title: B98

value: resection


title: B76

status: Public on Jun 22 2008

type: genomic

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

country: USA

institute: University of North Carolina

description: 103 hepatocellular carcinomas and 95 adjacent cirrhotic, non-tumoral liver tissue were obtained at the time of surgical resection of orthotopic transplantation.

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Copy numbers were estimated by the GenePattern SNPFileCreator module

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: hepatocellular carcinoma

label_protocol: Affymetrix standard procedure

growth_protocol: Tumors obtained at time of surgical resection or transplantation, according to institutional review board approved protocols

extract_protocol: Genomic DNA was extracted with the ChargeSwitch gDNA mini kit (Invitrogen) according to manufacturer's instructions, followed by phenol-chloroform extraction

value: A

tag: Age

tag: Sex

value: F

tag: Class

tag: AFP

tag: TP53 mutation

tag: CTNNB1 mutation

tag: Immunocytochemistry

value: pRPS6 :1

value: pIGFR1 :0

value: pAkt :0

value: CTNNB1 :1


title: B74

value: C

value: M

value: Proliferation

value: pAkt :1

value: CTNNB1 :0


title: B94

value: pRPS6 :0


title: B80

value: Polysomy chr7


title: B78


title: B82

value: Unannotated


title: B70


title: B72

value: Inflammation


title: WT strain, replicate 3

status: Public on Jun 21 2008

type: RNA

city: Indianapolis

first: Mark

last: Goebl

state: IN

address: 1345 West 16th St.

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: no additional

hyb_protocol: The cRNA is purified using Qiagen RNeasy columns, quantitated and then  fragmented by incubation at high temperature with magnesium. Fifteen μg of biotinylated cRNA is added to a total hybridization cocktail of 300 μl, and 200 μl is hybridized to a GeneChip® after adding control oligonucleotides. Hybridization is at 45°C for 17 h with constant rotation. The hybridization mixture is then removed and the GeneChips® are washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station. To reduce non-random error, balanced groups of samples are handled in parallel.

scan_protocol: Arrays are then scanned using the dedicated scanner, controlled by Affymetrix GCOS software. Images are examined for defects.

data_processing: The Affymetrix® Microarray Suite version 5 (MAS5) algorithm analyzes the hybridization intensity data from GeneChip® expression probe arrays and calculates a set of metrics that describe probe set performance. The average intensity on each array is normalized by global scaling to a target intensity of 1000.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: total RNA, experimental variables include CDC34tm mutation, a nourseothricin resistance gene, partial disruption of PST1 3' region and leu2-3,112 allele

label_protocol: For samples of 2 microgram or more, we do single cycle labeling. This involves synthesizing cDNA using a T7 promoter-dT24 oligonucleotide as primer with the Invitrogen Life Technologies SuperScript Choice system. Following second strand cDNA synthesis and incubation with T4 DNA polymerase, the products are purified using an Affymetrix Cleanup Module. Biotinylated cRNA is made using the Affymetrix IVT kit.

growth_protocol: The Saccharomyces cerevisiae CDC34tm strain (RRC85, MATα, CDC34tm(NatR)) which is marked by a nourseothricin resistance gene (NatR) and an isogenic wild type strain (DBY2059, MATα, leu2-3, 112) were inoculated from stationary phase cultures into a synthetic defined medium containing 2% dextrose, 0.17% yeast nitrogen base minus amino acids and ammonium sulfate, 0.25% L-glutamine, 0.025% magnesium sulfate and 25.2 mg/L L-Leucine. Four separate cultures of each strain were grown at 30°C, allowing between three and four doublings and cells were collected at approximately 8 x 10e6cells/ml.

extract_protocol: Total RNA was extracted using a hot acid phenol-chloroform protocol as previously described (Schmitt et al. 1990).  RNA quality was verified with OD260/280 readings and a 1.5% agarose gel.

treatment_protocol: Cells frozen in liquid nitrogen

tag: WT


title: B68


title: WT strain, replicate 4

description: no additional


title: WT strain, replicate 1

description: no additional


title: B66

value: B


title: WT strain, replicate 2

description: no additional


title: CDC34tm strain, replicate 3

description: no additional

tag: CDC34tm confers only slightly slow growth phenotype


title: B37

value: transplant


title: CDC34tm strain, replicate 1

description: no additional


title: B41


title: B35

value: A

value: resection


title: B27


title: B33


title: B31


title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -2 (separate feeding)

status: Public on Jun 20 2008

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007). Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics. 8:25.

data_processing: GCOS version 2.1 calculated intensity data with global scaling to 150

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

source_name: Steady state Aerobic formaldehyde-glucose limited chemostat culture (separate feeding)

growth_protocol:
Aerobic chemostat cultivation was performed at 30ºC in 1.5 L laboratory fermenters (Applikon, Schiedam, the Netherlands) with a stirrer speed of 800 rpm. The working volume was kept at 1 L by a Masterflex peristaltic effluent pump (Barrington IL, USA) coupled to an electric level sensor. The pH was kept at 5.0 using an Applikon ADI 1030 biocontroller via automatic addition of 2.0 M potassium hydroxide. Cultures were sparged with air at a flow rate of 0.5 L.min-1 using Brooks 5876 mass-flow controllers. The dissolved oxygen tension (DOT) was continuously monitored with an oxygen electrode (Ingold, model 34.100.3002, Mettler, Utrecht, the Netherlands) and remained above 50% of air saturation in all chemostat cultures. The dilution rate (in steady-state cultures equal to the specific growth rate) was set to 0.10 h-1.
Synthetic medium was prepared as described previously (Verduyn et al., 1992) with glucose (7.5 g.L 1) as the sole carbon source. Filter sterilized vitamins were either added directly to the medium or were added from a separate reservoir. Formaldehyde was prepared by hydrolysing para-formaldehyde in 15 mM ammonium hydroxide (30 min. incubation at 100ºC) and aseptically added to the medium reservoir at various concentrations as indicated in the results section. When formaldehyde was co-fed, S. cerevisiae was first cultivated in batch on glucose alone, followed by 3-days with 30 mM formaldehyde in the medium vessel after which the medium was switched to the final amount of formaldehyde until a steady state was obtained. Steady state was defined as the situation in which at least five volume changes had passed since the last change in culture parameters, and in which the biomass concentration, as well as all other specific production or consumption rates, had remained constant (<2% variation) for at least two volume changes.

treatment_protocol: Liquid nitrogen quenching

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Kotter, Frankfurt, Germany.


title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -1 (separate feeding)

scan_protocol: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007). Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics. 8:25.


title: B15


title: B19

value: pRPS6 :1

value: pIGFR1 :1


title: B25

value: pAkt :0


title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -2 (co feeding)

source_name: Steady state Aerobic formaldehyde-glucose limited chemostat culture (co feeding)

label_protocol:
Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were
performed as described previously (Knijnenburg et al 2007).
Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
BMC Genomics. 8:25.


title: B29

value: pIGFR1 :0


title: CDC34tm strain, replicate 4

description: no additional


title: B17

value: F


title: B21


title: B13

value: M


title: B23


title: B39


title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -1 (co feeding)

extract_protocol:
Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007).
Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
BMC Genomics. 8:25.

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. KoÂ¨tter, Frankfurt, Germany.


title: Bb infection of H4 cells replicate 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Bb infection of H4 cells replicate 2

hyb_protocol: Following fragmentation, 3-6 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Borreliella burgdorferi

source_name: H4 with Bb infection replicate 2

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

growth_protocol:
Human cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, Virginia, USA). The human neuroglial cell line (H4) was grown in Dulbecco’s Modified Eagle’s Medium (DMEM) with 4 mM L-glutamine containing 4.5 g / L glucose, 1.5 g / L sodium bicarbonate, and supplemented with 10% fetal bovine serum.  Cells were grown at 37°C with 5% CO2 in a humidified cell incubator.  Cells were harvested from confluent monolayers using 0.05% trypsin with 10 mM EDTA and enumerated with a hemacytometer
B. burgdorferi strains used are derivatives of strain B31.  B31 clone A (B31-A) is a high-passage non-infectious derivative of type strain B31 (ATCC 35210), and B31 A3 is a clonal, low-passage infectious strain (Elias et al., 2002).  Frozen stocks of all B. burgdorferi strains were maintained in 60% glycerol at -70° C.  All bacterial strains were grown in liquid Barbour-Stoenner-Kelly (BSK-II) complete medium at 35° C with 5% CO2

extract_protocol: After incubation with B. burgdorferi for 20 hours, monolayers were washed 3 times in phosphate buffered saline (PBS) to remove unassociated spirochetes.  Cells were then scraped from the flask and suspended in PBS.  The cells were centrifuged at 125 x G for 5 minutes and total RNA was isolated from infected monolayers using the RNAqueous-Midi kit (Ambion, Austin, TX.).  Polyadenylated host RNA was removed by using MicrobEnrich columns (Ambion).  RNA samples were subjected to DNAse treatment using Turbo DNA-free (Ambion).  RNA samples were tested for contaminating DNA by PCR analysis for flaB (flagellin gene) prior to use in the cDNA synthesis, microarray, and qRT-PCR assays

treatment_protocol: Mammalian cells were allowed to grow to confluence on a T-225 flask (Corning) and were trypsinized and enumerated the morning of the experiment.  After trypsinization, the cells were allowed to re-attach to the flasks for 4 h at 37° C.  B. burgdorferi were grown for 3 days until they reached mid-logarithmic phase and enumerated using a Petroff Hausser counting chamber.  Bacteria were centrifuged at 500 x g for 20 minutes and resuspended in pre-warmed DMEM.  B. burgdorferi were added to the mammalian cells at a multiplicity of infection (MOI) of 40, and were incubated at 35 C with 5% CO2 for approx. 20 h

tag: Bb infection of H5


title: B84

value: CTNNB1 :1


title: Bb infection of H4 cells replicate 1

description: Gene expression data from_Bb infection of H4 cells replicate 1

source_name: H4 with Bb infection replicate 1

tag: Bb infection of H4


title: H4 negative control replicate 2

description: Gene expression data from_H4 cells replicate 2

source_name: H4 only replicate 2

tag: H4 cells


title: Bb infection of H4 cells replicate 3

description: Gene expression data from_Bb infection of H4 cells replicate 3

source_name: H4 with Bb infection replicate 3

tag: Bb infection of H6


title: H4 negative control replicate 1

description: Gene expression data from_H4 cells replicate 1

source_name: H4 only replicate 1


title: 72hr D v A Slide 4B

status: Public on Jun 18 2008

city: Mississippi State

first: Jeff

last: Wilkinson

state: MS

institute: Mississippi State University

description: Hybridized slides were scanned using a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) and the independent TIFF images from each channel were analyzed using TIGR Spotfinder software program.

hyb_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900TM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900TM Kit (Genisphere) according to the manufacturer’s protocol. Each experiment consisted of one aflatoxigenic parental strain and one nonaflatoxigenic progeny, compared after 48- or 72-hr growth. Each comparison was repeated with duplicate dye-flip. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing following Genisphere’s instructions. Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49C for 4 h in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA) and followed by washes to remove non-specific background.

data_processing: To remove the non-specific background signals, the raw data were normalized using a local regression technique, LOWESS (LOcally WEighted Scatterplot Smoothing), using the MIDAS software tool. The LOWESS normalized dye-flips were then combined to minimize any artifacts introduced by the Cy3 or Cy5 dyes. The resulting data were averaged over duplicate gene features on each array for each replicate experiment. Some genes are represented by two separate non-overlapping fragments, therefore since a gene may be detected by each fragment they are defined as features so that gene count will not be over reported. All calculated gene expression ratios were log2-transformed and aflatoxin biosynthetic gene expressions were examined by cross comparison between experiments using TIGR MeV.  To determine genes that were significantly expressed across all experiments the expression ratios were log2-transformed. Differentially expressed genes at the 95% confidence level for each reference set were determined by assuming the log2 ratios for each data set form a normal distribution, and selecting genes with log2 (ratio) values >1.96 standard deviations from the mean. This filtration of the significantly expressed genes was conducted using MIDAS, and the resulting lists of the genes were examined further by cross comparison between experiments using TIGR MeV.

organism: Aspergillus flavus

source_name: Aspergillus flavus 459B-20-2

growth_protocol: For each strain used for total RNA preparation, an aliquot of spore suspension was added to 100 ml potato dextrose broth (PDB, Beckton and Dickinson Company, Sparks, MD) to give a final concentration of 5 × 106 per milliliter. The medium containing spores was dispensed onto five Petri dishes (100 × 15 mm, FALCON® 1029), each having 20 ml. Stationary cultures were incubated at 30oC in darkness. After 48- and 72-h growth, mycelia from each of the five culture plates were harvested by filtration, pooled, and rinsed by sterilized distilled water. Mycelia were pulverized to a fine powder with a mortar and pestle in the presence of liquid nitrogen.

extract_protocol: Total RNA was prepared using TRIzol® reagent (Invitrogen, Carlsbad, CA). Three micrograms of total RNA was used to generate cDNA using Genispheres RT primers with Supercript II, Dithiotreitol and 5X SuperScript II First Strand Buffer (Invitrogen) following the manufacturer’s instructions.

treatment_protocol: Aspergillus flavus NRRL 29459, NRRL 29474, and NRRL 29490 are aflatoxigenic strains originated from soil collection in a peanut field (Terrell Co., Georgia, USA). Strains 459B-20-2, 474A-20, and 499A-20 were nonaflatoxigenic isolates obtained after 20 serial transfers of the parental strains on potato dextrose agar slants (Horn and Dorner 2002).

tag: Aspergillus flavus 459B-20-2 72 hr growth

source_name: Aspergillus flavus NRRL 29459

tag: Aspergillus flavus NRRL 29459 72 hr growth


title: Bb cDNA positive control replicate 2

description: Gene expression data from_Bb cDNA positive control replicate 2

source_name: Bb replicate 2

tag: Bb


title: 48hr J vs C Slide 3B

scan_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900TM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900TM Kit (Genisphere) according to the manufacturer’s protocol. Each experiment consisted of one aflatoxigenic parental strain and one nonaflatoxigenic progeny, compared after 48- or 72-hr growth. Each comparison was repeated with duplicate dye-flip. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing following Genisphere’s instructions. Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49C for 4 h in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA) and followed by washes to remove non-specific background.

source_name: Aspergillus flavus 499A-20

tag: Aspergillus flavus 499A-20 48 hr growth

source_name: Aspergillus flavus NRRL 29499

tag: Aspergillus flavus NRRL 29499 48 hr growth


title: 48hr G vs B Slide 2B

source_name: Aspergillus flavus 474A-20

label_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900TM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900TM Kit (Genisphere) according to the manufacturer’s protocol. Each experiment consisted of one aflatoxigenic parental strain and one nonaflatoxigenic progeny, compared after 48- or 72-hr growth. Each comparison was repeated with duplicate dye-flip. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing following Genisphere’s instructions. Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49C for 4 h in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA) and followed by washes to remove non-specific background.

tag: Aspergillus flavus 474A-20 48 hr growth

source_name: Aspergillus flavus NRRL 29474

tag: Aspergillus flavus NRRL 29474 48 hr growth


title: Bb cDNA positive control replicate 1

description: Gene expression data from_Bb cDNA positive control replicate 1

source_name: Bb replicate 1


title: 72hr J vs C Slide 6B

tag: Aspergillus flavus 499A-20 72 hr growth

tag: Aspergillus flavus NRRL 29499 72 hr growth


title: 72 hr G vs B Slide 5B

tag: Aspergillus flavus 474A-20 72 hr growth

tag: Aspergillus flavus NRRL 29474 72 hr growth


title: 48hr C vs J Slide 3A


title: 72hr B vs G Slide 5A


title: 48hr B vs G Slide 2A


title: Bb cDNA positive control replicate 3

description: Gene expression data from_Bb cDNA positive control replicate 3

source_name: Bb replicate 3


title: 48hr D vs A Slide 1B

tag: Aspergillus flavus 459B-20-2 48 hr growth

tag: Aspergillus flavus NRRL 29459 48 hr growth


title: 72hr A vs D Slide 4A


title: 48hr A vs D Slide 1A

tag: Aspergillus flavus 459B-20-2  48 hr growth


title: 72hr C vs J Slide 6A


title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -3 (separate feeding)

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Kotter, Frankfurt, Germany.


title: BW25113 w/t LB glu 24 hr biofilm cells

status: Public on Jun 17 2008

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 24 hours of growth at 37C in LB glu with glasswool

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB glu medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: BW25113 w/t LB glu 4 hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 4 hours of growth at 37C in LB glu with glasswool.

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181)

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB glu medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 hha mutant LB glu 15 hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 hha mutant after 15 hours of growth at 37C in LB glu with glasswool


title: BW25113 hha deletion mutant LB 4hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 hha mutant after 4 hours of growth at 37C in LB with glasswool

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 w/t LB glu 15 hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 15 hours of growth at 37C in LB glu with glasswool.


title: BW25113 w/t LB 4hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 4 hours of growth at 37C in LB with glasswool.

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software

scan_protocol: ollowing affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS)

extract_protocol: “The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: CDC34tm strain, replicate 2

description: no additional

source_name: total RNA, experimental variables include CDC34tm mutation, a nourseothricin resistance gene, partial disruption of PST1 3' region and leu2-3,112 allele

tag: CDC34tm confers only slightly slow growth phenotype


title: Steady-state-based anaerobic glucose pulse t= 5 min - 2

status: Public on Jun 16 2008

hyb_protocol: EukGE-ws2s4 Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

scan_protocol: Affymetrix scanner 3000

data_processing: GeneChip® Operating Software (GCOS), version 1.2. Samples scaled to 150.

label: Biotynylated UTP- SAPE

source_name: 5 min time point after anaerobic glucose pulse

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at 30 °C in 2-l bioreactors with a working volume of 1.5 l as described via an electrical level sensor. Removal of effluent from the center of the culture ensured that biomass concentrations in the effluent line differed by less than 1% from those in the culture. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. A stirrer speed of 800 rpm and air flow of 0.75 liter•min-1 were applied to keep the dissolved-oxygen concentration, as measured with an oxygen electrode, above 60% of air saturation in all chemostat cultivations performed. Steady-state samples were taken after  10 volume changes to avoid strain adaptation due to long-term cultivation. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant over at least three volume changes.
Anaerobic glucose-pulse experiments were started by sparging the medium reservoir of a steady-state glucose-limited aerobic chemostat (airflow of 0.5 liter•min-1) with pure nitrogen gas. Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. Two min after nitrogen sparging and just before adding the glucose, the medium pump was switched off. The 200 mM glucose pulse was injected aseptically through a rubber septum. Samples for RNA extraction were taken for each time point after the perturbation (5, 10, 30, 60 and 120 min) from two independently cultured replicates, while steady state data were taken from three independent chemostats.

extract_protocol:
Sampling of cells from chemostats and total RNA extraction was performed as previously described1. Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
1- Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.

treatment_protocol: liquid nitrogen quenching

tag: Strain

value: CENPK113.7D; Genotype:MATa MAL2-8c SUC2


title: Steady-state-based anaerobic glucose pulse t=60 min - 2

source_name: 60 min time point after anaerobic glucose pulse

label_protocol: Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).


title: H4 negative control replicate 3

description: Gene expression data from_H4 cells replicate 3

source_name: H4 only replicate 3

tag: H4 cells


title: BW25113 hha mutant LB glu 4 hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 hha mutant after 4 hours of growth at 37C in LB glu with glasswool.


city: London

first: Maria

last: Ocampo-Hafalla

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK London Research Institute

description: SUPernatant file for whole genome tiling arrays. [Figures 2 and 3]

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Reference: Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4).

source_name: SUPernatant fraction (equal to Whole Cell Extract)

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

extract_protocol:
Extraction was performed as previously described (Katou et al. 2003).
Reference:
Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

treatment_protocol: Cells were synchronized in G1 with α-factor and released into metaphase arrest in medium containing nocodazole. Scc2 was inactivated by temperature shift before addition of galactose to the medium.

tag: Strain 2270 = Scc1-9PK-TRP, scc2-4


title: Steady-state-based anaerobic glucose pulse 1=30 min - 2

source_name: 30 min time point after anaerobic glucose pulse


title: Steady-state-based anaerobic glucose pulse t=120 min - 2

source_name: 120 min time point after anaerobic glucose pulse


title: Steady-state-based anaerobic glucose pulse t=60 min -1

hyb_protocol: EukGE-ws2v4 Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). 1- Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. epub ahead

label: Biotynylated UTP -SAPE

extract_protocol:
Sampling of cells from chemostats and total RNA extraction was performed as previously described in (1). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions.
1- Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. epub ahead

value: Strain:CENPK113.7D; Genotype:MATa MAL2-8c SUC2


title: Steady-state-based anaerobic glucose pulse t=120 min -1


title: Steady-state-based anaerobic glucose pulse 1=10 min - 2

source_name: 10 min time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse t=5min - 1

data_processing: GeneChip® Operating Software (GCOS), version 1.2.

label: Biotynylated -UTP + SAPE

source_name: 5-min time point after anaerobic glucose pulse

label_protocol:
EukGE-ws2v4
Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies) (1).
1. Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.

extract_protocol:
Sampling of cells from chemostats and total RNA extraction was performed as previously described 1. Probe preparation and hybridization to Affymetrix Genechip®
1. Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.


title: BW25113 hha mutant LB glu 24 hr biofilm cells

description:
Following affymetrix protocol.
After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

scan_protocol: affymetrix

tag: RNA extracted from biofilm cells of E. coli K-12 hha mutant after 24 hours of growth at 37C in LB glu with glasswool


title: Steady-state based anaerobic glucose pulse t=10 min - 1

hyb_protocol: Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies) (1). 1. Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.


title: Steady-state-based anaerobic glucose pulse -t=30 min -1


title: Thymus, technical replicate 1

status: Public on Jun 15 2008

city: Providence

first: Fenghai

last: Duan

state: RI

address: 121 S. Main Street

department: Biostatistics

institute: Brown University

description: Gene expression data from thymus

hyb_protocol: Following fragmentation, the biotinylated cRNA were hybridized for 16 hr at 45C on Rhesus Macaque Genome Array or Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned on Affymetrix scanner 3000

data_processing: The data were preprossed with GC-Robust Multichip Analysis (RMA).

organism: Macaca mulatta

source_name: rhesus macaques thymus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: Tissue

value: thymus


title: Testis, technical replicate 2

description: Gene expression data from testis

source_name: rhesus macaques testis

value: testis


title: Thymus, technical replicate 2

description: Gene expression data from thymus


title: Testis, technical replicate 1

description: Gene expression data from testis


title: Pancreas, technical replicate 2

description: Gene expression data from pancreas

source_name: rhesus macaques pancreas

value: pancreas


title: 500 uM hemin (500A)

status: Public on Jun 13 2008

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: no additional information

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray data were verified with Microarray Suite 5.0 (Affymetrix) and Robust Multichip Average Method (RMA, R package)

organism: Caenorhabditis elegans

source_name: 500 uM hemin

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

treatment_protocol: For microarray analysis, synchronized F2 larvae were re-inoculated in mCeHR-2 medium supplemented with 4, 20 or 500 uM hemin and harvested at the late L4 stage for mRNA prep and probe hybridization to Affymetrix C. elegans Whole Genome Expression Arrays.

tag: L4 stage


title: Fibroblasts, technical replicate 1

description: Gene expression data from immortalized fibroblasts

source_name: rhesus macaques fibroblasts

tag: Cell Line

value: immortalized fibroblasts


title: Fibroblasts, technical replicate 2


title: 20 uM hemin (20B)

description: no additional information

source_name: 20 uM hemin


title: Cerebral cortex, technical replicate 2

description: Gene expression data from cerebral cortex

source_name: rhesus macaques cerebral cortex

value: cerebral cortex


title: Ethanol Control 2 (Clutch A, Group 2, N6)

status: Public on Jun 14 2008

city: New Haven

first: Geffrey

middle: Foresman

last: Stopper

state: CT

address: 165 Prospect St.

department: Department of Ecology & Evolutionary Biology

institute: Yale University

description: Ethanol Control 2 Normalized Expression Value (Clutch A, Group 2, N6)

hyb_protocol: Hybridized according to standard Affymetrix protocols, performed by the Yale University W. M. Keck Foundation Biotechnology Resource Laboratory

scan_protocol: Scanned according to standard Affymetrix protocols, performed by the Yale University W. M. Keck Foundation Biotechnology Resource Laboratory

data_processing: Data were normalized by the Yale University W. M. Keck Foundation Biotechnology Resource Laboratory.  GeneChip Operating Software was used to calculate the overall intensity of each arrray by averaging the intensity values of every probe set on the array with the exception of the top and bottom 2% of the probe set intensities.  For each array, the average intensity of the array was multiplied by a scaling factor for that array to bring it to an arbitrary target intensity value common to all arrays.

organism: Xenopus laevis

source_name: whole hindlimbs, ethanol exposed, 24 hours

label_protocol: Labeled according to standard Affymetrix protocols, performed by the Yale University W. M. Keck Foundation Biotechnology Resource Laboratory

growth_protocol: Approximately 200 tadpoles from each of two clutches (designated “clutch A” and “clutch B”) of the species Xenopus laevis were obtained from Nasco Biology for a total of approximately 400 tadpoles.  Animals arrived at approximately stage 45.  All animals were kept in a room with an air temperature of 25ºC ± 1ºC.  After one day of equilibrating to room temperature, animals were moved to an Aquatic Habitats aquatic housing unit (http://www.aquatichabitats.com/, Apopka, FL).  Thirteen tadpoles were put into each of twenty-four tanks, without mixing clutches, for a total of 156 animals of each clutch.  Each tank was filled to 9 liters with treated water.  Tap water was treated and aged for at least one day with approximately 1ml Stress Coat (Aquarium Pharmaceuticals, Chalfont, PA) for every 22 liters of water.  To decrease temperature-based variability in developmental rates between clutches due to slight temperature variations in the room, tanks were oriented on the rack in four rows of six tanks, with tanks along each row or column alternating between clutches.  To decrease temperature-based variability in developmental rates within clutches, every three days, tanks on the top row were switched with those on the bottom row, and the middle two rows were similarly exchanged.  All animals were staged each day, and animals at stage 52 (Nieuwkoop and Faber, 1994) were set aside for exposure.  The population of animals at stage 52 from each clutch was divided in half indiscriminately, resulting in four groups: (1) a control group for clutch A, (2) an experimental group for clutch A, (3) a control group for clutch B, and (4) an experimental group for clutch B.  These groups were then moved to new plastic exposure tanks.  If a group was over twenty animals it was split among more than one exposure tank so that no tank had more than twenty animals.  Each exposure tank was filled with 150ml treated water per tadpole.  All exposure groups throughout the experiment had at least ten individuals, so exposure tank volumes ranged from 1,500ml (for ten individuals) to 3,000ml (for twenty individuals).

extract_protocol: Both hindlimb buds were dissected off of each animal at the base of the limb using surgical scissors.  For animals from exposure tanks with over eleven individuals, limbs were divided into sub-groups of between eighteen and twenty-two limbs.  This resulted in six groups of limbs per clutch for control groups and six groups of limbs per clutch for experimental groups, or a total of twenty-four groups of limbs.  All limbs were placed in fresh vials of RNAlater, and returned to -20ºC for continued storage.   Twenty-four total RNA preparations were extracted, in several batches of between four and six preparations each batch, using the RNeasy Mini Kit and optional RNase-Free DNase Set (QIAGEN, Valencia, CA), with the following notes.  Limbs were put into 1.5ml microcentrifuge tube, residual RNAlater was pipetted off.  Limbs were crushed with a homegenizer in 200μl buffer RLT, then 300μl buffer RLT was added.  Elution was carried out with two washes of 50μl RNase-free water.    Extracted total RNA was stored at -80ºC and transferred to the W. M. Keck Foundation Biotechnology Resource Center, Affymetrix Resource Center (Yale University, New Haven, Connecticut).  All samples were again run through DNase treatment.  Eight of the twenty-four RNA extractions were chosen for hybridization.

treatment_protocol: Immediately after sorting all animals into the appropriate tanks, 30μl per animal of 5mg/ml cyclopamine solution was added to all experimental tanks (to a final concentration of 1 μg/ml, and 30μl per animal of 100% ethanol was added to each control tank.  Tanks were rocked gently to distribute cyclopamine and ethanol.  Exposures were carried out for 24 hours and ended with fixation of treated animals.

tag: 24 hours after Nieuwkoop and Faber stage 52


title: Cyclopamine 2 (Clutch A, Group 2, M6)

description: Cyclopamine Experimental 2 Normalized Expression Value (Clutch A, Group 2, M6)

source_name: whole hindlimbs, Cyclopamine exposed, 24 hours


title: Pancreas, technical replicate 1

description: Gene expression data from pancreas


title: Ethanol Control 4 (Clutch B, Group 2, P4)

description: Ethanol Control 4 Normalized Expression Value (Clutch B, Group 2, P4)


title: 4 uM hemin (4B)

description: no additional information

source_name: 4 uM hemin


title: Ethanol Control 1 (Clutch A, Group 1, N1)

description: Ethanol Control 1 Normalized Expression Value (Clutch A, Group 1, N1)


title: Cyclopamine 1 (Clutch A, Group 1, M1)

description: Cyclopamine Experimental 1 Normalized Expression Value (Clutch A, Group 1, M1)


title: 500 uM hemin (500B)

description: no additional information


title: 500 uM hemin (500C)

description: no additional information


title: 20 uM hemin (20C)

description: no additional information


title: Cyclopamine 3 (Clutch B, Group 1, O2)

description: Cyclopamine Experimental 3 Normalized Expression Value (Clutch B, Group 1, O2)


title: 20 uM hemin (20A)

description: no additional information


title: Cyclopamine 4 (Clutch B, Group 2, O4)

description: Cyclopamine Experimental 4 Normalized Expression Value (Clutch B, Group 2, O4)


title: Genetic interactions involving the yng2 query mutation

status: Public on Jun 12 2008

city: Baltimore

first: Daniel

last: Yuan

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

institute: Johns Hopkins Univ School of Medicine

description: Matched comparison of the viability of yng2 xxxN vs xxxN cells

hyb_protocol: Labeled extracts were hybridized overnight to microarray slides at 42 degrees C. See PubMed ID 15994458.

scan_protocol: Images were acquired with a GenePix 4000B scanner.

data_processing: Paired image files were analyzed with the GenePix Pro software package (MDS Analytical Technologies, version 5.1). Feature intensities were quantified as the 'F532 Median - B532' or 'F635 Median - B635' values. The two channels were compared using the log2 ratio. Global intensity normalization factors were specific to the type of gene-specific probe (UpTag or DnTag) and were calculated as the log2 ratio of total signal intensity in features 1:6018 (UpTag) or 10972:16989 (DnTag). Ratios were ignored when intensities of the control features [635] were less than 400.

source_name: Cells selected for the query mutation

label_protocol: UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458.

growth_protocol:
Growth medium: -Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

extract_protocol: Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520.

tag: Query mutation

source_name: A matched aliquot of cells, grown in parallel but without selection for the query mutation

growth_protocol:
Growth medium: +Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Ethanol Control 3 (Clutch B, Group 1, P2)

description: Ethanol Control 3 Normalized Expression Value (Clutch B, Group 1, P2)


title: Cerebral cortex, technical replicate 1


title: 4 uM hemin (4C)

description: no additional information


title: Genetic interactions involving the swc4-23 query mutation at 32 degrees C

description: Matched comparison of the viability of swc4-23 xxxN vs xxxN cells at 32 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 32 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

value: swc4-delta::natMX with swc4-23 (ts allele) in URA3 CEN plasmid

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 32 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the yaf9 query mutation

description: Matched comparison of the viability of yaf9 xxxN vs xxxN cells


title: 4 uM hemin (4A)

description: no additional information


title: Genetic interactions involving the swc4-23 query mutation at 31 degrees C

description: Matched comparison of the viability of swc4-23 xxxN vs xxxN cells at 31 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 31 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 31 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the hpa2 query mutation

description: Matched comparison of the viability of hpa2 xxxN vs xxxN cells


title: Genetic interactions involving the rtt109 query mutation

description: Matched comparison of the viability of rtt109 xxxN vs xxxN cells


title: Genetic interactions involving the hpa3 query mutation

description: Matched comparison of the viability of hpa3 xxxN vs xxxN cells


title: Genetic interactions involving the swc4-23 query mutation at 30 degrees C

description: Matched comparison of the viability of swc4-23 xxxN vs xxxN cells at 30 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the sas2 query mutation

description: Matched comparison of the viability of sas2 xxxN vs xxxN cells


title: Genetic interactions involving the sas3 query mutation

description: Matched comparison of the viability of sas3 xxxN vs xxxN cells


title: Genetic interactions involving the hos1 query mutation

description: Matched comparison of the viability of hos1 xxxN vs xxxN cells


title: Genetic interactions involving the sin3 query mutation

description: Matched comparison of the viability of sin3 xxxN vs xxxN cells


title: Genetic interactions involving the hda1 query mutation

description: Matched comparison of the viability of hda1 xxxN vs xxxN cells


title: Genetic interactions involving the sap30 query mutation

description: Matched comparison of the viability of sap30 xxxN vs xxxN cells


title: Genetic interactions involving the hos2 query mutation

description: Matched comparison of the viability of hos2 xxxN vs xxxN cells


title: Genetic interactions involving the esa1-531 query mutation at 32 degrees C

description: Matched comparison of the viability of esa1-531 xxxN vs xxxN cells at 32 degrees C

value: esa1-delta::natMX with esa1-531 (ts allele) in URA3 CEN plasmid


title: Genetic interactions involving the spt8 query mutation

description: Matched comparison of the viability of spt8 xxxN vs xxxN cells


title: Genetic interactions involving the hat1 query mutation

description: Matched comparison of the viability of hat1 xxxN vs xxxN cells


title: Genetic interactions involving the epl1-1 query mutation at 30 degrees C

description: Matched comparison of the viability of epl1-1 xxxN vs xxxN cells at 30 degrees C

value: epl1-delta::natMX with epl1-1 (ts allele) in URA3 CEN plasmid


title: Genetic interactions involving the esa1-531 query mutation at 30 degrees C

description: Matched comparison of the viability of esa1-531 xxxN vs xxxN cells at 30 degrees C


title: Genetic interactions involving the pho23 query mutation

description: Matched comparison of the viability of pho23 xxxN vs xxxN cells


title: Genetic interactions involving the hda2 query mutation

description: Matched comparison of the viability of hda2 xxxN vs xxxN cells


title: Genetic interactions involving the esa1-531 query mutation at 31 degrees C

description: Matched comparison of the viability of esa1-531 xxxN vs xxxN cells at 31 degrees C


title: Genetic interactions involving the hos3 query mutation

description: Matched comparison of the viability of hos3 xxxN vs xxxN cells


title: Genetic interactions involving the eaf5 query mutation

description: Matched comparison of the viability of eaf5 xxxN vs xxxN cells


title: Genetic interactions involving the eaf6 query mutation

description: Matched comparison of the viability of eaf6 xxxN vs xxxN cells


title: Genetic interactions involving the elp3 query mutation

description: Matched comparison of the viability of elp3 xxxN vs xxxN cells


title: Genetic interactions involving the rpd3 query mutation

description: Matched comparison of the viability of rpd3 xxxN vs xxxN cells


title: Genetic interactions involving the epl1-1 query mutation at 31 degrees C

description: Matched comparison of the viability of epl1-1 xxxN vs xxxN cells at 31 degrees C


title: Genetic interactions involving the nut1 query mutation

description: Matched comparison of the viability of nut1 xxxN vs xxxN cells


title: Genetic interactions involving the eaf7 query mutation

description: Matched comparison of the viability of eaf7 xxxN vs xxxN cells


title: Genetic interactions involving the eaf3 query mutation

description: Matched comparison of the viability of eaf3 xxxN vs xxxN cells


title: Genetic interactions involving the epl1-1 query mutation at 29 degrees C

description: Matched comparison of the viability of epl1-1 xxxN vs xxxN cells at 29 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 29 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 29 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the eaf1 query mutation

description: Matched comparison of the viability of eaf1 xxxN vs xxxN cells

growth_protocol:
Growth medium: +Nourseothricin+Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin+Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the ada2 query mutation

description: Matched comparison of the viability of ada2 xxxN vs xxxN cells


title: Genetic interactions involving the cdc20-1 query mutation at 34 degrees C

description: Matched comparison of the viability of cdc20-1 xxxN vs xxxN cells at 34 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 34 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

value: cdc20-delta::natMX with cdc20-1 (ts allele) in URA3 CEN plasmid

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 34 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the arp4-7 query mutation at 30 degrees C

description: Matched comparison of the viability of arp4-7 xxxN vs xxxN cells at 30 degrees C

value: arp4-delta::natMX with arp4-7 (ts allele) in URA3 CEN plasmid


title: Genetic interactions involving the arp4-7 query mutation at 31 degrees C

description: Matched comparison of the viability of arp4-7 xxxN vs xxxN cells at 31 degrees C


title: Genetic interactions involving the cdc20-1 query mutation at 32 degrees C

description: Matched comparison of the viability of cdc20-1 xxxN vs xxxN cells at 32 degrees C


title: Genetic interactions involving the cdc20-1 query mutation at 33 degrees C

description: Matched comparison of the viability of cdc20-1 xxxN vs xxxN cells at 33 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 33 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 33 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: Genetic interactions involving the arp4-7 query mutation at 29 degrees C

description: Matched comparison of the viability of arp4-7 xxxN vs xxxN cells at 29 degrees C


title: Genetic interactions involving the arp4-7 query mutation at 28 degrees C

description: Matched comparison of the viability of arp4-7 xxxN vs xxxN cells at 28 degrees C

growth_protocol:
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 28 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.

growth_protocol:
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 28 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny.  See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.


title: RT4 cells grown on Matrigel, 7 days after grown on Plastic

status: Public on Jun 10 2008

city: Oklahoma City

first: Robert

middle: Evan

last: Hurst

state: OK

address: 920 S. L. Young Blvd

department: Urology

institute: Oklahoma University Health Sciences Center

description: Details about microarray handling/processing techniques can be obtained from platform’s manufacturer

hyb_protocol: Ventana Discovery 9h, 58 C washed to 0.1xSSC

scan_protocol: scanned on Agilient G2505B scanner Imagene 5.0

data_processing: Data were normalized as was described previously in Dozmorov I et al., Nucleic Acids Res. 2004 Oct 28;32(19). In general, intensities were converted to expression and normalized to low-expressed genes, which provide possible technical noise level. The arrays are then adjusted to each other by robust linear regression and this Log10 transformed data presented for each sample. Group of low-expressed genes is  selected by normal distribution fitting. This group provides internal standard of measurement noise (ISMN). Genes above 5SD from mean of ISMN were selected as expressed

source_name: RT4 papilloma cell line

label_protocol: Omniscript reverse-transcriptase, 37 C, 2 hrs

growth_protocol: Cells were maintained for 10 days and media replenished underneath the insert twice a week.  Cells were harvested at 12 hrs, 24hrs, 2 days, 3 days, 4days, 6 days, 7 days, 8 days, and 9 days of growth in culture using Matrisperse (Falcon, Becton-Dickinson Labware, Franklin Lakes, NJ) and RNA collected

extract_protocol: RNA was isolated at each time point with RNAeasy kit (QIAGEN Inc.,Valencia, CA) according to manufacturer’s protocol

treatment_protocol:
Three dimensional gel cultures with Matrigel were performed by layering 0.8 mls of ice cold Matrigel onto polyethylene terephthalate membranes of 6-well cell culture inserts (Falcon, Becton-Dickinson Labware, Franklin Lakes, NJ). Gels were solidified at 37º C.
RT4 cells were trypsinized, brought up on 20 mls McCoys media with 10% Fetal Calf Serum (FCS).  Cells were centrifuged  then brought up in McCoys media with 10% FCS to a concentration of 500,000 cells/250µl.   250µl added on top of each solidified matrigel disc and 2mls of McCoys with 10% FCS layered underneath each culture insert

tag: RT4 cell line is a urinary bladder transitional cell papilloma cell line from the American Type Culture Collection, Manassas Virginia


title: RT4 cells grown on Matrigel, 2 days after grown on Plastic


title: RT4 cells grown on Matrigel, 6 days after grown on Plastic


title: RT4 cells grown on Matrigel, 8 days after grown on Plastic

tag: RT4 cell line is a urinary bladder transitional cell papilloma cell line from the American Type Culture Collection, Manassas Virginia.


title: RT4 cells grown on Matrigel, 4 days after grown on Plastic


title: RT4 cells grown on Matrigel, 3 days after grown on Plastic


title: RGZ treated HCT-116 cells

city: Knoxville

first: Seung

middle: Joon

last: Baek

state: TN

address: 2407 River Dr

department: Pathobiology

institute: University of Tennessee

description: RGZ treated replicates 1-4

hyb_protocol: The purified probes from both control and treated samples were mixed and hybridized with the long-oligo microarray by the Microarray Hybridization Kit (Corning, Inc., Corning, NY) on a MAUI hybridization station (Bio Micro Systems Inc., Salt Lake City, UT) according to the manufacturer’s instruction. Dye swap experiments were included to eliminate dye-specific bias. For each sample set of treated versus control, the treated mRNA was first labeled with Cy5 and the control with Cy3.

scan_protocol: After hybridization, the microarray slides were washed and scanned in a GenePix 4000 scanner (Axon Instrument, Union City, CA), and the images were processed by GenePix Pro software (Axon Instrument).

data_processing: The resultant file was analyzed with Bioconductor (http://www.bioconductor.org), where local background subtraction and Lowess normalization were carried out for each microarray slide. Linear models from limma package of Bioconductor were applied to derive a p value and average of logarithm 2-based ratio. Changes in gene expression pattern were considered statistically significant at p<0.05*.

label: Cy3, Cy5

source_name: HCT-116 cell line

label_protocol: One hundred microgram of total RNA was labeled for each sample with a Superscript III direct Labeling Kit (Invitrogen) according to the instructions of the manufacturer.

growth_protocol: Human colorectal adenocarcinoma cell line HCT-116 was obtained from American Type Culture Collection (ATCC, Manassas, VA). The cells were maintained in McCoy's 5A modified medium supplemented with 10% fetal bovine serum, 100 I.U. penicillin and 100 ug/ml streptomycin and grown in an atmosphere of 5% CO2 at 37˚C.

extract_protocol: Total RNA was isolated from treated cell samples using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: HCT-116 cells were grown in 100 mm dishes (2x106) in complete media overnight, and then washed twice with PBS and treated with 5 uM MCC-555, 5 uM RGZ, or 1 uM PGJ2 in serum free media for an additional 24 h.

tag: RGZ Treated or DMSO Vechicle Treated


title: RT4 cells grown on Matrigel, 9 days after grown on Plastic


title: RT4 cells grown on Matrigel, 12 hours after grown on Plastic


title: PGJ treated HCT-116 cells

description: PGJ treated replicates 1-4

tag: PGJ Treated or DMSO Vechicle Treated


title: RT4 cells grown on Plastic, replicate 2; Matrigel next


title: MCCC5 treated HCT-116 cells

description: MCCC5 treated replicates 1-4

tag: MCCC5 Treated or DMSO Vechicle Treated


title: BAF250b-/- #7B(72hrs) Repl#2 (251411710246)

status: Public on Jun 09 2008

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

description: BAF250b-/- #7 (72 hrs)

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
We used 12 new arrays in this Series plus 14 old arrays we submitted earlier (ie, GSM175328-GSM175341). We used only the raw values of Cy3/Cy5 channels in the old arrays to normalize with the 12 new arrays.  See VALUE definition below for further details.

organism: Mus musculus

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: One ml of Trizol (Invitrogen) was added to one well. Total RNA was extracted according to the manufacturer's protocol.

tag: ES

value: hybrid of B6,129 and CD1

tag: Gender

value: unknown sex

tag: Age

value: 2 months

tag: Development stage

value: 3.5 dpc blastocysts

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: BAF250b-/- #7B(18hrs) Repl#2 (251411710244)

description: BAF250b-/- #7 (18 hrs)

tag: Strain


title: BAF250b WT #3B(72 hrs) Repl#2 (251411710237)

description: BAF250b WT #3 (72 hours)

source_name: BAF250b WT #3 (72 hours)


title: RT4 cells grown on Matrigel, 1 day after grown on Plastic


title: BAF250b WT #3A(72 hrs) Repl#1 (251411710236)

description: BAF250b WT #3 (72 hours)


title: BAF250b-/- #7A(18hrs) Repl#1 (251411710243)

description: BAF250b-/- #7 (18 hrs)


title: BAF250b-/- #4B(72hrs) Repl#2 (251411710241)

description: BAF250b-/- #4 (72 hrs)


title: BAF250b-/- #4B(18 hrs) Repl#2 (251411710239)

description: BAF250b-/- #4 (18 hrs)


title: BAF250b-/- #4A(72hrs) Repl#1 (251411710240)

description: BAF250b-/- #4 (72 hrs)


title: BAF250b-/- #7A(72hrs) Repl#1 (251411710245)

description: BAF250b-/- #7 (72 hrs)


title: BAF250b WT #3A (18 hrs) Repl#2 (251411710235)

description: BAF250b WT #3 (18 hours)

source_name: BAF250b WT #3 (18 hours)


title: BAF250b-/- #4A(18 hrs) Repl#1 (251411710238)

description: BAF250b-/- #4 (18 hrs)


title: RT4 cells grown on Plastic, replicate 1

data_processing: Data were normalized as was described previously in Dozmorov I et al., Nucleic Acids Res. 2004 Oct 28;32(19). In general, intensities were converted to expression and normalized to low-expressed genes, which provide possible technical noise level. The arrays are then adjusted to each other by robust linear regression and this Log10 transformed data presented for each sample. Group of low-expressed genes is  selected by normal distribution fitting. This group provides internal standard of measurement noise (ISMN). Genes above 5SD from mean of ISMN were selected as expressed.


title: Steady-state based anaerobic glucose pulse, sfp1delta_t60_2

first: Chiara

last: Cipollina

department: Biotechnology

hyb_protocol: Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies) (1). (1). Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.

source_name: 60-minute time point after anaerobic glucose pulse

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain sfp1 null mutant (MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2) was grown at 30 °C in 2-l bioreactors with a working volume of 1.5 l. Removal of effluent from the center of the culture ensured that biomass concentrations in the effluent line differed by less than 1% from those in the culture. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. A stirrer speed of 800 rpm and air flow of 0.75 liter•min-1 were applied to keep the dissolved-oxygen concentration, as measured with an oxygen electrode, above 60% of air saturation in all chemostat cultivations performed. Steady-state samples were taken after 10 volume changes to avoid strain adaptation due to long-term cultivation. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant over at least three volume changes.
Anaerobic glucose-pulse experiments were started by sparging the medium reservoir of a steady-state glucose-limited aerobic chemostat (airflow of 0.5 liter•min-1) with pure nitrogen gas. Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. Two min after nitrogen sparging and just before adding the glucose, the medium pump was switched off. The 200 mM glucose pulse was injected aseptically through a rubber septum. Samples for RNA extraction were taken at 5, 10, 30, 60 and 120 minutes after the perturbation from two independently cultured replicates, while steady state data were taken from three independent chemostats.

extract_protocol:
Sampling of cells from chemostats and total RNA extraction was performed as previously described (1).
(1). Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.

tag: strain

value: sfp1Δ, genotype:MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2


title: Steady-state based anaerobic glucose pulse, sfp1delta_t30_2

source_name: 30-minute time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse, sfp1delta_t30_1


title: Steady-state based anaerobic glucose pulse, sfp1delta_t60_1

source_name: 60-min time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse, sfp1delta_t5_1

source_name: 5-min time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse, sfp1delta_t120_2

source_name: 120-minute time point after anaerobic glucose pulse


title: BAF250b WT #3A (18 hrs) Repl#1 (251411710234)

description: BAF250b WT #3 (18 hours)


title: Steady-state based anaerobic glucose pulse, sfp1delta_t10_2

source_name: 10-minute time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse, sfp1delta_t5_2

source_name: 5-minute time point after anaerobic glucose pulse


title: Steady-state based anaerobic glucose pulse, sfp1delta_t10_1


title: Steady-state based anaerobic glucose pulse, sfp1delta_t120_1


title: Steady-state based anaerobic glucose pulse, sfp1delta_SS_1

source_name: Steady State Samples


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t10_1

data_processing: GeneChip® Operating Software (GCOS), version 1.2

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at 30 °C in 2-l bioreactors with a working volume of 1.5 l. Removal of effluent from the center of the culture ensured that biomass concentrations in the effluent line differed by less than 1% from those in the culture. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. A stirrer speed of 800 rpm and air flow of 0.75 liter•min-1 were applied to keep the dissolved-oxygen concentration, as measured with an oxygen electrode, above 60% of air saturation in all chemostat cultivations performed. Steady-state samples were taken after 10 volume changes to avoid strain adaptation due to long-term cultivation. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant over at least three volume changes.
Anaerobic glucose-pulse experiments were started by sparging the medium reservoir of a steady-state glucose-limited aerobic chemostat (airflow of 0.5 liter•min-1) with pure nitrogen gas. Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. Two min after nitrogen sparging and just before adding the glucose, the medium pump was switched off. The 200 mM glucose pulse was injected aseptically through a rubber septum. Samples for RNA extraction were taken at 5, 10, 30, 60 and 120 minutes after the perturbation from two independently cultured replicates, while steady state data were taken from three independent chemostats.

value: CENPK113.7D; Genotype:MATa MAL2-8c SUC2


title: Steady-state based anaerobic glucose pulse CENPK113-7D_SS_3


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t60_2


title: Steady-state based anaerobic glucose pulse CENPK113-7D_SS_2

source_name: Steady State Sample


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t10_2


title: Steady-state based anaerobic glucose pulse CENPK113-7D_t5_1

tag: CENPK113.7D; Genotype

value: MATa MAL2-8c SUC2


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t60_1


title: Steady-state based anaerobic glucose pulse, sfp1delta_SS_2

source_name: Steady State SAmple

growth_protocol:
The S. cerevisiae sfp1 null mutant (MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2) was grown at 30 °C in 2-l bioreactors with a working volume of 1.5 l. Removal of effluent from the center of the culture ensured that biomass concentrations in the effluent line differed by less than 1% from those in the culture. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. A stirrer speed of 800 rpm and air flow of 0.75 liter•min-1 were applied to keep the dissolved-oxygen concentration, as measured with an oxygen electrode, above 60% of air saturation in all chemostat cultivations performed. Steady-state samples were taken after 10 volume changes to avoid strain adaptation due to long-term cultivation. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant over at least three volume changes.
Anaerobic glucose-pulse experiments were started by sparging the medium reservoir of a steady-state glucose-limited aerobic chemostat (airflow of 0.5 liter•min-1) with pure nitrogen gas. Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. Two min after nitrogen sparging and just before adding the glucose, the medium pump was switched off. The 200 mM glucose pulse was injected aseptically through a rubber septum. Samples for RNA extraction were taken at 5, 10, 30, 60 and 120 minutes after the perturbation from two independently cultured replicates, while steady state data were taken from three independent chemostats.

value: sfp1Δ; genotype:MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2


title: Steady-state based anaerobic glucose pulse, sfp1delta_SS_3


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t120_1


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t120_2


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t30_1


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t30_2


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_t5_2


title: Steady-state based anaerobic glucose pulse, CENPK113-7D_SS_1

source_name: Steady state sample

value: CENPK113.7D; Genotype:MATa MAL2-8c SUC2;


title: BW25113 w/t 7h LB 30C biofilm

status: Public on Jun 05 2008

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 w/t after 7 hours of growth in LB with glasswool at 30ºC

hyb_protocol: Followed Affymetrix protocol Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

source_name: Channel 1

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 luxS LB 37C free-living cells 100 uM AI2 3h

description: RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 37ºC in LB, 100 uM AI2 was added in and 3-h further incubation was applied)

hyb_protocol: Followed Affymetrix protocol Prepared hybridization cocktail for Single Probe Array (169 Format) with total 90 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 0.8 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli 2.0 Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 37°C with shaking (250 rpm) to OD600 0.5, 100 uM AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 sdiA LB 30C OD 4.0 free-living cells

description: RNA extracted from free living cells of E. coli K-12 BW25113 sdiA mutant when growth to OD600 4.0 at 30ºC in LB

data_processing: MAS 5.0 Expression Analysis Default Setting.

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 4.0, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 tnaA Biofilm DMF 7h LB 37C

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and DMF at 37ºC

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 tnaA Biofilm 100 uM indole 7h LB 30C

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and with 100 uM indole at 30ºC

hyb_protocol: Followed Affymetrix protocol Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and with 100 uM indole for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 luxS LB 37C free-living cells no AI2 3h

description: RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 37ºC in LB, no AI2 was added in and 3-h further incubation was applied)

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 37°C with shaking (250 rpm) to OD600 0.5, no AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 luxS LB 30C free-living cells no AI2 for 3h

description: RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 30ºC in LB, no AI2 was added in and 3-h further incubation was applied)

hyb_protocol: Followed Affymetrix protocol Prepared hybridization cocktail for Single Probe Array (49 Format) with total 90 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 0.8 ug fragmented and labelled cDNA.After loading of hybridization cocktail in Affymetrix E. coli 2.0 Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 0.5, no AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 w/t 7h LB 30C free-living

description: RNA extracted from suspension cells of E. coli K-12 BW25113 w/t after 7 hours of growth in LB with glasswool at 30ºC

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) for 7 hours, 2.0 ml of cell culture was removed from suspension part and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 tnaA Biofilm 100 uM indole 7h LB 37C

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and 100 uM indole at 37ºC

hyb_protocol: Followed Affymetrix protocol Prepared hybridization cocktail for Single Probe Array (169 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli 2.0 Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and with 100 uM indole for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 luxS LB 30C free-living cells 100 uM AI2 3h

description: RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 30ºC in LB, 100 uM AI2 was added in and 3-h further incubation was applied)

extract_protocol: The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 0.5, 100 uM AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: BW25113 w/t LB 30C OD 4.0 free-living cells

description: RNA extracted from free living cells of E. coli K-12 BW25113 wild type when growth to OD600 4.0 at 30ºC in LB


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_1mM_HG-U133A_2_YCHSUP501

status: Public on Jun 03 2008

city: Research Triangle Park

first: Yin

address: 6 Davis Dr.

department: Division of Translational Biology

institute: Hamner Institutes for Health Sciences

description: H465_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

source_name: Sample Type: human cellular RNA, Cell Line: primary airway epithelial cells, Cell Type: tracheobronchial

growth_protocol: Growth Media: C media, Growth Conditions: 37C, 5%CO2

extract_protocol: Extraction Method: Rneasy mini-kit

tag: Additional Information

value: please return the leftover samples to PI.

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ug

tag: Ratio


title: BW25113 tnaA LB 30C biofilm cells with DMF 7h

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and DMF at 30ºC

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_Con_HG-U133A_2_YCHSUP501

description: H465_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_0.4mM_HG-U133A_2_YCHSUP501

description: H421_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_0.4mM_HG-U133A_2_YCHSUP501

description: H465_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_4mM_HG-U133A_2_YCHSUP501

description: H421_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_Con_HG-U133A_2_YCHSUP501

description: H511_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_0.4mM_HG-U133A_2_YCHSUP501

description: H465_6h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_4mM_HG-U133A_2_YCHSUP501

description: H465_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_1mM_HG-U133A_2_YCHSUP501

description: H421_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_1mM_HG-U133A_2_YCHSUP501

description: H421_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_1mM_HG-U133A_2_YCHSUP501

description: H511_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.


title: human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_4mM_HG-U133A_2_YCHSUP501

description: H421_6h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.