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

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

source_name: T. thermophilus HB8, (-)crp, 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 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.42).

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.

value: (-)crp


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

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: (-)crp strain at 100 (min) after ϕYS40 infection 2

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

growth_protocol: The T. thermophilus HB8 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.05).

tag: genotype


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

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

growth_protocol: The T. thermophilus HB8 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.60).


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

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

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

growth_protocol: The T. thermophilus HB8 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 2.44).


title: Aire1

status: Public on Oct 16 2010

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description: 293T cells transfected with pCMV-Aire expression vector

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

scan_protocol: GeneChips were scanned using  GeneArray Scanner.

data_processing: The data were normalized and analyzed with Genepattern software.

organism: Homo sapiens

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: 293T cells were grown on 10cm plates in DMEM containing 10% FBS under standard TC conditions

extract_protocol: Total RNA was extracted 48 hrs post transfection by Trizol extraction  according to the manufacturer's instructions.

treatment_protocol: 293T cells were transfected either by pCMV-Aire (6ug/plate) or empty pCMV (6ug/plate) using Mirus reagent, according to manufacturer's instructions

tag: cell type


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

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

growth_protocol: The T. thermophilus HB8 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 2.31).


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

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

growth_protocol: The T. thermophilus HB8 (-)crp 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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 1.96).


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

description: (-)crp strain ϕYS40 pre-infection 3

source_name: T. thermophilus HB8, (-)crp strain, rich medium, phage ϕYS40 pre-infection

growth_protocol: The T. thermophilus HB8 (-)crp 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 360 min (OD600nm = ~ 0.78).


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

description: (-)crp strain ϕYS40 pre-infection 2

growth_protocol: The T. thermophilus HB8 (-)crp 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 360 min (OD600nm = ~ 0.90).


title: tumor tissue versus the adjacent non-tumor tissue. biological replicates#3

city: Taipei

first: Yi-Shing

last: Lin

address: NanGang

country: Taiwan

institute: Welgene Biotech.co., Ltd

description: Biological replicate 3 of 4.  tumor tissue versus the adjacent non-tumor tissue

hyb_protocol: Both Cy-labeled cRNAs were fragmented to about 50-100 nucleotides and then pooled and hybridized to Agilent Whole Human Genome Oligo Microarray 44K (Agilent Technologies, USA) at 60oC for 17 h.

scan_protocol: After washing and drying by nitrogen blowing, microarrays were scanned with an Agilent microarray scanner at 535 nm for Cy3 and 625 nm for Cy5.  The scanned images were analyzed by Feature Extraction 9.1 software (Agilent Technologies)

data_processing: Feature Extraction 9.1 software (Agilent Technologies, USA) to quantify the signal and background intensity for each feature, and normalization of the data was performed by rank-consistency-filtering LOWESS method.  Only the features with the signal-to-noise ratio >2.6 in either Cy3 or Cy5 channel were retrieved for further analysis.

source_name: tumor tissue  of colorectal cancer

label_protocol: RNA samples (0.5 mg for each), chosen from the tumor tissues and the corresponding non-tumor tissues of two patients with metastasis and two patients without metastasis, were amplified by Low RNA Input Fluor Linear Amp kit (Agilent Technologies, USA) and labeled with Cy3- or Cy5-dUTP (GE Healthcare, Piscataway, NJ).  The RNA from tumor parts was labeled with Cy5 and the RNA from the corresponding non-tumor parts was labeled with Cy3.

extract_protocol: Each tissue sample with 2 mg of tissue pieces, together with 1 ml of Trizol reagent (Invitrogen, Carlsbad, CA), was put into a ceramic beads-containing homogenizer tube (Roche, Penzberg, Germany).  Homogenization was performed in MagNA Lyser (Roche) by 5 cycles of oscillation at 6500 rpm for 20 sec and chilling on ice for 1 min.  Tissue lysates were further for RNA isolation by RNeasy protocol (Qiagen).

tag: sample id

tag: disease state

value: tumor tissue

source_name: adjacent non-tumor tissue of colorectal cancer

value: non-tumor tissue


title: tumor tissue versus the adjacent non-tumor tissue. biological replicates#4

description: Biological replicate 4 of 4.  tumor tissue versus the adjacent non-tumor tissue


title: wild-type strain cultured for 420 min_2 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 420 min, rep 2

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).

source_name: T. thermophilus HB8, wild-type, rich medium, 420 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 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 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 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 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.

value: wild-type

tag: time

value: 420 min


title: wild-type strain cultured for 420 min_3 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 420 min, rep 3


title: tumor tissue versus the adjacent non-tumor tissue. biological replicates#1

description: Biological replicate 1 of 4.  tumor tissue versus the adjacent non-tumor tissue


title: wild-type strain cultured for 480 min_2 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 480 min, rep 2

source_name: T. thermophilus HB8, wild-type, rich medium, 480 min

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 480 min.

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.

value: 480 min


title: wild-type strain cultured for 480 min_3 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 480 min, rep 3


title: wild-type strain cultured for 480 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 480 min, rep 1


title: wild-type strain cultured for 420 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 420 min, rep 1


title: wild-type strain cultured for 540 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 540 min, rep 1

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

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 540 min.

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.

value: 540 min


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

description: (-)crp strain ϕYS40 pre-infection 1

growth_protocol: The T. thermophilus HB8 (-)crp 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 360 min (OD600nm = ~ 0.69).


title: wild-type strain cultured for 760 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 760 min, rep 1

source_name: T. thermophilus HB8, wild-type, rich medium, 760 min

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 760 min.

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.

value: 760 min


title: wild-type strain cultured for 680 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 680 min, rep 1

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

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 680 min.

value: 680 min


title: tumor tissue versus the adjacent non-tumor tissue. biological replicates#2

description: Biological replicate 2 of 4.  tumor tissue versus the adjacent non-tumor tissue


title: 4302_CD133-, untreated

city: Durham

first: Igor

last: Shats

state: NC

address: 101 Science Drive

institute: Duke University

description: Gene expression data from breast cancer cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A plus 2.0 arrays. Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (Robust Multichip Average) using Bioconductor

source_name: Cultured cell line

label_protocol: Biotinylated cRNA were prepared using Ambion MessageAmp Premier labeling kit.

growth_protocol: CD133+ and CD133- glioma cells were separated from tumor xenografts (4105 and 4302), cultured in serum-free media for 48 hours in the presence of absence of laminin, which led to adherent growth of glioma stem cells while preserving stemness.

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: No treatment

tag: tissue

value: glioblastoma xenografts


title: wild-type strain cultured for 600 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 600 min, rep 1

source_name: T. thermophilus HB8, wild-type, rich medium, 600 min

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 600 min.

value: 600 min


title: wild-type strain cultured for 360 min_2 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 360 min, rep 2

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

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 360 min.

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.

value: 360 min


title: wild-type strain cultured for 360 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 360 min, rep 1


title: 4105_CD133-, untreated


title: wild-type strain cultured for 300 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 300 min, rep 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 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 300 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 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.

value: 300 min


title: wild-type strain cultured for 240 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 240 min, rep 1

source_name: T. thermophilus HB8, wild-type, rich medium, 240 min

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 240 min.

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.

value: 240 min


title: TTHA1359-deficient strain_1240_1

description: TTHA1359-deficient strain cultivated for 1240 min_1

source_name: T. thermophilus HB8, TTHA1359 deletion mutant, rich medium, 1240 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 manufacturer’s instructions (Affymetrix).

growth_protocol: The TTHA1359-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 1240 min.

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 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: TTHA1359-deficient strain


title: wild-type strain cultured for 180 min_1 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 180 min, rep 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 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 min.

value: 180 min


title: ko_1

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

label: Biotin

organism: Mus musculus

source_name: E12.5 DRG RNA from Erk1/2CKO(Wnt1) mice

label_protocol: Biotin

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and a Qiagen RNeasy Mini kit per manufacturer’s instructions.

treatment_protocol: E12.5 DRGs from control and Erk1/2CKO(Wnt1) embryos derived from three independent litters were dissected in PBS supplemented with 10% RNAlater (Qiagen) and frozen on dry ice.

tag: genotype/variation

value: E12.5 Erk1/2CKO(Wnt1)

value: E12.5 dorsal root ganglia (DRG)


title: wild-type strain cultured for 360 min_3 (labeling:ENZO)

description: T. thermophilus wild-type strain cultured for 360 min, rep 3


title: TTHA1359-deficient strain_1120_4

description: TTHA1359-deficient strain cultivated for 1120 min_4

source_name: T. thermophilus HB8, TTHA1359 deletion mutant, rich medium, 1120 min

growth_protocol: The TTHA1359-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 1120 min.


title: TTHA1359-deficient strain_1120_5

description: TTHA1359-deficient strain cultivated for 1120 min_5


title: TTHA1359-deficient strain_1120_3

description: TTHA1359-deficient strain cultivated for 1120 min_3


title: TTHA1359-deficient strain_1120_2

description: TTHA1359-deficient strain cultivated for 1120 min_2


title: TTHA1359-deficient strain_1120_1

description: TTHA1359-deficient strain cultivated for 1120 min_1


title: TTHA1359-deficient strain_680_1

description: TTHA1359-deficient strain cultivated for 680 min_1

source_name: T. thermophilus HB8, TTHA1359 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA1359-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 680 min.

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.


title: TTHA1359-deficient strain_680_4

description: TTHA1359-deficient strain cultivated for 680 min_4

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.


title: dTTHA0995_1mM_FeSO4_0min_1

description: TTHA0995-deficient strain grown on a TT medium, non-addition of FeSO4

source_name: T. thermophilus HB8, TTHA0995-deficient strain, rich medium, 1 mM FeSO4, 0 min

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.53).

value: TTHA0995-deficient strain


title: TTHA1359-deficient strain_680_2

description: TTHA1359-deficient strain cultivated for 680 min_2


title: TTHA1359-deficient strain_680_3

description: TTHA1359-deficient strain cultivated for 680 min_3


title: TTHA0175-deficient strain_600_2

description: TTHA0175-deficient strain cultivated for 600 min_2

source_name: T. thermophilus HB8, TTHA0175 deletion mutant, rich medium, 600 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 TTHA0175-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 680 min.

value: TTHA0175-deficient strain


title: dTTHA0995_1mM_FeSO4_30min_2

description: TTHA0995-deficient strain grown on a TT medium, 30 min time point after addition of 1.0 mM FeSO4

source_name: T. thermophilus HB8, TTHA0995-deficient strain, rich medium, 1 mM FeSO4, 30 min

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.30). A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.


title: TTHA0175-deficient strain_600_1

description: TTHA0175-deficient strain cultivated for 600 min_1


title: dTTHA0995_1mM_FeSO4_30min_3

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.46). A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.


title: Wild_Fe_osaka_30min_2

description: wild-type strain grown on a synthetic medium, 1 mM FeSO4, 30 min_2

source_name: T. thermophilus HB8, wild type, synthetic medium, 1 mM FeSO4, 30 min

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 4 h in 5 ml of TT medium. The cells were inoculated into synthetic medium so that the dilution rate to be 100 fold and then cultivated at 70°C until OD600nm being 1.0 . The synthetic medium was made by the same way as described in this section of GSM296605.

extract_protocol: Cells were collected at 30 min time point after the adition of FeSO4, 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: wild-type


title: Wild_Fe_osaka_30min_1

description: wild-type strain grown on a synthetic medium, 1 mM FeSO4, 30 min_1


title: TTHA0175-deficient strain_480_1

description: TTHA0175-deficient strain cultivated for 480 min_1

source_name: T. thermophilus HB8, TTHA0175 deletion mutant, rich medium, 480 min

growth_protocol: The TTHA0175-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 480 min.


title: dTTHA0995_1mM_FeSO4_30min_1

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.53). A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.


title: dTTHA0995_1mM_FeSO4_0min_3

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.46).


title: TTHA0175-deficient strain_300_2

description: TTHA0175-deficient strain cultivated for 300 min_2

source_name: T. thermophilus HB8, TTHA0175 deletion mutant, rich medium, 300 min

growth_protocol: The TTHA0175-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 300 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: TTHA0175-deficient strain_480_2

description: TTHA0175-deficient strain cultivated for 480 min_2


title: TTHA0175-deficient strain_300_1

description: TTHA0175-deficient strain cultivated for 300 min_1


title: TTHA1431-deficient strain_360_3

description: TTHA1431-deficient strain cultivated for 360 min_3

source_name: T. thermophilus HB8, TTHA1431 deletion mutant, rich medium, 360 min

growth_protocol: The TTHA1431-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 L of the same medium and then cultivated at 70°C for 360 min.

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.

value: TTHA1431-deficient strain


title: TTHA1939-deficient strain_800_4

description: TTHA1939-deficient strain cultivated for 800 min_4

source_name: T. thermophilus HB8, TTHA1939 deletion mutant, synthetic medium, 800 min

growth_protocol: Wild-type and the mutant strains were precultured in rich medium (TR medium) for two times at 70 oC and then subcultured to minimum essential medium (CS medium). These cells were harvested during the logarithmic growth phase (800 minutes from the start of culture).

extract_protocol: Cells were collected from 20 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: TTHA1939-deficient strain


title: TTHA1939-deficient strain_800_3

description: TTHA1939-deficient strain cultivated for 800 min_3


title: TTHA1939-deficient strain_800_2

description: TTHA1939-deficient strain cultivated for 800 min_2


title: TTHA1939-deficient strain_800_1

description: TTHA1939-deficient strain cultivated for 800 min_1


title: TTHA1431-deficient strain_360_1

description: TTHA1431-deficient strain cultivated for 360 min_1


title: Wild_Fe_osaka_30min_3

description: wild-type strain grown on a synthetic medium, 1 mM FeSO4, 30 min_3


title: dTTHA0995_1mM_FeSO4_0min_2

description: TTHA0995-deficient strain grown on a TT medium, non-addition of FeSO4

growth_protocol: T. thermophilus HB8 TTHA0995-deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 h (OD600nm = ~ 1.30).


title: TTHA0845-deficient strain_420_3

description: TTHA0845-deficient strain cultivated for 420 min_3

source_name: T. thermophilus HB8, TTHA0845 deletion mutant, rich medium, 420 min

growth_protocol: The TTHA0845-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 L of the same medium and then cultivated at 70°C for 420 min.

value: TTHA0845-deficient strain


title: TTHA1431-deficient strain_360_2

description: TTHA1431-deficient strain cultivated for 360 min_2


title: ko_3


title: TTHA0845-deficient strain_420_2

description: TTHA0845-deficient strain cultivated for 420 min_2


title: TTHA0845-deficient strain_420_1

description: TTHA0845-deficient strain cultivated for 420 min_1


title: TTHA1634-deficient strain_600_2

description: TTHA1634-deficient strain cultivated for 600 min_2

source_name: T. thermophilus HB8, TTHA1634 deletion mutant, rich medium, 600 min

growth_protocol: The TTHA1634-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 L of the same medium and then cultivated at 70°C for 420, and 600 min.

value: TTHA1634-deficient strain


title: TTHA1634-deficient strain_600_1

description: TTHA1634-deficient strain cultivated for 600 min_1


title: crp-deficient strain_480_1

description: crp-deficient strain cultivated for 480 min_1

source_name: T. thermophilus HB8, TTHA1437 deletion mutant, rich medium, 480 min

growth_protocol: THA1437 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).

value: crp-deficient strain


title: crp-deficient strain_360_3

description: crp-deficient strain cultivated for 360 min_3

source_name: T. thermophilus HB8, TTHA1437 deletion mutant, rich medium, 360 min

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).


title: TTHB186-deficient strain_480_1

description: TTHB186-deficient strain cultivated for 480 min_1

source_name: T. thermophilus HB8, TTHB186 deletion mutant, rich medium, 480 min

growth_protocol: The TTHB186-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 500 mL of the same medium and then cultivated at 70°C for 360, and 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: TTHB186-deficient strain


title: crp-deficient strain_480_3

description: crp-deficient strain cultivated for 480 min_3


title: crp-deficient strain_360_1

description: crp-deficient strain cultivated for 360 min_1


title: TTHB186-deficient strain_480_2

description: TTHB186-deficient strain cultivated for 480 min_2


title: crp-deficient strain_480_2

description: crp-deficient strain cultivated for 480 min_2


title: TTHA1634-deficient strain_420_1

description: TTHA1634-deficient strain cultivated for 420 min_1

source_name: T. thermophilus HB8, TTHA1634 deletion mutant, rich medium, 420 min


title: TTHB186-deficient strain_480_3

description: TTHB186-deficient strain cultivated for 480 min_3


title: crp-deficient strain_360_2

description: crp-deficient strain cultivated for 360 min_2


title: TTHB186-deficient strain_360_3

description: TTHB186-deficient strain cultivated for 360 min_3

source_name: T. thermophilus HB8, TTHB186 deletion mutant, rich medium, 360 min


title: TTHA1634-deficient strain_420_2

description: TTHA1634-deficient strain cultivated for 420 min_2


title: TTHB186-deficient strain_360_2

description: TTHB186-deficient strain cultivated for 360 min_2


title: TTHA0252-deficient strain_680_2

description: TTHA0252-deficient strain cultivated for 680 min_2

source_name: T. thermophilus HB8, TTHA0252 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0252-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 500 mL of the same medium and then cultivated at 70°C for 360, 540, and 680 min.

value: TTHA0252-deficient strain


title: TTHA0252-deficient strain_680_1

description: TTHA0252-deficient strain cultivated for 680 min_1


title: TTHA0252-deficient strain_540_2

description: TTHA0252-deficient strain cultivated for 540 min_2

source_name: T. thermophilus HB8, TTHA0252 deletion mutant, rich medium, 540 min


title: TTHB186-deficient strain_360_1

description: TTHB186-deficient strain cultivated for 360 min_1


title: TTHA0252-deficient strain_540_1

description: TTHA0252-deficient strain cultivated for 540 min_1


title: TTHA0252-deficient strain_360_1

description: TTHA0252-deficient strain cultivated for 360 min_1

source_name: T. thermophilus HB8, TTHA0252 deletion mutant, rich medium, 360 min


title: TTHA0101-deficient strain_680_2

description: TTHA0101-deficient strain cultivated for 680 min_2

source_name: T. thermophilus HB8, TTHA0101 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0101-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 680 min.

value: TTHA0101-deficient strain


title: TTHA0101-deficient strain_680_3

description: TTHA0101-deficient strain cultivated for 680 min_3


title: TTHB211 deletion mutant strain_8h_3

description: TTHB211 deletion mutant strain grown on a rich medium for 480 min

source_name: T. thermophilus HB8, TTHB211 deletion mutant, TT medium, 480 min

growth_protocol: TTHB211 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).

value: TTHB211 deletion mutant strain


title: wild_type_5%_etoh_30min_3

description: wild-type strain grown on a TT medium, 30 min time point after addition of 5% ethanol

source_name: T. thermophilus HB8, wild-type, TT medium, 6.5 hrs, 30 min time point after addition of 5% ethanol

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 mL of TT medium. The cells (0.5 mL) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.95). A 5% (final) of ethanol was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ethanol.


title: TTHA0101-deficient strain_680_1

description: TTHA0101-deficient strain cultivated for 680 min_1


title: wild_type_5%_etoh_30min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 mL of TT medium. The cells (0.5 mL) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.56). A 5% (final) of ethanol was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ethanol.


title: wild_type_5%_etoh_30min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 mL of TT medium. The cells (0.5 mL) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.57). A 5% (final) of ethanol was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ethanol.


title: TTHA0252-deficient strain_360_2

description: TTHA0252-deficient strain cultivated for 360 min_2


title: wild_type_10mM_Tet_5min_1

description: wild-type strain grown on a rich medium, 5 min time point after addition of 10 mM tetracycline

source_name: T. thermophilus HB8, wild-type, TT medium, 305 min, 5 min time point after addition of 10 mM tetracycline

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5 h (OD600nm = ~ 0.45). A 10 mM (final) of tetracycline was added into medium and the cultivation was continued. The cells were collected at 5 min time point after addition of tetracycline.


title: wild_type_10mM_Tet_5min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5 h (OD600nm = ~ 0.47). A 10 mM (final) of tetracycline was added into medium and the cultivation was continued. The cells were collected at 5 min time point after addition of tetracycline.


title: wild_type_10mM_Tet_5min_3


title: wild_type_10mM_diamide_10min_3

description: wild-type strain grown on a synthetic medium, 10 min time point after addition of 10 mM diamide

source_name: T. thermophilus HB8, wild-type, synthetic medium, 490 min, 10 min time point after addition of 10 mM diamide

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.34). A 10 mM (final) of diamide was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of diamide. The synthetic medium was made by the same way as described in this section of GSM296605.


title: TTHB211 deletion mutant strain_8h_1


title: TTHB211 deletion mutant strain_8h_2


title: wild_type_10mM_diamide_10min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.22). A 10 mM (final) of diamide was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of diamide. The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_10mM_diamide_0min_3

description: wild-type strain grown on a synthetic medium, non-addition of diamide

source_name: T. thermophilus HB8, wild-type, synthetic medium, 480 min

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.34). The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_10mM_diamide_10min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.23). A 10 mM (final) of diamide was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of diamide. The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_10mM_diamide_0min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.23). The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_10mM_diamide_0min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.22). The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_50mM_Tet_10min_2

description: wild-type strain grown on a rich medium, 10 min time point after addition of 50 mM tetracycline

source_name: T. thermophilus HB8, wild-type, TT medium, 370 min, 10 min time point after addition of 50 mM tetracycline

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.59).  A 50 mM (final) of tetracycline was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of tetracycline.


title: wild_type_50mM_Tet_10min_3

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.53).  A 50 mM (final) of tetracycline was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of tetracycline.


title: wild_type_50mM_Tet_0min_2

description: wild-type strain grown on a rich medium, non-addition of tetracycline

source_name: T. thermophilus HB8, wild-type, TT medium, 360 min

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.59).


title: wild_type_50mM_Tet_0min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.62).


title: wild_type_10mM_H2O2_30min_3

description: wild-type strain grown on a rich medium, 30 min time point after addition of 10 mM H2O2

source_name: T. thermophilus HB8, wild-type, TT medium, 360 min, 30 min time point after addition of 10 mM H2O2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.55). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_15min_3

description: wild-type strain grown on a rich medium, 15 min time point after addition of 10 mM H2O2

source_name: T. thermophilus HB8, wild-type, TT medium, 345 min, 15 min time point after addition of 10 mM H2O2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.55). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 15 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_0min_3

description: wild-type strain grown on a rich medium, non-addition of H2O2

source_name: T. thermophilus HB8, wild-type, TT medium, 330 min

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.55).


title: wild_type_50mM_Tet_0min_3

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.53).


title: wild_type_10mM_H2O2_30min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.52). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_15min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.52). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 15 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_5min_2

description: wild-type strain grown on a rich medium, 5 min time point after addition of 10 mM H2O2

source_name: T. thermophilus HB8, wild-type, TT medium, 335 min, 5 min time point after addition of 10 mM H2O2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.52). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 5 min time point after addition of H2O2.


title: wild_type_50mM_Tet_10min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium. The cells (2 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 h (OD600nm = ~ 0.62).  A 50 mM (final) of tetracycline was added into medium and the cultivation was continued. The cells were collected at 10 min time point after addition of tetracycline.


title: wild_type_10mM_H2O2_0min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.52).


title: wild_type_10mM_H2O2_15min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.51). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 15 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_30min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.51). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_5min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.51). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 5 min time point after addition of H2O2.


title: wild_type_10mM_H2O2_0min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.51).


title: wild_type_10mM_H2O2_5min_3

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 2 ml of TT medium. The cells (1 ml) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6.5 h (OD600nm = ~ 0.55). A 10 mM (final) of H2O2 was added into medium and the cultivation was continued. The cells were collected at 5 min time point after addition of H2O2.


title: wild-type strain cultured for 600 min_3

description:
T. thermophilus wild-type strain cultured for 600 min, rep 3.
wild-type strain 600_3

source_name: T. thermophilus HB8, wild-type, rich medium, 600 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 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, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min.

extract_protocol: Cells were collected from 5-200 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

value: 600 min


title: wild-type strain cultured for 760 min_3

description:
T. thermophilus wild-type strain cultured for 760 min, rep 3.
wild-type strain 760_3

source_name: T. thermophilus HB8, wild-type, rich medium, 760 min

value: 760 min


title: wild-type strain cultured for 680 min_1

description:
T. thermophilus wild-type strain cultured for 680 min, rep 1.
wild-type strain 680_1

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

value: 680 min


title: wild-type strain cultured for 600 min_2

description:
T. thermophilus wild-type strain cultured for 600 min, rep 2.
wild-type strain 600_2


title: wild-type strain cultured for 680 min_2

description:
T. thermophilus wild-type strain cultured for 680 min, rep 2.
wild-type strain 680_2


title: wild-type strain cultured for 600 min_1

description:
T. thermophilus wild-type strain cultured for 600 min, rep 1.
wild-type strain 600_1


title: wild-type strain cultured for 680 min_3

description:
T. thermophilus wild-type strain cultured for 680 min, rep 3.
wild-type strain 680_3


title: wild-type strain cultured for 760 min_1

description:
T. thermophilus wild-type strain cultured for 760 min, rep 1.
wild-type strain 760_1


title: wild-type strain cultured for 540 min_3

description:
T. thermophilus wild-type strain cultured for 540 min, rep 3.
wild-type strain 540_3

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

value: 540 min


title: wild-type strain cultured for 540 min_2

description:
T. thermophilus wild-type strain cultured for 540 min, rep 2.
wild-type strain 540_2


title: wild-type strain cultured for 360 min_2

description:
T. thermophilus wild-type strain cultured for 360 min, rep 2.
wild-type strain 360_2

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

value: 360 min


title: wild-type strain cultured for 540 min_1

description:
T. thermophilus wild-type strain cultured for 540 min, rep 1.
wild-type strain 540_1


title: wild-type strain cultured for 300 min_3

description:
T. thermophilus wild-type strain cultured for 300 min, rep 3.
wild-type strain 300_3

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

value: 300 min


title: wild-type strain cultured for 300 min_2

description:
T. thermophilus wild-type strain cultured for 300 min, rep 2.
wild-type strain 300_2


title: wild-type strain cultured for 480 min_2

description:
T. thermophilus wild-type strain cultured for 480 min, rep 2.
wild-type strain 480_2

source_name: T. thermophilus HB8, wild-type, rich medium, 480 min

value: 480 min


title: wild-type strain cultured for 480 min_1

description:
T. thermophilus wild-type strain cultured for 480 min, rep 1.
wild-type strain 480_1

value: wild-type


title: wild-type strain cultured for 360 min_3

description:
T. thermophilus wild-type strain cultured for 360 min, rep 3.
wild-type strain 360_3


title: wild-type strain cultured for 420 min_3

description:
T. thermophilus wild-type strain cultured for 420 min, rep 3.
wild-type strain 420_3

source_name: T. thermophilus HB8, wild-type, rich medium, 420 min

value: 420 min


title: wild-type strain cultured for 760 min_2

description:
T. thermophilus wild-type strain cultured for 760 min, rep 2.
wild-type strain 760_2


title: wild-type strain cultured for 420 min_1

description:
T. thermophilus wild-type strain cultured for 420 min, rep 1.
wild-type strain 420_1


title: wild-type strain cultured for 420 min_2

description:
T. thermophilus wild-type strain cultured for 420 min, rep 2.
wild-type strain 420_2


title: wild-type strain cultured for 480 min_3

description:
T. thermophilus wild-type strain cultured for 480 min, rep 3.
wild-type strain 480_3


title: wild-type strain cultured for 300 min_1

description:
T. thermophilus wild-type strain cultured for 300 min, rep 1.
wild-type strain 300_1


title: wild-type strain cultured for 180 min_2

description:
T. thermophilus wild-type strain cultured for 180 min, rep 2.
wild-type strain 180_2

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

value: 180 min


title: wild-type strain cultured for 240 min_1

description:
T. thermophilus wild-type strain cultured for 240 min, rep 1.
wild-type strain 240_1

source_name: T. thermophilus HB8, wild-type, rich medium, 240 min

value: 240 min


title: wild-type strain cultured for 240 min_3

description:
T. thermophilus wild-type strain cultured for 240 min, rep 3.
wild-type strain 240_3


title: wild-type strain cultured for 240 min_2

description:
T. thermophilus wild-type strain cultured for 240 min, rep 2.
wild-type strain 240_2


title: wild-type strain cultured for 180 min_1

description:
T. thermophilus wild-type strain cultured for 180 min, rep 1.
wild-type strain 180_1


title: wild-type strain cultured for 180 min_3

description:
T. thermophilus wild-type strain cultured for 180 min, rep 3.
wild-type strain 180_3


title: wild-type strain cultured for 360 min_1

description:
T. thermophilus wild-type strain cultured for 360 min, rep 1.
wild-type strain 360_1


title: wild_type_0.5%_NaCl_30min_3

description:
Wild-type strain grown for 30 min in the presence of 0.5% NaCl.
0.5%_NaCl_30min_3

source_name: T. thermophilus HB8, wild-type, TT medium 6 hrs, 0.5% NaCl 0.5 hrs

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium.  The cells (1 ml) were inoculated into 1 L of a rich (TT)  medium, and then cultivated at 70°C for 6 hours.  Then NaCl was added into the medium to a final concentration of 0.5%, and cultivation was continued. Cells were collected at 30 min time point after the addition of excess NaCl.

extract_protocol: Cells were collected from 15 or 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.

tag: treatment

value: 0.5% NaCl


title: wild_type_0.5%_NaCl_30min_2

description:
Wild-type strain grown for 30 min in the presence of 0.5% NaCl.
0.5%_NaCl_30min_2


title: wild_type_none_3

description:
Wild-type strain, before addition of excess NaCl.
none_3

source_name: T. thermophilus HB8, wild-type, TT medium 6 hrs

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium.  The cells (1 ml) were inoculated into 1 L of a rich (TT)  medium.  After 6 hours, the cells were collected.

value: untreated


title: wild_type_0.5%_NaCl_30min_1

description:
Wild-type strain grown for 30 min in the presence of 0.5% NaCl.
0.5%_NaCl_30min_1


title: wild_type_none_2

description:
Wild-type strain, before addition of excess NaCl.
none_2


title: wild_type_none_1

description:
Wild-type strain, before addition of excess NaCl.
none_1


title: wild_type_1.5%_NaCl_30min_3

description:
Wild-type strain grown for 30 min in the presence of 1.5% NaCl.
1.5%_NaCl_30min_3

source_name: T. thermophilus HB8, wild-type, TT medium 6 hrs, 1.5% NaCl 0.5 hrs

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT medium.  The cells (1 ml) were inoculated into 1 L of a rich (TT)  medium, and then cultivated at 70°C for 6 hours.  Then NaCl was added into the medium to a final concentration of 1.5%, and cultivation was continued. Cells were collected at 30 min time point after the addition of excess NaCl.

value: 1.5% NaCl


title: wild-type_non-treated_1

description:
Wild-type strain grown on a rich medium, non-treated.
non-treated_1

source_name: T. thermophilus HB8, wild-type, rich medium, 70C 6 hrs

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 (0.5 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 6 h.


title: wild-type_non-treated_2

description:
Wild-type strain grown on a rich medium, non-treated.
non-treated_2


title: wild-type_80°C_30min_2

description:
Wild-type strain grown on a rich medium, treated at 80°C for 30 min.
80°C_30min_2

source_name: T. thermophilus HB8, wild-type, rich medium, 70C 6 hrs, 80C 0.5 hrs

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 (0.5 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 6 h. Then, the growth temperature was shifted up to 80°C, and cultivation continued for 30 min.

value: heat shock


title: wild-type_1.0mM_FeSO4_0min_3

description: wild-type strain grown on a synthetic medium, non-addition of ZnSO4

source_name: T. thermophilus HB8, wild-type, synthetic medium, 9 hrs

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.31).  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.0mM_FeSO4_30min_1

description: wild-type strain grown on a synthetic medium, 30 min time point after addition of 1.0 mM ZnSO4

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.27).  A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild_type_1.5%_NaCl_30min_1

description:
Wild-type strain grown for 30 min in the presence of 1.5% NaCl.
1.5%_NaCl_30min_1


title: wild_type_1.5%_NaCl_30min_2

description:
Wild-type strain grown for 30 min in the presence of 1.5% NaCl.
1.5%_NaCl_30min_2


title: TTHA1438-deficient strain_760_2

description: TTHA1438-deficient strain cultivated for 760 min_2

source_name: T. thermophilus HB8, TTHA1438 deletion mutant, rich medium, 760 min

growth_protocol: The TTHA1438-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 760 min.

value: TTHA1438-deficient strain


title: wild-type_non-treated_3

description:
Wild-type strain grown on a rich medium, non-treated.
non-treated_3


title: wild-type_1.0mM_FeSO4_0min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.27).  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.0mM_FeSO4_0min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.29).  The synthetic medium was made by the same way as described in this section of GSM296605.


title: TTHA1438-deficient strain_600_2

description: TTHA1438-deficient strain cultivated for 600 min_2

source_name: T. thermophilus HB8, TTHA1438 deletion mutant, rich medium, 600 min

growth_protocol: The TTHA1438-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 600 min.


title: wild-type_1.0mM_FeSO4_30min_3

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.31).  A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: TTHA1438-deficient strain_760_1

description: TTHA1438-deficient strain cultivated for 760 min_1


title: wild-type_1.0mM_FeSO4_30min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 4 ml of synthetic medium. The cells (2 ml) were inoculated into 200 ml of the same medium and then cultivated at 70°C for 9 h (OD600nm = ~ 0.29).  A 1.0 mM (final) of FeSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of FeSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_80°C_30min_3

description:
Wild-type strain grown on a rich medium, treated at 80°C for 30 min.
80°C_30min_3


title: TTHA1438-deficient strain_360_2

description: TTHA1438-deficient strain cultivated for 360 min_2

source_name: T. thermophilus HB8, TTHA1438 deletion mutant, rich medium, 360 min

growth_protocol: The TTHA1438-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 360 min.


title: wild-type_80°C_30min_1

description:
Wild-type strain grown on a rich medium, treated at 80°C for 30 min.
80°C_30min_1


title: TTHA1438-deficient strain_600_1

description: TTHA1438-deficient strain cultivated for 600 min_1


title: TTHA1438-deficient strain_240_1

description: TTHA1438-deficient strain cultivated for 240 min_1

source_name: T. thermophilus HB8, TTHA1438 deletion mutant, rich medium, 240 min

growth_protocol: The TTHA1438-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 240 min.

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.


title: TTHA1438-deficient strain_480_1

description: TTHA1438-deficient strain cultivated for 480 min_1

source_name: T. thermophilus HB8, TTHA1438 deletion mutant, rich medium, 480 min

growth_protocol: The TTHA1438-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 480 min.


title: TTHA1438-deficient strain_480_2

description: TTHA1438-deficient strain cultivated for 480 min_2


title: TTHA0995-deficient strain_680_2

description: TTHA0995-deficient strain cultivated for 680 min_2

source_name: T. thermophilus HB8, TTHA0995 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0995-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 680 min.

value: TTHA0995-deficient strain


title: TTHA0995-deficient strain_680_1

description: TTHA0995-deficient strain cultivated for 680 min_1


title: TTHA0995-deficient strain_680_3

description: TTHA0995-deficient strain cultivated for 680 min_3


title: TTHA0344-deficient strain_680_1

description: TTHA0344-deficient strain cultivated for 680 min_1

source_name: T. thermophilus HB8, TTHA0344 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0344-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 680 min.

value: TTHA0344-deficient strain


title: TTHA0344-deficient strain_680_3

description: TTHA0344-deficient strain cultivated for 680 min_3


title: TTHA1438-deficient strain_360_1

description: TTHA1438-deficient strain cultivated for 360 min_1


title: Wild-type strain_45_120_2

description: Wild-type strain cultivated for 120 min at 45oC_2

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).

source_name: T. thermophilus HB8, wild-type strain, rich medium, 120 min after shifted the growth temperature down to 45 oC

growth_protocol: Wild-type and TTHA0175-deficient strains were each 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 (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0, 30, and 120 min after temperature shift.

value: wild type


title: TTHA0344-deficient strain_680_2

description: TTHA0344-deficient strain cultivated for 680 min_2


title: Wild-type strain_45_30_2

description: Wild-type strain cultivated for 30 min at 45oC_2

source_name: T. thermophilus HB8, wild-type strain, rich medium, 30 min after shifted the growth temperature down to 45 oC


title: Wild-type strain_45_120_1

description: Wild-type strain cultivated for 120 min at 45oC_1


title: Wild-type strain_45_0_2

description: Wild-type strain cultivated for 0 min after shifted the growth temperature down to 45 oC_2

source_name: T. thermophilus HB8, wild-type strain, rich medium, 0 min after shifted the growth temperature down to 45 oC


title: TTHA0175-deficient strain_45_120_2

description: TTHA0175-deficient strain cultivated for 120 min at 45oC_2

source_name: T. thermophilus HB8, TTHA0175-deficient strain, rich medium, 120 min after shifted the growth temperature down to 45 oC

value: TTHA0175-deficient strain


title: Wild-type strain_45_30_1

description: Wild-type strain cultivated for 30 min at 45oC_1


title: TTHA0175-deficient strain_45_30_2

description: TTHA0175-deficient strain cultivated for 30 min at 45oC_2

source_name: T. thermophilus HB8, TTHA0175-deficient strain, rich medium, 30 min after shifted the growth temperature down to 45 oC


title: TTHA0175-deficient strain_45_30_1

description: TTHA0175-deficient strain cultivated for 30 min at 45oC_1


title: TTHA0175-deficient strain_45_0_2

description: TTHA0175-deficient strain cultivated for 0 min after shifted the growth temperature down to 45 oC_2

source_name: T. thermophilus HB8, TTHA0175-deficient strain, rich medium, 0 min after shifted the growth temperature down to 45 oC


title: TTHA0655-deficient strain_680_3

description: TTHA0655-deficient strain cultivated for 680 min_3

source_name: T. thermophilus HB8, TTHA0655 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0655-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 360 or 680 min.

value: TTHA0655-deficient strain


title: TTHA0973-deficient strain_680_2

description: TTHA0973-deficient strain cultivated for 680 min_2

source_name: T. thermophilus HB8, TTHA0973 deletion mutant, rich medium, 680 min

growth_protocol: The TTHA0973-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 680 min.

value: TTHA0973-deficient strain


title: TTHA0655-deficient strain_680_1

description: TTHA0655-deficient strain cultivated for 680 min_1


title: TTHA0973-deficient strain_680_1

description: TTHA0973-deficient strain cultivated for 680 min_1


title: TTHA0973-deficient strain_680_3

description: TTHA0973-deficient strain cultivated for 680 min_3


title: TTHA0655-deficient strain_360_1

description: TTHA0655-deficient strain cultivated for 360 min_1

source_name: T. thermophilus HB8, TTHA0655 deletion mutant, rich medium, 360 min


title: TTHA0655-deficient strain_360_2

description: TTHA0655-deficient strain cultivated for 360 min_2


title: TTHA0175-deficient strain_45_120_1

description: TTHA0175-deficient strain cultivated for 120 min at 45oC_1


title: TTHA0655-deficient strain_680_2

description: TTHA0655-deficient strain cultivated for 680 min_2


title: TTHA0655-deficient strain_360_3

description: TTHA0655-deficient strain cultivated for 360 min_3


title: Wild-type strain_45_0_1

description: Wild-type strain cultivated for 0 min after shifted the growth temperature down to 45 oC_1


title: TTHB099-deficient strain_420_4

description: TTHB099-deficient strain cultivated for 420 min_4

source_name: T. thermophilus HB8, TTHB099 deletion mutant, rich medium, 420 min

growth_protocol: The TTHB099-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 360 or 420 min.

value: TTHB099-deficient strain


title: TTHB099-deficient strain_360_4

description: TTHB099-deficient strain cultivated for 360 min_4

source_name: T. thermophilus HB8, TTHB099 deletion mutant, rich medium, 360 min


title: TTHA0175-deficient strain_45_0_1

description: TTHA0175-deficient strain cultivated for 0 min after shifted the growth temperature down to 45 oC_1


title: TTHB099-deficient strain_420_3

description: TTHB099-deficient strain cultivated for 420 min_3


title: TTHB099-deficient strain_360_3

description: TTHB099-deficient strain cultivated for 360 min_3


title: wild-type_10h_syn2

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

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

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.


title: wild-type_20h_syn2

description: wild-type strain grown in a synthetic medium for 20 h

source_name: T. thermophilus HB8, wild-type, synthetic medium, 20 h

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 20 h.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_10h_syn3


title: wild-type_20h_syn3


title: TTHB099-deficient strain_420_2

description: TTHB099-deficient strain cultivated for 420 min_2


title: TTHB099-deficient strain_420_1

description: TTHB099-deficient strain cultivated for 420 min_1


title: TTHB099-deficient strain_360_2

description: TTHB099-deficient strain cultivated for 360 min_2


title: TTHB099-deficient strain_360_1

description: TTHB099-deficient strain cultivated for 360 min_1


title: wild-type_20h_syn1