title: TTHB212 deletion mutant strain 3

description: TTHB212 deletion mutant strain 3

growth_protocol: The T. thermophilus HB8 TTHB212 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR 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 7 h (OD600nm = ~ 0.45).


title: wild-type strain 680_1

status: Public on Aug 03 2008

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: wild-type strain 680_1

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 image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating Software, version 1.1 (Affymetrix, Santa Clara, CA).

label: biotin

molecule: total RNA

organism: Thermus thermophilus HB8

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

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: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR 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 680 min (OD600nm = ~ 5.2).

extract_protocol: Cells were collected from 5 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: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 680 min


title: Hum 60d-3

status: Public on Sep 11 2009

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: GF female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of : fresh anaerobic cultures of fecal homogenate from SFB mono-associated mice, fresh feces from Cv mice (Cvd) or from a healthy human donor (Hum). All mice were sacrificed on d8, 20 and 60 post-colonization in parallel to age-matched Cv and GF controls.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip NuGO Mouse Array (NuGO_Mm1a520177). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.

label: Biotin

organism: Mus musculus

source_name: ileal tissue, Hum 60d

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 5 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: C3H/HeN mice were bred at the INRA facilities in Jouy-en-Josas. GF mice were maintained in plastic isolators and fed ad libitum on a commercial diet (R03-40; UAR) sterilized by γ-irradiation (40 kGy).

extract_protocol: Ileal tissue was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: GF female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh feces from a healthy human donor, and sacrificed on d60 post-colonization as age-match to Cv, GF, Hum and SFB mice.

tag: culture

value: Hum 60d

tag: strain

tag: gender

value: female

tag: age

value: 8-9 weeks

tag: tissue

value: ileum


title: wild-type strain_8h_2

status: Public on Sep 04 2007

description: no additional information

hyb_protocol: 3’-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix, Santa Clara, CA).  The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 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 GeneArray Scanner (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix, Santa Clara, CA).

source_name: wild-type strain grown on a rich (TT) medium for 8 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 35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37oC for 10 min, and after inactivation at 98oC for 10 min, the cDNA fragments were labeled with biotin-dideoxy UTP, using terminal transferase according to the manufacturer’s instructions (ENZO Biochem. Inc., Farmingdale, NY).

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 8 h (OD600nm = ~ 4.5).

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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 8 h


title: TTHB212 deletion mutant strain 1

status: Public on Jul 16 2008

description: TTHB212 deletion mutant strain 1

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating Software, version 1.2 (Affymetrix, Santa Clara, CA).

source_name: T. thermophilus HB8, TTHB212 deletion mutant, rich medium, 7h

growth_protocol: The T. thermophilus HB8 TTHB212 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR 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 7 h (OD600nm = ~ 0.33).

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.

tag: TTHB212 deletion mutant strain grown on a rich (TR) medium for 7 h


title: wild-type strain_8h_1

description: no additional information


title: wild-type strain 180_1

description: wild-type strain 180_1

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

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR 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 min (OD600nm = ~ 0.06).

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: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 180 min


title: wild-type strain_760_2

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 760 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 760 min (OD600nm = ~ 7.0).

extract_protocol: Cells were collected from 5 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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 760 min


title: wild-type strain_760_3

description: no additional information


title: wild-type strain_600_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 600 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 600 min (OD600nm = ~ 6.0).

extract_protocol: Cells were collected from 10 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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 600 min


title: wild-type strain_600_1

description: no additional information


title: wild-type strain_600_2

description: no additional information


title: wild-type strain_760_1

description: no additional information


title: wild-type strain 300_1

description: wild-type strain 300_1

source_name: T. thermophilus HB8, wild-type, rich medium, 300 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR 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 300 min (OD600nm = ~ 0.27).

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.

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 300 min


title: MuRF1 transgene_2

status: Public on May 15 2008

city: Mannheim

first: Stephanie

last: Hirner

department: Universitätsklinikum Mannheim

country: Germany

institute: institute of anaesthesiology and intensive care

description: TG/WT at 12 weeks of age were compared.

hyb_protocol: Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2007)

scan_protocol: Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2007)

data_processing: quantile normalization (SAS GEnomics 3.0)

source_name: TG2 M. quadriceps

label_protocol: Between 15 to 40 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

extract_protocol: Total RNA was isolated from skeletal muscles using RNeasy mini kit (Qiagen) according to manufacturer’s protocol.

value: FVBN

tag: genotype/variation

value: MuRF1 overexpression

value: male

value: 3 month

value: skeletal muscle


title: wild-type strain_540_1

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 540 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 540 min (OD600nm = ~ 5.5).

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 540 min


title: wild-type strain_680_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 680 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 680 min (OD600nm = ~ 6.5).

tag: Thermus thermophilus HB8 strain grown on TT medium for 680 min


title: WT2

description: TG/WT at 12 weeks of age were compared.

source_name: M. quadriceps

value: wildtype


title: WT1

description: TG/WT at 12 weeks of age were compared.

source_name: WT1 M. quadriceps


title: wild-type strain_540_2

description: no additional information

tag: Thermus thermophilus HB8 strain grown on TT medium for 540 min


title: wild-type strain_540_3

description: no additional information


title: wild-type strain_480_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 480 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 480 min (OD600nm = ~ 4.5).

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 480 min


title: wild-type strain_420_1

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 420 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 420 min (OD600nm = ~ 4.0).

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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 420 min


title: wild-type strain_360_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 360 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 360 min (OD600nm = ~ 3.0).

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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 360 min


title: wild-type strain_300_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 300 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 300 min (OD600nm = ~ 1.0).

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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 300 min


title: wild-type strain_420_2

description: no additional information


title: wild-type strain_420_3

description: no additional information


title: wild-type strain_360_1

description: no additional information


title: wild-type strain_360_2

description: no additional information


title: wild-type strain_680_1

description: no additional information

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 680 min


title: MuRF1 transgene_1

description: TG/WT at 12 weeks of age were compared.

tag: strain

tag: gender

tag: age


title: wild-type strain_300_1

description: no additional information


title: wild-type strain_480_1

description: no additional information


title: wild-type strain_480_2

description: no additional information


title: wild-type strain_240_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 240 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 240 min (OD600nm = ~ 0.5).

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 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  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 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC 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 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 240 min


title: wild-type strain_680_2

description: no additional information


title: wild-type strain_180_3

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 180 min

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 180 min (OD600nm = ~ 0.2).

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 180 min


title: wild-type strain_240_1

description: no additional information


title: wild-type strain_6h_2

status: Public on Aug 05 2007

description: no additional information

source_name: wild-type strain grown on a rich (TT) medium for 6 h

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC 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 70oC for 6 h (OD600nm = ~ 2.5).

tag: wild-type Thermus thermophilus HB8 strain grown on TT medium for 6 h


title: wild-type strain_240_2

description: no additional information


title: TTHA1437 deletion mutant strain_8h_3

description: no additional information

source_name: TTHA1437 deletion mutant strain grown on a rich (TT) medium for 8 h

growth_protocol: TTHA1437 deletion mutant strain was pre-cultured at 70oC 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 70oC for 8 h (OD600nm = ~ 4.5).

tag: TTHA1437 deletion mutant strain grown on TT medium for 8 h


title: wild-type strain_180_2

description: no additional information


title: wild-type strain_180_1

description: no additional information


title: TTHA1437 deletion mutant strain_8h_2

description: no additional information


title: TTHA1437 deletion mutant strain_6h_1

description: no additional information

source_name: TTHA1437 deletion mutant strain grown on a rich (TT) medium for 6 h

growth_protocol: TTHA1437 deletion mutant strain was pre-cultured at 70oC 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 70oC for 6 h (OD600nm = ~ 2.5).

tag: TTHA1437 deletion mutant strain grown on TT medium for 6 h


title: TTHA1437 deletion mutant strain_8h_1

description: no additional information


title: TTHA1437 deletion mutant strain_6h_2

description: no additional information


title: wild-type strain_300_2

description: no additional information


title: TTHA1437 deletion mutant strain_6h_3

description: no additional information


title: wild-type strain_6h_3

description: no additional information


title: wild-type strain_6h_1

description: no additional information


title: ER negative human primary breast tumor EA02014_41299_H133A_JA-2021

status: Public on May 14 2007

city: Chicago

first: Andy

middle: J

last: Minn

state: IL

address: 924 E. 57th Street

country: USA

institute: University of Chicago

description: Gene expression data from ER negative human primary breast tumor

hyb_protocol: cRNA were hybridized to the Affymetrix U133a GeneChip according to manufacturer's protocols.

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

organism: Homo sapiens

source_name: Primary human breast tumor

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

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

tag: ID

tag: cohort

value: Erasmus

tag: metastasis

tag: lung met first event

tag: lung met all

tag: metastasis free survival (yr)

tag: lung met free survival (yr)

tag: lms status


title: ER negative human primary breast tumor EA02014_41295_H133A_JA-1976


title: ER negative human primary breast tumor EA02014_41288_H133A_JA-1853


title: ER negative human primary breast tumor EA02014_41292_H133A_JA-1949


title: ER negative human primary breast tumor EA02014_41270_H133A_JA-1501


title: ER negative human primary breast tumor EA02014_41284_H133A_JA-854


title: ER negative human primary breast tumor EA02014_41275_H133A_JA-1568


title: ER negative human primary breast tumor EA02014_41267_H133A_JA-1455


title: ER negative human primary breast tumor EA02014_41274_H133A_JA-1563


title: ER negative human primary breast tumor EA02014_41256_H133A_JA-872


title: ER negative human primary breast tumor EA02014_41259_H133A_JA-929


title: ER negative human primary breast tumor EA02014_41258_H133A_JA-282


title: ER negative human primary breast tumor EA02014_41272_H133A_JA-1416


title: ER negative human primary breast tumor EA02014_41264_H133A_JA-1487


title: ER negative human primary breast tumor EA02014_41263_H133A_JA-1582


title: ER negative human primary breast tumor EA02014_41302_H133A_JA-2024


title: ER negative human primary breast tumor EA02014_41248_H133A_JA-131


title: ER negative human primary breast tumor EA02014_41289_H133A_JA-1871


title: Lentinula edodes-mature fruit body after spore formation

status: Public on Feb 09 2006

type: SAGE

anchor: NlaIII

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

department: Biology

country: China

institute: The Chinese University of Hong Kong

description: To analyze gene expression profiles at different developmental stages and identify differentially expressed genes that may relate to sporulation by comparing transcriptomes of mature fruit body before and after sporulation.

organism: Lentinula edodes

source_name: Strain L54 of Lentinula edodes (Shiitake mushroom)

tag: The gene expression profiles of L. edodes strain L54 mature fruit body after spore formation. Fruit bodies were germinated from L54 dikaryotic mycelium grown on sadust.


title: Lentinula edodes-mature fruit body before sporulation

tag: The gene expression profiles of L. edodes strain L54 mature fruit body before sporulation. Fruit bodies were germinated from L54 dikaryotic mycelium grown on sawdust.


title: ER negative human primary breast tumor EA02014_41255_H133A_JA-838


title: ER negative human primary breast tumor EA02014_41247_H133A_JA-120


title: ER negative human primary breast tumor EA02014_41261_H133A_JA-1060


title: ER negative human primary breast tumor EA02014_41253_H133A_JA-755


title: HNF4 CONTROL_406

status: Public on Jan 01 2006

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: D-Chip, PM/MM model with defaults

source_name: E18.5 Embryo Colon

label_protocol: Standard Affymetrix protocol

extract_protocol: Qiagen RNeasy mini

tag: strain

value: HNF4LoxP/+ FoxA3Cre

tag: tissue

value: Fetal Colon


title: HNF4 CONTROL_421

tag: age


title: HNF4 null_60

value: HNF4LoxP/LoxP FoxA3Cre


title: HNF4 null_426


title: HNF4 null_59


title: HNF4 Control_1193

status: Public on Dec 31 2005

source_name: E18.5 Embryonic Liver

value: Fetal Liver


title: ER negative human primary breast tumor EA02014_41246_H133A_JA-401


title: HNF4 Control_1192


title: HNF4 Null_190

description: HNF4 null small intestine

source_name: HNF4loxp/-villin cre

value: HNF4 loxP/- villin cre

value: 1 month

value: small intestine

tag: sex


title: HNF4 Control_8

extract_protocol: Qiagen RNeasy Mini


title: HNF4 Null_61

value: HNF4LoxP/LoxP AlfpCre


title: HNF4 Null_278

description: HNF4 null small intestine

value: HNF4 null

value: female


title: HNF4 Null_1191


title: HNF4 CONTROL_277

description: HNF4 control small intestine

source_name: HNF4loxp/+villin cre

value: HNF4LoxP/+  Villin Cre


title: HNF4 Null_1195


title: MDA-MB-231 SCP#26

status: Public on Jul 28 2005

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: RNA was extracted using a Quiagen RNeasy kit from subconfluent cells grown on plastic.

data_processing: MAS 5.0

source_name: Breast cancer cell line

extract_protocol: RNA was extracted using a Qiagen RNeasy kit from homogenized frozen tumors

tag: tissue type

value: Breast cancer cell line


title: B96-T

description: RNA was extracted using a Quiagen RNeasy kit from homogenized frozen tumors

source_name: Primary Breast Cancer

tag: name

tag: age at dx

tag: tumor size (cm)

tag: pos lymph nodes

tag: all lymph nodes

tag: path er status

value: P

tag: path pr status

tag: her2 status

value: N

tag: van't veer signature

value: Good Prognosis

tag: binary 5y met event

tag: met event

tag: mfs (yr)

tag: lm event

tag: lmfs (yr)

tag: bm event

tag: bmfs (yr)


title: MDA-MB-231 SCP#28

tag: tissue type


title: MDA-MB-231 SCP#21


title: MDA-MB-231 SCP#2


title: MDA-MB-231 SCP#25


title: B11-T

tag: name


title: 11B

status: Public on Aug 31 2005

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description:
phosgene exposed mouse lung
CG
32 mg
1
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.

source_name: lung


title: MDA-MB-231 SCP#3


title: MDA-MB-231 SCP#43


title: B9-T

tag: age at dx


title: MCF10A


title: 158A

description:
phosgene exposed mouse lung
Air
1
72
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: HNF4 CONTROL_191

description: HNF4 control small intestine

tag: strain

value: HNF4LoxP/- no Cre

tag: age

tag: tissue

tag: sex

value: male


title: MDA-MB-231 SCP#32


title: 142B

description:
phosgene exposed mouse lung
Air
1
48
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: 158B

description:
phosgene exposed mouse lung
Air
1
72
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: 154B

description:
phosgene exposed mouse lung
None
None
0
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: MDA-MB-231 #2295


title: MDA-MB-231 SCP#46


title: 116B

description:
phosgene exposed mouse lung
Air
1
4
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: MDA-MB-231 #1833


title: 22B

description:
phosgene exposed mouse lung
CG
32 mg
8
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC

.CEL file unavailable for this chip.


title: MDA-MB-231 #3481


title: MDA-MB-231 SCP#6


title: MDA-MB-231 #4142


title: MDA-MB-231 #2293


title: MDA-MB-231 #1834


title: 4175

description:
In vivo selected subpopulation of MDA-MB-231 harvested in tissue culture.
Keywords = Breast cancer
Keywords = Lung metastasis

source_name: Subpopulation of MDA-MB-231

value: Subpopulation of MDA-MB-231


title: 4173


title: Parental MDA-MB-231 Replicate B

description:
Parental MDA-MB-231 cells harvested in tissue culture, replicate B.
Keywords = Breast cancer
Keywords = Lung metastasis

source_name: Breast cancer cell line MDA-MB-231

value: Breast cancer cell line MDA-MB-231


title: Parental_A

description:
Parental MDA-MB-231 cells harvested in tissue culture
Keywords = Breast cancer
Keywords = Lung metastasis

source_name: MDA-MB-231 breast cancer cell line

value: MDA-MB-231 breast cancer cell line


title: B17-T

tag: tumor size (cm)

tag: pos lymph nodes

tag: all lymph nodes

tag: path er status

tag: path pr status


title: 4180

source_name: in vivo selected subpopulation of MDA-MB-231


title: Hum 8d-2

source_name: ileal tissue, Hum 8d

growth_protocol: C3H/HeN mice were bred at the INRA facilities in Jouy-en-Josas. GF mice were maintained in plastic isolators and fed ad libitum on a commercial diet (R03-40; UAR) sterilized by γ-irradiation (40 kGy).

treatment_protocol: GF female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh feces from a healthy human donor, and sacrificed on d8 post-colonization as age-match to Cv, GF, Hum and SFB mice.

tag: culture

value: Hum 8d

tag: gender

value: 8-9 weeks

value: ileum