
phase (A620 = 0.6). Bacteria were then transferred to grow at 37 °C for 1 h. Samples were collected 1 h after shock at 10 °C.

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 0.5 M NaCl for 20 min.

source_name: Yersinia pestis_without high salinity

tag: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) avirulent to humans, belonging to a newly established biovar, Microtus was grown at 26 °C in a chemically defined TMH medium to the middle exponential growth phase (A620nm approximately 0.8). Cell cultures were diluted 1:20 in fresh TMH medium, and the cells were grown for at least 10 generations at 26 °C until reaching A620nm of approximately 0.6. The cultures were then transformed to 37 °C for 1 hr. Bacterial cells were then exposed to 0.9% NaCl for 20 min.


title: miRNA BM-MSC_donor1–P11

description: miRNA Donor1-P11

source_name: bone marrow mesenchymal stem cells of donor1 - passage 11

treatment_protocol: Cells were harvested by trypsination after passage 11

tag: Passage 11


title: miRNA BM-MSC_donor1–P6

description: miRNA Donor1-P6

source_name: bone marrow mesenchymal stem cells of donor1 - passage 6

treatment_protocol: Cells were harvested by trypsination after passage 6

tag: Passage 6


title: miRNA BM-MSC_donor1–P5

description: miRNA Donor1-P5

source_name: bone marrow mesenchymal stem cells of donor1 - passage 5

treatment_protocol: Cells were harvested by trypsination after passage 5

tag: Passage 5


title: miRNA BM-MSC_donor1–P3

description: miRNA Donor1-P3

source_name: bone marrow mesenchymal stem cells of donor1 - passage 3

tag: Passage 3


title: miRNA BM-MSC_donor1–P7

description: miRNA Donor1-P7

source_name: bone marrow mesenchymal stem cells of donor1 - passage 7

tag: Passage 7


title: miRNA BM-MSC_donor1–P2

description: miRNA Donor1-P2

source_name: bone marrow mesenchymal stem cells of donor1 - passage 2

tag: Passage 2


title: CD8+ T cells (spleen), 0 to 6 divisions

status: Public on Jul 25 2008

city: Worcester

first: Raymond

middle: M

last: Welsh

state: MA

address: 55 Lake Ave. North

department: Pathology

institute: UMASS Medical School

description: slowly proliferating (CFSE-high) CD8 cell population

hyb_protocol: 5 ug of cRNA  hybridized for 16 hr at 45C on GeneChip Mus Musculus Genome Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

source_name: Homeostatically Proliferated CFSE-labeled CD8+ T cells (spleen), 0 to 6 divisions

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

extract_protocol: Extraction of total RNA was performed using the Qiagen RNAeasy Kit.

tag: Strain

tag: Age

value: 10 weeks

tag: Tissue

value: Spleen


title: Barley seeds with P. aeruginosa PA5021 mutant for 12hr

city: College Station

first: Akihiro

last: Ueda

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description: barley seeds RNA was extracted after 12hr infection of P. aeruginosa PA5021 mutant at 25C

hyb_protocol: Standard protocol, available from the following website, http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: MAS 5.0 Expression Analysis Default Setting

label: Biotin

organism: Hordeum vulgare

extract_protocol: Total RNA was extracted by SDS-phenol method, and then purified with a Qiagen RNeasy Mini Kit.


description: rapidly proliferating (CFSE-low) CD8 cell population

source_name: Homeostatically Proliferated CFSE-labeled CD8+ T cells (spleen), less than 8 divisions


title: Normal lung 403N sample

status: Public on Jul 22 2008

city: Madrid

first: Barbara

last: Angulo

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology Program

country: Spain

institute: Spanish National Cancer Centre

description: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to  be used as a reference for microarray gene-profiling experiments. Equal quantities of DNase-treated total RNA from each cell line (adenocarcinoma, mammary gland; melanoma;  hepatoblastoma, liver; liposarcoma; adenocarcinoma, cervix; histiocytic lymphoma; macrophage; embryonal carcinoma, testis; lymphoblastic leukemia, T lymphoblast; glioblastoma, brain; plasmacytoma; myeloma; B lymphocyte) were pooled to make the Universal Human Reference RNA.

hyb_protocol: 1.- Slide pre-washing and denaturation: slide was incubated in SDS 0.1% at room temperature for 5min (x2). After rinse with miliQ-water, slide was transfered to 95º-100ºC water bath for 2min and then to miliQ-water at room temperature. 2.- Slide pre-hybridization: slide was sinked in a staining dish containing pre-warmed pre-hybridization buffer (4x SCC, 0.1% SDS and 0.002% BSA) and was incubated at 65ºC for 45min. After rinse with miliQ-water, slide was dried using centrifuge (300g, 3min). 3.- Hybridization: the probe (mix Cy3-labeled and Cy5-labeled cDNAs) was centrifuged at full speed for 5min at room temperature. Then it was applied (approx. 44µl, leave 2µl from the bottom of the tube behind in order to avoid transferring any sediment to the slide) to a clean cover-slip and place on the pre-hybridized microarray. The slide was placed in a hybridization chamber with the printed area and the cover-slip at the top, and was incubated overnight (15-20h) at 55ºC in an oven. 4.- Post-hybridization washes: low- and high-stringency wash buffers were prepared from 20x SCC and 10% SDS stocks solutions (wash buffer 1: 2x SSC, 0.5% SDS; wash buffer 2: 0.5x SSC, 0.5% SDS). Wash buffer 1 was pre-warmed and kept at the temperature used for the hybridization,  wash buffer 2 was kept at room temperature. Slide was placed in a falcon with wash buffer 1 until the cover-slip has fallen from the slide. Wash slide 3 times in pre-warmed wash buffer 1, 10min each, with shaking at room temeprature. Wash slide in wash buffer 2 with shaking, 15min for the first wash and 5min for the last ones. Slide was dried using a centrifuge (300g, 3min). Scanning as soon as possible and protect from direct light.

scan_protocol: Slides were scanned for Cy3 and Cy5 fluorescence on a Agilent G2565BA Microarray Scanner System. 1.- Place each slide in a cassette as follows: orient the slide so that it is array-side down and to the left; take cassette flat side down, place on flat surface and push down on the two buttons; with the buttons pressed, insert the slide (keeping everything flat); release buttons when slide has been fully inserted. 2.- Place cassettes into carousel. The etched side should now face to the left, and you should be looking at the back of the slide. Note: the cassette must start with the first slot. The scanner recognizes an empty slot as a sign to stop scanning. Close the scanner top. 3.- Double-click on the Agilent Scanner icon. When it opens, the scanner will go through some initialization steps. Also, if the lasers are not fully warm, there will be a warning sign that will give an approximate time that the lasers will be ready. 4.- Enter your name under Operator and check to see that the controls are set for the following: output directory is D:\niehs; both Red and Green channels are checked and are set to 100%; the size is 10 microns. 5.- Click on Options: choose to scan default slide area under Scan Region Options; specify slide area to largest area under Default Scan Region;  click on Instrument serial number under Automatic File Naming (it will then be highlighted). Choose and type in your identifier for that day. Leave the Slot Number as is. 6.- Fill out log in the Scanner Cassette Log with your name, date and the order you put your slides into the carousel. This is important to assure proper renaming after scanning is complete. Click on OK to close the Options window. 7.- Double check that all the settings are properly set and click on Scan. 8.- After scan is complete, you will need to change the names to format pxxsxx. To do this: with the right mouse button, click on the Start menu and choose Explorer. Navigate your way through the files by clicking on the D drive on the far left hand side of the screen. Double click on D drive then double click onniehs. This folder contains all of the scanned files. Locate your slides by looking for the identifier you used for the scan. Click once to highlight name and click once more to get a cursor in the file name. Type in the proper name using the log you filled out earlier. Once all of the names have been changed, highlight the newest slides and move them into the appropriate boxes on Witchfire. 9.- Once you are done, log out of the computer, take the cassettes out of the carousel and your slides out of the cassettes. Turn off scanner.

data_processing:
Cy3 and Cy5 fluorescent signals were quantified using GenePix Pro 5.0 (Axon Instruments Inc.). Substandard spots were manually flagged and discarded for further analysis.
The Cy5/Cy3 ratios were normalized to the median ratio value using the DNMAD tool, based on a print-tip loess method. The conditions for the normalization were: 1) use negative flags, that means that the flagged spots are not used for the normalization and are turned into missing values; 2) do not use background correction.
The normalized and semi-logarithmic transformed data were preprocessing using GEPAS software. Conditions for data pre-processing were: 1) merge replicates (the Cy5/Cy3 ratios of replicated spots were averaged); 2) filter missing values in order to exclude for further analysis any gene with data missing in more than 10% of the samples.
For unsupervised hierarchical clustering, we used a complete-linkage method with correlation distance. Genes whose expression levels varied by a factor of less than 3 across the samples were eliminated to leave only the mos variably expressed transcripts.The SOTARRAY Clustering Program was used for the hierarchical clustering of the samples and the Gene Cluster/Tree View program was used to view gene expression profiles.
To identify the genes that are important for distinguishing subgroups defined by histological type or gene alterations, we did t-tests with 200.000 random permutations to compute significance. To account for the effect of multiple hypothesis testing on the identification of significance, adjusted P-values were computed to control for the false discovery rate (FDR). The differentially expressed genes were functionaly classified manually on the basis of exhaustive searches in Pubmed an in Gene Ontology databases.

source_name: RNA from NSCLC tumor 403N labeled with Cy5

label_protocol:
1.- 2.5µg of amplified RNA from each sample (lung tumors, normal lung tissues and Universal Human Reference RNA) were primed with 3µl of random hexamers d(N)6 0.5mg/ml (Promega) at 70ºC for 10min. For each labeling reaction, a master mix was prepared: 5µl First Strand buffer 5x, 2.5µl DTT 0.1M, 0.5µl unlabeled dNTPs 50x (dATP/dCTP/dGTP:dTTP 25:5), 1.5µl Cy5-dUTP 10mM (for lung tumor or normal lung samples) or Cy3-dUTP 10mM (for Universal Human Reference RNA), 0.63µl RNasin Inhibitor and 1.25µl SuperScript II (200U/µl). The labeling reaction was incubated at room temperature for 10min and then incubated at 42ºC for 2h. Tubes were protected from direct light.
2.- Each fluorescent labeled cDNA was purified with CyScribe GFX Purification kit (Amersham) following manufacturer's instructions.
3.- The Cy3-labeled and Cy5-labeled cDNAs for each hybridization were combined into a single tube. 10µg of Human Cot-1 DNA (Invitrogen) were added.
4.- To precipitate each hybridization probe, 0.1 volumes of sodium acetate 0.1M and 2.5 volumes of absolute ethanol were added.
5.- Each probe was resuspended in 4µl of filtered EDTA 10mM ph 8 and denatured at 95ºC for 10min. 40µl of SlideHyb buffer 1x (Ambion), prewarmed at 65ºC, and blocking agents (mix of polyA and yeast tRNA, 10µg and 4µg in 2µl of final volume) were added.

extract_protocol:
1.- Total RNA  from lung tumors and normal lung tissues was isolated in two steps using TRIZOL reagent (Invitrogen), followed by purification with RNeasy mini kit (QIAGEN) and digestion with RNase-free DNase I (QIAGEN) following the manufacturer's instructions. Universal Human Reference RNA (Stratagene), the reference used in all the hybridizations, is provided in a solution of 70% ethanol and 0.1M sodium acetate; it was prepared by centrifugation and washing with 70% ethanol.
2.- cDNA was synthesized from 4µg of each total RNA using SuperScript II Rnase H- Reverse Transcriptase (Invitrogen). Subsequent amplification was carried out with MegaScript T7 Kit (Ambion) following the manufacturer's instruction for assembling the in vitro transcription reaction. The amplified RNA was cleaned up with RNeasy mini kit (QIAGEN).

value: lung

tag: Normal lung

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3

tag: no additional information


title: NSCLC tumor 447T sample

source_name: RNA from NSCLC tumor 447T labeled with Cy5

tag: Gender

value: female

tag: Smoking status

value: smoker

tag: Histological type

value: adenocarcinoma

tag: Genetic background

value: P53- / KRAS- / LKB1- / EGFR+

tag: Degree of differentiation

value: well

tag: Tumor size

tag: Lymph node involvement


title: Normal lung 359N sample

source_name: RNA from NSCLC tumor 359N labeled with Cy5


title: NSCLC tumor 368T sample

source_name: RNA from NSCLC tumor 368T labeled with Cy5

value: squamous cell carcinoma


title: NSCLC tumor 386T sample

source_name: RNA from NSCLC tumor 386T labeled with Cy5

value: P53- / KRAS- / LKB1- / EGFR- / PIK3CA- / BRAF-


title: NSCLC tumor 362T sample

source_name: RNA from NSCLC tumor 362T labeled with Cy5

value: poor


title: NSCLC tumor 438T sample

source_name: RNA from NSCLC tumor 438T labeled with Cy5

value: non-smoker

value: P53+ / KRAS- / LKB1- / EGFR- / PIK3CA- / BRAF-

value: moderate


title: NSCLC tumor 434T sample

source_name: RNA from NSCLC tumor 434T labeled with Cy5

value: P53+ / KRAS- / LKB1- / EGFR+ / BRAF-


title: NSCLC tumor 388T sample

source_name: RNA from NSCLC tumor 388T labeled with Cy5

value: P53+ / PIK3CA-


title: NSCLC tumor 402T sample

source_name: RNA from NSCLC tumor 402T labeled with Cy5

value: male


title: NSCLC tumor 396T sample

source_name: RNA from NSCLC tumor 396T labeled with Cy5

value: large cell carcinoma

value: P53- / KRAS+ / LKB1+ / EGFR- / PIK3CA-

value: X


title: NSCLC tumor 400T sample

source_name: RNA from NSCLC tumor 400T labeled with Cy5

value: lung

value: female


title: NSCLC tumor 358T sample

source_name: RNA from NSCLC tumor 358T labeled with Cy5

value: smoker

value: adenocarcinoma


title: NSCLC tumor 372T sample

source_name: RNA from NSCLC tumor 372T labeled with Cy5


title: NSCLC tumor 360T sample

source_name: RNA from NSCLC tumor 360T labeled with Cy5


title: NSCLC tumor 374T sample

source_name: RNA from NSCLC tumor 374T labeled with Cy5

value: P53- / PIK3CA-

value: well


title: NSCLC tumor 354T sample

source_name: RNA from NSCLC tumor 354T labeled with Cy5

value: P53+ / KRAS+ / LKB1- / EGFR- / PIK3CA- / BRAF-


title: NSCLC tumor 390T sample

source_name: RNA from NSCLC tumor 390T labeled with Cy5

value: poor

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3


title: NSCLC tumor 380T sample

source_name: RNA from NSCLC tumor 380T labeled with Cy5

value: P53+ / KRAS- / LKB1+ / EGFR- / PIK3CA+ / BRAF-


title: Normal lung 369N sample

source_name: RNA from NSCLC tumor 369N labeled with Cy5


title: NSCLC tumor 446T sample

source_name: RNA from NSCLC tumor 446T labeled with Cy5

value: P53+ / KRAS- / LKB1- / EGFR- / BRAF-


title: Barley seeds control in Hoagland solution for 12hr

description: barley seeds RNA was extracted after 12hr imbibition in Hoagland solution at 25C

scan_protocol: Standard protocol, available from the following website, http://www.affymetrix.com/support/technical/manual/expression_manual.affx


title: Barley seeds with P. aeruginosa PAO1 for 12hr

description: barley seeds RNA was extracted after 12hr infection of P. aeruginosa PAO1 at 25C

label_protocol:
Standard protocol, available from the following website,
http://www.affymetrix.com/support/technical/manual/expression_manual.affx


title: NSCLC tumor 348T sample

source_name: RNA from NSCLC tumor 348T labeled with Cy5

value: non-smoker

value: P53- / KRAS+ / LKB1- / EGFR- / PIK3CA- / BRAF-


title: H3K4me3 kidney NimbleGen Mouse Chr11:36912182-99375819 tiling array array number 59251

status: Public on Jul 26 2008

type: genomic

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5).

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: log2R normalized using the limma R package method=loess

molecule: genomic DNA

source_name: Chromatin immunoprecipitated DNA from kidney cells using H3K4me3 antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: kidney immunoprecipitated chromatin

source_name: Input Chromatin kidney cells.

extract_protocol: input chromatin

value: kidney input chromatin


title: NSCLC tumor 240T sample

source_name: RNA from NSCLC tumor 240T labeled with Cy5

value: male

value: squamous cell carcinoma

value: P53+ / PIK3CA-

value: moderate


title: NSCLC tumor 273T sample

source_name: RNA from NSCLC tumor 273T labeled with Cy5

value: lung

value: X


title: NSCLC tumor 230T sample

source_name: RNA from NSCLC tumor 230T labeled with Cy5

value: female

value: adenocarcinoma

value: P53+ / KRAS- / LKB1- / EGFR- / PIK3CA- / BRAF-


title: NSCLC tumor 264T sample

source_name: RNA from NSCLC tumor 264T labeled with Cy5

value: smoker

value: P53- / PIK3CA+


title: NSCLC tumor 252T sample

source_name: RNA from NSCLC tumor 252T labeled with Cy5


title: NSCLC tumor 268T sample

source_name: RNA from NSCLC tumor 268T labeled with Cy5

value: P53- / KRAS- / LKB1- / EGFR- / BRAF-

value: well


title: NSCLC tumor 245T sample

source_name: RNA from NSCLC tumor 245T labeled with Cy5

value: P53- / KRAS+ / LKB1- / EGFR-  / BRAF-


title: NSCLC tumor 276T sample

source_name: RNA from NSCLC tumor 276T labeled with Cy5

value: P53+ / PIK3CA+


title: H3K4me3 heart NimbleGen Mouse Chr11:36912182-99375819 tiling array array number 59358

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from heart cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5).

source_name: Chromatin immunoprecipitated DNA from heart cells using H3K4me3 antibody

value: heart immunoprecipitated chromatin

source_name: Input Chromatin heart cells.

value: heart input chromatin


title: NSCLC tumor 258T sample

source_name: RNA from NSCLC tumor 258T labeled with Cy5

value: male

value: large cell carcinoma

value: poor

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3


title: NSCLC tumor 237T sample

source_name: RNA from NSCLC tumor 237T labeled with Cy5

value: squamous cell carcinoma

value: P53+ / PIK3CA-

value: moderate


title: NSCLC tumor 270T sample

source_name: RNA from NSCLC tumor 270T labeled with Cy5

value: lung


title: NSCLC tumor 261T sample

source_name: RNA from NSCLC tumor 261T labeled with Cy5

value: adenocarcinoma


title: NSCLC tumor 251T sample

source_name: RNA from NSCLC tumor 251T labeled with Cy5

value: P53- / PIK3CA-


title: NSCLC tumor 267T sample

source_name: RNA from NSCLC tumor 267T labeled with Cy5

value: smoker


title: NSCLC tumor 269T sample

source_name: RNA from NSCLC tumor 269T labeled with Cy5


title: NSCLC tumor 227T sample

source_name: RNA from NSCLC tumor 227T labeled with Cy5

value: P53+ / KRAS- / LKB1+ / EGFR- / PIK3CA- / BRAF-


title: NSCLC tumor 181T sample

source_name: RNA from NSCLC tumor 181T labeled with Cy5


title: NSCLC tumor 256T sample

source_name: RNA from NSCLC tumor 256T labeled with Cy5


title: H3K4me3 brain NimbleGen Mouse Chr11:36912182-99375819 tiling array array number 61037

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from brain cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5).

source_name: Chromatin immunoprecipitated DNA from brain cells using H3K4me3 antibody

value: brain immunoprecipitated chromatin

source_name: Input Chromatin brain cells.

value: brain input chromatin


title: NSCLC tumor 229T sample

source_name: RNA from NSCLC tumor 229T labeled with Cy5

value: P53+  / PIK3CA+

value: well

value: X


title: Normal lung 171N sample

source_name: RNA from NSCLC tumor 171N labeled with Cy5


title: NSCLC tumor 174T sample

source_name: RNA from NSCLC tumor 174T labeled with Cy5

value: female

value: P53- / KRAS+ / LKB1- / EGFR- / PIK3CA- / BRAF-


title: H3K4me3 liver NimbleGen Mouse Chr11:36912182-99375819 tiling array array number 61062

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5).

source_name: Chromatin immunoprecipitated DNA from liver cells using H3K4me3 antibody

value: liver immunoprecipitated chromatin

source_name: Input Chromatin liver cells.

value: liver input chromatin


title: NSCLC tumor 170T sample

source_name: RNA from NSCLC tumor 170T labeled with Cy5

value: male

value: squamous cell carcinoma

value: P53- / PIK3CA+

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3


title: Normal lung 169N sample

source_name: RNA from NSCLC tumor 169N labeled with Cy5

value: lung


title: NSCLC tumor 224T sample

source_name: RNA from NSCLC tumor 224T labeled with Cy5


title: NSCLC tumor 185T sample

source_name: RNA from NSCLC tumor 185T labeled with Cy5

value: non-smoker

value: adenocarcinoma

value: P53- / KRAS- / LKB1- / EGFR+ / PIK3CA- / BRAF-

value: poor


title: NSCLC tumor 280T sample

source_name: RNA from NSCLC tumor 280T labeled with Cy5

value: smoker

value: P53+ / KRAS- / LKB1- / EGFR- / PIK3CA- / BRAF-


title: NSCLC tumor 168T sample

source_name: RNA from NSCLC tumor 168T labeled with Cy5


title: NSCLC tumor 167T sample

source_name: RNA from NSCLC tumor 167T labeled with Cy5

value: P53- / PIK3CA-


title: NSCLC tumor 166T sample

source_name: RNA from NSCLC tumor 166T labeled with Cy5

value: moderate


title: NSCLC tumor 160T sample

source_name: RNA from NSCLC tumor 160T labeled with Cy5

value: well


title: NSCLC tumor 165T sample

source_name: RNA from NSCLC tumor 165T labeled with Cy5

value: P53+ / PIK3CA-


title: NSCLC tumor 134T sample

source_name: RNA from NSCLC tumor 134T labeled with Cy5


title: NSCLC tumor 159T sample

source_name: RNA from NSCLC tumor 159T labeled with Cy5

value: P53+  / PIK3CA-


title: Normal lung 140N sample

source_name: RNA from NSCLC tumor 140N labeled with Cy5


title: NSCLC tumor 156T sample

source_name: RNA from NSCLC tumor 156T labeled with Cy5

value: P53+ / PIK3CA+


title: NSCLC tumor 149T sample

source_name: RNA from NSCLC tumor 149T labeled with Cy5


title: NSCLC tumor 162T sample

source_name: RNA from NSCLC tumor 162T labeled with Cy5


title: NSCLC tumor 127T sample

source_name: RNA from NSCLC tumor 127T labeled with Cy5

value: P53- / KRAS+ / LKB1- / EGFR- / BRAF-


title: NSCLC tumor 133T sample

source_name: RNA from NSCLC tumor 133T labeled with Cy5

value: female

value: P53- / KRAS- / LKB1- / EGFR- / PIK3CA- / BRAF-

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3


title: NSCLC tumor 136T sample

source_name: RNA from NSCLC tumor 136T labeled with Cy5

value: male

value: P53- / KRAS+ / LKB1+ / EGFR-/ PIK3CA- / BRAF-


title: NSCLC tumor 139T sample

source_name: RNA from NSCLC tumor 139T labeled with Cy5

value: lung

value: squamous cell carcinoma


title: NSCLC tumor 143T sample

source_name: RNA from NSCLC tumor 143T labeled with Cy5


title: NSCLC tumor 157T sample

source_name: RNA from NSCLC tumor 157T labeled with Cy5

value: large cell carcinoma

value: P53+ / KRAS- / LKB1- / EGFR- / PIK3CA-


title: NSCLC tumor 131T sample

source_name: RNA from NSCLC tumor 131T labeled with Cy5

value: non-smoker

value: adenocarcinoma

value: P53- / KRAS- / LKB1- / EGFR- / BRAF-


title: NSCLC tumor 120T sample

source_name: RNA from NSCLC tumor 120T labeled with Cy5

value: smoker

value: P53- / PIK3CA+

value: moderate


title: NSCLC tumor 116T sample

source_name: RNA from NSCLC tumor 116T labeled with Cy5

value: poor


title: NSCLC tumor 108T sample

source_name: RNA from NSCLC tumor 108T labeled with Cy5

value: well

value: X


title: NSCLC tumor 155T sample

source_name: RNA from NSCLC tumor 155T labeled with Cy5

value: P53+ / KRAS+ / LKB1- / EGFR- / PIK3CA- / BRAF-