title: Diabetic heart #3

status: Public on Jan 26 2008

type: RNA

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

country: USA

institute: Cleveland VA Medical Center

description: Standard Affy

hyb_protocol: Standard Affy

scan_protocol: Standard Affy

data_processing: Standard Affy

label: Standard Affy

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat diabetic heart, left vent

label_protocol: Standard Affy

extract_protocol: Standard Affy

tag: 12 week old rat, at 8 weeks got streptozotocin


title: Diabetic heart #1

description: Standard Affy


title: Normal heart #2

description: Standard Affy

source_name: Rat normal heart, left vent

tag: 12 week old rat


title: Diabetic heart #2

description: Standard Affy


title: Normal heart #3

description: Standard Affy


title: Perirenal old 3

status: Public on Jan 09 2008

city: Boston

first: Marc

middle: E.

last: Lenburg

state: MA

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

description: Separate groups of animals were used for each experiment.  All experiments were conducted in parallel and animals were autopsied to exclude gross pathology.  Macrophage markers in the preadipocyte cultures did not differ with aging or among depots.

hyb_protocol: For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases.  10 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm.  Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).

scan_protocol: The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: MAS5.0, target intensity = 500

label: biotin

source_name: isolated preadipocytes from perirenal fat depot

label_protocol: Using a poly-dT primer incorporating a T7 promoter, double-stranded cDNA was synthesized from 10 micrograms total RNA using a cDNA synthesis kit (SuperScript double-stranded cDNA synthesis kit; Invitrogen, Carlsbad, CA).  Biotin-labeled cRNA was generated from the double-stranded cDNA template through in-vitro transcription with T7 polymerase using an RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).

growth_protocol: Fat depots were minced, digested in collagenase solution (1mg/ml HBSS per 3ml/g of tissue), filtered and centrifuged (10 minutes @ 12,000 rpm).  Pellet was resuspended in alphaMEM-10%FBS and plated for 20 hours.  Cells were trypsinized until 90% of cells lifted, replated at 4X10^4 cells/cm2 and cultured to confluence for RNA extraction.

extract_protocol: Total RNA was isolated from preadipocytes by the TRIzol method.

tag: Strain

value: Brown Norway Rats, barrier reared, specific pathogen free

tag: Gender

value: male

tag: age of rat

value: 30 months

tag: preadipocyte source

value: perirenal fat depot

tag: animal number

value: old rat 3


title: Epididymal old 3

source_name: isolated preadipocytes from epididymal fat depot

value: epididymal fat depot


title: Epididymal young 3

value: 3 months

value: young rat 3


title: Perirenal young 1

value: young rat 1


title: Pulmonary myofibroblast from patient with idiopathic pulmonary fibrosis 1

status: Public on Jan 17 2008

city: Fukushima

first: Yoshimi

last: Homma

state: Fukushima

address: 1 Hikarigaoka

department: Department of Biomolecular Science

country: Japan

institute: Fukushima Medical University

description: Cells from passage 2-5 were used for RNA extraction.

hyb_protocol: Hybridization was carried out for 16 hr at 60 rpm at 45? using Affymetrix® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The probe array was scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Analysis of the microarray data was carried out using GeneChip® Operating Software (GCOS) version 1.1.

organism: Homo sapiens

source_name: pulmonary tissue from patient with IPF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS.  The medium was changed every 3 days.

extract_protocol: Total RNA extraction was performed by using Isogen (NIPPON GENE) according to the manufacturer's instructions.

tag: Cell type

value: myofibroblast, Gender:male, Tissue:lung, Disease:idiopathic pulmonary fibrosis


title: Epididymal young 1


title: Pulmonary myofibroblast from another patient with idiopathic pulmonary fibrosis 2

source_name: plumonary tissue from another patient with IPF


title: Epididymal young 2

value: young rat 2


title: Kidney(Nas1) WT Cy3 vs KO Cy5_2

status: Public on Jan 24 2008

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: Pairwise comparison of total kidney RNA extracted from Nas1 knockout mice versus total kidney RNA extracted from wildtype mice(dye swap)

hyb_protocol: Followed protocol described in: PMID: 15998744

data_processing: Imagene5.0, Lowess Normalisation (R)

organism: Mus musculus

source_name: WT Kidney

label_protocol: Indirect aRNA Ambion

extract_protocol: RNAAmplification Ambion

tag: RNA extract of Wildtype Kidney tissue

source_name: Nas1 -/- Kidney

tag: RNA extract of Nas1 Knockout Kidney tissue


title: Epididymal old 2

value: old rat 2


title: Epididymal old 1

value: old rat 1


title: Human pulmonary fibroblast

hyb_protocol: Hybridization was carried out for 16 hr at 60 rpm at 45? using Affymetrix® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA)

source_name: human embryonic pulmonary tissue

value: fibroblast, Gender:male, Tissue:fetus lung


title: Kidney(Nas1) KO Cy3 vs WT Cy5_1

description: Pairwise comparison of total kidney RNA extracted from Nas1 knockout mice versus total kidney RNA extracted from wildtype mice

scan_protocol: Followed protocol described in: PMID: 15998744


title: Normal heart #1

description: Standard Affy


title: Kidney(Nas1) KO Cy3 vs WT Cy5_3


title: Hippocampal CA3 at T30m, biological rep 2

status: Public on Jan 08 2008

city: Lawrence

first: Xinkun

last: Wang

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

description: total RNA extracted from organotypic hippocampal slice culture

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA

source_name: Hippocampal CA3

label_protocol: two-cycle target labeling

extract_protocol: standard Affymetrix procedures

tag: Sprague-Dawley, male


title: Perirenal old 2


title: Hippocampal CA3 at T30m, biological rep 1


title: Perirenal old 1


title: Kidney(Nas1) WT Cy3 vs KO Cy5_4


title: Perirenal young 3


title: Hippocampal CA3 at T0, biological rep 1


title: Perirenal young 2


title: Hippocampal CA1 at T30m, biological rep 2

source_name: Hippocampal CA1


title: Hippocampal CA3 at T12h, biological rep 2


title: Hippocampal CA3 at T0, biological rep 2


title: Hippocampal CA3 at T3h, biological rep 2


title: Hippocampal CA3 at T3h, biological rep 1


title: Hippocampal CA3 at T12h, biological rep 1


title: Leaf_sucrose1

status: Public on Jan 05 2008

city: Potsdam

first: Joost

middle: T.

last: van Dongen

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description: source leaves of Wild type Arabidopsis thaliana Col0 rosette plants.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

organism: Arabidopsis thaliana

source_name: leaf

label_protocol: 10µg total RNA was biotin labelled

growth_protocol: Plants were grown in a phytotron with a 14h day / 10h night. Temperature: 20°C / 16°C. Humidity: 60% / 75%. Lightintensity: .

extract_protocol: Total RNA extraction using TRIzol Total RNA Isolation Reagent, according to the protocol supplied by the manufacturer GibcoBRL Life-Technologies.

treatment_protocol: Source leaves were cut at the end of the day from non-flowering plants. Leaf peteoles were recut under buffer (2mM MES, pH6.5) and placed in buffer + 100mM sucrose for 13hours in the dark. After incubation discs were snap-frozen in liquid nitrogen.

tag: sucrose feeding belonging to control (leaf_sorbitol1)

tag: ecotype

tag: developmental stage

value: full grown leaves of non-flowering plants


title: Day12_N3

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: Day 12, repeat 3

source_name: podocytes


title: Day12_N2

description: Day 12, repeat 2


title: Day9_N2

description: Day 9, repeat 2


title: Day9_N1

description: Day 9, repeat 1


title: Hippocampal CA1 at T12h, biological rep 2


title: Leaf_sorbitol1

treatment_protocol: Source leaves were cut at the end of the day from non-flowering plants. Leaf peteoles were recut under buffer (2mM MES, pH6.5) and placed in buffer + 100mM sorbitol for 13hours in the dark. After incubation discs were snap-frozen in liquid nitrogen.

tag: control for sucrose feeding (leaf_sucrose1)


title: Day3_N1

description: Day 3, repeat 1


title: Day0_N3

description: Day 0, repeat 3


title: Low vs High_CompC_2

status: Public on Jan 03 2008

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

institute: INRA

description: The signal and background mean intensities for the Cy3 and Cy5 channels from each spot were obtained using ImaGene 6.0 software (BioDiscovery, Inc).

hyb_protocol: 43 pmol of Cy3-labeled cDNA and 43 pmol of Cy5-labeled cDNA were co-hybridized at 42°C for 16 h on the oligoarray “URH-TALL _Bovine_Operon V1.1_1”. The pre-hybridization treatments, hybridization and washes were performed using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

scan_protocol: The slide was scanned for both dye channels at 532 and 635 nm with an Affymetrix 428 Array Scanner (MWG Biotech) at 10 µm resolution.

data_processing: After base-2 logarithm transformation, data were corrected for systematic dye bias by Lowess normalization using GeneSight 4.1 software (BioDiscovery, Inc).

organism: Capra hircus

label_protocol: 5 µg of purified total RNA was labeled with Cy3-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen life technologies) according to the manufacturer’s instructions and further purified with the SV Total RNA Isolation System (Promega). RNA concentration and purity were determined by spectrophotometry at 260, 280 and 320 nm and RNA integrity was verified using a Bioanalyser 2100 (Agilent Technologies).

tag: Goat no.

tag: Tissue

value: lactating mammary gland,

tag: Treatment

value: 48-h food-deprivation,

tag: Genotype

value: Low CSN1S1

label_protocol: 5 µg of purified total RNA was labeled with Cy5-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

value: High CSN1S1


title: Day3_N3

description: Day 3, repeat 3


title: Hippocampal CA1 at T3h, biological rep 2


title: Hippocampal CA1 at T0, biological rep 2


title: Hippocampal CA1 at T3h, biological rep 1


title: Hippocampal CA1 at T12h, biological rep 1


title: Hippocampal CA1 at T0, biological rep 1


title: Day9_N3

description: Day 9, repeat 3


title: Leaf_sucrose2

tag: sucrose feeding belonging to control(leaf_sorbitol2)


title: Low vs High_CompB_2


title: Hippocampal CA1 at T30m, biological rep 1


title: Leaf_sorbitol2

tag: control for sucrose feeding (leaf_sucrose2)


title: Day12_N1

description: Day 12, repeat 1


title: Low vs High_CompB_1


title: Day3_N2

description: Day 3, repeat 2


title: Mcm/ stationary phase/ replica 3

status: Public on Jan 01 2008

type: genomic

city: Gif-sur-Yvette

first: LAWRENCE

last: AGGERBECK

address: Avenue de la Terrasse

department: Centre de Génétique Moléculaire

institute: Centre National de la Recherche Scientifique

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, third replica

data_processing: Log base 2 ratio of median values of channel 1 to channel 2

molecule: genomic DNA

organism: Pyrococcus abyssi

source_name: DNA from mock-treated cell extract and archaebacteria treated in exponential phase, third replica


title: Cdc 6/exponential phase replica 4

description: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, fourth replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in exponential phase, fourth replica


title: Day0_N1

description: Day 0, repeat 1


title: Cdc 6/stationary phase

description: ChiP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase

source_name: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, first replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in stationary phase, first replica

tag: DNA from mock-treated cell extract


title: Cdc 6/stationary phase replica 2

description: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, second replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica


title: Low vs High_CompC_1


title: Day0_N2

description: Day 0, repeat 2


title: Low vs High_CompA_2


title: Low vs High_CompA_1


title: proband K7 Monocytes

status: Public on Dec 31 2007

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

institute: University Hospital Jena

description: proband K7 Monocytes

hyb_protocol: 10 µg biotinylated RNA were hybridised for 16h at 45°C on geneChip human U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics station 400.

scan_protocol: GeneChips were scanned with the Affymetrix Scanner 3000.

data_processing: The data were first analysed with Affymetrix GCOS 1.4 using default analysis settings.

source_name: human peripheral Monocytes

label_protocol: biotinylated RNA was prepared from 1 µg total RNA according to the Affymetrix manual (2005)

extract_protocol: RNA was extracted from Trizol through addition of chloroform and phase separation using PLG tubes. Additionally RNA was cleaned up using the Rneasy Micro Kit with a Dnase step.

treatment_protocol: 8ml of whole blood were collected in BD Vacutainer CPT tubes. 200 µl of RosetteSep Tcell Enrichment cocktail were added immediately following the blood withdrawal. Tubes were inverted five times and incubated for 20 minutes at room temperature. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml, spun down for 10 minutes at 500g at 4°C, the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.

tag: control


title: Low vs High_Comp3_2

value: control diet ad libitum,


title: proband K5 T-lymphocytes

description: proband K5 T-lymphocytes

source_name: human peripheral T-lymphocytes

treatment_protocol: 4ml of whole blood were collected in BD Vacutainer CPT tubes. 200 µl of RosetteSep Tcell Enrichment cocktail were added immediately following the blood withdrawal. Tubes were inverted five times and incubated for 20 minutes at room temperature. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml, spun down for 10 minutes at 500g at 4°C, the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.


title: Low vs High_Comp2_2


title: Low vs High_Comp3_1


title: proband K6 T-lymphocytes

description: proband K6 T-lymphocytes


title: Mcm/ exponential phase/ replica 4

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, fourth replica

tag: DNA from mock-treated cell extract and archaebacteria treated in exponential phase, fourth replica


title: Low vs High_Comp2_1


title: proband K2 Monocytes

description: proband K2 Monocytes


title: Low vs High_Comp1_2


title: Low vs High_Comp1_1


title: proband K2 T-lymphocytes

description: proband K2 T-lymphocytes


title: proband K4 T-lymphocytes

description: proband K4 T-lymphocytes


title: Mcm/ exponential phase/ replica 1

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, first replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in exponential phase, first replica


title: Mcm/ stationary phase/ replica 4

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, fourth replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in stationary phase, fourth replica


title: Mcm/ stationary phase/ replica 2

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, second replica

tag: DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica


title: Mcm/ exponential phase/ replica 2

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, second replica

source_name: DNA from mock-treated cell extract and archaebacteria treated in exponential phase, second replica


title: peripheral monocytes, B7 Baseline

source_name: human peripheral monocytes

treatment_protocol: 8 ml of whole blood were collected in BD Vacutainer CPT tubes. 200 µl of RosetteSep Monocyte Enrichment cocktail were added immediately following the blood withdrawal. Tubes were inverted five times and incubated for 20 minutes at room temperature. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml spun down for 10 minutes at 500g at 4°C the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.

tag: peripheral monocytes


title: peripheral monocytes, B5 Baseline


title: peripheral monocytes, B6 Baseline


title: peripheral monocytes, B4 Baseline


title: Mcm/ stationary phase/ replica 1

description: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, first replica

tag: DNA from mock-treated cell extract and archaebacteria treated in stationary phase, first replica


title: Cdc 6/exponential phase replica 2

description: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, second replica

tag: DNA from mock-treated cell extract and archaebacteria treated in exponential phase


title: peripheral monocytes, B1 Baseline


title: peripheral monocytes, F9 in Fromentine


title: peripheral monocytes, B3 Baseline


title: peripheral monocytes, F10 in Fromentine


title: peripheral monocytes, F4 in Fromentine


title: peripheral monocytes, F3 in Fromentine


title: peripheral monocytes, F5 in Fromentine


title: proband K5 Monocytes

description: proband K5 Monocytes


title: Cdc 6/exponential phase replica 1

description: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, first replica


title: Cdc 6/stationary phase replica 4

description: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, fourth replica

tag: DNA from mock-treated cell extract and archaebacteria treated in stationary phase


title: proband K7 T-lymphocytes

description: proband K7 T-lymphocytes


title: peripheral monocytes, F1 in Fromentine


title: peripheral monocytes, F2 in Fromentine


title: Cdc 6/puromycin

source_name: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria treated with puromycin, fourth replica

source_name: DNA from mock-treated cell extract and archaebacteria treated with puromycin, fourth replica


title: proband K8 T-lymphocytes

description: proband K8 T-lymphocytes


title: peripheral monocytes, E8 in St. Etienne


title: proband K6 Monocytes

description: proband K6 Monocytes


title: proband K1 T-lymphocytes

description: proband K1 T-lymphocytes


title: peripheral monocytes, E2 in St. Etienne


title: peripheral monocytes, E4 in St. Etienne


title: proband K4 Monocytes

description: proband K4 Monocytes


title: proband K8 Monocytes

description: proband K8 Monocytes


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E1

treatment_protocol: 4ml of whole blood were collected in BD Vacutainer CPT tubes. 200 µl of RosetteSep Tcell Enrichment cocktail were added immediately following the blood withdrawal. Tubes were inverted five times and incubated for 20 minutes at room temperature. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml. spun down for 10 minutes at 500g at 4°C, the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.

tag: blood withdrawal in St. Etienne, human peripheral T-lymphocytes


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F2

tag: blood withdrawal Fromentine, human peripheral T-lymphocytes


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E2

tag: blood withdrawal  in St. Etienne, human peripheral T-lymphocytes


title: proband K3 Monocytes

description: proband K3 Monocytes

source_name: human peripheral Monocyte


title: Blood withdrawal baseline, human peripheral T-lymphocytes B3

tag: blood withdrawal  baseline, human peripheral T-lymphocytes


title: proband K9 Monocytes

description: proband K9 Monocytes


title: proband K3 T-lymphocytes

description: proband K3 T-lymphocytes


title: Blood withdrawal baseline, human peripheral T-lymphocytes B1


title: Blood withdrawal baseline, human peripheral T-lymphocytes B6


title: Blood withdrawal baseline, human peripheral T-lymphocytes B4


title: peripheral monocytes, B2 Baseline


title: peripheral monocytes, F8 in Fromentine


title: Blood withdrawal baseline, human peripheral T-lymphocytes B5


title: peripheral monocytes, F7 in Fromentine


title: peripheral monocytes, F6 in Fromentine


title: peripheral monocytes, E9 in St. Etienne


title: peripheral monocytes, E5 in St. Etienne


title: peripheral monocytes, E7 in St. Etienne


title: peripheral monocytes, E6 in St. Etienne


title: peripheral monocytes, E3 in St. Etienne


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F7

tag: blood withdrawal  in Fromentine, human peripheral T-lymphocytes


title: peripheral monocytes, E1 in St. Etienne


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#10_rep2

status: Public on Dec 29 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: The pertinent metric in the manuscript Dynamics of genomic-library enrichment and identification of solvent-tolerance genes in Clostridium acetobutylicum was each gene's relative rank after a given number of challenge transfers.  Enriched genes were those showing an increase in relative rank over successive challenge transfers.

hyb_protocol: Oppositely labeled microarray probe pairs (1 microgram of each) were mixed together, dried in a rotary SpeedVac, and redissolved in Pronto Universal Hybridization Solution. The samples were incubated at 95 degrees C for 5 min and loaded on the microarray under a LifterSlip (Erie Scientific, Portsmouth, NH, USA). The microarrays were placed in a Corning hybridization chamber with 50 microL 10xSSC (1xSSC is 0.15 M NaCl and 0.015 M sodium citrate) to maintain humidity. Microarrays were hybridized for 14-16 h in a 42 degrees C water bath. Following hybridization, microarrays were washed in TeleChem (Sunnyvale, CA, USA) wash buffers A (42 degrees C, 5 min), B (room temperature, 5 min), and C (room temperature, 2 min) and water. Slides were then spun dry at 240xg for 10 min.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometer resolution.

data_processing: GenePix software (Molecular Devices, Union City, CA, USA) (v. 5.x) was used to assess spot quality and extract feature intensity statistics; spot intensity data were exported into Xcel, non-specific background signal was subtracted, and duplicate spots per gene were averaged.  Genes were then ranked in order of decreasing average intensity.

organism: Clostridium acetobutylicum

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_unstressed inoculum_rep2

label_protocol: A PCR-based labeling approach was followed where 0.1 microl of extracted plasmid DNA was PCR amplified for 20 rounds in the presence of 275 mM dATP, 180 mM dGTP, 180 mM dCTP, 90 mM dTTP, and 180 mM aa-dUTP, and 2.5 units of Taq DNA polymerase in Taq Polymerase buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, pH 8.3).  PCR products were purified using a Microcon YM-30 column and washed twice with 450 mL distilled water.  The samples were dried in a rotary SpeedVac, redissolved in 4.5 microL of a 0.1 M sodium carbonate buffer (pH 9.0), and combined with 54 nmol NHS-ester Cy3 or Cy5 monofunctional dye (Amersham Biosciences) dissolved in an equal volume of DMSO. The mixture was incubated in the dark for 1 h. To purify the labeled cDNA, 35 microL of a 100 mM sodium acetate solution (pH 5.2) was added before purifying on a Qiagen Qiaquick PCR purification column (Valencia, CA, USA). cDNA quantity, quality, and dye incorporation was measured (A260, A280, A550 [Cy3 probe], and A649 [Cy5 probe]) on a spectrophotometer. Only samples with a dye incorporation of at least 10 dye molecules per 1,000 nucleotides were hybridized on microarrays. Samples were stored at -20 degrees C for up to 3 weeks until microarray hybridization.

growth_protocol: C. acetobutylicum was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) buffered with 30 mM sodium acetate and supplemented with 80 g/liter glucose to stationary phase for plasmid DNA isolation and transfer to the next challenge flask.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of culture at 5,000xg for 10 min, 4 degrees C. Cells were washed twice with 750 microl Wash Buffer (100mM EDTA, 50mM Tris-HCl, 500mM KCl, pH8.0) and washed once with 750 microl SET buffer (25% wt/vol sucrose, 50mM Tris-HCl, 50mM EDTA) then lysed by resuspending in 390 microL SET buffer with 5 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 10 min. Impurities were precipitated by adding 390 microl of alkaline SDS (10% vol/vol SDS, 200mM NaOH) and 390 microl 3M K+5M Acetate buffer.  Precipitate was removed by centrifugation at 13,000xg for 5 min, and plasmid DNA in the supernatant purified with two rounds of extraction with an equal volume of Phenol-chloroform Isoamyl alcohol (24:1:1) followed by one round with an equal volume of chloroform-isoamyl alcohol.  Plasmid DNA was precipitated with an equal volume of isopropanol and held at -20C for 20 minutes, washed once with 70% ethanol, and the DNA pellet resuspended in 20 microl of TE buffer (10mM Tris-HCl, 1mM EDTA, pH 8.0)

treatment_protocol: This culture was not subject to butanol challenge and serves as a control for the initial plasmid library population.  Culture was grown to stationary phase for plasmid DNA isolation and then used to inoculate the first challenge flask containing butanol.

tag: Clostridium acetobutylicum ATCC 824 containing genomic library pLib1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #10_rep2

label_protocol: Same as channel 1

growth_protocol: Same as channel 1

extract_protocol: Same as channel 1

treatment_protocol: This culture contained 1.30% v/v butanol and was inoculated from stationary phase cells from the ninth challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#7_rep1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_unstressed inoculum_rep1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #7_rep1

treatment_protocol: This culture contained 0.97% v/v butanol and was inoculated from stationary phase cells from the sixth challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F1


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E3


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E4


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E8


title: butanol_stress_50_mM_720_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_720_min_S1

hyb_protocol: Oppositely labeled microarray probe pairs (5 microg of each) were mixed together, dried in a rotary SpeedVac, and redissolved in Pronto Universal Hybridization Solution. The samples were incubated at 95 degrees C for 5 min and loaded on the microarray under a LifterSlip (Erie Scientific, Portsmouth, NH, USA). The microarrays were placed in a Corning hybridization chamber with 50 microL 10xSSC (1xSSC is 0.15 M NaCl and 0.015 M sodium citrate) to maintain humidity. Microarrays were hybridized for 14-16 h in a 42 degrees C water bath. Following hybridization, microarrays were washed in TeleChem (Sunnyvale, CA, USA) wash buffers A (42 degrees C, 5 min), B (room temperature, 5 min), and C (room temperature, 2 min) and water. Slides were then spun dry at 240xg for 10 min.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 microm resolution.

data_processing: GenePix software (Molecular Devices, Union City, CA, USA) (v. 5.x) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127).

source_name: Wild type not stressed 720 min

label_protocol: An indirect labeling approach was followed where cDNA was first made in the presence of nucleotides and aminoallyl dUTP, purified, and then the aminoallyl dUTP groups were coupled to a monoreactive dye (Cy3 or Cy5). Total RNA (25 microg) was mixed with 15 microg random hexamers (Roche, Indianapolis, IN, USA) and the volume brought up to 18.5 microL with RNase-free water. Samples were incubated at 70 degrees C for 10 min and then snap-frozen in a dry ice/ethanol bath for 30 sec. Deoxynucleotide triphosphates (Invitrogen; 0.6 mM dATP, 0.4 mM dCTP, 0.4 mM dGTP, and 0.36 mM dTTP), 0.24 mM aminoallyl dUTP (Sigma), 400 units SuperScript II reverse transcriptase (Invitrogen), First Strand Buffer (Invitrogen), and 6 microM dithiothreitol were added to a final volume of 30 microL. The samples were incubated for 3 h to overnight at 42°C, and the reaction was stopped by addition of 0.5 M EDTA (pH 8.0). The remaining RNA was degraded by addition of NaOH (final concentration 11 mM), incubation at 65oC for 15 min, and neutralization with HCl (final concentration 11 mM). The cDNA was purified by bringing up the volume to 450 microL with sterile water and concentrating three times on a Millipore YM-30 column. The samples were dried in a rotary SpeedVac, redissolved in 4.5 microL of a 0.1 M sodium carbonate buffer (pH 9.0), and combined with 54 nmol NHS-ester Cy3 or Cy5 monofunctional dye (Amersham Biosciences) dissolved in an equal volume of DMSO. The mixture was incubated in the dark for 1 h. To purify the labeled cDNA, 35 microL of a 100 mM sodium acetate solution (pH 5.2) was added before purifying on a Qiagen Qiaquick PCR purification column (Valencia, CA, USA). cDNA quantity, quality, and dye incorporation was measured (A260, A280, A550 [Cy3 probe], and A649 [Cy5 probe]) on a spectrophotometer. Only samples with a dye incorporation of at least 10 dye molecules per 1,000 nucleotides were hybridized on microarrays. Samples were stored at -20 degrees C for up to 3 weeks until microarray hybridization.

growth_protocol: C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA) was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose until they reached an A600 ca. 0.6 (corresponding to midexponential growth).  The cultures were then split equally into two bottles, one was stressed with butyrate and the other was used as control. Both were sampled at the same time points through the length of the experiment.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min, 4 degrees C. Cells were then lysed by resuspending in 200 microL SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) with 20 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 4 min. One milliliter of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. Samples were immediately stored at -85 degrees C and used within one month to minimize RNA degradation. To isolate and purify the RNA, samples were thawed at room temperature; 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified following manufacturer's instructions. The RNA was resuspended in 20-30 microL RNase-free water and quantitated in a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8. RNA integrity was also verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA were stored at -85 degree C and used within one week of purification.

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 720 minutes after the challenge.

tag: Clostridium acetobutylicum ATCC 824

source_name: Wild type 720 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 720 minutes after the challenge.


title: Blood withdrawal baseline, human peripheral T-lymphocytes B2


title: butanol_stress_50_mM_360_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_360_min_S2

source_name: Wild type 360 min after butanol stress (50 mM, 0.46% v/v)

growth_protocol: C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA) was stored at -85 degree C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose until they reached an A600 ca. 0.6 (corresponding to midexponential growth).  The cultures were then split equally into two bottles, one was stressed with butyrate and the other was used as control. Both were sampled at the same time points through the length of the experiment.

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 360 minutes after the challenge.

source_name: Wild type not stressed 360 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 360 minutes after the challenge.


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E7


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E5


title: Blood withdrawal in St. Etienne, human peripheral T-lymphocytes E6


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F10


title: butanol_stress_50_mM_120_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_120_min_S1

source_name: Wild type not stressed 120 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 120 minutes after the challenge.

source_name: Wild type 120 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 120 minutes after the challenge.


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F9

source_name: human peripheral T-lymphocytes

tag: blood withdrawal in Fromentine, human peripheral T-lymphocytes


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F6


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F4


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#4_rep2

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #4_rep2

treatment_protocol: This culture contained 0.74% v/v butanol and was inoculated from stationary phase cells from the third challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: butanol_stress_50_mM_60_min_S4

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_60_min_S4

source_name: Wild type 60 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 60 minutes after the challenge.

source_name: Wild type not stressed 60 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 60 minutes after the challenge.


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F3


title: butanol_stress_50_mM_45_min_S4

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_45_min_S4

source_name: Wild type 45 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 45 minutes after the challenge.

source_name: Wild type not stressed 45 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 45 minutes after the challenge.


title: butanol_stress_50_mM_45_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_45_min_S2


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F5


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#4_rep1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #4_rep1

treatment_protocol: This culture contained 0.86% v/v butanol and was inoculated from stationary phase cells from the third challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: Blood withdrawal in Fromentine, human peripheral T-lymphocytes F8


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#13_rep1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #13_rep1

treatment_protocol: This culture contained 1.56% v/v butanol and was inoculated from stationary phase cells from the twelfth challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: butanol_stress_50_mM_30_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_30_min_S2

source_name: Wild type not stressed 30 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 30 minutes after the challenge.

source_name: Wild type 30 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 30 minutes after the challenge.


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#10_rep1

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_unstressed inoculum_rep1

treatment_protocol: This culture was not subject to butanol challenge and serves as a control for the initial plasmid library population.  Culture was grown to stationary phase for plasmid DNA isolation and then used to inoculate the first challenge flask containing butanol.

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #10_rep1

treatment_protocol: This culture contained 1.30% v/v butanol and was inoculated from stationary phase cells from the ninth challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: butanol_stress_50_mM_1440_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_1440_min_S1

source_name: Wild type not stressed 1440 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 1440 minutes after the challenge.

source_name: Wild type 1440 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 1440 minutes after the challenge.


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#13_rep2

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_unstressed inoculum_rep2

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #13_rep2


title: butanol_stress_50_mM_1440_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_1440_min_S2


title: butanol_stress_50_mM_10_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_10_min_S1

source_name: Wild type not stressed 10 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 10 minutes after the challenge.

source_name: Wild type 10 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 10 minutes after the challenge.


title: butanol_stress_50_mM_720_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_720_min_S2

source_name: Wild type 720 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 720 minutes after the challenge.

source_name: Wild type not stressed 720 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 720 minutes after the challenge.


title: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol_stress_Transfer#7_rep2

source_name: Clostridium_acetobutylicum_ATCC 824 (pLib1)_butanol stressed transfer #7_rep2

treatment_protocol: This culture contained 0.98% v/v butanol and was inoculated from stationary phase cells from the sixth challenge flask.  The flask was grown to stationary phase for plasmid DNA isolation


title: butanol_stress_50_mM_120_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_120_min_S2

source_name: Wild type not stressed 120 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 120 minutes after the challenge.

source_name: Wild type 120 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 120 minutes after the challenge.


title: butanol_stress_50_mM_60_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_60_min_S2

source_name: Wild type not stressed 60 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 60 minutes after the challenge.

source_name: Wild type 60 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 60 minutes after the challenge.


title: butanol_stress_50_mM_360_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_360_min_S1

source_name: Wild type not stressed 360 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 360 minutes after the challenge.

source_name: Wild type 360 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 360 minutes after the challenge.


title: butanol_stress_50_mM_120_min_S3

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_120_min_S3


title: butyrate_stress_29_mM_120_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_120_min_S1

source_name: Wild type 120 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 120 minutes after the challenge.


title: butyrate_stress_29_mM_720_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_720_min_S1

source_name: Wild type 720 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 720 minutes after the challenge.


title: butyrate_stress_29_mM_360_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_360_min_S2

source_name: Wild type 360 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 360 minutes after the challenge.


title: butyrate_stress_29_mM_45_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_45_min_S2

source_name: Wild type 45 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 45 minutes after the challenge.

source_name: Wild type not stressed 45 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 45 minutes after the challenge.


title: butanol_stress_50_mM_60_min_S3

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_60_min_S3


title: butanol_stress_50_mM_60_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_60_min_S1


title: butyrate_stress_29_mM_60_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_60_min_S2

source_name: Wild type 60 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 60 minutes after the challenge.


title: butyrate_stress_29_mM_30_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_30_min_S2

source_name: Wild type 30 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 30 minutes after the challenge.

source_name: Wild type not stressed 30 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 30 minutes after the challenge.


title: butanol_stress_50_mM_45_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_45_min_S1

source_name: Wild type 45 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 45 minutes after the challenge.


title: butyrate_stress_29_mM_30_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_30_min_S1


title: butanol_stress_50_mM_45_min_S3

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_45_min_S3


title: butanol_stress_50_mM_30_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_30_min_S1

source_name: Wild type 30 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 30 minutes after the challenge.


title: butanol_stress_50_mM_30_min_S3

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_30_min_S3


title: acetate_stress_43 mM_1440_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_1440_min_S2

source_name: Wild type 1440 min after acetate stress (43 mM)

growth_protocol: C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA) was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose until they reached an A600 ca. 0.6 (corresponding to midexponential growth).  The cultures were then split equally into two bottles, one was stressed with acetate and the other was used as control. Both were sampled at the same time points through the length of the experiment.

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 1440 minutes after the challenge.

source_name: Wild type not stressed 1440 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 1440 minutes after the challenge.


title: acetate_stress_43 mM_720_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_720_min_S2

source_name: Wild type 720 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 720 minutes after the challenge.

source_name: Wild type not stressed 720 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 720 minutes after the challenge.


title: acetate_stress_43 mM_720_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_720_min_S1


title: acetate_stress_43 mM_1440_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_1440_min_S1


title: acetate_stress_43 mM_45_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_45_min_S1

source_name: Wild type 45 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 45 minutes after the challenge.


title: acetate_stress_43 mM_60_min_S3

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_60_min_S3

source_name: Wild type 60 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 60 minutes after the challenge.

source_name: Wild type not stressed 60 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 60 minutes after the challenge.


title: acetate_stress_43 mM_120_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_120_min_S1

source_name: Wild type not stressed 120 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 120 minutes after the challenge.

source_name: Wild type 120 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 120 minutes after the challenge.


title: E61 96h 00uM_rep1

description: primary T cell response to oxidative stress under the context of T-cell activaiton

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

source_name: T cells, control, 96 hours

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

growth_protocol: Grown in AIM V with 2% Human AB Serum, 37degC, 5% CO2

extract_protocol: Agilent RNA isolation mini-kit

treatment_protocol: activated with CD3/CD28 and IL2 for 96 hours

tag: primary T cells, donor 2

source_name: Human Thymus Total RNA

extract_protocol: Extraction performed by the manufacturer

tag: Human Thymus Total RNA


title: butanol_stress_50_mM_10_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butanol_stress_50_mM_10_min_S2

source_name: Wild type 10 min after butanol stress (50 mM, 0.46% v/v)

treatment_protocol: This bottle was challenged with a sublethal amount of butanol (50 mM, 0.46% v/v). This sample was taken 10 minutes after the challenge.

source_name: Wild type not stressed 10 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 10 minutes after the challenge.


title: butyrate_stress_29_mM_120_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_120_min_S2

source_name: Wild type 120 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 120 minutes after the challenge.


title: E61 10h 00uM_rep1

source_name: T cells, control, 10 hours

treatment_protocol: activated with CD3/CD28 and IL2 for 10 hours


title: butyrate_stress_29_mM_60_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_60_min_S1

source_name: Wild type 60 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 60 minutes after the challenge.


title: butyrate_stress_29_mM_45_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_45_min_S1

source_name: Wild type not stressed 45 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 45 minutes after the challenge.

source_name: Wild type 45 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 45 minutes after the challenge.


title: butyrate_stress_29_mM_720_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_720_min_S2

source_name: Wild type 720 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 720 minutes after the challenge.


title: E61 48h 00uM_rep1

source_name: T cells, control, 48 hours

treatment_protocol: activated with CD3/CD28 and IL2 for 48 hours


title: E61 10h 25uM_rep1

source_name: T cells, H2O2, 10 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 10 hours


title: acetate_stress_43 mM_60_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_60_min_S2


title: E61 04h 25uM_rep1

source_name: T cells, H2O2, 4 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 4 hours


title: butyrate_stress_29_mM_10_min_S2

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_10_min_S2

source_name: Wild type 10 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 10 minutes after the challenge.


title: butyrate_stress_29_mM_10_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_10_min_S1


title: E61 00h_rep1

source_name: T cells,  0 hour

treatment_protocol: No treatment


title: E59 96h 25uM_rep1

source_name: T cells, H2O2, 96 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 96 hours

tag: primary T cells, donor 1


title: E61 96h 25uM_rep1


title: acetate_stress_43 mM_360_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_360_min_S1

source_name: Wild type not stressed 360 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 360 minutes after the challenge.

source_name: Wild type 360 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 360 minutes after the challenge.


title: butyrate_stress_29_mM_360_min_S1

description: Clostridium_acetobutylicum_ATCC 824_butyrate_stress_29_mM_360_min_S1

source_name: Wild type 360 min after butyrate stress (29 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of butyrate (29 mM). Before addition, the butyrate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 360 minutes after the challenge.


title: acetate_stress_43 mM_120_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_120_min_S2

source_name: Wild type 120 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 120 minutes after the challenge.

source_name: Wild type not stressed 120 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 120 minutes after the challenge.


title: acetate_stress_43 mM_60_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_60_min_S1

source_name: Wild type not stressed 60 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 60 minutes after the challenge.

source_name: Wild type 60 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 60 minutes after the challenge.


title: acetate_stress_43 mM_30_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_30_min_S1

source_name: Wild type not stressed 30 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 30 minutes after the challenge.

source_name: Wild type 30 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 30 minutes after the challenge.


title: E61 48h 25uM_rep2

source_name: T cells, H2O2, 48 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 48 hours

source_name: Human Thymus Total RNA


title: acetate_stress_43 mM_360_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_360_min_S2


title: E61 48h 00uM_rep2

source_name: T cells, control, 48 hours


title: E59 00h_rep2


title: E59 96h 00uM_rep1

source_name: T cells, control, 96 hours

treatment_protocol: activated with CD3/CD28 and IL2 for 96 hours


title: E61 48h 25uM_rep1


title: E103 96h 25uM_rep2

tag: primary T cells, donor 3


title: acetate_stress_43 mM_10_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_10_min_S2

source_name: Wild type 10 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 10 minutes after the challenge.

source_name: Wild type not stressed 10 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 10 minutes after the challenge.


title: acetate_stress_43 mM_10_min_S1

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_10_min_S1


title: acetate_stress_43 mM_30_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_30_min_S2


title: acetate_stress_43 mM_45_min_S2

description: Clostridium_acetobutylicum_ATCC 824_acetate_stress_43 mM_45_min_S2

source_name: Wild type 45 min after acetate stress (43 mM)

treatment_protocol: This bottle was challenged with a sublethal amount of acetate (43 mM). Before addition, the acetate solution was adjusted for pH with NaOH to within 0.1 pH units of the culture to minimize any pH effects. This sample was taken 45 minutes after the challenge.

source_name: Wild type not stressed 45 min

treatment_protocol: This bottle was not subject to any challenge and it is used as a control. This sample was taken 45 minutes after the challenge.


title: E59 10h 25uM_rep1

description: primary T cell response to oxidative stress under the context of T-cell activaiton

source_name: T cells, H2O2, 10 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 10 hours


title: E103 96h 00uM_rep2


title: E61 00h_rep2

source_name: T cells,  0 hour

treatment_protocol: No treatment


title: E61 04h 00uM_rep1

source_name: T cells, control, 4 hours

treatment_protocol: activated with CD3/CD28 and IL2 for 4 hours


title: E103 48h 00uM_rep1

treatment_protocol: activated with CD3/CD28 and IL2 for 48 hours


title: E103 48h 25uM_rep2


title: E59 10h 00uM_rep1

source_name: T cells, control, 10 hours

treatment_protocol: activated with CD3/CD28 and IL2 for 10 hours


title: E59 04h 25uM_rep1

source_name: T cells, H2O2, 4 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 4 hours


title: E103 48h 25uM_rep1


title: E59 48h 25uM_rep1


title: E103 10h 00uM_rep1


title: E103 10h 25uM_rep2


title: E103 96h 00uM_rep1


title: E59 48h 25uM_rep2


title: E59 96h 25uM_rep2

source_name: T cells, H2O2, 96 hours

treatment_protocol: treated with H2O2, activated with CD3/CD28 and IL2 for 96 hours


title: E59 48h 00uM_rep1


title: E103 04h 00uM_rep1


title: B4 392 b4-/- after nicotine-induced seizures

status: Public on Dec 26 2007

city: Tel Aviv

first: Avi

last: Orr-Urtreger

address: 6 Weizmann St

department: Genetic Institute

country: Israel

institute: Tel Aviv Sourasky Medical Center

description: Total RNA was extracted from whole brain. Total RNA isolation, target preprocessing and hybridization to the U74Av2 microarray were conducted according to Affymetrix’s instructions.

hyb_protocol: Fragmented cRNAs were hybridized overnight at 45°C to Affymetrix Gene Chip Murine Genome U74Avr2 arrays (Affymetrix, Inc.).

scan_protocol: Affymetrix Gene-Array Scanner

data_processing: The signal values were generated by statistical algorithm implanted in Affymetrix Suite Version 5.0 software (MAS5, Affymetrix, Inc.) The detection calls were calculated, based on the detection p-value, as following: probe sets with p-value of more than 0.06 were designated as absent, p-value of more than 0.04 and less than 0.06 as marginal and p-value of less than 0.04 as present. For interarray comparisons, data from each array was scaled using MAS5 software, and the mean intensity for each array was adjusted by a scaling factor to a set target intensity of 150.

label: biotin-labeled

source_name: Beta4 nAChR subunit null mice following nicotine-induced seizures

label_protocol: 10 mg of total RNA were used to synthesize double-stranded cDNA with the Superscript Choice System (Invitrogen, Carlsbad, CA) and 100 pmole of oligo-dT primer attached to a T7 promoter sequence (Genset, Paris, France). The double-stranded cDNAs were phenol/chloroform extracted with Phase Lock Gels tubes (Eppendorf, Hamburg, Germany). In vitro transcription (IVT) of the double-stranded cDNA products was performed with an Enzo BioArray High Yield Transcript labeling kit in the presence of biotin-labeled nucleotides (Affymetrix, Inc., Santa Clara, CA). Following purification by an RNeasy mini kit (Qiagen Sciences), the biotin-labeled cRNA products were subjected to alkaline lysis (200mM Tris-acetate pH 8.1, 500mM potassium acetate, 150mM magnesium acetate).

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

tag: Strain

tag: Gender

value: M

tag: Age

value: 8 weeks

tag: Treatment

value: 1 hour following nicotine-induced seizures


title: E59 00h_rep1

source_name: T cells, 0 hour


title: E59 04h 00uM_rep1


title: B4 363 b4-/- untreated

source_name: Beta4 nAChR subunit null mice without treatment

value: 6 weeks

value: untreated


title: B4 436 b4-/- after nicotine-induced seizures

value: F


title: B4 365 b4-/- untraeted

value: 9 weeks


title: LT 411 +/T after nicotine-induced seizures

source_name: Alpha7 L250T heterozygous mice following nicotine-induced seizures


title: E103 96h 25uM_rep1

source_name: Human Thymus Total RNA


title: E103 48h 00uM_rep2

source_name: T cells, control, 48 hours


title: LT 407 +/T after nicotine-induced seizures


title: B4 437 b4-/- untreated


title: B4 424 b4-/- untreated


title: LT 410 +/T after nicotine-induced seizures


title: LT 435 +/T after nicotine-induced seizures


title: LT 344 +/T untreated

source_name: Alpha7 nAChR subunit L250T heterozygous mice without treatment


title: E59 48h 00uM_rep2


title: B4 398 b4-/- untreated

value: 7 weeks


title: B4 391 b4-/- after nicotine-induced seizures


title: E103 10h 25uM_rep1


title: LT 436 +/T untreated


title: LT 341 +/T untreated


title: E103 00h_rep1


title: B4 528 b4-/- after nicotine-induced seizures


title: E103 04h 25uM_rep1


title: LT 434 +/T after nicotine-induced seizures


title: B4 422 wild-type after nicotine-induced seizures

source_name: Wild-type mice following nicotine-induced seizures


title: B4 394 wild-type untreated

source_name: Wild-type mice without treatment


title: LT 342 +/T untreated


title: LT489 wild-type after nicotine-induced seizures


title: B4 527 wild-type after nicotine-induced seizures


title: LT346 wilt-type untreated


title: PC-3 siGFP_2 (Contol cell line with slienceing of  GFP)

status: Public on Dec 20 2007

first: Towia

middle: A

last: Libermann

address: 99 Brookline Ave.

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from Contol PC-3 cells by slienceing the GFP gene using the SiRNA specific for the gene.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C. GeneChips were washed and stained on the Affymetrix High-throughput array platform

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip HT Scanner

data_processing: dChip

source_name: Pc-3 Cell line

label_protocol: Biotinylated cRNA were prepared using GeneChip HT IVT Labelling Kit according to  the standard Affymetrix protocol

extract_protocol: RNAeasy mini Kit from Qiagen has benn used to extract total RNA.  The extraction of RNA has been performed according to the manufacturer's instructions

tag: Prostate cancer cell line


title: PC-3 siPDEF_2 (Experimental cell line with slienceing of  PDEF)

description: Gene expression data from experimental PC-3 cells by slienceing the PDEF gene using the SiRNA.

source_name: PC-3 cell line

tag: Prostate cancer cell line with slienceing of PDEF gene using siRNA


title: B4 367 wild-type untreated


title: B4 395 wild-type untreated


title: LT345 wild-type untreated


title: PC-3 siPDEF_1 (Experimental cell line with slienceing of  PDEF)

tag: Prostate cancer cell line with slienceing of PDEF gene using siRNA.


title: R28 - Vb16 TIL - mAdbID:64372

status: Public on Dec 15 2007

city: Bethesda

first: Keith

last: Kerstann

state: MD

department: Surgery Branch

institute: National Institutes of Health

description: mAdb experiment ID: 64372

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

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.39;; 3.54 Temperature: 27.36

data_processing:
mAdb Standard Data Processing Protocol
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Universal Human Reference RNA - Cy3

label_protocol:
Cy3 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: Other

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: R28 - Vb16 TIL

label_protocol:
Ambion Message Amp - Cy5
Label method: amino allyl conjugation
Other: Approximately 0.5 Ÿ 1.0 ug of total RNA was then linearly amplified for one round using Amino Allyl Message Amp kits as recommended by the manufacturer (Ambion). All TIL antisense RNA (aRNA) were conjugated with Cyanine 5 while equivalently amplified control aRNA was conjugated with Cyanine 3.

extract_protocol:
Qiagen RNeasy Columns
Other: All RNA was isolated from respective TIL samples using Qiashredder homogenization columns followed by RNeasy columns (Qiagen) according to manufactures directions. RNA yield was determined using a Nanodrop photospectrometer.

treatment_protocol:
Treatment type: Adoptive Cell Transfer
Treatment dose: 1.1-13.7 x 10e10 cells

value: male

tag: Cell type

value: Vb16 tumor infiltrating lymphocytes

tag: Disease state

value: metastatic melanoma

tag: Individual

tag: genotype/variation

value: Persisting clonotype


title: PC-3 siGFP_1 (Contol cell line with slienceing of  GFP)

source_name: Prostate cancer cell line

tag: Prostate cancer cell line PC-3.


title: R9 - F4 MART TIL - mAdbID:64378

description: mAdb experiment ID: 64378

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.44;; 3.53 Temperature: 25.41

source_name: R9- F4 MART TIL

value: F4 MART tumor infiltrating lymphocytes


title: R30 - Vb17 TIL - mAdbID:64370

description: mAdb experiment ID: 64370

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.38;; 3.54 Temperature: 27.09

source_name: R30 - Vb17 TIL

value: Vb17 MART tumor infiltrating lymphocytes

value: Non-persisting clonotype


title: R10 - Vb5 TIL - mAdbID:64381

description: mAdb experiment ID: 64381

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.39;; 3.51 Temperature: 27.97

source_name: R10 - Vb5 TIL

value: Vb5 tumor infiltrating lymphocytes


title: R30 - Vb11 TIL - mAdbID:64369

description: mAdb experiment ID: 64369

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.4;; 3.54 Temperature: 26.75

source_name: R30 - Vb11 TIL

value: Vb11 MART tumor infiltrating lymphocytes


title: R9 - F5 MART TIL - mAdbID:64379

description: mAdb experiment ID: 64379

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.44;; 3.51 Temperature: 26.45

source_name: R9- F5 MART TIL

value: F5 MART tumor infiltrating lymphocytes


title: R10 - Vb7 TIL - mAdbID:64380

description: mAdb experiment ID: 64380

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.37;; 3.48 Temperature: 28.43

source_name: R10 - Vb7 TIL

value: Vb7 tumor infiltrating lymphocytes


title: LT 339 +/T untreated

value: 6 weeks


title: R28 - Vb13 TIL - mAdbID:64371

description: mAdb experiment ID: 64371

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.38;; 3.54 Temperature: 27.64

value: Vb13.1 tumor infiltrating lymphocytes


title: W10 - Cloned TIL - mAdbID:64364

description: mAdb experiment ID: 64364

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.25;; 3.53 Temperature: 32.64

source_name: W10 - Cloned TIL

value: tumor infiltrating lymphocyte clone

value: Non-responder


title: R32- Bulk TIL - mAdbID:64350

description: mAdb experiment ID: 64350

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.36;; 3.5 Temperature: 31.42

source_name: R32 - Bulk TIL

value: female

value: bulk tumor infiltrating lymphocytes

value: Responder


title: R16- Bulk TIL - mAdbID:64349

description: mAdb experiment ID: 64349

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.4;; 3.51 Temperature: 30.9

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: R16 - Bulk TIL

value: male


title: R19 - Vb8 TIL - mAdbID:64365

description: mAdb experiment ID: 64365

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.41;; 3.53 Temperature: 25.38

source_name: R19- Vb8 TIL

value: Vb8 tumor infiltrating lymphocytes

value: metastatic melanoma

value: Persisting clonotype


title: LT340 wild-type untreated

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD).

value: M

value: untreated


title: R9 - Cloned TIL - mAdbID:64363

description: mAdb experiment ID: 64363

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.27;; 3.53 Temperature: 32.52

source_name: R9 - Cloned TIL


title: T8 - Cloned TIL - mAdbID:64362

description: mAdb experiment ID: 64362

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.25;; 3.53 Temperature: 32.09

source_name: T8 - Cloned TIL


title: R34- Bulk TIL - mAdbID:64351

description: mAdb experiment ID: 64351

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.33;; 3.5 Temperature: 32.09

source_name: R34 - Bulk TIL


title: R19 - Vb3 TIL - mAdbID:64366

description: mAdb experiment ID: 64366

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.42;; 3.54 Temperature: 25.72

source_name: R19- Vb3 TIL

value: Vb3 tumor infiltrating lymphocytes

value: Non-persisting clonotype


title: B1 - Cloned TIL - mAdbID:64354

description: mAdb experiment ID: 64354

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.36;; 3.53 Temperature: 29.78

source_name: Universal Human Reference RNA - Cy3

source_name: B1 - Cloned TIL


title: NR11- Bulk TIL - mAdbID:64345

description: mAdb experiment ID: 64345

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.48;; 3.5 Temperature: 28.07

source_name: NR11 - Bulk TIL


title: L7 - Cloned TIL - mAdbID:64361

description: mAdb experiment ID: 64361

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.26;; 3.53 Temperature: 31.94

source_name: L7 - Cloned TIL


title: R25 - Vb17 TIL - mAdbID:64368

description: mAdb experiment ID: 64368

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.42;; 3.54 Temperature: 26.42

source_name: R25 - Vb17 TIL

value: Vb17 MART tumor infiltrating lymphocytes


title: NR3- Bulk TIL - mAdbID:64344

description: mAdb experiment ID: 64344

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.47;; 3.5 Temperature: 27.3

source_name: NR3 - Bulk TIL


title: NR23- Bulk TIL - mAdbID:64346

description: mAdb experiment ID: 64346

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.44;; 3.5 Temperature: 28.83

source_name: NR23 - Bulk TIL


title: CO3 - Cloned TIL - mAdbID:64357

description: mAdb experiment ID: 64357

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.34;; 3.53 Temperature: 30.51

source_name: CO3 - Cloned TIL


title: NR12- Bulk TIL - mAdbID:64343

description: mAdb experiment ID: 64343

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.51;; 3.5 Temperature: 26.39

source_name: NR12 - Bulk TIL


title: NR7- Bulk TIL - mAdbID:64348

description: mAdb experiment ID: 64348

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.39;; 3.5 Temperature: 30.23

source_name: NR7 - Bulk TIL


title: R25 - Vb8 TIL - mAdbID:64367

description: mAdb experiment ID: 64367

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.41;; 3.54 Temperature: 26.05

source_name: R25 - Vb8 TIL

value: Vb8 MART tumor infiltrating lymphocytes


title: K6 - Cloned TIL - mAdbID:64360

description: mAdb experiment ID: 64360

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.32;; 3.52 Temperature: 31.82

source_name: K6 - Cloned TIL


title: CA2 - Cloned TIL - mAdbID:64356

description: mAdb experiment ID: 64356

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.37;; 3.53 Temperature: 30.02

source_name: CA2 - Cloned TIL


title: D4 - Cloned TIL - mAdbID:64358

description: mAdb experiment ID: 64358

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.31;; 3.53 Temperature: 31.51

source_name: D4 - Cloned TIL


title: NR20- Bulk TIL - mAdbID:64347

description: mAdb experiment ID: 64347

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.48;; 3.5 Temperature: 29.5

source_name: NR20 - Bulk TIL


title: J5 - Cloned TIL - mAdbID:64359

description: mAdb experiment ID: 64359

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.31;; 3.53 Temperature: 31.58

source_name: J5 - Cloned TIL


title: R6 - Bulk TIL - mAdbID:64337

description: mAdb experiment ID: 64337

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.41;; 3.49 Temperature: 30.57

source_name: R6 - Bulk TIL


title: R33- Bulk TIL - mAdbID:64335

description: mAdb experiment ID: 64335

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.46;; 3.48 Temperature: 28.49

source_name: Universal Human Reference RNA - Cy3

source_name: R33 - Bulk TIL


title: NR14- Bulk TIL - mAdbID:64338

description: mAdb experiment ID: 64338

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.37;; 3.49 Temperature: 31.67

source_name: NR14 - Bulk TIL


title: NR24- Bulk TIL - mAdbID:64342

description: mAdb experiment ID: 64342

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.26;; 3.38 Temperature: 34.6

source_name: NR24 - Bulk TIL


title: NR5- Bulk TIL - mAdbID:64341

description: mAdb experiment ID: 64341

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.28;; 3.5 Temperature: 33.99

source_name: NR5 - Bulk TIL


title: IMR90hTERTpd134  cells with long telomeres and telomerase positive

status: Public on Dec 07 2007

city: Dallad

first: zhenjun

last: Lou

state: TX

address: 5323 Harry Hines Blvd.

department: Cell Biology

institute: The University of Texas Southwestern Medical Center at Dallas

description: not applicable

hyb_protocol: spotted array, available on UT Southwestern Microarray Facility website

data_processing: raw data

source_name: Cy5, Reference RNA

label_protocol: PE asas RNA labeling kit

extract_protocol: not known

tag: comerially available, used as reference in all experiments

source_name: Cy 3, Experimental RNA

extract_protocol: Qiagen RNA extraction kit

tag: RNAs from IMR90 cells with long telomeres and telomerase positive


title: NR22- Bulk TIL - mAdbID:64339

description: mAdb experiment ID: 64339

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.35;; 3.5 Temperature: 32.95

source_name: NR22 - Bulk TIL


title: NR27- Bulk TIL - mAdbID:64340

description: mAdb experiment ID: 64340

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.28;; 3.5 Temperature: 33.56

source_name: NR27 - Bulk TIL


title: R28 - Bulk TIL - mAdbID:57731

description: mAdb experiment ID: 57731

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.44;; 3.5 Temperature: 30.11

source_name: R28 - Bulk TIL


title: HME31E6/7pd69 cells with short telomeres

description: not applicable

scan_protocol: spotted array, available on UT Southwestern Microarray Facility website

data_processing: Raw data

label: Cy 5

label_protocol: PE ASAP RNA labeling kit

extract_protocol: Qiage RNA kit

tag: RNAs from HME31 cells with short telomeres


title: IMR90pd67  cells with short telomeres

description: not applicable

tag: RNAs from IMR90 cells with short telomeres


title: NR8- Bulk TIL - mAdbID:64333

description: mAdb experiment ID: 64333

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.23;; 3.48 Temperature: 34.66

source_name: NR8 - Bulk TIL


title: NR15- Bulk TIL - mAdbID:57735

description: mAdb experiment ID: 57735

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.35;; 3.5 Temperature: 32.8

source_name: NR15 - Bulk TIL


title: R30- Bulk TIL - mAdbID:57730

description: mAdb experiment ID: 57730

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.47;; 3.5 Temperature: 28.43

source_name: R30 - Bulk TIL


title: R17- Bulk TIL - mAdbID:64336

description: mAdb experiment ID: 64336

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.48;; 3.48 Temperature: 28.92

source_name: R17 - Bulk TIL


title: HME31hTERTpd67 cells with long telomeres and telomerase positive

description: not applicable

extract_protocol: Not known

extract_protocol: Qiagen RNA kit

tag: RNAs from HME31 cells with long telomeres and telomerase positive


title: IMR90E6/7pd84  cells with short telomeres

description: not applicable


title: R21- Bulk TIL - mAdbID:64334

description: mAdb experiment ID: 64334

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.5;; 3.47 Temperature: 27.18

source_name: R21 - Bulk TIL

tag: Gender


title: IMR90pd26 cells with long telomeres

description: not applicable

tag: RNAs from IMR90 cells with long telomeres


title: BJB14 with short telomeres and telomerase positive

description: not applicable

data_processing: raw

source_name: Cy5, for Reference RNA

extract_protocol: not known.

tag: Reference RNA, comercially available, used as control for all the experiments

source_name: Cy3, experimental RNA

tag: RNAs from BJB14 cells with short telomeres and telomerase positive


title: NR13- Bulk TIL - mAdbID:64329

description: mAdb experiment ID: 64329

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.26;; 3.39 Temperature: 34.41

source_name: Universal Human Reference RNA - Cy3

source_name: NR13 - Bulk TIL


title: NR18- Bulk TIL - mAdbID:64326

description: mAdb experiment ID: 64326

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.3;; 3.39 Temperature: 33.74

source_name: NR18 - Bulk TIL


title: NR29- Bulk TIL - mAdbID:64322

description: mAdb experiment ID: 64322

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.3;; 3.5 Temperature: 33.5

source_name: NR29 - Bulk TIL


title: BJhtert-168 with long telomeres and telomerase positive

description: not applicable

source_name: Cy 5 reference RNA

source_name: Cy3 experiment RNA

tag: RNAs from BJhTERT-168 cells with long telomeres and telomerase positive


title: R31- Bulk TIL - mAdbID:57729

description: mAdb experiment ID: 57729

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.53;; 3.49 Temperature: 26.94

source_name: R31 - Bulk TIL


title: HME31PD26 cells with long telomeres

description: not applicable

source_name: Cy5, Reference RNAs

tag: Comerially available, Used as reference in all experiments

tag: RNA from HME31 cells with long telomeres


title: BJ-78 with short telomeres

description: not applicable

tag: RNAs from BJ cells with short telomeres


title: BJ-18 with long telommeres

description: not applicable

source_name: Cy5, for reference RNAs

label_protocol: chemical labeling using PE ASAP RNA labeling kit

extract_protocol: Comercially availible

tag: Reference RNA, comercially availible, used as control for all the experiments

label_protocol: chemicallabeling using PE ASAP RNA labeling kit

tag: RNA from BJ cells with long telomeres


title: R26- Bulk TIL - mAdbID:57734

description: mAdb experiment ID: 57734

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.39;; 3.5 Temperature: 32.06

tag: Other

source_name: R26 - Bulk TIL

tag: Cell type

tag: Disease state

tag: Individual

tag: genotype/variation


title: R19- Bulk TIL - mAdbID:57732

description: mAdb experiment ID: 57732

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [94874] ScanPower: 100;; 100 LaserPower: 3.45;; 3.5 Temperature: 31.03

source_name: R19 - Bulk TIL


title: Liver control pool2 Affy

status: Public on Nov 27 2007

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.

scan_protocol: MIcroarrays were scanned using a laser scanner (Affymetrix).

data_processing: Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).

source_name: liver, untreated

label_protocol: All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

tag: Strain

tag: Age

value: 9 - 12 weeks

tag: Tissue

value: liver

tag: Treatment

value: vehicle only (5% DMSO in corn oil)


title: Liver control pool3 Affy

description: No additional data.

tag: Gender


title: Liver cholesterol pool1 Affy

description: No additional data.

scan_protocol: Microarrays were scanned using a laser scanner (Affymetrix).

data_processing: Raw data were first normalized using log2-transformed expression measure summaries of the probe sets which were computed and normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group and transcript levels further analyzed using Gene Spring Software (Silicon Genetics, Redwood, USA).

source_name: liver, high cholesterol diet

label_protocol: All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10μg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10 h they were sacrificed.

tag: Diet

value: 1% cholesterol diet


title: Staphylococcus aureus_hypochlorite_10min_replicate1

status: Public on Aug 01 2007

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Hypochlorite treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_hypochlorite

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 4.4mM hypochlorite immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 10 min incubation with hypochlorite using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: hypochlorite (4.4mM)

tag: NCTC 8325 Wild type


title: Liver control pool1 Affy

description: No additional data.


title: Liver phenobarbital pool4 Affy

description: No additional data.

source_name: liver, phenobarbital treated

treatment_protocol: Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

value: 50 mg/kg of phenobarbital


title: Liver phenobarbital pool1 Affy

description: No additional data.


title: Liver cholesterol pool3 Affy

description: No additional data.


title: Liver phenobarbital pool2 Affy

description: No additional data.


title: Staphylococcus aureus_hypochlorite_20min_replicate2

description: Hypochlorite treatment

extract_protocol: Total RNA was isolated after 20 min incubation with hypochlorite using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: Liver phenobarbital pool3 Affy

description: No additional data.


title: Staphylococcus aureus_hypochlorite_20min_replicate1

description: Hypochlorite treatment


title: Staphylococcus aureus_hypochlorite_20min_replicate3

description: Hypochlorite treatment