description: T. thermophilus wild-type strain cultured for 1240 min_L2

source_name: T. thermophilus HB8, wild-type, rich medium, 1240 min_L

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions (Affymetrix).

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 180, 360, 540, 680, 880, 1000, 1120, and 1240 min.

tag: medium

value: rich


status: Public on Oct 15 2010

type: RNA

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

description: T. thermophilus wild-type strain cultured for 1120 min_L4

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm and normalized by global scaling method using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA). The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, wild-type, rich medium, 1120 min_L

extract_protocol: Cells were collected from 200 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: strain

tag: genotype

value: wild-type

tag: time


description: T. thermophilus wild-type strain cultured for 1120 min_L2


description: T. thermophilus wild-type strain cultured for 1120 min_L3


description: T. thermophilus wild-type strain cultured for 1120 min_L1


description: T. thermophilus wild-type strain cultured for 1000 min_L1

source_name: T. thermophilus HB8, wild-type, rich medium, 1000 min_L


description: T. thermophilus wild-type strain cultured for 880 min_L2

source_name: T. thermophilus HB8, wild-type, rich medium, 880 min_L

value: 880 min


description: T. thermophilus wild-type strain cultured for 880 min_L1


description: T. thermophilus wild-type strain cultured for 680 min_L4

source_name: T. thermophilus HB8, wild-type, rich medium, 680 min_L

value: 680 min


description: T. thermophilus wild-type strain cultured for 680 min_L3


description: T. thermophilus wild-type strain cultured for 1240 min_L1


title: wild-type_10h_syn1

description: wild-type strain grown in a synthetic medium for 10 h

source_name: T. thermophilus HB8, wild-type, synthetic medium, 10 h

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturerâ€™s instructions (Affymetrix).

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 500 ml of the synthetic medium and then cultivated at 70°C for 10 h.  The synthetic medium was made by the same way as described in this section of GSM296605.

extract_protocol: Cells were collected from 50 ml (10 h culture) or 10 ml (20 h culture) of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: genotype/variation


description: T. thermophilus wild-type strain cultured for 540 min_L2

source_name: T. thermophilus HB8, wild-type, rich medium, 540 min_L

value: 540 min


description: T. thermophilus wild-type strain cultured for 180 min_L2

source_name: T. thermophilus HB8, wild-type, rich medium, 180 min_L

value: 180 min


description: T. thermophilus wild-type strain cultured for 360 min_L2

source_name: T. thermophilus HB8, wild-type, rich medium, 360 min_L

value: 360 min


description: T. thermophilus wild-type strain cultured for 540 min_L1


description: T. thermophilus wild-type strain cultured for 360 min_L1


description: T. thermophilus wild-type strain cultured for 680 min_L2


description: T. thermophilus wild-type strain cultured for 680 min_L1


description: T. thermophilus wild-type strain cultured for 1000 min_L2


description: T. thermophilus wild-type strain cultured for 180 min_L1


title: wild-type strain on a rich medium, 100 (min) time point after phage ϕYS40 infection (2)

description: wild-type strain at 100 (min) after ϕYS40 infection 2

source_name: T. thermophilus HB8, wild-type, rich medium, 100 (min) after phage ϕYS40 infection

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturers instructions (Affymetrix).

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C.

extract_protocol: Cells were collected from 50 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: Cells were infected by ϕYS40 bacteriophage and harvested at 25 (OD600nm = ~ 0.98), 50 (OD600nm = ~ 1.66), 75 (OD600nm = ~ 2.02), and 100 min (OD600nm = ~ 2.68) post-infection.

value: wild type HB8

tag: protocol

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium, harvested at 100 (min) after infection of bacteriophage ϕYS40


title: wild-type strain on a rich medium, 50 (min) time point after phage ϕYS40 infection (3)

description: wild-type strain at 50 (min) after ϕYS40 infection 3

source_name: T. thermophilus HB8, wild-type, rich medium, 50 (min) after phage ϕYS40 infection

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium, harvested at 50 (min) after infection of bacteriophage ϕYS40


title: wild-type strain on a rich medium, 75 (min) time point after phage ϕYS40 infection (3)

description: wild-type strain at 75 (min) after ϕYS40 infection 3

source_name: T. thermophilus HB8, wild-type, rich medium, 75 (min) after phage ϕYS40 infection

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium, harvested at 75 (min) after infection of bacteriophage ϕYS40


title: wild-type strain on a rich medium, 100 (min) time point after phage ϕYS40 infection (1)

description: wild-type strain at 100 (min) after ϕYS40 infection 1


title: wild-type strain on a rich medium, 75 (min) time point after phage ϕYS40 infection (2)

description: wild-type strain at 75 (min) after ϕYS40 infection 2


title: wild-type strain on a rich medium, 50 (min) time point after phage ϕYS40 infection (1)

description: wild-type strain at 50 (min) after ϕYS40 infection 1


title: wild-type strain on a rich medium, 50 (min) time point after phage ϕYS40 infection (2)

description: wild-type strain at 50 (min) after ϕYS40 infection 2


title: wild-type strain on a rich medium, 100 (min) time point after phage ϕYS40 infection (3)

description: wild-type strain at 100 (min) after ϕYS40 infection 3


title: wild-type strain on a rich medium, 25 (min) time point after phage ϕYS40 infection (3)

description: wild-type strain at 25 (min) after ϕYS40 infection 3

source_name: T. thermophilus HB8, wild-type, rich medium, 25 (min) after phage ϕYS40 infection

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium, harvested at 25 (min) after infection of bacteriophage ϕYS40


title: wild-type strain on a rich medium, 25 (min) time point after phage ϕYS40 infection (1)

description: wild-type strain at 25 (min) after ϕYS40 infection 1


title: wild-type strain on a rich medium, 25 (min) time point after phage ϕYS40 infection (2)

description: wild-type strain at 25 (min) after ϕYS40 infection 2


title: TTHB212-deficient strain_480_2

description: TTHB212-deficient strain cultivated for 480 min_2

source_name: T. thermophilus HB8, TTHB212-deficient strain, rich medium, 480 min

growth_protocol: The TTHB212-deficient T. thermophilus HB8 strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 420 or 480 min.

extract_protocol: Cells were collected from 25 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

value: TTHB212-deficient strain


title: TTHB212-deficient strain_480_3

description: TTHB212-deficient strain cultivated for 480 min_3


title: TTHB212-deficient strain_480_1

description: TTHB212-deficient strain cultivated for 480 min_1


title: wild-type strain on a rich medium, 75 (min) time point after phage ϕYS40 infection (1)

description: wild-type strain at 75 (min) after ϕYS40 infection 1


title: wild-type strain on a rich medium, phage ϕYS40 pre-infection (1)

description: wild-type strain ϕYS40 pre-infection 1

source_name: T. thermophilus HB8, wild-type, rich medium, phage ϕYS40 pre-infection

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium for 360 min, harvested before infection of bacteriophage ϕYS40


title: wild-type strain on a rich medium, phage ϕYS40 pre-infection (3)

description: wild-type strain ϕYS40 pre-infection 3


title: wild-type strain on a rich medium, phage ϕYS40 pre-infection (2)

description: wild-type strain ϕYS40 pre-infection 2


title: TTHB212-deficient strain_420_3

description: TTHB212-deficient strain cultivated for 420 min_3

source_name: T. thermophilus HB8, TTHB212-deficient strain, rich medium, 420 min


title: TTHB212-deficient strain_420_1

description: TTHB212-deficient strain cultivated for 420 min_1


title: TIL 15_Rep1

type: genomic

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

description: 382040_A09_Cy3_TIL 15

hyb_protocol: 20ug genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing:
Data from each test genotype single-channel hybridization was compared to the B73 reference. This reference was generated from the following raw data files: GSM586152_382546A09_635_grid.pair, GSM586153_382546A09_532_grid.pair, GSM586154_382128A02_635_grid.pair, GSM586155_382128A04_532_grid.pair, GSM586156_382116A10_635_grid.pair, GSM586158_382546A11_635_grid.pair, GSM586159_382116A04_635_grid.pair, GSM586160_382068A05_532_grid.pair, GSM586161_382116A04_532_grid.pair
Array images were quantified and data were processed using NimbleScan software. The DNAcopy algorithm was used to produce spatially normalized hybridization values for all probes for the 71 samples using NimbleScan (Roche NimbleGen). A robust B73 average (henceforth termed B73avg) was generated from nine replicate samples of B73 hybridization. Subsequently, the log2(signal/B73avg) was calculated for each probe for all 71 samples. The distribution of these ratios were normalized so that the mode of the distribution of log2(signal/B73avg) for each genotype equaled zero using custom R scripts.

molecule: genomic DNA

organism: Zea mays subsp. parviglumis

source_name: TIL 15, above ground tisuse

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

growth_protocol: 1-2 week old seedlings were grown at the University of Minnesota (St. Paul campus) in September-October 2009. The conditions were set to 15 hours of full lights and 9 hours with lights off. Plants were watered daily as needed.

extract_protocol: Genomic DNAs were isolated using the CTAB method (Saghai-Maroof et al., 1984).

tag: sample type

value: pooled 5 seedlings

value: TIL 15

tag: classification

organism: Zea mays

source_name: B73 Reference

value: averaged data across B73

value: Stiff-stalk


title: Tx303_Rep1

source_name: Tx303, above ground tisuse

value: Tropical


title: TIL 17_Rep1

description: 382076_A02_Cy3_TIL 17

source_name: TIL 17, above ground tisuse

value: TIL 17


title: P39_Rep1

source_name: P39, above ground tisuse

value: mixed


title: PHJ40_Rep1

source_name: PHJ40, above ground tisuse

value: single seedling

value: ex-PVP


title: TIL 9_Rep2

description: 382040_A10_Cy3_TIL 9

source_name: TIL 9, above ground tisuse

value: TIL 9


title: TTHB212-deficient strain_420_2

description: TTHB212-deficient strain cultivated for 420 min_2


title: PHG84_Rep1_2

source_name: PHG84, above ground tisuse


title: PHG39_Rep1

source_name: PHG39, above ground tisuse


title: PHG84_Rep1


title: wild synthetic medium 1440, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 1440 min.

source_name: T. thermophilus

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of synthetic medium. The cells (2 ml) were inoculated into 1 litter of the same medium and then cultivated at 70°C.  The synthetic medium was made by mixing 500 ml of solutions A (4% sucrose) and B, 5 ml of solution C, 1 ml of solution D and 0.1 ml of each metal solution. Solution B was composed of 4% sodium glutamate, 0.11% K2HPO4, 0.036% KH2PO4, 0.4% NaCl and 0.1% (NH4)2SO4, which was adjusted to pH 7.3 with 3 M NaOH. Solution C was composed of 2.5% MgCl2·6H2O and 0.5% CaCl2·2H2O. Solution D was composed of 1% biotin and 10% thiamine. The matal solutions were as follows: 10% FeSO4·7H2O, 1.2% Na2MoO4·2H2O, 0.1% VOSO4·xH2O, 0.5% MnCl2·4H2O, 0.06% ZnSO4·7H2O, 0.015% CuSO4·5H2O, 0.8% CoCl2·6H2O and 0.02% NiCl2·6H2O.

value: wild-type

tag: timepoint


title: Oh7b_Rep1

source_name: Oh7b, above ground tisuse

value: Non-stiff stalk


title: wild synthetic medium 1200, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 1200 min.

extract_protocol: Cells were collected from 30 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.


title: wild synthetic medium 1320, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 1320 min.


title: wild synthetic medium 1080, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 1080 min.


title: TIL 1_Rep2

description: 382068_A07_Cy3_TIL 1

source_name: TIL 1, above ground tisuse

value: TIL 1


title: Ms71_Rep2_2

source_name: Ms71, above ground tisuse


title: wild synthetic medium 840, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 840 min.


title: wild synthetic medium 960, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 960 min.


title: Ms71_Rep2


title: wild synthetic medium 600, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 600 min.


title: PHZ51_Rep1

source_name: PHZ51, above ground tisuse


title: wild synthetic medium 360, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 360 min.

extract_protocol: Cells were collected from 300 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.


title: wild synthetic medium 480, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 480 min.


title: wild synthetic medium 720, biological rep2

description: Gene expression data from wild-type strain grown on a synthetic medium at 720 min.

extract_protocol: Cells were collected from 100 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.


title: Oh43_Rep1

source_name: Oh43, above ground tisuse


title: wild synthetic medium 1440, biological rep1


title: Mo17.1_Rep1b_2

source_name: Mo17, above ground tisuse


title: Mo17.2_Rep1


title: Mo17.1_Rep1c


title: Mo17.3_Rep1_2


title: wild synthetic medium 1320, biological rep1


title: wild synthetic medium 1200, biological rep1


title: wild synthetic medium 960, biological rep1


title: wild synthetic medium 1080, biological rep1


title: wild synthetic medium 840, biological rep1


title: wild synthetic medium 720, biological rep1


title: Mo17.3_Rep1


title: Mo17.1_Rep1b


title: LH82_Rep1_2

source_name: LH82, above ground tisuse


title: wild synthetic medium 480, biological rep1


title: Mo17.1_Rep1a_2


title: Mo17.1_Rep1a


title: wild synthetic medium 360, biological rep1


title: wild 480 ethanol collection, biological rep3

description: Gene expression data from wild-type strain grown on a rich medium at 480 min, cold shock avoided collection.

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA).

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1000 ml of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 2.57).

extract_protocol: Cells were collected from 15 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: Cells were harvested after arrest the growth on ice or addition of cold ethanol.

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium for 480 min, harvested after addition of cold ethanol

tag: cell type

value: cold-shock avoided cells


title: Mo17.4_Rep1


title: M37W_Rep1

source_name: M37W, above ground tisuse


title: wild 480 normal collection, biological rep3

description: Gene expression data from wild-type strain grown on a rich medium at 480 min, normal collection.

value: wild-type Thermus thermophilus HB8 strain grown on a rich medium for 480 min, harvested after arrested the growth on ice

value: normal cells


title: LH82_Rep1

source_name: B73 Reference


title: wild 480 ethanol collection, biological rep2


title: LH1_Rep1

source_name: LH1, above ground tisuse


title: wild 480 normal collection, biological rep2


title: wild 480 ethanol collection, biological rep1


title: IA 36.3_Rep1

description: 382128_A06_Cy5_I.A. 36.3

source_name: IA 36, above ground tisuse

value: IA 36


title: LH1_Rep1_2


title: IA 36.4_Rep1

description: 382199_A06_Cy3_I.A. 36.4


title: IA 36.1_Rep1

description: 382546_A03_Cy3_I.A. 36.1


title: Ki11_Rep1

source_name: Ki11, above ground tisuse

value: pooled 5 seedlings


title: wild 480 normal collection, biological rep1


title: IA 36.2_Rep1

description: 382128_A12_Cy3_I.A. 36.2

value: averaged data across B73


title: IA 31.2_Rep1_2

description: 382546_A12_Cy5_I.A. 31.2

source_name: IA 31, above ground tisuse

value: IA 31

value: Stiff-stalk


title: IA 29.6_Rep1

description: 382116_A01_Cy3_I.A. 29.6

source_name: IA 29, above ground tisuse

value: IA 29


title: IA 31.2_Rep1

description: 382546_A10_Cy3_I.A. 31-2


title: IA 29.3_Rep1_2

description: 382128_A04_Cy5_I.A. 29-3


title: Hp301_Rep2b

source_name: Hp301, above ground tisuse

value: mixed


title: IA 29.5_Rep1

description: 382199_A03_Cy3_I.A. 29-5

value: single seedling


title: IA 29.2_Rep1

description: 382546_A04_Cy5_I.A. 29.2


title: UTMB_91

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description:
Clinical sample TVP-11191 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing Ross River virus.
Cy3 9mer

hyb_protocol: Arrays were hybridized with labeled DNA for 16 hr at 42 C on a MAUI hybridization station.

scan_protocol: Arrays were scanned on an Axon 4000B scanner at 5 um resolution per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Feature extraction was performed using NimbleScan software. Probe intensities were analyzed using custom software developed at LLNL.

organism: Homo sapiens

label_protocol: DNA or cDNA from cell culture preparations was labeled using Cy-3 labeled nonamers from Trilink Biotechnologies.   Samples from the DeRisi lab were amplified for an additional 15 cycles to incorporate aminoallyl-dUTP and labeled with Cy3NHS ester (GE Healthcare (Piscataway, NJ).

extract_protocol: RNA from cell cultures was treated with Trizol reagent,  precipitated with isopropanol and washed with 70% ethanol. The RNA pellet was dried and reconstituted with RNase free water. 1 µg of RNA was transcribed into double-strand cDNA with random hexamers using SuperscriptTM double-stranded cDNA synthesis kit from Invitrogen (Carlsbad, CA). Clinical samples from the DeRisi lab were extracted and partially purified  using Round A and Round B protocols (Wang et al, 2003).

tag: sample

value: Vero cell culture

tag: provider

value: R. Tesh/UTMB

tag: provider id

tag: confirmed content

value: Ross River virus

tag: amplification


title: IA 29.1_Rep1

description: 382546_A04_Cy3_I.A. 29.1


title: UTMB_89

description:
Clinical sample TVP-11189 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing vesicular stomatitis virus strain NJ.
Cy3 9mer

value: Vesicular stomatitis virus strain NJ


title: UTMB_90

description:
Uninfected Vero cells, provided by R. Tesh, University of Texas Medical Branch.
Cy3 9mer

organism: Chlorocebus aethiops

source_name: Uninfected Vero cells

value: Uninfected Vero cells


title: CML247_Rep1

source_name: CML247, above ground tisuse

value: Tropical


title: B73_Rep1

description: 382116_A04_Cy5_B73 Pooled

source_name: B73, above ground tisuse


title: IA 29.3_Rep1

description: 382128_A02_Cy3_I.A. 29.3


title: I205_Rep1_2

source_name: I205, above ground tisuse

value: Non-stiff stalk


title: UTMB_85

description:
Clinical sample TVP-11185 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing Ilheus virus.
Cy3 9mer

value: Ilheus virus


title: B73_Rep1a


title: UTMB_86

description:
Clinical sample TVP-11186 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing epizootic hemorrhagic disease virus.
Cy3 9mer

value: Epizootic hemorrhagic disease virus


title: B73.4_Rep1b


title: Hp301_Rep2


title: UTMB_88

description:
Clinical sample TVP-11188 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing sandfly fever Sicilian virus.
Cy3 9mer

value: Sandfly fever Sicilian virus


title: UTMB_84

description:
Clinical sample TVP-11184 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing Cache Valley virus.
Cy3 9mer

value: Cache Valley virus


title: UTMB_83

description:
Clinical sample TVP-11183 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing Colorado tick fever virus.
Cy3 9mer

value: Colorado tick fever virus


title: B73.4_Rep1a

value: averaged data across B73


title: B73.1_Rep1a

value: Stiff-stalk


title: B73.1_Rep1


title: B73.2_Rep1b


title: UTMB_87

description:
Clinical sample TVP-11187 provided by R. Tesh, cultured in Vero cellsconfirmed by UTMB as containing La Crosse virus.
Cy3 9mer

value: La Crosse virus


title: B73.3_Rep1


title: B73_Rep1b

description: 382116_A04_Cy3_B73 Pooled

value: pooled 5 seedlings


title: UTMB_81

description:
Clinical sample TVP-11181 provided by R. Tesh, cultured in Vero cells, confirmed by UTMB as containing Thogoto virus.
Cy3 9mer

value: Thogoto virus


title: UTMB_82

description:
Clinical sample TVP-11182 provided by R. Tesh, cultured in Vero cells confirmed by UTMB as containing Dengue virus type 4.
Cy3 9mer

value: Vero cell culture

value: Dengue virus type 4


title: DeRset2_3

type: other

description:
Human clinical fecal sample 3 provided by J. DeRisi, confirmed by PCR as containing chicken anemia virus.
aminoallyl dUTP/Cy3

molecule: other

source_name: DeRisi sample # 3 2nd set

value: Human fecal sample

value: J. DeRisi/UCSF

value: Chicken anemia virus

value: DeR random PCR


title: UTMB_80

description:
Clinical sample TVP-11180 provided by R. Tesh, cultured in Vero cells, confirmed by UTMB as containing Punto Toro virus.
Cy3 9mer

value: R. Tesh/UTMB

value: Punto Toro virus


title: B73.2_Rep1a

value: single seedling


title: DeRset2_1

description:
Human clinical fecal sample 1 provided by J. DeRisi, confirmed by PCR as containing human parechovirus and Streptococcus thermophilus.
aminoallyl dUTP/Cy3

source_name: DeRisi sample # 1 2nd set

value: Human parechovirus; Streptococcus thermophilus


title: DeRset2_4

description:
Human clinical fecal sample 4 provided by J. DeRisi, confirmed by PCR as containing Staphylococcus aureus, Shigella dysenteriae, E. coli, Streptococcus sanguinis and Lactococcus lactis plasmid DNA.
aminoallyl dUTP/Cy3

source_name: DeRisi sample # 4 2nd set

value: Staphylococcus aureus; Shigella dysenteriae; E. coli; Streptococcus sanguinis; Lactococcus lactis plasmid


title: DeRset2_2

description:
Human clinical fecal sample 2 provided by J. DeRisi, confirmed by PCR as containing E. coli and Norwalk virus.
aminoallyl dUTP/Cy3

source_name: DeRisi sample # 2 2nd set

value: E. coli; Norwalk virus


title: SLE_11612

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Data for Dr. Quan Li and Nancy Olsen's paper :Risk Factors for ANA Positivity in Healthy Persons

hyb_protocol: 1.5ug labeled cRNA from each sample was hybed to Illumina HumanWG-6 chip following Illumina protocol

scan_protocol: Illumina iScan protocol

data_processing:
data was processed using Illumina Genostudio software v2.0
version number of BeadStudio software and normalization algorithm: Module Gene Expression 3.3.8 and Quantile normalization.

source_name: blood PBMC

label_protocol: 250ng total RNA was labeled using Ambion TotalPrep Illumina RNA amplification and labeling kit following vendor's protocol

extract_protocol: 2ml blood was draw into PAXgene tubes and total RNA extracted using Qiagen Rneasy mini kit following Qiagen protocol

tag: tissue

value: blood

value: PBMCs

tag: patient status

value: SLE patients (SLE)

tag: ana status

value: ANA+

tag: sample number


title: SLE_92508


title: secondary xylem-Control vs PtaHB1-rep4

city: Québec

first: John

middle: J

last: MacKay

state: Québec

address: 1030 avenue de la medecine

department: Wood and forestery Departement

country: Canada

institute: Laval University - ARBOREA

hyb_protocol: The poplar 3.4K microarray slides were pre-hybridised for 2 hours at 42°C in a solution containing 5X SSC, 0.1% SDS, 0.02% BSA (w/v), 0.01% herring sperm DNA (w/v), and 50% formamide. The slides were then washed twice in 0.1X SSC, once in water, rinsed in 2-propanol, and finally dried by centrifugation. The labelled targets (3.5 μL) were mixed with 52.5μL of hybridisation solution containing 5X SSC, 0.1% SDS, 0.01% herring sperm DNA (w/v), and 50% deionised formamide. The mixture was heat-denatured for 4 min at 95°C and cooled for 5 min on ice prior to hybridisation to the microarray. The microarray was then covered with a LifterSlip (Erie Scientific Company, Portsmouth, NH, USA) and placed in a hybridisation chamber II with increased depth (Corning, Lowell, MA, USA) and incubated for 12h at 45°C in a model 1012 hybridisation oven (Shel Lab, Cornelius, OR, USA). After hybridisation, the slides were iteratively washed for 15 min in 2X SSC + 0.5% SDS, 0.5X SSC + 0.1% SDS and 0.1X SSC solutions at 45°C.

scan_protocol: The slides were scanned using a ScanArrayTM Express scanner (Packard BioScience, Meriden, CT, USA) and the image files were analysed using QuantArray® software (Packard BioScience, Meriden, CT, USA). Scan intensities were comparable between sets of slides for a given hybridisation.

data_processing: Data analysis was carried out using Bioconductor packages (www.bioconductor.org) distributed in R (R Development Core Team 2008). Median foreground intensity minus median background intensity was the response variable used for the statistical analysis. Data quality was assessed using graphical analysis tools in the marray and olin packages available in Bioconductor, and by assessment of within- and between-slide Pearson product-moment correlation coefficients (r), which were calculated both from the raw intensities and after normalisation. The composite normalisation method (Yang et al., 2002) was applied by using the two functions maNorm2D and maNormLoess in the marray package (Dudoit & Yang, 2002). We identified differentially expressed sequences with the SAM package (release 3.0; Efron et al., 2001) using a false discovery rate (FDR, Benjamini & Hochberg 1995) threshold set to 5% (q < 5.00).

organism: Populus tremula x Populus alba

source_name: secondary xylem, control

label_protocol: Each microarray hybridisation used 1 μg of total RNA that was amplified using the SuperScript™ Indirect RNA Amplification System (Invitrogen, Carlsbad, CA, USA) and 5 μg of the aRNA were labelled with Alexa Fluor®555 and 647 dyes (Invitrogen Carlsbad, CA, USA)), for use in dye-swap experiments

growth_protocol: plants were grown in a greenhouse with 16 hours light per day, with a temperature regime of 22/17oC (day/night), and relative humidity of at least 70%. Natural daylight was supplemented with light from HQI-TS 400W/DH metal halogen lamps (Osram, Munich, Germany). Plants were fertilised weekly with 1 g L-1 20/20/20 (N-P-K) and supplemented with calcium every two weeks.

extract_protocol: Total RNA extractions were carried out using the CTAB method of Chang et al. (1993)

treatment_protocol: Over-expression constructs were obtained by inserting the complete coding sequences of PtaHB1 from P. tremula x P. albabetween the maize ubiquitin promoter (Christensen et al., 1992) and a 35S terminator into the pCambia1305.2 vector (www.cambia.org). The resulting plasmids were then transferred into A. tumefaciens strain C58 pGV2260 (Hellens et al., 2000).

value: secondary xylem

value: control

tag: clone

source_name: secondary xylem, PtaHB1 transgene

value: PtaHB1 transgene


title: DeRset1_5

description:
Partially amplified human serum sample provided by J. DeRisi, containing hepatitis B virus.
aminoallyl dUTP/Cy3

source_name: DeRisi clinical sample #5

value: Human serum sample

value: Hepatitis B virus


title: SLE_80259


title: secondary xylem-Control vs PtaHB1-rep1


title: secondary xylem-Control vs PtaHB1-rep3


title: secondary xylem-Control vs PtaHB1-rep2


title: I205_Rep1

tag: genotype

value: Non-stiff stalk

source_name: B73 Reference

value: averaged data across B73

value: Stiff-stalk


title: SLE_82827


title: Her_Vac_1

description:
Mixture of vaccinia virus strain Lister and human herpes virus 6B purified DNA.
Cy3 9mer

organism:
Vaccinia virus Lister
Human betaherpesvirus 6B

source_name: Vaccinia Lister/HHV6B

value: Vaccinia virus strain Lister; human herpes virus 6B

value: Advanced Biotechnologies

value: Vaccinia virus Lister; HHV6B


title: SLE_48210


title: secondary xylem-PtaHB1 vs Control-rep4

tag: genotype/variation


title: secondary xylem-PtaHB1 vs Control-rep2


title: secondary xylem-PtaHB1 vs Control-rep3


title: BVD_rndPCR2ng_1

description:
Bovine viral diarrhea virus type 1
Cy3 9mer

organism: Bovine viral diarrhea virus 1

source_name: BVDV type 1

value: Bovine viral diarrhea virus type 1

value: National Veterinary Lab

value: BVDV type 1

value: DeR random PCR


title: SLE_42563

value: blood

value: PBMCs

value: SLE patients (SLE)


title: CML277_Rep1

source_name: CML277, above ground tisuse

value: pooled 5 seedlings

value: Tropical


title: SLE_96250

value: ANA+


title: secondary xylem-PtaHB1 vs Control-rep1

value: secondary xylem

value: PtaHB1 transgene

value: control


title: BVD_1

description:
Bovine viral diarrhea virus type 1 strain Singer
Cy3 9mer

tag: layout version


title: SLE_11798


title: SLE_28042


title: Adeno_1

description:
Adenovirus type 7 strain Gomen
Cy3 9mer

organism: Human adenovirus 7

source_name: Adenovirus type 7 strain Gomen

value: Adenovirus type 7 strain Gomen


title: Atg7-conditional knockout mice and Atg7-conditional knockout mice in Nrf2-null background exp7 rev

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

hyb_protocol: For each two-color comparison, 825 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using appropriate gains on the PMT in both channels, with a scan resolution of 5um.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5.1), using default for all parameters.

organism: Mus musculus

source_name: Mouse liver

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: To induce Cre from Mx1 promoter, mice were treated with pIpC for 4 weeks.

extract_protocol: Total RNA was extracted from livers using TRIzol (Invitrogen). RNA was further purified using an RNeasy Mini Kit (Qiagen).

value: Atg7F/F:Mx1-Cre:Nrf2-/- mice


title: DeRset1_1

description:
Human clinical induced sputum sample provided by J. DeRisi/UCSF
aminoallyl dUTP/Cy3

source_name: DeRisi clinical sample #1 1st set

value: Human induced sputum sample

value: J. DeRisi/UCSF

value: Human respiratory syncytial virus; human coronavirus HKU1


title: Atg7-conditional knockout mice and Atg7-conditional knockout mice in Nrf2-null background exp8


title: SLE_64513


title: SLE_30353


title: Viral_mix_3

description:
Mixture of purified commercially purchased viral DNA from vaccinia virus strain Lister and human herpesvirus 6B
Cy3 9mer

source_name: Human herpesvirus 6B; vaccinia virus strain Lister

value: Advanced Biotechnologies


title: Viral_mix_5

description:
Mixture of viral DNA and RNA from human herpesvirus 6B, vaccinia virus strain Lister, bluetongue virus type 2, and respiratory syncytial virus B1
Cy3 9mer

organism:
Vaccinia virus Lister
Human betaherpesvirus 6B
Bluetongue virus 2
Human respiratory syncytial virus B1

source_name: Herpes 6B/Vaccina lister/Blue tongue type 2/RSV B1

value: Human herpesvirus 6B; vaccinia virus strain Lister; bluetongue virus type 2; respiratory syncytial virus B1

value: and Advanced Biotechnologies (vaccinia, HHV6B)


title: SLE_13161

value: blood


title: SLE_43923

value: PBMCs


title: Viral_mix_4

description:
Mixture of viral DNA and RNA from bluetongue virus type 2 and respiratory syncytial virus B1
Cy3 9mer

organism:
Bluetongue virus 2
Human respiratory syncytial virus B1

source_name: Bluetongue virus type 2/RSV B1

value: Bluetongue virus type 2; respiratory syncytial virus B1

value: National Veterinary Lab


title: Atg7-conditional knockout mice and Atg7-conditional knockout mice in Nrf2-null background exp8 rev


title: Viral_mix_2

description:
Mixture of viral DNA and RNA from adenovirus type 7 strain Gomen, bovine viral diarrhea virus type 1 strain Singer, and respiratory syncytial virus strain Long A
Cy3 9mer

organism:
Human adenovirus 7
Bovine viral diarrhea virus 1
Human respiratory syncytial virus A strain Long

source_name: Adenovirus type 7 strain Gomen; bovine viral diarrhea virus type 1 strain Singer; respiratory syncytial virus strain Long A


title: wild type and Atg7F/F:Mx1-Cre:Nrf2-/- mice exp6 rev

value: wild type


title: wild type and Atg7F/F:Mx1-Cre:Nrf2-/- mice exp6


title: SLE_83279

value: SLE patients (SLE)

value: ANA+


title: wild type and Atg7-conditional knockout mice exp5


title: wild type and Atg7-conditional knockout mice exp5 rev


title: SLE_14947


title: Atg7-conditional knockout mice and Atg7-conditional knockout mice in Nrf2-null background exp7


title: wild type and Nrf2-null mice exp4 rev


title: HC_95621

value: healthy control (HC)

value: ANA-


title: wild type and Nrf2-null mice exp1


title: wild type and Nrf2-null mice exp4


title: wild type and Atg7F/F:Mx1-Cre:Nrf2-/- mice exp3 rev


title: wild type and Atg7-conditional knockout mice exp2 rev


title: wild type and Nrf2-null mice exp1 rev


title: wild type and Atg7F/F:Mx1-Cre:Nrf2-/- mice exp3


title: HC_26806


title: HC_98590


title: FDR_99879

value: first degree relative of SLE patientw (FDR)


title: FDR_39959


title: HC_40597


title: FDR_86896


title: FDR_99440


title: wild type and Atg7-conditional knockout mice exp2


title: HC_21559


title: HC_38621


title: HC_40984


title: FDR_28226


title: HC_10215


title: HC_99382


title: FDR_82198


title: HC_45843


title: whole lungs (pooled in triplicate) PR/8/34/AdeltaNS1 treated 24hpi

city: New York

first: Benjamin

last: tenOever

state: NY

address: 430 East 29th Street, Room 540

department: Microbiology

institute: New York University

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7GGeneChips were scanned using the GeneChip Array Scanner 7G

data_processing:
The data were analyzed with GeneChip Operating Software (GCOS) ver 1.3
MAS5-calculated Signal Intensity

source_name: whole lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA

growth_protocol: See Schmid et. Al. JBC 2010

extract_protocol: Trizol

treatment_protocol: See Schmid et. Al. JBC 2010

value: whole lung

tag: strain

tag: treatment group

value: influenza deltaNS1, 24hpi


title: whole lungs (pooled in triplicate) PR/8/34/A treated 12hpi

value: influenza wt, 12, hpi


title: whole lungs (pooled in triplicate) PR/8/34/A treated 24hpi

value: influenza wt, 24, hpi


title: whole lungs (pooled in triplicate) mock treated 24hpi

value: mock treated, 24hpi


title: whole lungs (pooled in triplicate) mock treated 12hpi

value: mock treated, 12hpi


title: whole lungs (pooled in triplicate) mock treated 48hpi

value: mock treated, 48hpi


title: BMSC-GC

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

description:
Bone marrow stromal cells-ground control (bmsc-gc): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in growth medium in manual-operated hardwares (normal gravity)
Gene expression data from bone marrow stromal cells - ground control experiment (normal gravity).

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Mouse Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were subsequently scanned using a confocal laser GeneChip Scanner 3000 7G and GeneChip Command Console (Affymetrix).

data_processing: GC Robust Multi-array Average (GCRMA)

label: Biotin

source_name: bone marrow from cells from ground experiments

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes.

growth_protocol: Mice were bred and maintained at the Institution's animal facility. The care and use of the animals were in compliance with laws of the Italian Ministry of Health and the guidelines of the European Community.

extract_protocol: Total RNA was isolated using RNeasy® MinElute columns (Qiagen,Valencia, CA). RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol:
Mice between 6 and 8 weeks of age were killed, and bone marrow cells were collected by flushing nucleate cells out of the femurs and tibiae with cold PBS. Cells were cultured (2x106 nucleated cells/10-cm petri dish) in a growth medium [Coon's modified Ham's F12 medium (Biochrom AG, Berlin, Germany)] supplemented with 10% fetal calf serum (GIBCO, Italy), 1% glutamine, 1% penicillin-streptomycin]. No cytokines were added at any stage. Cultures were incubated at 37°C in a 5% CO2 atmosphere. After 3 days, nonadherent cells were removed. When 80% confluent, the adherent cells were trypsinized (0.05% trypsin/EDTA at 37°C for 10 min) and expanded (P1 stage).
Cells from the same initial bone marrow sample were cultured at an initial plating density of 1x106 nucleated cells per dish to evaluate their CFU-f (CFU-fibroblast) as a quality control. After 2 weeks of culture, plates were washed with PBS, fixed with 3.7% paraformaldehyde, stained with 1% methylene blue, and colonies were counted. As an additional quality control, we tested BMSC cultures for their ability to undergo differentiation into chondrocytes, osteocytes, and adipocytes.

value: bone marrow stromal cells

tag: sample type

value: ground control

tag: gravity type

value: normal

tag: osteo-induced

value: no


title: FDR_38175

source_name: blood PBMC

value: blood

tag: cell type

value: PBMCs


title: FDR_34386

value: ANA+


title: whole lungs (pooled in triplicate) PR/8/34/A treated 48hpi

value: influenza wt, 48hpi


title: HC_93371

value: healthy control (HC)


title: FDR_42222

value: first degree relative of SLE patientw (FDR)


title: whole lungs (pooled in triplicate) PR/8/34/AdeltaNS1 treated 12hpi

value: whole lung

value: influenza deltaNS1, 12hpi


title: FDR_93562


title: BOI-GC

description:
Bone marow stromal cells-osteoinduced-ground control (boi-gc): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in osteoinductive medium in manual-operated hardwares (normal gravity).
Gene expression data from bone marrow stromal cells osteoinducted - ground control experiment (normal gravity).

data_processing: GC Robust Multi-array Average (GCRMA).

source_name: Bone marrow from cells from ground experiments

extract_protocol: Total RNA was isolated using RNeasy® MinElute columns (Qiagen,Valencia, CA). RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity

value: yes


title: BOI-FC

description:
Bone marrow stromal cells-osteoinduced-flight control (boi-fc): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in growth medium in fully automated hardware inside the KUBIK incubator (ESA) on a 1g centrifuge in the KUBIK incubator.
Gene expression data from bone marrow stromal cells in osteoinductive medium, on a 1g centrifuge - flight experiment.

source_name: Bone marrow from flight experiments on a 1g centrifuge, maintained in osteo-inductive conditions

value: flight control

value: microgravity


title: BMSC-FE

description:
Bone marrow stromal cells-flight experiment (bmsc-fe): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in growth medium in fully automated hardware inside the KUBIK incubator (ESA) (microgravity)
Gene expression data from bone marrow stromal cells - flight experiment (microgravity).

source_name: Bone marrow from flight experiments

value: flight experiment


title: BOI-LC

description:
Bone marrow stromal cells-osteoinduced-laboratory control (boi-lc): Cells/skelite constructs, maintained in 24-well cell culture dishes with osteoinductive medium (normal gravity);
Gene expression data from bone marrow stromal cells in osteoinductive medium and incubated under routine laboratory conditions (normal gravity).

source_name: Bone marrow from cells from laboratory control

value: laboratory control


title: BMSC-FC

description:
Bone marrow stromal cells-flight control experiment (bmsc-fc): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in growth medium in fully automated hardware inside the KUBIK incubator (ESA) on a 1g centrifuge in the KUBIK incubator.
Gene expression data from bone marrow stromal cells on a 1g centrifuge - flight experiment.

source_name: Bone marrow from flight experiments on a 1g centrifuge

value: bone marrow stromal cells


title: whole lungs (pooled in triplicate) PR/8/34/AdeltaNS1 treated 48hpi

value: influenza deltaNS1, 48hpi


title: HC_89765


title: HC_45914


title: FDR_39812


title: BOI-FE

description:
Bone marrow stromal cells-osteoinduced-flight experiment (boi-fe): Cells/skelite constructs, assembled in incubation units (Kayser Italia), maintained in osteoinductive medium in fully automated hardware inside the KUBIK incubator (ESA) (microgravity)
Gene expression data from bone marrow stromal cells osteoinduced - flight experiment (microgravity).

source_name: Bone marrow from flight experiments (microgravity), maintained in osteo-inductive conditions


title: HC_49821

description: Data for Dr. Quan Li and Nancy Olsen's paper :Risk Factors for ANA Positivity in Healthy Persons


title: FDR_92483


title: SCO1-48h

description:
GBM TICs were obtained from tumor samples of patients subjected to surgery at Neurosurgery Department of the San Martino Hospital in Genova. An informed consent was obtained from all patients before surgery as required by the Ethic Board.
Cells isolation was described in detail elsewhere (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity.
Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Human Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

data_processing: Affymetrix raw data files (CEL files) are used as input files in expression console environment (Affymetrix, Inc., Santa Clara, CA). Briefly, Cel files were processed using Robust Multi-Array Analysis procedure (Irizarry et al., 2003). The RMA method was used, first, to convert the intensities from the multiple probes in a probeset into a single expression value with greater precision and reduced background noise, relying on the perfect match probes only (ignoring the mismatch probes) and, after, to normalize by sketch quantile normalization. Also quality assessement were performed in expression console environment.

source_name: Human glioblastoma (GBM) tumor initiating cells (TICs).

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes

growth_protocol:
Proliferation medium was DMEM-F12/Neurobasal additioned with 1% v/v B27 supplement, (Gibco Ltd, Paisley, Scotland), 2 mM L-glutamine (Gibco Ltd), recombinant human fibroblast growth factor (FGF-2, 10 ng/ml Peprotech, London, UK), recombinant human epidermal growth factor (EGF, 20 ng/ml Peprotech). The medium was changed twice a week. Under these conditions, TICs were grown as a monolayer in flasks coated with Matrigel (BD Biosciences, San Jose, CA) express stem cell markers, maintained intact self-renewal capacity, partial multilineage differentiation ability and gave rise to tumor when injected orthotopically in nude mice (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity.
Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).

extract_protocol:
miRNeasy Mini Kit (Qiagen) with DNase treatment.
RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: GBM TICs were treated with Demethyl fructiculin, a diterpenoid quinone component of the exudates from Salvia corrugata (SCO-1) leafes and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

tag: agent

value: Demethyl fructiculin A (Sco-1)

tag: time

value: 48 hours


title: HC_77184

value: blood


title: HC_74869

value: PBMCs


title: DMSO_24h

treatment_protocol: GBM TICs were treated with vehicle alone (DMSO) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).

value: vehicle alone (DMSO)

value: 24 hours


title: AcH3

status: Public on Oct 14 2010

city: Boston

first: Jonghwan

last: Kim

state: MA

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

hyb_protocol: According to standard Affymetrix protocols.

data_processing: MAT (Johnson et al., 2006) was used to process the raw CEL files. The following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10 were used. BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv36.NR.bpmap.

source_name: Pan AcH3 ChIP DNA from mouse ES cells

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

growth_protocol: Normal J1 ES growth condition

extract_protocol: For biotin-mediated ChIP, approximately, 5 × 107 mES cells expressing both BirA and biotinylated proteins were used. Briefly, cells were cross-linked by addition of final 1% formaldehyde for 7 min at room temperature. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. Collected cell pellet was resuspended in SDS ChIP buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, and protease inhibitors). Cells were sonicated and fragmented DNA was visualized on an agarose gel (average size 0.5-1 kb). The sample was centrifuged at 12000 rpm at 4°C for 10 min and supernatant was collected. Sample was pre-cleared with protein A beads at 4°C for 1 hr and incubated with streptavidin beads (Dynabeads® MyOne™ Streptavidin T1) at 4°C overnight. For reference sample, J1 ES cells expressing BirA enzyme without biotinylated protein were used. Immunoprecipitated complexes were successively washed with buffer I (2% SDS), buffer II (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), buffer III (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 8 min at room temperature. SDS elution buffer was added and incubated at 65°C overnight to reverse crosslink protein-DNA complexes. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25μl of water.

treatment_protocol: Normal J1 ES growth condition

value: wt J1 mES cells

tag: fraction

value: ChIP

tag: target

source_name: Mock ChIP DNA from mouse ES cells

value: reference (mock ChIP)


title: AcH4

scan_protocol: According to standard Affymetrix protocols.

source_name: Pan AcH4 ChIP DNA from mouse ES cells


title: bioGcn5

source_name: bioGcn5 ChIP DNA from mouse ES cells

value: bioGcn5 J1 mES cells

source_name: Mock biotin ChIP DNA from ES cells expressing BirA

value: BirA expressing J1 mES cells


title: bioTip60

source_name: bioTip60 ChIP DNA from mouse ES cells

value: bioTip60 J1 mES cells


title: DMSO_48h

treatment_protocol: GBM TICs were treated with vehicle alone (DMSO) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: bioDmap1

source_name: bioDmap1 ChIP DNA from mouse ES cells

value: bioDmap1 J1 mES cells


title: bioMax

source_name: bioMax ChIP DNA from mouse ES cells

value: bioMax J1 mES cells

value: Max


title: HC_73452

tag: tissue

tag: patient status

value: healthy control (HC)

value: ANA+


title: HC_27976

tag: ana status

tag: sample number


title: SCO1_24h

treatment_protocol: GBM TICs were treated with Demethyl fructiculin, a diterpenoid quinone component of the exudates from Salvia corrugata (SCO-1) leafes and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24h).

value: Demethyl fructiculin A (Sco-1)


title: HC_21466


title: bioE2F4

source_name: bioE2F4 ChIP DNA from mouse ES cells

value: bioE2F4 J1 mES cells


title: RB_535_09_TR1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Human retinoblastoma 2

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the 7G scanner in Sankara Nethralaya.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data was analyzed using GeneSpring GX v 10.0.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Quantile normalization
Summarization Algorithm: ExonRMA16
Transcript level: CORE
Technology: Affymetrix.HuGene-1_0-st-v1
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: Retinoblastoma -NO Chemotreated

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: No growth conditions

extract_protocol: RNA was isolated from 1mg of Retinoblastoma tumors with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The extracted RNA was quantified using nanodrop and the purity was analysed by Agilant Bioanalyser with RNA nano chip and the RNAs with RIN values of 6 and above were considered for further processing.

treatment_protocol: chemotherapy of one sample (139-09) is 10 cycles and other sample (984-09) is 8 cycles.

value: cadeveric eye

value: primary tumor


title: RB_984_09_TR1

description: Human retinoblastoma 3

source_name: Retinoblastoma -Chemotreated


title: RB_984_09_TR2

description: Human retinoblastoma 3


title: RB_139_09_TR1

description: Human retinoblastoma 1


title: nox5-py (40173202)

status: Public on Oct 13 2010

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Microarray scanning, data acquisition and identification of probe sets showing a significant difference (p=0.05) in expression level between the two culture conditions considered were performed by Roche-NimbleGen as in previous studies (Samolski et al., 2009). Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
5015 genes passed t-test of transformant versus wild type strain replicates. Transcripts showing significantly up-regulated expression (2-fold and 5-fold changes) were annotated using Gene Ontology (GO) (Gotz et al., 2008) for TrichoEST derived transcripts and the eukaryotic orthologous groups (KOG) classification (Tatusov et al., 2003) for the genes indentified in the genomes of T. atroviride and T. virens. Considering a differential expression with a fold-change greater than 2.0, 2024 transcripts were identified (1051 up-regulated and 973 down-regulated). With a fold-change greater than 5.0, just 288 genes displayed differential expression (261 up-regulated and 27 down-regulated).

organism:
Trichoderma harzianum
Globisporangium ultimum

source_name: mycelium

label_protocol: High quality purified RNAs were submitted to Roche-NimbleGene (40 μg per 3-microarray set) where cDNAs were synthesized, amplified and labeled and then used for subsequent hybridization. Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Agar plugs cut from the growing edge of a 4-day colony of Trichoderma and Pythium were placed 2 cm from the border on the opposite side of the same petri plates containing PDA covered with sterile cellophane sheets. Dual cultures were allowed to grow at 25 ºC and mycelia were collected from the interaction zone in confrontations between P. ultimum and T. harzianum T34 or Tnox5 strains.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Freeze-dried mycelia from T. harzianum-P. ultimum interactions were ground in liquid nitrogen using a mortar and pestle.

value: mycelium


title: nox5-py (40150802)


title: nox5-py (40162402)


title: RB_984_09_TR3

description: Human retinoblastoma 3


title: HC_89564

source_name: blood PBMC

value: blood

value: PBMCs


title: RB_535_09_TR2

description: Human retinoblastoma 2


title: RB_139_09_TR3

description: Human retinoblastoma 1


title: RB_139_09_TR2

description: Human retinoblastoma 1


title: BMSC-LC

description:
Bone marrow stromal cells-laboratory control (bmsc-lc): Cells/skelite constructs, maintained in 24-well cell culture dishes with growth medium (normal gravity).
Gene expression data from bone marrow stromal cells incubated under routine laboratory conditions (normal gravity).

source_name: Bone marrow from laboratory control

value: bone marrow stromal cells

value: laboratory control

value: normal

value: no


title: T34-py (40173402)

value: T34 wild type


title: T34-py (40148202)


title: colon of mouse treated with DSS for 6 day, D6M1

city: Shreveport

first: Kevil

middle: G

last: Christopher

state: LA

address: 1501 Kings Highway

department: Pathology

institute: Louisiana State University Health Science Center, Shreveport

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 500 as normalization method.

source_name: colon

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

growth_protocol: C57BL/6J mice aged 12-14 weeks old were housed according to institutional IACUC regulations and the National Research Council's Guide for Care and Use of Laboratory Animals.

extract_protocol: Total RNA was isolated by using Qiagen RNA easy kits according the manufacture's instruction.

treatment_protocol: A 3% Dextran Sodium Sulphate solution was administered in the drinking water for the mice.

tag: time point (day)

value: 3% Dextran Sodium Sulphate


title: colon of mouse treated with DSS for 6 day, D6M21


title: colon of mouse treated with DSS for 6 day, D6M3


title: JEKO BR replicate2

city: Bethesda

first: Patricia

last: Perez-Galan

state: MD

address: 10 center drive

department: Hematology Branch

institute: NHLBI-NIH

description: mantle cell lymphoma cell lines, phenotype of BR vs PT

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: GeneChip operating software version 1.4 was used to calculate signal intensity and present calls on the hybridized chip. Then, the MAS5 signal-intensity values were transformed with an adaptive variance-stabilizing, quantile-normalizing transformation algorithm referred to as S10 (Symmetric Adapted transformed, base 10) available at http://abs.cit.nih.gov/MSCLtoolbox/ (P.J. Munson, MSCL Analyst's tool box, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001).

source_name: cultured JEKO

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: RNA was isolated from cells in logaritmic growth phase

extract_protocol: Total RNA was extracted using Qiagen RNA extraction kit

tag: cell line

value: JEKO

value: mantle cell lymphoma cell lines

tag: culture variation

value: Bortezomib-induced resistant


title: colon of mouse treated with DSS for 6 day, D6M4

tag: strain


title: FDR_92264

value: first degree relative of SLE patientw (FDR)

value: ANA+


title: colon of mouse treated with DSS for 6 day, D6M29


title: JEKO BR replicate1


title: RB_535_09_TR3

description: Human retinoblastoma 2


title: JEKO PT replicate2


title: colon of mouse treated with DSS for 4 day, D4M6


title: colon of mouse treated with DSS for 4 day, D4M4


title: colon of mouse treated with DSS for 4 day, D4M7


title: colon of mouse treated with DSS for 6 day, D6M7


title: colon of mouse treated with DSS for 4 day, D4M1


title: colon of mouse treated with DSS for 2 day, D2M17


title: colon of mouse treated with DSS for 4 day, D4M8


title: colon of mouse treated with DSS for 4 day, D4M3


title: colon of mouse treated with DSS for 2 day, D2M52


title: HBL2 BR replicate3

source_name: cultured HBL2


title: HBL2 BR replicate2


title: HBL2 BR replicate1


title: JEKO PT replicate1


title: colon of mouse treated with DSS for 2 day, D2M8


title: HBL2 PT replicate2


title: HBL2 PT replicate3


title: HBL2 PT replicate1


title: Wild type erythroblasts expressing ectopic Myc at supraphysiological levels 48hours 3

city: Singapore

first: Senthil Raja

last: Jayapal

address: #08-01, Genome, 60 Biopolis Street

department: Stem cell and developmental biology

country: Singapore

institute: Genome Institute of singapore

description:
Biological replicate 3
D2 Myc-GFPhigh3

hyb_protocol: 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing: The microarray data was subjected to background subtraction and quantile normalization on the BeadStudio Data Analysis software (Illumina).

source_name: E13.5 mouse fetal liver

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, USA).

growth_protocol: Fetal livers were isolated from E13.5 C57BL/6 mice embryos and mechanically dissociated by pipetting in PBS containing 20% fetal bovine serum (FBS). The dissociated cells were passed through 70 and 30 micron strainers to obtain single-cell suspensions. The cells were labeled with magnetic microbead-conjugated antibodies for TER119 and CD11b and passed through LD columns according to the manufacturer’s instructions for negative selection (Miltenyi Biotec). The purified TER119-negative, CD11b-negative erythroid progenitor cells were seeded in fibronectin coated plates and cultured in Iscove’s modified Dulbecco medium (IMDM) containing 15% FBS, 1% detoxified bovine serum albumin (StemCell Technologies), 200 μg/mL holo-transferrin (Sigma),10 μg/mL recombinant human insulin (Sigma), 2 mM L-glutamine, 10-4 M β-mercaptoethanol, and 2 U/mL erythropoietin.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Germany) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent, USA) using the RNA 6000 Nano Chip kit (Agilent, USA) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8) for all samples.

treatment_protocol: Purified mouse fetal liver erythroblasts were cultured for 48 hours after infection with retroviruses encoding Myc or were cultured as uninfected cells for control.

tag: treatment

value: Infection with MSCV-c-Myc-IRES-GFP encoding retroviruses at 0 hours in culture, followed by FACS sorting for highly GFP positive cells at 48 hours post infection

tag: genotype/variation

value: Myc at supraphysiological levels

tag: time in culture

value: 48 hours


title: Wild type erythroblasts expressing ectopic Myc at supraphysiological levels 48hours 1

description:
Biological replicate 1
D2 Myc-GFPhigh1


title: Wild type erythroblasts expressing ectopic Myc at supraphysiological levels 48hours 2

description:
Biological replicate 2
D2 Myc-GFPhigh2


title: colon of mouse treated with DSS for 2 day, D2M6


title: colon of mouse treated with DSS for 2 day, D2M7


title: normal mouse colon, D0M5


title: Wild type erythroblasts expressing ectopic Myc at Physiological levels 48hours 3

description:
Biological replicate 3
D2 Myc-GFPlow3

value: Infection with MSCV-c-Myc-IRES-GFP encoding retroviruses at 0 hours in culture, followed by FACS sorting for moderately GFP positive cells at 48 hours post infection

value: Myc at physiological levels


title: Wild type erythroblasts expressing ectopic Myc at Physiological levels 48hours 1

description:
Biological replicate 1
D2 Myc-GFPlow1


title: Wild type erythroblasts expressing ectopic Myc at Physiological levels 48hours 2

description:
Biological replicate 2
D2 Myc-GFPlow2


title: normal mouse colon, D0M4


title: Wild type erythroblasts-uninfected 48hours 1

description:
Biological replicate 1
D2 WT1

value: control (uninfected)


title: Wild type erythroblasts-uninfected  0hours 2

description:
Biological replicate 2
D0 WT2

value: 0 hours


title: Wild type erythroblasts-uninfected  0hours 3

description:
Biological replicate 3
D0 WT3


title: colon of mouse treated with DSS for 2 day, D2M1


title: GIST882 Imatinib Rep3

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: SAMPLE 18

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina HumanHT-12 v3  chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Genespring 10.0.2 for normalization. Detection P-value >0.8 is called present and <0.6 is called absent. Raw signal is threhold to 1.0. The signal is log2 transformed and quartile normalized between samples.

source_name: GIST882 Cell line

label_protocol: ~500 ng of total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

growth_protocol: GIST882 cells are grown in RPMI with 15% serum

extract_protocol: RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: Cells were treated in triplicate in either 0.1% DMSO or 1 μM Imatinib for 8 hours

value: Imatinib

tag: dose

tag: replicate


title: GIST882 Imatinib Rep1

description: SAMPLE 16

tag: agent


title: GIST882 DMSO Rep2

description: SAMPLE 14

value: DMSO (control)


title: normal mouse colon, D0M3


title: normal mouse colon, D0M2


title: Wild type erythroblasts-uninfected 48hours 3

description:
Biological replicate 3
D2 WT3


title: Wild type erythroblasts-uninfected 48hours 2

description:
Biological replicate 2
D2 WT2


title: Wild type erythroblasts-uninfected 24hours 3

description:
Biological replicate 3
D1 WT3

value: 24 hours


title: Wild type erythroblasts-uninfected  0hours 1

description:
Biological replicate 1
D0 WT1


title: Wild type erythroblasts-uninfected 24hours 1

description:
Biological replicate 1
D1 WT1


title: Glycine soja, young leaves, 50 mM NaHCO3, 24 hour, replicate 2

city: Harbin

first: Yanming

last: Zhu

state: Heilongjiang

address: Wood Street 59

department: Life sciences

country: China

institute: Northeast Agriculture University

description:
Gene expression data from Glycine soja leaves of 21 days old after 24h NaHCO3 stress.
24h_leaf_r2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The computation of expression values was conducted using dChip software. Sample wise normalization to the median probe cell intensity (CEL) of all 14 arrays. Model-based gene expression was obtained from normalized CEL intensities based on a Perfect Match-only model.

organism: Glycine soja

source_name: leaf after 24h stress

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Glycine soja seeds were grown in a culture room with 60 % relative humidity, 24℃ and a light regime of 12h light/12h dark. Germinated seedlings were grown in the growth boxes containing 1/4 strength Hoagland's solution.

extract_protocol: Total RNA was extracted from frozen leaves with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions from the manufacturer.

treatment_protocol: 21-day-old seedlings were transferred into the growth boxes containing 1/4 strength Hoagland’s solution with 50mmol/L NaHCO3 (pH 8.5).

tag: line

value: leaf

tag: age

value: 21 days after germination

tag: time


title: GIST882 DMSO Rep3

description: SAMPLE 15


title: GIST882 Imatinib Rep2

description: SAMPLE 17


title: stationary phase-repbiol2

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

country: France

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

description: Direct transcriptomic comparisons between VAR* and TT01alpha grown in LB broth and harvested in in in stationary phase (replicate 2)

hyb_protocol: Micro-array slides were pre-hybridized for 1 hour at 42°C in the saturation buffer (5 x SSC, 0,1 % bovine serum albumin, 0,1 % SDS), rinsed under continuous flow of deionized water and, after a rapid isopropanol bath, blow-dried using compressed gas. Hybridization was performed at 42°C for 12 hours in the automated slide processor (APS) chamber of Amersham.  The micro-arrays were washed for ten minutes in water, for four minutes in 1 x SSC, 0,2% SDS, and four additional minutes in 0,1 x SSC, 0,2% SDS. Micro-array slides were briefly washed in isopropanol and air-dried.

scan_protocol: Micro-array were  scanned for fluorescence intensity by using an Amersham scanner. The intensity of the signal for each microarray spot was determined with ArrayVision software (Amersham).

data_processing: Microarray data were normalized and statistical analyses were carried out with Spotfire DecisionSite Functional Genomic. The raw intensities were normalized as follow: for a given hybridization, the median intensity of a given variable is adjusted such that it is equal to the median intensity of the control variable (logR-logG = 0, where R and G are the summed intensities for each variable) without the designation of a baseline. As such, intensity levels of the two channels are mutually adjusted (dye normalization). The trimmed median method was used to calculate a median value for which the effect of outliers was minimized. The trim cutoff was set at 10%, resulting in the exclusion of the top 5% and the bottom 5% of values from the calculation. The dye-normalized values were used for a global normalization process in which intensities were rescaled with respect to a baseline intensity control. After normalization, the fold change value (FC) was calculated as follow: FC=R if R>1 and -1/R if R<1, where R=[median of normalized intensity for VAR*] / [median of normalized intensity for TT01alpha]. We used t-test to identify statistically significant differences between groups. The original hypothesis (null hypothesis) was that the median expression levels of a gene did not differ between the two groups. The null hypothesis was then either rejected or accepted for each gene considered. The results are expressed in terms of p-values, indicating the significance of the differences observed. These values correspond to the probability of a type I error leading to the conclusion that two median expression values for a given gene are different when there is, in fact, no difference. A significant difference is considered to exist if the p-value obtained is below 0.01.

organism: Photorhabdus laumondii subsp. laumondii TTO1

source_name: TT01alpha in stationary phase (45-hour-old culture, 5 x 108 cfu/ml)

label_protocol: We synthesized cDNA targets from 10 µg of TT01alpha and VAR* RNA and labeled them as follows: each RNA preparation was heated at 70°C for 10 minutes with random hexamer (0.1 µg/µl; Roche, Meylan, France) and cooled at room temperature for ten minutes. The RNA was then reverse transcribed by incubation at 42°C, for two hours, with SuperScript II (10 U/µl; Invitrogen, Carlsbad, California, USA), DTT (5 mM; Invitrogen), a mixture of dNTPs (1 µl; RPK0147; Amersham, GE Healthcare Europe GmbH, Munich, Germany) and dCTP-Cy3 or dCTP-Cy5 (50 µM; Amersham). The remaining RNA was subjected to alkaline lysis by incubation with 0.2 M NaOH for 10 minutes at 37°C. The labeled cDNAs were neutralized by adding HEPES pH 8 (625 mM) and immediately purified with a Qiaquick PCR purification kit (Qiagen, Courtaboeuf, France), used according to the manufacturer’s recommendations, but with two additional washes in PE buffer. Cy5- and Cy3-labeled cDNAs were mixed, dried under vacuum and resuspended in hybridization buffer (30 % formamide, 5 x SSC, 0,1 % SDS).

growth_protocol: Bacterial cells were grown in LB broth.

extract_protocol: Total RNA was extracted with TRIzol reagent, according to the manufacturer’s instructions (Invitrogen, Carlsbad, California, USA) and then purified with the High Pure RNA Isolation kit (Roche, Meylan, France), including a DNase I treatment step.

tag: growth phase

source_name: VAR* in stationary phase (45-hour-old culture, 5 x 108 cfu/ml)

value: VAR*


title: normal mouse colon, D0M1


title: Glycine soja, young leaves, 50 mM NaHCO3, 24 hour, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 24h NaHCO3 stress.
24h_leaf_r1

tag: tissue


title: exponential growth phase-repbiol1

description: Direct transcriptomic comparisons between VAR* and TT01alpha grown in LB broth and harvested in in exponential growth phase (replicate 1)

source_name: TT01alpha in exponential growth phase (6-hour-old culture, 5 x 107 cfu/ml)

source_name: VAR* in exponential growth phase (6-hour-old culture, 5 x 107 cfu/ml)


title: exponential growth phase-repbiol2

description: Direct transcriptomic comparisons between VAR* and TT01alpha grown in LB broth and harvested in in exponential growth phase (replicate 2)

value: exponential growth phase (6-hour-old culture, 5 x 107 cfu/ml)


title: stationary phase-repbiol1

description: Direct transcriptomic comparisons between VAR* and TT01alpha grown in LB broth and harvested in in in stationary phase(replicate 1)

value: stationary phase (45-hour-old culture, 5 x 108 cfu/ml)


title: Glycine soja, young leaves, 50 mM NaHCO3, 12 hour, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old after 12h NaHCO3 stress.
12h_leaf_r2

source_name: leaf after 12h stress


title: Glycine soja, young leaves, 50 mM NaHCO3, 12 hour, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 12h NaHCO3 stress.
12h_leaf_r1


title: Wild type erythroblasts-uninfected 24hours 2

description:
Biological replicate 2
D1 WT2


title: GIST48 ETV1sh2 Rep2

description: no additional information

hyb_protocol: The amplified, biotin-labeled antisense RNA (aRNA) was purified and quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization reagents and heated at 65C for 10min. After cooled to room temperature, total 15 ul of the hyb solution was applied to Illumina HumanHT-12 v3 chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing and staining with streptavidin-Cy3, the chip was scanned using Illumina BeadArray Reader. The scanning was done using standard DirectHyb Gene Expression protocol with the following settings: Factor=1, PMT=587, Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio software without normalization. Raw data was imported into Genespring 10.0.2 for normalization. Detection P-value >0.8 is called present and <0.6 is called absent. Raw signal is threhold to 1.0. The signal is log2 transformed and quartile normalized between samples.

source_name: GIST48 Cell line

label_protocol: ~500 ng of total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791, Applied Biosystems, Foster City, CA). Briefly, 500 ng of total RNA was used to synthesize the first strand of cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer bearing a T7 promoter. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase I in the presence of /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA was served as a template for in vitro transcription in a reaction containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

growth_protocol: GIST48 cells are grown in F10 media supplemented with MITO+, bovine pituitary extract and 15% serum. GIST882 cells are grown in RPMI with 15% serum.

extract_protocol: RNA is extracted using RNeasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: Two GIST cell lines (GIST48 and GIST882) were infected in duplicate with three shRNA viruses (Scrambled, ETV1sh1-B11TRCN0000013923, ETV1sh2-TRCN0000013925). Four days after infection, RNA was harvested for expression profiling.

tag: cell type

value: Gastrointestinal stromal tumor cells

tag: shrna


title: Glycine soja, young leaves, 50 mM NaHCO3, 6 hour, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old after 6h NaHCO3 stress.
6h_leaf_r2

source_name: leaf after 6h stress


title: control (ch1) vs. BF-1 6 h (ch2)

city: Kunitachi

first: Yukio

last: Shirasawa

state: Tokyo

address: 1796 Yaho

department: Central Institute for microbiological research

institute: Yakult Honsha Co., Ltd.

description: US22502557_SLOT03_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: The sample was fragmented and suspended in Hybridization Buffer HI-PRM (Agilent) before application to the microarray for hybridization. The microarray was incubated for 17 h at 65°C with 10 rpm rotation in a hybridization chamber. After hybridization, the microarray was washed with 37°C pre-warmed Gene Expression Wash Buffer (Agilent), acetonitrile (Sigma-Aldrich Co., St. Louis, MO), and Stabilization and Drying solution (Agilent).

scan_protocol: The microarray was scanned using the Agilent 2505B scanner.

data_processing: Image processing was performed using the Feature Extraction V9.5 software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GCIY cells

label_protocol: Total RNA was reverse transcribed and labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color to produce cyanine-3(Cy3) or -5(Cy5) labeled cRNA. The cRNAs were purified with RNeasy columns and quantified.

growth_protocol: H. pylori cultured in Brucella broth (Becton Dickinson Co., Sparks, MD) with 10% heat-inactivated horse serum under microaerobic conditions using AnaeroPack Helico (MITSUBISHI GAS CHEMICAL Co., Inc. Tokyo, Japan) with mild shaking (140 rpm) at 37°C for 48 h. BF-1 was cultured in mILS broth under anaerobic conditions using AnaeroPack (MITSUBISHI GAS CHEMICAL Co., Inc.). Human gastric epithelial cell line GCIY (RCB0555) cells were cultured in Eagle minimal essential medium (MEM; Nissui, Osaka, Japan), containing 15% fetal bovine serum (Gibco; invitrogen, Carlsbad, Calif.) with 100 U/ml Penicillin G and 100 g/ml Streptomycin sulfate at 37°C in humidified air containing 5% CO2.

extract_protocol: Infected cells were washed 3 times with MEM and treated with RNAlater (Qiagen, Dusseldorf, Germany) for 16 h to stabilize RNA. After removing the RNAlater, total RNA was extracted using the RNeasy Mini kit (Qiagen). RNA quality was evaluated with the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) and RNA yield was determined spectrophotometrically.

treatment_protocol: H. pylori YIT10238 and BF-1 were cultured as described above, washed and re-suspended in MEM without antibiotics. H. pylori infection studies were performed with GCIY cells in vitro. GCIY cells, which were maintained in MEM supplemented with 15% fetal serum, were seeded into collagen-coated 6-well tissue culture plates and grown to confluence at 37°C. BF-1 at a concentration of 10^9 CFU/ml or control medium was added to the tissue culture plates and co-incubated with GCIY cells. After 3 h of incubation, cells were washed 3 times with medium. Then H. pylori at 10^7 CFU/ml or control medium was added to the cells and incubated for 4 or 6 h.

value: gastric epithelial cell line

value: GCIY

tag: treatment group

value: control

tag: treatment time

value: 6 h


title: control (ch1) vs. BF-1 dye-exchange (ch2)

description: US22502557_SLOT02_S01_GE2-v5_95_Feb07_1_4.txt

tag: cell line

value: 4 h


title: GIST882 DMSO Rep1

description: SAMPLE 13


title: Glycine soja, young leaves, 50 mM NaHCO3, 3 hour, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 3h NaHCO3 stress.
3h_leaf_r1

source_name: leaf after 3h stress


title: control (ch1) vs. infected 6 h (ch2)

description: US22502557_SLOT03_S01_GE2-v5_95_Feb07_1_1.txt

value: infected


title: GIST48 ETV1sh1 Rep2

description: no additional information


title: Glycine soja, young leaves, 50 mM NaHCO3, 6 hour, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 6h NaHCO3 stress.
6h_leaf_r1


title: BF-1+non-infected (ch1) vs BF-1+infected 6 h (ch2)

description: US22502557_SLOT03_S01_GE2-v5_95_Feb07_1_2.txt


title: infected (ch1) vs BF-1+infected 6 h (ch2)

description: US22502557_SLOT03_S01_GE2-v5_95_Feb07_1_3.txt


title: GIST48 ETV1sh2 Rep1

description: no additional information


title: GIST48 shScr Rep2

description: no additional information

value: shScr


title: GIST48 ETV1sh1 Rep1

description: no additional information


title: Glycine soja, young leaves, 50 mM NaHCO3, 3 hour, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old after 3h NaHCO3 stress.
3h_leaf_r2


title: 1266 SN Cm

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Standard method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)

data_processing: MAS5.0 normalized in Gene Expression Console 1.0 (Affymetrix)

source_name: Postmortem brain whole substantia nigra

label_protocol: Standard Two-Cycle cRNA IVT method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)

extract_protocol: RNeasy (Qiagen)

tag: disease state

value: Control

tag: gender

value: male

tag: brain region

value: Whole substantia nigra from postmortem brain


title: 1134 SN Cm

scan_protocol: Standard method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)


title: GIST882 ETV1sh2 Rep2

description: no additional information


title: infected (ch1) vs BF-1+infected dye-exchange (ch2)

description: US22502557_SLOT02_S01_GE2-v5_95_Feb07_1_3.txt


title: 3132 SN Cm


title: GIST48 shScr Rep1

description: no additional information


title: Glycine soja, young leaves, 50 mM NaHCO3, 1 hour, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old after 1h NaHCO3 stress.
1h_leaf_r2

source_name: leaf after 1h stress

tag: treatment


title: BF-1+non-infected (ch1) vs BF-1+infected dye-exchange (ch2)

description: US22502557_SLOT02_S01_GE2-v5_95_Feb07_1_2.txt


title: control (ch1) vs. infected dye-exchage (ch2)

description: US22502557_SLOT02_S01_GE2-v5_95_Feb07_1_1.txt


title: GIST882 ETV1sh1 Rep2

description: no additional information


title: control (ch1) vs. BF-1 4 h (ch2)

description: US22502557_SLOT01_S01_GE2-v5_95_Feb07_1_4.txt


title: GIST882 ETV1sh1 Rep1

description: no additional information


title: Glycine soja, young leaves, 50 mM NaHCO3, 30 minutes, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 0.5h NaHCO3 stress.
0.5h_leaf_r1

source_name: leaf after 0.5h stress


title: 5386 PT Cm

source_name: Postmortem brain putamen

value: Putamen from postmortem brain


title: GIST882 shScr Rep2

description: no additional information


title: BF-1+non-infected (ch1) vs BF-1+infected 4 h (ch2)

description: US22502557_SLOT01_S01_GE2-v5_95_Feb07_1_2.txt


title: 3132 PT Cm


title: 1266 PT Cm


title: GIST882 ETV1sh2 Rep1

description: no additional information


title: Glycine soja, young leaves, 50 mM NaHCO3, 1 hour, replicate 1

description:
Gene expression data from Glycine soja leaves of 21 days old after 1h NaHCO3 stress.
1h_leaf_r1

value: leaf


title: 3747 PT Cm


title: Glycine soja, young leaves, 50 mM NaHCO3, 30 minutes, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old after 0.5h NaHCO3 stress.
0.5h_leaf_r2

value: 21 days after germination


title: Glycine soja, young leaves, standard condition, replicate 2

description:
Gene expression data from Glycine soja leaves of 21 days old without stress.
0h_leaf_r2

source_name: leaf at 0h as control


title: control (ch1) vs. infected 4 h (ch2)

description: US22502557_SLOT01_S01_GE2-v5_95_Feb07_1_1.txt


title: infected (ch1) vs BF-1+infected 4 h (ch2)

description: US22502557_SLOT01_S01_GE2-v5_95_Feb07_1_3.txt


title: 1134 PT Cm


title: GIST882 shScr Rep1

description: no additional information